0:00:00.000037 INFO: Moved old log file /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/log.txt to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/log.0.bkp.txt
0:00:00.000186 INFO: Output directory: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output/work/97/9b8eeeabbd37645883b822d592a7d1.
0:00:00.000219 INFO: User provided config file: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.014645 PROGRESS:           _      _         ___ ___   _   
0:00:00.014714 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014741 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014762 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014787 PROGRESS:            |_|                           
0:00:00.014810 PROGRESS: 
0:00:00.014829 PROGRESS: version: 2.1.1
0:00:00.014847 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.014874 INFO: hostname: thestral
0:00:00.014904 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.014931 PROGRESS: python: 3.11.11 (CPython)
0:00:00.014985 INFO: date: 2026-07-08 17:24:58
0:00:00.015007 INFO: ================ AlphaX Environment ===============
0:00:00.015026 INFO: alphabase       : 1.8.1
0:00:00.015044 INFO: alpharaw        : 0.5.0
0:00:00.015061 INFO: alphatims       : 1.0.9
0:00:00.015078 INFO: alphapeptdeep   : 1.4.2
0:00:00.015094 INFO: directlfq       : 0.3.3
0:00:00.015109 INFO: ===================================================
0:00:00.015125 INFO: ================= Pip Environment =================
0:00:00.084371 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
0:00:00.084478 INFO: ===================================================
0:00:00.084507 INFO: =================== Running step 'library' ===================
0:00:00.084583 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
0:00:00.096825 INFO: loading additional config provided via CLI
0:00:00.096904 INFO: loading additional config provided via CLI parameters
0:00:00.097278 INFO: Updating config with 'user defined'
0:00:00.097351 INFO: Updating config with 'user defined (cli)'
0:00:00.097421 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/AstralAlphaDIA/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': 0, 'target_ms2_tolerance': 0, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': False}}, {'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/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library'}]
0:00:00.097629 INFO: Updating config with 'user defined'
0:00:00.097672 INFO: Updating config with 'user defined (cli)'
0:00:00.097691 INFO: Updating config with 'multistep search'
0:00:00.097739 INFO: ├──version: None
0:00:00.097762 INFO: ├──workflow_name: None
0:00:00.097782 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library [multistep search, default: None][0m
0:00:00.097802 INFO: ├──library_path: None
0:00:00.097818 INFO: ├──raw_paths:
0:00:00.097837 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.097876 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.097895 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.097915 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.097933 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.097959 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.097980 INFO: ├──fasta_paths:
0:00:00.097998 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.098016 INFO: ├──quant_directory: None
0:00:00.098033 INFO: ├──general
0:00:00.098054 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.098072 INFO: │   ├──transfer_step_enabled: False
0:00:00.098090 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.098108 INFO: │   ├──reuse_calibration: False
0:00:00.098125 INFO: │   ├──reuse_quant: False
0:00:00.098143 INFO: │   ├──log_level: INFO
0:00:00.098160 INFO: │   ├──use_gpu: True
0:00:00.098180 INFO: │   ├──save_figures: True
0:00:00.098198 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.098216 INFO: │   ├──save_flat_library: False
0:00:00.098233 INFO: │   ├──input_library_type: base
0:00:00.098250 INFO: │   ├──save_mbr_library: True
0:00:00.098268 INFO: │   ├──random_state: None
0:00:00.098286 INFO: │   └──fail_fast: False
0:00:00.098304 INFO: ├──library_loading
0:00:00.098323 INFO: │   └──drop_decoys: False
0:00:00.098340 INFO: ├──library_prediction
0:00:00.098358 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.098375 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.098393 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.098411 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.098429 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.098447 INFO: │   ├──missed_cleavages: 1
0:00:00.098465 INFO: │   ├──precursor_len:
0:00:00.098483 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.098500 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.098517 INFO: │   ├──precursor_charge:
0:00:00.098533 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.098549 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.098566 INFO: │   ├──precursor_mz:
0:00:00.098583 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
0:00:00.098600 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
0:00:00.098616 INFO: │   ├──fragment_mz:
0:00:00.098632 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
0:00:00.098649 INFO: │   │   - 2000.0
0:00:00.098666 INFO: │   ├──nce: 25.0
0:00:00.098682 INFO: │   ├──fragment_types:
0:00:00.098699 INFO: │   │   - b
0:00:00.098716 INFO: │   │   - y
0:00:00.098733 INFO: │   ├──max_fragment_charge: 2
0:00:00.098750 INFO: │   ├──instrument: Lumos
0:00:00.098767 INFO: │   ├──peptdeep_model_path: None
0:00:00.098783 INFO: │   ├──peptdeep_model_type: generic
0:00:00.098801 INFO: │   ├──predict_charge: False
0:00:00.098818 INFO: │   └──min_charge_probability: 0.1
0:00:00.098835 INFO: ├──custom_modifications:
0:00:00.098853 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.098871 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098893 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.098910 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098927 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.098944 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098961 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.098978 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.098996 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.099017 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.099035 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.099054 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.099071 INFO: │   ├──name: Label:13C(12)@K
0:00:00.099088 INFO: │   └──composition: C(12)
0:00:00.099104 INFO: ├──search
0:00:00.099122 INFO: │   ├──extraction_backend: rust
0:00:00.099138 INFO: │   [32;20m├──target_ms1_tolerance: 0 [user defined, default: 5][0m
0:00:00.099156 INFO: │   [32;20m├──target_ms2_tolerance: 0 [user defined, default: 10][0m
0:00:00.099173 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.099190 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.099208 INFO: │   ├──quant_window: 3
0:00:00.099224 INFO: │   ├──target_num_candidates: 3
0:00:00.099241 INFO: │   ├──channel_filter: 
0:00:00.099258 INFO: │   ├──compete_for_fragments: True
0:00:00.099275 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.099292 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.099309 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.099325 INFO: │   ├──optimized_peak_group_score: False
0:00:00.099342 INFO: │   ├──exclude_shared_ions: True
0:00:00.099360 INFO: │   ├──quant_all: True
0:00:00.099378 INFO: │   └──experimental_xic: True
0:00:00.099394 INFO: ├──calibration
0:00:00.099413 INFO: │   ├──batch_size: 1000
0:00:00.099430 INFO: │   ├──optimization_lock_target: 1000
0:00:00.099448 INFO: │   ├──max_steps: 20
0:00:00.099465 INFO: │   ├──min_steps: 5
0:00:00.099483 INFO: │   ├──max_skips: 1
0:00:00.099500 INFO: │   ├──max_fragments: 5000
0:00:00.099518 INFO: │   └──min_correlation: 0.7
0:00:00.099534 INFO: ├──search_initial
0:00:00.099552 INFO: │   ├──num_candidates: 1
0:00:00.099569 INFO: │   ├──ms1_tolerance: 30
0:00:00.099586 INFO: │   ├──ms2_tolerance: 30
0:00:00.099604 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.099622 INFO: │   └──rt_tolerance: 0.5
0:00:00.099639 INFO: ├──library_multiplexing
0:00:00.099657 INFO: │   ├──enabled: False
0:00:00.099674 INFO: │   ├──input_channel: 0
0:00:00.099691 INFO: │   └──multiplex_mapping:
0:00:00.099708 INFO: ├──multiplexing
0:00:00.099725 INFO: │   ├──enabled: False
0:00:00.099741 INFO: │   ├──target_channels: 4,8
0:00:00.099758 INFO: │   ├──decoy_channel: 12
0:00:00.099775 INFO: │   ├──reference_channel: 0
0:00:00.099792 INFO: │   └──competitive_scoring: True
0:00:00.099809 INFO: ├──fdr
0:00:00.099826 INFO: │   ├──fdr: 0.01
0:00:00.099842 INFO: │   ├──group_level: proteins
0:00:00.099859 INFO: │   ├──inference_strategy: heuristic
0:00:00.099876 INFO: │   ├──competitive_scoring: True
0:00:00.099893 INFO: │   ├──keep_decoys: False
0:00:00.099910 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.099928 INFO: │   ├──channel_wise_fdr: False
0:00:00.099945 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.099961 INFO: ├──search_output
0:00:00.099978 INFO: │   ├──file_format: parquet
0:00:00.099995 INFO: │   ├──precursor_level_lfq: True
0:00:00.100012 INFO: │   ├──peptide_level_lfq: True
0:00:00.100029 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.100046 INFO: │   ├──min_k_fragments: 12
0:00:00.100063 INFO: │   ├──min_correlation: 0.9
0:00:00.100080 INFO: │   ├──num_samples_quadratic: 50
0:00:00.100097 INFO: │   ├──min_nonnan: 3
0:00:00.100115 INFO: │   ├──normalization_method: directlfq
0:00:00.100132 INFO: │   [32;20m└──normalize_directlfq: False [user defined, default: True][0m
0:00:00.100149 INFO: ├──optimization
0:00:00.100166 INFO: │   ├──order_of_optimization: None
0:00:00.100183 INFO: │   ├──ms2_error
0:00:00.100203 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.100222 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.100241 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.100259 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.100276 INFO: │   │   ├──try_narrower_values: True
0:00:00.100294 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.100311 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.100328 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.100345 INFO: │   ├──ms1_error
0:00:00.100362 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.100379 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.100397 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.100414 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.100431 INFO: │   │   ├──try_narrower_values: False
0:00:00.100448 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.100465 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.100482 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.100498 INFO: │   ├──mobility_error
0:00:00.100516 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.100533 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.100551 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.100569 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.100586 INFO: │   │   ├──try_narrower_values: False
0:00:00.100603 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.100621 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.100638 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.100655 INFO: │   └──rt_error
0:00:00.100672 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.100690 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.100708 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.100726 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.100743 INFO: │       ├──try_narrower_values: True
0:00:00.100761 INFO: │       ├──maximal_decrease: 0.1
0:00:00.100778 INFO: │       ├──favour_narrower_optimum: False
0:00:00.100795 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.100813 INFO: ├──optimization_manager
0:00:00.100831 INFO: │   ├──fwhm_rt: 5
0:00:00.100849 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.100866 INFO: │   └──score_cutoff: 0
0:00:00.100883 INFO: ├──transfer_library
0:00:00.100900 INFO: │   ├──enabled: False
0:00:00.100917 INFO: │   ├──fragment_types:
0:00:00.100933 INFO: │   │   - b
0:00:00.100950 INFO: │   │   - y
0:00:00.100966 INFO: │   ├──max_charge: 2
0:00:00.100983 INFO: │   ├──top_k_samples: 3
0:00:00.101000 INFO: │   ├──norm_delta_max: True
0:00:00.101018 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.101035 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.101051 INFO: └──transfer_learning
0:00:00.101069 INFO:     ├──enabled: False
0:00:00.101086 INFO:     ├──batch_size: 2000
0:00:00.101103 INFO:     ├──max_lr: 0.0001
0:00:00.101120 INFO:     ├──train_fraction: 0.7
0:00:00.101137 INFO:     ├──validation_fraction: 0.2
0:00:00.101155 INFO:     ├──test_fraction: 0.1
0:00:00.101171 INFO:     ├──test_interval: 1
0:00:00.101188 INFO:     ├──lr_patience: 3
0:00:00.101206 INFO:     ├──epochs: 51
0:00:00.101223 INFO:     ├──warmup_epochs: 5
0:00:00.101239 INFO:     ├──nce: 25
0:00:00.101257 INFO:     └──instrument: Lumos
0:00:00.106420 INFO: Moved existing config file /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/frozen_config.yaml to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/frozen_config.0.bkp.yaml
0:00:00.106634 INFO: Registering 7 custom modifications
0:00:00.140774 INFO: Searching 6 files:
0:00:00.140861 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.140885 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.140903 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.140920 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.140937 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.140955 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.140971 INFO: Using 1 fasta files:
0:00:00.140988 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.141006 INFO: Using library: None
0:00:00.141021 INFO: Saving output to: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library
0:00:00.141044 PROGRESS: Loading spectral library
0:00:00.141067 PROGRESS: No library provided. Building library from fasta files.
0:00:00.141101 INFO: Running FastaDigest
0:00:00.142730 INFO: Digesting fasta file
0:00:07.042688 INFO: Adding modifications
0:01:55.676613 INFO: Removing non-canonical amino acids
0:02:02.004798 INFO: Fasta library contains 6,091,314 precursors
0:02:02.005010 PROGRESS: Predicting library properties.
0:02:02.005098 INFO: Running PeptDeepPrediction
0:02:02.006209 INFO: Device set to cpu
0:02:04.038080 INFO: Loading PeptDeep models of type generic
0:02:05.419404 INFO: Predicting RT, MS2 and mobility
0:02:05.419585 INFO: Using multiprocessing with 100 processes ...
0:02:05.818417 INFO: Predicting rt,ms2,mobility ...
0:08:43.799984 INFO: Adding fragment mz information
0:08:44.103919 INFO: Adding fragment intensity information
0:08:44.404807 INFO: Adding precursor information
0:08:44.769531 INFO: Running PrecursorInitializer
0:08:44.793117 INFO: Running AnnotateFasta
0:09:10.934817 INFO: Running IsotopeGenerator
0:09:10.936092 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:13:39.434424 INFO: Running RTNormalization
0:13:39.434797 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:13:39.434911 INFO: Saving library to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/speclib.hdf
0:14:14.121724 INFO: Running DecoyGenerator
0:16:13.817142 INFO: Running FlattenLibrary
0:16:42.734099 INFO: Running InitFlatColumns
0:16:42.973081 INFO: Running LogFlatLibraryStats
0:16:42.973221 INFO: ============ Library Stats ============
0:16:42.973255 INFO: Number of precursors: 12,150,378
0:16:44.542361 INFO: 	thereof targets:6,091,314
0:16:44.542512 INFO: 	thereof decoys: 6,059,064
0:16:44.622618 INFO: Number of elution groups: 6,091,314
0:16:44.622753 INFO: 	average size: 1.99
0:16:44.916826 INFO: Number of proteins: 117,993
0:16:44.949427 INFO: Number of channels: 1 ([0])
0:16:44.949599 INFO: Isotopes Distribution for 4 isotopes
0:16:44.949629 INFO: =======================================
0:16:44.949675 PROGRESS: =================== Starting Search Workflows for step library ===================
0:16:44.949747 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:16:44.949787 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant
0:16:44.949888 INFO: Initializing TimingManager
0:16:44.950531 INFO: Initializing RawFileManager
0:16:55.304766 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:16:55.313248 INFO: Determining DIA cycle
0:16:55.627865 INFO: Found cycle with start 0.00 min and length 300.
0:16:55.792418 INFO: RT (min)            : 0.0 - 26.9
0:16:55.792506 INFO: RT duration (sec)   : 1611.2
0:16:55.792535 INFO: RT duration (min)   : 26.9
0:16:55.792560 INFO: Cycle len (scans)   : 300
0:16:55.792580 INFO: Cycle len (sec)     : 1.65
0:16:55.792600 INFO: Number of cycles    : 977
0:16:55.792620 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:16:55.792646 INFO: Creating DIA data object took: 10.842020273208618
0:16:56.610075 INFO: Creating DIA data NG object took: 0.81730055809021
0:16:57.780384 INFO: Initializing CalibrationManager
0:16:57.780740 INFO: Setting up calibration estimators ..
0:16:57.780807 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:16:57.780881 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:16:57.780956 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:16:57.781011 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:16:57.781065 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:16:57.781116 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:16:57.781165 INFO: Done setting up calibration estimators.
0:16:57.781361 INFO: Initializing OptimizationManager
0:16:57.781497 INFO: initial parameter: ms1_error = 30
0:16:57.781552 INFO: initial parameter: ms2_error = 30
0:16:57.781600 INFO: initial parameter: rt_error = 805.5992431640625
0:16:57.781644 INFO: initial parameter: mobility_error = 0.1
0:16:57.781687 INFO: initial parameter: num_candidates = 1
0:16:57.781728 INFO: initial parameter: fwhm_rt = 5
0:16:57.781770 INFO: initial parameter: fwhm_mobility = 0.01
0:16:57.781813 INFO: initial parameter: score_cutoff = 0
0:16:57.781865 INFO: initial parameter: classifier_version = -1
0:16:57.781938 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:16:57.782185 INFO: FDRManager: loading saved state not requested, will be initialized.
0:16:57.782218 INFO: Initializing FDRManager
0:16:57.782256 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:16:59.165765 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:17:00.631466 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:17:00.631839 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:17:00.631945 PROGRESS: Starting initial search for precursors.
0:17:00.632032 INFO: Starting optimization step 0.
0:17:00.632097 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:17:00.632155 INFO: Using rust extraction backend
0:17:00.632214 PROGRESS: Extracting batch of 1970 precursors
0:17:00.637101 INFO: === Search parameters used ===
0:17:00.637196 INFO: rt_error       : 805.5992431640625
0:17:00.637246 INFO: mobility_error : 0.1
0:17:00.637291 INFO: num_candidates : 1
0:17:00.637334 INFO: ms1_error      : 30
0:17:00.637376 INFO: ms2_error      : 30
0:17:00.637416 INFO: fwhm_rt        : 5
0:17:00.637460 INFO: quant_window   : 3
0:17:00.637501 INFO: ==============================================
0:17:00.667149 INFO: performing precursor FDR with 40 features
0:17:00.667275 INFO: Decoy channel: -1
0:17:00.667300 INFO: competitive: True
0:17:00.668634 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:00.671003 INFO: Estimating optimal hyperparameters - samples: 1,560, batch_size: 128, learning_rate: 1.77e-04
0:17:00.671998 INFO: Using random state 761126 for train-test-split
0:17:00.834655 INFO: Test AUC: 0.537
0:17:00.834745 INFO: Train AUC: 0.548
0:17:00.834773 INFO: AUC difference: 2.07%
0:17:01.119790 INFO: Resetting torch num_threads to 100
0:17:01.121396 PROGRESS: === Extracted 1950 precursors and 9278 fragments ===
0:17:01.121753 INFO: === FDR correction performed with classifier version -1 ===
0:17:01.122284 PROGRESS: ============================= Precursor FDR =============================
0:17:01.122373 PROGRESS: Total precursors accumulated: 622
0:17:01.122431 PROGRESS: Target precursors: 616 (99.04%)
0:17:01.122482 PROGRESS: Decoy precursors: 6 (0.96%)
0:17:01.122536 PROGRESS: 
0:17:01.122580 PROGRESS: Precursor Summary:
0:17:01.123734 PROGRESS: Channel   0:	 0.050 FDR:   616; 0.010 FDR:   616; 0.001 FDR:   616
0:17:01.123816 PROGRESS: 
0:17:01.123870 PROGRESS: Protein Summary:
0:17:01.125253 PROGRESS: Channel   0:	 0.050 FDR:   605; 0.010 FDR:   605; 0.001 FDR:   605
0:17:01.125335 PROGRESS: =========================================================================
0:17:01.125513 INFO: Target number of precursors not reached yet.
0:17:01.209952 INFO: Starting optimization step 1.
0:17:01.210187 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:17:01.210270 INFO: Using rust extraction backend
0:17:01.210333 PROGRESS: Extracting batch of 3942 precursors
0:17:01.219106 INFO: === Search parameters used ===
0:17:01.219238 INFO: rt_error       : 805.5992431640625
0:17:01.219291 INFO: mobility_error : 0.1
0:17:01.219336 INFO: num_candidates : 1
0:17:01.219378 INFO: ms1_error      : 30
0:17:01.219418 INFO: ms2_error      : 30
0:17:01.219458 INFO: fwhm_rt        : 5
0:17:01.219498 INFO: quant_window   : 3
0:17:01.219536 INFO: ==============================================
0:17:01.260179 INFO: performing precursor FDR with 40 features
0:17:01.260268 INFO: Decoy channel: -1
0:17:01.260293 INFO: competitive: True
0:17:01.264340 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:01.266627 INFO: Estimating optimal hyperparameters - samples: 4,685, batch_size: 128, learning_rate: 1.77e-04
0:17:01.266727 INFO: Using random state 75901 for train-test-split
0:17:01.720863 INFO: Test AUC: 0.510
0:17:01.720971 INFO: Train AUC: 0.571
0:17:01.720999 INFO: AUC difference: 10.70%
0:17:01.721022 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:01.959016 INFO: Resetting torch num_threads to 100
0:17:01.962573 PROGRESS: === Extracted 5857 precursors and 27832 fragments ===
0:17:01.962960 INFO: === FDR correction performed with classifier version -1 ===
0:17:01.963660 PROGRESS: ============================= Precursor FDR =============================
0:17:01.963741 PROGRESS: Total precursors accumulated: 2,395
0:17:01.963796 PROGRESS: Target precursors: 2,372 (99.04%)
0:17:01.963843 PROGRESS: Decoy precursors: 23 (0.96%)
0:17:01.963887 PROGRESS: 
0:17:01.963931 PROGRESS: Precursor Summary:
0:17:01.965575 PROGRESS: Channel   0:	 0.050 FDR: 2,372; 0.010 FDR: 2,372; 0.001 FDR: 2,372
0:17:01.965660 PROGRESS: 
0:17:01.965712 PROGRESS: Protein Summary:
0:17:01.968036 PROGRESS: Channel   0:	 0.050 FDR: 2,219; 0.010 FDR: 2,219; 0.001 FDR: 2,219
0:17:01.968140 PROGRESS: =========================================================================
0:17:01.968408 INFO: Target number of precursors reached.
0:17:01.974635 INFO: fragments_df: keeping 3597 of 27832 [sum(precursor_idx_mask)=11009 sum(mass_error_mask)=27832 stop_rank=3597
0:17:02.102671 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:02.470976 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:02.969130 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:17:02.969610 INFO: Using score_cutoff 6.189774375486374 (fac=0.99, q=1)
0:17:02.970039 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:17:02.970124 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:17:02.970181 INFO: Updating optimization_manager: score_cutoff        : 0 -> 6.189774375486374
0:17:02.970246 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:02.974660 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:02.983411 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
0:17:02.983517 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:17:02.983602 INFO: Starting optimization step 2.
0:17:02.983675 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:02.983745 INFO: Using rust extraction backend
0:17:02.983808 PROGRESS: Extracting batch of 5912 precursors
0:17:02.996127 INFO: === Search parameters used ===
0:17:02.996242 INFO: rt_error       : 805.5992431640625
0:17:02.996306 INFO: mobility_error : 0.1
0:17:02.996354 INFO: num_candidates : 3
0:17:02.996398 INFO: ms1_error      : 30
0:17:02.996439 INFO: ms2_error      : 30
0:17:02.996480 INFO: fwhm_rt        : 3.0
0:17:02.996520 INFO: quant_window   : 3
0:17:02.996559 INFO: ==============================================
0:17:03.104235 INFO: performing precursor FDR with 40 features
0:17:03.104342 INFO: Decoy channel: -1
0:17:03.104367 INFO: competitive: True
0:17:03.108992 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:03.112924 INFO: Estimating optimal hyperparameters - samples: 14,036, batch_size: 128, learning_rate: 1.77e-04
0:17:03.113045 INFO: Using random state 126228 for train-test-split
0:17:04.456489 INFO: Test AUC: 0.526
0:17:04.456599 INFO: Train AUC: 0.565
0:17:04.456627 INFO: AUC difference: 6.82%
0:17:04.456648 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:05.148517 INFO: Resetting torch num_threads to 100
0:17:05.150904 PROGRESS: === Extracted 17545 precursors and 81471 fragments ===
0:17:05.151273 INFO: === FDR correction performed with classifier version 1 ===
0:17:05.151948 PROGRESS: ============================= Precursor FDR =============================
0:17:05.152030 PROGRESS: Total precursors accumulated: 2,222
0:17:05.152085 PROGRESS: Target precursors: 2,200 (99.01%)
0:17:05.152133 PROGRESS: Decoy precursors: 22 (0.99%)
0:17:05.152175 PROGRESS: 
0:17:05.152217 PROGRESS: Precursor Summary:
0:17:05.153806 PROGRESS: Channel   0:	 0.050 FDR: 2,200; 0.010 FDR: 2,200; 0.001 FDR: 2,200
0:17:05.153904 PROGRESS: 
0:17:05.153968 PROGRESS: Protein Summary:
0:17:05.156168 PROGRESS: Channel   0:	 0.050 FDR: 2,069; 0.010 FDR: 2,069; 0.001 FDR: 2,069
0:17:05.156260 PROGRESS: =========================================================================
0:17:05.156626 INFO: Target number of precursors reached.
0:17:05.170622 INFO: fragments_df: keeping 5000 of 81471 [sum(precursor_idx_mask)=29986 sum(mass_error_mask)=81471 stop_rank=5000
0:17:05.298017 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:05.620176 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:06.278869 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:06.279322 INFO: Using score_cutoff 6.540447775125504 (fac=0.99, q=1)
0:17:06.279634 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:06.279707 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:06.279757 INFO: Updating optimization_manager: score_cutoff        : 6.189774375486374 -> 6.540447775125504
0:17:06.279814 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:06.284025 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:06.292599 INFO: === checking if optimization conditions were reached ===
0:17:06.292725 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 5 ===
0:17:06.294757 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.617030461748435
0:17:06.294857 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.6170.
0:17:06.294929 INFO: ==============================================
0:17:06.295001 INFO: Starting optimization step 3.
0:17:06.295059 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:06.295119 INFO: Using rust extraction backend
0:17:06.295175 PROGRESS: Extracting batch of 5912 precursors
0:17:06.306695 INFO: === Search parameters used ===
0:17:06.306803 INFO: rt_error       : 805.5992431640625
0:17:06.306855 INFO: mobility_error : 0.1
0:17:06.306900 INFO: num_candidates : 3
0:17:06.306942 INFO: ms1_error      : 30
0:17:06.306982 INFO: ms2_error      : 7.617030461748435
0:17:06.307022 INFO: fwhm_rt        : 3.0
0:17:06.307061 INFO: quant_window   : 3
0:17:06.307101 INFO: ==============================================
0:17:06.406670 INFO: performing precursor FDR with 40 features
0:17:06.406783 INFO: Decoy channel: -1
0:17:06.406808 INFO: competitive: True
0:17:06.411347 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:06.415265 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
0:17:06.415384 INFO: Using random state 126228 for train-test-split
0:17:07.800694 INFO: Test AUC: 0.547
0:17:07.800809 INFO: Train AUC: 0.569
0:17:07.800840 INFO: AUC difference: 3.95%
0:17:08.046735 INFO: Resetting torch num_threads to 100
0:17:08.049208 PROGRESS: === Extracted 17726 precursors and 98799 fragments ===
0:17:08.049602 INFO: === FDR correction performed with classifier version 1 ===
0:17:08.050313 PROGRESS: ============================= Precursor FDR =============================
0:17:08.050404 PROGRESS: Total precursors accumulated: 2,460
0:17:08.050467 PROGRESS: Target precursors: 2,436 (99.02%)
0:17:08.050520 PROGRESS: Decoy precursors: 24 (0.98%)
0:17:08.050569 PROGRESS: 
0:17:08.050616 PROGRESS: Precursor Summary:
0:17:08.052280 PROGRESS: Channel   0:	 0.050 FDR: 2,436; 0.010 FDR: 2,436; 0.001 FDR: 2,436
0:17:08.052374 PROGRESS: 
0:17:08.052432 PROGRESS: Protein Summary:
0:17:08.054781 PROGRESS: Channel   0:	 0.050 FDR: 2,267; 0.010 FDR: 2,267; 0.001 FDR: 2,267
0:17:08.054876 PROGRESS: =========================================================================
0:17:08.055294 INFO: Target number of precursors reached.
0:17:08.072288 INFO: fragments_df: keeping 5000 of 98799 [sum(precursor_idx_mask)=39229 sum(mass_error_mask)=98799 stop_rank=5000
0:17:08.199336 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:08.545933 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:09.262440 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:09.263011 INFO: Using score_cutoff 4.334595952749252 (fac=0.99, q=1)
0:17:09.263418 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:09.263498 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:09.263554 INFO: Updating optimization_manager: score_cutoff        : 6.540447775125504 -> 4.334595952749252
0:17:09.263627 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:09.268167 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:09.276618 INFO: === checking if optimization conditions were reached ===
0:17:09.276735 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 5 ===
0:17:09.278951 INFO: Updating optimization_manager: ms2_error           : 7.617030461748435 -> 7.693248046325405
0:17:09.279069 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.6932.
0:17:09.279136 INFO: ==============================================
0:17:09.279211 INFO: Starting optimization step 4.
0:17:09.279274 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:09.279343 INFO: Using rust extraction backend
0:17:09.279405 PROGRESS: Extracting batch of 5912 precursors
0:17:09.291352 INFO: === Search parameters used ===
0:17:09.291465 INFO: rt_error       : 805.5992431640625
0:17:09.291518 INFO: mobility_error : 0.1
0:17:09.291565 INFO: num_candidates : 3
0:17:09.291609 INFO: ms1_error      : 30
0:17:09.291651 INFO: ms2_error      : 7.693248046325405
0:17:09.291693 INFO: fwhm_rt        : 3.0
0:17:09.291745 INFO: quant_window   : 3
0:17:09.291786 INFO: ==============================================
0:17:09.392175 INFO: performing precursor FDR with 40 features
0:17:09.392285 INFO: Decoy channel: -1
0:17:09.392310 INFO: competitive: True
0:17:09.397424 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:09.401436 INFO: Estimating optimal hyperparameters - samples: 14,179, batch_size: 128, learning_rate: 1.77e-04
0:17:09.401563 INFO: Using random state 126228 for train-test-split
0:17:10.789735 INFO: Test AUC: 0.536
0:17:10.789843 INFO: Train AUC: 0.563
0:17:10.789881 INFO: AUC difference: 4.79%
0:17:11.032475 INFO: Resetting torch num_threads to 100
0:17:11.034992 PROGRESS: === Extracted 17724 precursors and 98741 fragments ===
0:17:11.035368 INFO: === FDR correction performed with classifier version 1 ===
0:17:11.036087 PROGRESS: ============================= Precursor FDR =============================
0:17:11.036168 PROGRESS: Total precursors accumulated: 2,574
0:17:11.036225 PROGRESS: Target precursors: 2,549 (99.03%)
0:17:11.036272 PROGRESS: Decoy precursors: 25 (0.97%)
0:17:11.036322 PROGRESS: 
0:17:11.036367 PROGRESS: Precursor Summary:
0:17:11.038064 PROGRESS: Channel   0:	 0.050 FDR: 2,549; 0.010 FDR: 2,549; 0.001 FDR: 2,549
0:17:11.038155 PROGRESS: 
0:17:11.038208 PROGRESS: Protein Summary:
0:17:11.040584 PROGRESS: Channel   0:	 0.050 FDR: 2,367; 0.010 FDR: 2,367; 0.001 FDR: 2,367
0:17:11.040676 PROGRESS: =========================================================================
0:17:11.041134 INFO: Target number of precursors reached.
0:17:11.059355 INFO: fragments_df: keeping 5000 of 98741 [sum(precursor_idx_mask)=41882 sum(mass_error_mask)=98741 stop_rank=5000
0:17:11.187648 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:11.549895 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:12.262686 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:12.263139 INFO: Using score_cutoff 4.405004875373841 (fac=0.99, q=1)
0:17:12.263451 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:12.263525 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:12.263576 INFO: Updating optimization_manager: score_cutoff        : 4.334595952749252 -> 4.405004875373841
0:17:12.263629 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:12.267810 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:12.275167 INFO: === checking if optimization conditions were reached ===
0:17:12.275276 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 5 ===
0:17:12.277403 INFO: Updating optimization_manager: ms2_error           : 7.693248046325405 -> 7.668673052134506
0:17:12.277497 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 7.6687.
0:17:12.277564 INFO: ==============================================
0:17:12.277629 INFO: Starting optimization step 5.
0:17:12.277683 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:12.277741 INFO: Using rust extraction backend
0:17:12.277796 PROGRESS: Extracting batch of 5912 precursors
0:17:12.289945 INFO: === Search parameters used ===
0:17:12.290059 INFO: rt_error       : 805.5992431640625
0:17:12.290111 INFO: mobility_error : 0.1
0:17:12.290154 INFO: num_candidates : 3
0:17:12.290195 INFO: ms1_error      : 30
0:17:12.290235 INFO: ms2_error      : 7.668673052134506
0:17:12.290275 INFO: fwhm_rt        : 3.0
0:17:12.290313 INFO: quant_window   : 3
0:17:12.290352 INFO: ==============================================
0:17:12.391612 INFO: performing precursor FDR with 40 features
0:17:12.391721 INFO: Decoy channel: -1
0:17:12.391744 INFO: competitive: True
0:17:12.396337 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:12.400266 INFO: Estimating optimal hyperparameters - samples: 14,179, batch_size: 128, learning_rate: 1.77e-04
0:17:12.400379 INFO: Using random state 126228 for train-test-split
0:17:13.797399 INFO: Test AUC: 0.553
0:17:13.797513 INFO: Train AUC: 0.558
0:17:13.797543 INFO: AUC difference: 0.99%
0:17:14.040200 INFO: Resetting torch num_threads to 100
0:17:14.042582 PROGRESS: === Extracted 17724 precursors and 98795 fragments ===
0:17:14.042956 INFO: === FDR correction performed with classifier version 1 ===
0:17:14.043659 PROGRESS: ============================= Precursor FDR =============================
0:17:14.043746 PROGRESS: Total precursors accumulated: 2,427
0:17:14.043812 PROGRESS: Target precursors: 2,403 (99.01%)
0:17:14.043865 PROGRESS: Decoy precursors: 24 (0.99%)
0:17:14.043913 PROGRESS: 
0:17:14.043963 PROGRESS: Precursor Summary:
0:17:14.045601 PROGRESS: Channel   0:	 0.050 FDR: 2,403; 0.010 FDR: 2,403; 0.001 FDR: 2,403
0:17:14.045690 PROGRESS: 
0:17:14.045746 PROGRESS: Protein Summary:
0:17:14.048104 PROGRESS: Channel   0:	 0.050 FDR: 2,248; 0.010 FDR: 2,248; 0.001 FDR: 2,248
0:17:14.048215 PROGRESS: =========================================================================
0:17:14.048587 INFO: Target number of precursors reached.
0:17:14.065695 INFO: fragments_df: keeping 5000 of 98795 [sum(precursor_idx_mask)=40357 sum(mass_error_mask)=98795 stop_rank=5000
0:17:14.197708 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:14.542922 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:15.255033 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:15.255483 INFO: Using score_cutoff 4.380340574741364 (fac=0.99, q=1)
0:17:15.255784 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:15.255860 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:15.255914 INFO: Updating optimization_manager: score_cutoff        : 4.405004875373841 -> 4.380340574741364
0:17:15.255971 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:15.260160 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:15.267705 INFO: === checking if optimization conditions were reached ===
0:17:15.267824 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 5 ===
0:17:15.269986 INFO: Updating optimization_manager: ms2_error           : 7.668673052134506 -> 7.653571723967804
0:17:15.270088 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 7.6536.
0:17:15.270169 INFO: ==============================================
0:17:15.270234 INFO: Starting optimization step 6.
0:17:15.270290 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:15.270350 INFO: Using rust extraction backend
0:17:15.270406 PROGRESS: Extracting batch of 5912 precursors
0:17:15.281905 INFO: === Search parameters used ===
0:17:15.282011 INFO: rt_error       : 805.5992431640625
0:17:15.282062 INFO: mobility_error : 0.1
0:17:15.282105 INFO: num_candidates : 3
0:17:15.282146 INFO: ms1_error      : 30
0:17:15.282186 INFO: ms2_error      : 7.653571723967804
0:17:15.282226 INFO: fwhm_rt        : 3.0
0:17:15.282264 INFO: quant_window   : 3
0:17:15.282303 INFO: ==============================================
0:17:15.382959 INFO: performing precursor FDR with 40 features
0:17:15.383070 INFO: Decoy channel: -1
0:17:15.383093 INFO: competitive: True
0:17:15.387743 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:15.391656 INFO: Estimating optimal hyperparameters - samples: 14,179, batch_size: 128, learning_rate: 1.77e-04
0:17:15.391772 INFO: Using random state 126228 for train-test-split
0:17:16.792681 INFO: Test AUC: 0.531
0:17:16.792795 INFO: Train AUC: 0.567
0:17:16.792823 INFO: AUC difference: 6.30%
0:17:16.792845 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:17.032102 INFO: Resetting torch num_threads to 100
0:17:17.034419 PROGRESS: === Extracted 17724 precursors and 98811 fragments ===
0:17:17.034789 INFO: === FDR correction performed with classifier version 1 ===
0:17:17.035458 PROGRESS: ============================= Precursor FDR =============================
0:17:17.035538 PROGRESS: Total precursors accumulated: 2,151
0:17:17.035593 PROGRESS: Target precursors: 2,130 (99.02%)
0:17:17.035640 PROGRESS: Decoy precursors: 21 (0.98%)
0:17:17.035684 PROGRESS: 
0:17:17.035727 PROGRESS: Precursor Summary:
0:17:17.037267 PROGRESS: Channel   0:	 0.050 FDR: 2,130; 0.010 FDR: 2,130; 0.001 FDR: 2,130
0:17:17.037349 PROGRESS: 
0:17:17.037399 PROGRESS: Protein Summary:
0:17:17.039524 PROGRESS: Channel   0:	 0.050 FDR: 1,998; 0.010 FDR: 1,998; 0.001 FDR: 1,998
0:17:17.039615 PROGRESS: =========================================================================
0:17:17.039988 INFO: Target number of precursors reached.
0:17:17.056258 INFO: fragments_df: keeping 5000 of 98811 [sum(precursor_idx_mask)=34141 sum(mass_error_mask)=98811 stop_rank=5000
0:17:17.202970 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:17.519826 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:18.235206 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:18.235654 INFO: Using score_cutoff 4.292720779466629 (fac=0.99, q=1)
0:17:18.235966 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:18.236044 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:18.236101 INFO: Updating optimization_manager: score_cutoff        : 4.380340574741364 -> 4.292720779466629
0:17:18.236168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:18.240333 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:18.247864 INFO: === checking if optimization conditions were reached ===
0:17:18.247983 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 5 ===
0:17:18.248738 INFO: Updating optimization_manager: ms2_error           : 7.653571723967804 -> 7.693248046325405
0:17:18.248863 INFO: Updating optimization_manager: classifier_version  : 1 -> 4
0:17:18.248960 INFO: Updating optimization_manager: score_cutoff        : 4.292720779466629 -> 4.405004875373841
0:17:18.249057 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:18.249146 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:18.249232 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.6932 found after 5 searches.
0:17:18.249291 INFO: ==============================================
0:17:18.249363 PROGRESS: Optimization finished for ms2_error.
0:17:18.375469 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:18.379721 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:18.390599 INFO: Starting optimization step 0.
0:17:18.390714 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:18.390792 INFO: Using rust extraction backend
0:17:18.390856 PROGRESS: Extracting batch of 5912 precursors
0:17:18.402332 INFO: === Search parameters used ===
0:17:18.402445 INFO: rt_error       : 805.5992431640625
0:17:18.402514 INFO: mobility_error : 0.1
0:17:18.402562 INFO: num_candidates : 3
0:17:18.402606 INFO: ms1_error      : 30
0:17:18.402648 INFO: ms2_error      : 7.693248046325405
0:17:18.402689 INFO: fwhm_rt        : 3.0
0:17:18.402730 INFO: quant_window   : 3
0:17:18.402769 INFO: ==============================================
0:17:18.506217 INFO: performing precursor FDR with 40 features
0:17:18.506328 INFO: Decoy channel: -1
0:17:18.506353 INFO: competitive: True
0:17:18.510944 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:18.514826 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
0:17:18.514944 INFO: Using random state 415073 for train-test-split
0:17:19.934154 INFO: Test AUC: 0.574
0:17:19.934267 INFO: Train AUC: 0.577
0:17:19.934296 INFO: AUC difference: 0.52%
0:17:20.177663 INFO: Resetting torch num_threads to 100
0:17:20.184016 PROGRESS: === Extracted 17723 precursors and 98738 fragments ===
0:17:20.184395 INFO: === FDR correction performed with classifier version 4 ===
0:17:20.185083 PROGRESS: ============================= Precursor FDR =============================
0:17:20.185168 PROGRESS: Total precursors accumulated: 2,314
0:17:20.185225 PROGRESS: Target precursors: 2,292 (99.05%)
0:17:20.185275 PROGRESS: Decoy precursors: 22 (0.95%)
0:17:20.185320 PROGRESS: 
0:17:20.185363 PROGRESS: Precursor Summary:
0:17:20.186977 PROGRESS: Channel   0:	 0.050 FDR: 2,292; 0.010 FDR: 2,292; 0.001 FDR: 2,292
0:17:20.187074 PROGRESS: 
0:17:20.187129 PROGRESS: Protein Summary:
0:17:20.189376 PROGRESS: Channel   0:	 0.050 FDR: 2,146; 0.010 FDR: 2,146; 0.001 FDR: 2,146
0:17:20.189470 PROGRESS: =========================================================================
0:17:20.189890 INFO: Target number of precursors reached.
0:17:20.206782 INFO: fragments_df: keeping 5000 of 98738 [sum(precursor_idx_mask)=37619 sum(mass_error_mask)=98738 stop_rank=5000
0:17:20.333083 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:20.662444 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:21.371457 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:21.371911 INFO: Using score_cutoff 4.138899412393569 (fac=0.99, q=1)
0:17:21.372216 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:21.372290 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:21.372342 INFO: Updating optimization_manager: score_cutoff        : 4.405004875373841 -> 4.138899412393569
0:17:21.372398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:21.376584 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:21.384098 INFO: === checking if optimization conditions were reached ===
0:17:21.384222 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:17:21.386935 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 968.7671789858168
0:17:21.387041 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 968.7672.
0:17:21.387104 INFO: ==============================================
0:17:21.387170 INFO: Starting optimization step 1.
0:17:21.387225 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:21.387283 INFO: Using rust extraction backend
0:17:21.387338 PROGRESS: Extracting batch of 5912 precursors
0:17:21.398800 INFO: === Search parameters used ===
0:17:21.398909 INFO: rt_error       : 968.7671789858168
0:17:21.398960 INFO: mobility_error : 0.1
0:17:21.399004 INFO: num_candidates : 3
0:17:21.399045 INFO: ms1_error      : 30
0:17:21.399084 INFO: ms2_error      : 7.693248046325405
0:17:21.399124 INFO: fwhm_rt        : 3.0
0:17:21.399165 INFO: quant_window   : 3
0:17:21.399204 INFO: ==============================================
0:17:21.500888 INFO: performing precursor FDR with 40 features
0:17:21.501001 INFO: Decoy channel: -1
0:17:21.501025 INFO: competitive: True
0:17:21.505770 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:21.509625 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
0:17:21.509741 INFO: Using random state 415073 for train-test-split
0:17:22.924469 INFO: Test AUC: 0.540
0:17:22.924579 INFO: Train AUC: 0.588
0:17:22.924607 INFO: AUC difference: 8.18%
0:17:22.924628 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:23.165369 INFO: Resetting torch num_threads to 100
0:17:23.167733 PROGRESS: === Extracted 17723 precursors and 98742 fragments ===
0:17:23.168107 INFO: === FDR correction performed with classifier version 4 ===
0:17:23.168792 PROGRESS: ============================= Precursor FDR =============================
0:17:23.168878 PROGRESS: Total precursors accumulated: 2,321
0:17:23.168938 PROGRESS: Target precursors: 2,299 (99.05%)
0:17:23.168990 PROGRESS: Decoy precursors: 22 (0.95%)
0:17:23.169037 PROGRESS: 
0:17:23.169084 PROGRESS: Precursor Summary:
0:17:23.170728 PROGRESS: Channel   0:	 0.050 FDR: 2,299; 0.010 FDR: 2,299; 0.001 FDR: 2,299
0:17:23.170819 PROGRESS: 
0:17:23.170875 PROGRESS: Protein Summary:
0:17:23.173126 PROGRESS: Channel   0:	 0.050 FDR: 2,153; 0.010 FDR: 2,153; 0.001 FDR: 2,153
0:17:23.173236 PROGRESS: =========================================================================
0:17:23.173625 INFO: Target number of precursors reached.
0:17:23.190281 INFO: fragments_df: keeping 5000 of 98742 [sum(precursor_idx_mask)=36865 sum(mass_error_mask)=98742 stop_rank=5000
0:17:23.317170 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:23.643599 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:24.351331 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:24.351781 INFO: Using score_cutoff 3.924411928510666 (fac=0.99, q=1)
0:17:24.352083 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:24.352159 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:24.352213 INFO: Updating optimization_manager: score_cutoff        : 4.138899412393569 -> 3.924411928510666
0:17:24.352274 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:24.356459 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:24.364104 INFO: === checking if optimization conditions were reached ===
0:17:24.364212 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:17:24.367014 INFO: Updating optimization_manager: rt_error            : 968.7671789858168 -> 982.3186958047352
0:17:24.367126 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 982.3187.
0:17:24.367188 INFO: ==============================================
0:17:24.367252 INFO: Starting optimization step 2.
0:17:24.367308 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:24.367376 INFO: Using rust extraction backend
0:17:24.367433 PROGRESS: Extracting batch of 5912 precursors
0:17:24.379089 INFO: === Search parameters used ===
0:17:24.379198 INFO: rt_error       : 982.3186958047352
0:17:24.379248 INFO: mobility_error : 0.1
0:17:24.379292 INFO: num_candidates : 3
0:17:24.379334 INFO: ms1_error      : 30
0:17:24.379373 INFO: ms2_error      : 7.693248046325405
0:17:24.379414 INFO: fwhm_rt        : 3.0
0:17:24.379454 INFO: quant_window   : 3
0:17:24.379493 INFO: ==============================================
0:17:24.478302 INFO: performing precursor FDR with 40 features
0:17:24.478411 INFO: Decoy channel: -1
0:17:24.478436 INFO: competitive: True
0:17:24.483017 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:24.486841 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
0:17:24.486958 INFO: Using random state 415073 for train-test-split
0:17:25.899142 INFO: Test AUC: 0.554
0:17:25.899251 INFO: Train AUC: 0.589
0:17:25.899279 INFO: AUC difference: 6.03%
0:17:25.899302 WARNING: AUC difference > 5%. This may indicate overfitting.
0:17:26.524851 INFO: Resetting torch num_threads to 100
0:17:26.527320 PROGRESS: === Extracted 17723 precursors and 98733 fragments ===
0:17:26.527695 INFO: === FDR correction performed with classifier version 4 ===
0:17:26.528406 PROGRESS: ============================= Precursor FDR =============================
0:17:26.528490 PROGRESS: Total precursors accumulated: 2,332
0:17:26.528546 PROGRESS: Target precursors: 2,309 (99.01%)
0:17:26.528594 PROGRESS: Decoy precursors: 23 (0.99%)
0:17:26.528639 PROGRESS: 
0:17:26.528684 PROGRESS: Precursor Summary:
0:17:26.530327 PROGRESS: Channel   0:	 0.050 FDR: 2,309; 0.010 FDR: 2,309; 0.001 FDR: 2,309
0:17:26.530420 PROGRESS: 
0:17:26.530475 PROGRESS: Protein Summary:
0:17:26.532773 PROGRESS: Channel   0:	 0.050 FDR: 2,157; 0.010 FDR: 2,157; 0.001 FDR: 2,157
0:17:26.532861 PROGRESS: =========================================================================
0:17:26.533231 INFO: Target number of precursors reached.
0:17:26.550336 INFO: fragments_df: keeping 5000 of 98733 [sum(precursor_idx_mask)=37748 sum(mass_error_mask)=98733 stop_rank=5000
0:17:26.677612 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:26.984150 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:27.697633 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:27.698079 INFO: Using score_cutoff 3.9152261544227605 (fac=0.99, q=1)
0:17:27.698386 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:27.698460 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:27.698511 INFO: Updating optimization_manager: score_cutoff        : 3.924411928510666 -> 3.9152261544227605
0:17:27.698561 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:27.702739 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:27.710279 INFO: === checking if optimization conditions were reached ===
0:17:27.710394 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:17:27.713299 INFO: Updating optimization_manager: rt_error            : 982.3186958047352 -> 977.5835210800019
0:17:27.713406 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 977.5835.
0:17:27.713470 INFO: ==============================================
0:17:27.713539 INFO: Starting optimization step 3.
0:17:27.713598 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:27.713655 INFO: Using rust extraction backend
0:17:27.713707 PROGRESS: Extracting batch of 5912 precursors
0:17:27.725544 INFO: === Search parameters used ===
0:17:27.725664 INFO: rt_error       : 977.5835210800019
0:17:27.725714 INFO: mobility_error : 0.1
0:17:27.725758 INFO: num_candidates : 3
0:17:27.725800 INFO: ms1_error      : 30
0:17:27.725841 INFO: ms2_error      : 7.693248046325405
0:17:27.725895 INFO: fwhm_rt        : 3.0
0:17:27.725936 INFO: quant_window   : 3
0:17:27.725976 INFO: ==============================================
0:17:27.831766 INFO: performing precursor FDR with 40 features
0:17:27.831877 INFO: Decoy channel: -1
0:17:27.831900 INFO: competitive: True
0:17:27.836749 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:27.840755 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
0:17:27.840878 INFO: Using random state 415073 for train-test-split
0:17:29.226720 INFO: Test AUC: 0.561
0:17:29.226831 INFO: Train AUC: 0.582
0:17:29.226860 INFO: AUC difference: 3.63%
0:17:29.466992 INFO: Resetting torch num_threads to 100
0:17:29.469362 PROGRESS: === Extracted 17720 precursors and 98746 fragments ===
0:17:29.469739 INFO: === FDR correction performed with classifier version 4 ===
0:17:29.470469 PROGRESS: ============================= Precursor FDR =============================
0:17:29.470560 PROGRESS: Total precursors accumulated: 2,358
0:17:29.470619 PROGRESS: Target precursors: 2,335 (99.02%)
0:17:29.470671 PROGRESS: Decoy precursors: 23 (0.98%)
0:17:29.470719 PROGRESS: 
0:17:29.470764 PROGRESS: Precursor Summary:
0:17:29.472391 PROGRESS: Channel   0:	 0.050 FDR: 2,335; 0.010 FDR: 2,335; 0.001 FDR: 2,335
0:17:29.472485 PROGRESS: 
0:17:29.472543 PROGRESS: Protein Summary:
0:17:29.474841 PROGRESS: Channel   0:	 0.050 FDR: 2,180; 0.010 FDR: 2,180; 0.001 FDR: 2,180
0:17:29.474934 PROGRESS: =========================================================================
0:17:29.475327 INFO: Target number of precursors reached.
0:17:29.492085 INFO: fragments_df: keeping 5000 of 98746 [sum(precursor_idx_mask)=38216 sum(mass_error_mask)=98746 stop_rank=5000
0:17:29.620237 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:29.955052 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:30.664217 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:30.664670 INFO: Using score_cutoff 4.194596736145019 (fac=0.99, q=1)
0:17:30.664978 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:30.665054 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:30.665107 INFO: Updating optimization_manager: score_cutoff        : 3.9152261544227605 -> 4.194596736145019
0:17:30.665160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:30.669349 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:30.676973 INFO: === checking if optimization conditions were reached ===
0:17:30.677091 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:17:30.679995 INFO: Updating optimization_manager: rt_error            : 977.5835210800019 -> 974.3757537567799
0:17:30.680100 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 974.3758.
0:17:30.680171 INFO: ==============================================
0:17:30.680240 INFO: Starting optimization step 4.
0:17:30.680296 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:17:30.680356 INFO: Using rust extraction backend
0:17:30.680409 PROGRESS: Extracting batch of 5912 precursors
0:17:30.692022 INFO: === Search parameters used ===
0:17:30.692142 INFO: rt_error       : 974.3757537567799
0:17:30.692205 INFO: mobility_error : 0.1
0:17:30.692250 INFO: num_candidates : 3
0:17:30.692290 INFO: ms1_error      : 30
0:17:30.692330 INFO: ms2_error      : 7.693248046325405
0:17:30.692368 INFO: fwhm_rt        : 3.0
0:17:30.692407 INFO: quant_window   : 3
0:17:30.692445 INFO: ==============================================
0:17:30.795249 INFO: performing precursor FDR with 40 features
0:17:30.795359 INFO: Decoy channel: -1
0:17:30.795383 INFO: competitive: True
0:17:30.800129 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:30.803989 INFO: Estimating optimal hyperparameters - samples: 14,177, batch_size: 128, learning_rate: 1.77e-04
0:17:30.804103 INFO: Using random state 415073 for train-test-split
0:17:32.198870 INFO: Test AUC: 0.569
0:17:32.198982 INFO: Train AUC: 0.584
0:17:32.199009 INFO: AUC difference: 2.51%
0:17:32.438936 INFO: Resetting torch num_threads to 100
0:17:32.441298 PROGRESS: === Extracted 17722 precursors and 98780 fragments ===
0:17:32.441668 INFO: === FDR correction performed with classifier version 4 ===
0:17:32.442356 PROGRESS: ============================= Precursor FDR =============================
0:17:32.442441 PROGRESS: Total precursors accumulated: 2,371
0:17:32.442498 PROGRESS: Target precursors: 2,348 (99.03%)
0:17:32.442545 PROGRESS: Decoy precursors: 23 (0.97%)
0:17:32.442590 PROGRESS: 
0:17:32.442638 PROGRESS: Precursor Summary:
0:17:32.444258 PROGRESS: Channel   0:	 0.050 FDR: 2,348; 0.010 FDR: 2,348; 0.001 FDR: 2,348
0:17:32.444342 PROGRESS: 
0:17:32.444395 PROGRESS: Protein Summary:
0:17:32.446703 PROGRESS: Channel   0:	 0.050 FDR: 2,199; 0.010 FDR: 2,199; 0.001 FDR: 2,199
0:17:32.446796 PROGRESS: =========================================================================
0:17:32.447168 INFO: Target number of precursors reached.
0:17:32.464078 INFO: fragments_df: keeping 5000 of 98780 [sum(precursor_idx_mask)=38964 sum(mass_error_mask)=98780 stop_rank=5000
0:17:32.590626 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:32.925347 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:33.634152 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:33.634606 INFO: Using score_cutoff 4.297803062582016 (fac=0.99, q=1)
0:17:33.634915 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:33.634990 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:33.635041 INFO: Updating optimization_manager: score_cutoff        : 4.194596736145019 -> 4.297803062582016
0:17:33.635091 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:33.639267 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:33.646867 INFO: === checking if optimization conditions were reached ===
0:17:33.646974 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:17:33.647681 INFO: Updating optimization_manager: rt_error            : 974.3757537567799 -> 974.3757537567799
0:17:33.647801 INFO: Updating optimization_manager: classifier_version  : 4 -> 11
0:17:33.647896 INFO: Updating optimization_manager: score_cutoff        : 4.297803062582016 -> 4.297803062582016
0:17:33.647981 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:33.648062 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:33.648144 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 974.3758 found after 5 searches.
0:17:33.648200 INFO: ==============================================
0:17:33.648260 PROGRESS: Optimization finished for rt_error.
0:17:33.775074 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:33.779367 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:33.786930 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:17:33.787037 PROGRESS: ==============================================
0:17:33.787108 PROGRESS: ms2_error      : 7.6932
0:17:33.787164 PROGRESS: rt_error       : 974.3758
0:17:33.787225 PROGRESS: ==============================================
0:17:33.787907 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:41.015707 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:57.551549 INFO: Using rust extraction backend
0:17:57.551992 PROGRESS: Extracting batch of 11997144 precursors
0:18:13.630598 INFO: === Search parameters used ===
0:18:13.631097 INFO: rt_error       : 974.3757537567799
0:18:13.631161 INFO: mobility_error : 0.1
0:18:13.631217 INFO: num_candidates : 3
0:18:13.631263 INFO: ms1_error      : 30
0:18:13.631305 INFO: ms2_error      : 7.693248046325405
0:18:13.631346 INFO: fwhm_rt        : 3.0
0:18:13.631390 INFO: quant_window   : 3
0:18:13.631435 INFO: ==============================================
0:18:48.914475 INFO: Removed 511385 precursors with score below cutoff 4.297803062582016
0:19:16.285206 INFO: performing precursor FDR with 40 features
0:19:16.285368 INFO: Decoy channel: -1
0:19:16.285397 INFO: competitive: True
0:19:19.958330 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:34.827666 INFO: Estimating optimal hyperparameters - samples: 28,383,752, batch_size: 4,096, learning_rate: 1.00e-03
0:19:34.918698 INFO: Using random state 745889 for train-test-split
0:28:36.821383 INFO: Test AUC: 0.622
0:28:36.821662 INFO: Train AUC: 0.623
0:28:36.821703 INFO: AUC difference: 0.08%
0:28:43.741831 INFO: Resetting torch num_threads to 100
0:28:45.870837 PROGRESS: ============================= Precursor FDR =============================
0:28:45.871155 PROGRESS: Total precursors accumulated: 77,322
0:28:45.871234 PROGRESS: Target precursors: 76,557 (99.01%)
0:28:45.871289 PROGRESS: Decoy precursors: 765 (0.99%)
0:28:45.871339 PROGRESS: 
0:28:45.871386 PROGRESS: Precursor Summary:
0:28:45.889907 PROGRESS: Channel   0:	 0.050 FDR: 76,557; 0.010 FDR: 76,557; 0.001 FDR: 26,347
0:28:45.890152 PROGRESS: 
0:28:45.890215 PROGRESS: Protein Summary:
0:28:45.915808 PROGRESS: Channel   0:	 0.050 FDR: 12,047; 0.010 FDR: 12,047; 0.001 FDR: 6,111
0:28:45.916059 PROGRESS: =========================================================================
0:28:46.103815 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:28:46.241493 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:28:46.439095 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:28:46.890643 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
0:28:46.890799 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant
0:28:46.890905 INFO: Initializing TimingManager
0:28:46.891580 INFO: Initializing RawFileManager
0:29:01.590388 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.
0:29:01.606420 INFO: Determining DIA cycle
0:29:01.624150 INFO: Found cycle with start 0.00 min and length 300.
0:29:01.860923 INFO: RT (min)            : 0.0 - 26.9
0:29:01.861022 INFO: RT duration (sec)   : 1611.2
0:29:01.861052 INFO: RT duration (min)   : 26.9
0:29:01.861073 INFO: Cycle len (scans)   : 300
0:29:01.861093 INFO: Cycle len (sec)     : 1.65
0:29:01.861111 INFO: Number of cycles    : 978
0:29:01.861131 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:29:01.861171 INFO: Creating DIA data object took: 14.969493627548218
0:29:02.562102 INFO: Creating DIA data NG object took: 0.7007944583892822
0:29:03.940015 INFO: Initializing CalibrationManager
0:29:03.940323 INFO: Setting up calibration estimators ..
0:29:03.940391 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:29:03.940471 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'}' ..
0:29:03.940575 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:29:03.940629 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:29:03.940686 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}}' ..
0:29:03.940740 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:29:03.940786 INFO: Done setting up calibration estimators.
0:29:03.940983 INFO: Initializing OptimizationManager
0:29:03.941111 INFO: initial parameter: ms1_error = 30
0:29:03.941163 INFO: initial parameter: ms2_error = 30
0:29:03.941209 INFO: initial parameter: rt_error = 805.6019897460938
0:29:03.941252 INFO: initial parameter: mobility_error = 0.1
0:29:03.941292 INFO: initial parameter: num_candidates = 1
0:29:03.941331 INFO: initial parameter: fwhm_rt = 5
0:29:03.941371 INFO: initial parameter: fwhm_mobility = 0.01
0:29:03.941413 INFO: initial parameter: score_cutoff = 0
0:29:03.941454 INFO: initial parameter: classifier_version = -1
0:29:03.941523 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:29:03.941799 INFO: FDRManager: loading saved state not requested, will be initialized.
0:29:03.941828 INFO: Initializing FDRManager
0:29:03.941885 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:29:05.377368 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:29:06.285530 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:29:06.285906 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:29:06.286016 PROGRESS: Starting initial search for precursors.
0:29:06.286105 INFO: Starting optimization step 0.
0:29:06.286170 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:29:06.286231 INFO: Using rust extraction backend
0:29:06.286294 PROGRESS: Extracting batch of 1970 precursors
0:29:06.291267 INFO: === Search parameters used ===
0:29:06.291372 INFO: rt_error       : 805.6019897460938
0:29:06.291423 INFO: mobility_error : 0.1
0:29:06.291469 INFO: num_candidates : 1
0:29:06.291513 INFO: ms1_error      : 30
0:29:06.291555 INFO: ms2_error      : 30
0:29:06.291601 INFO: fwhm_rt        : 5
0:29:06.291643 INFO: quant_window   : 3
0:29:06.291685 INFO: ==============================================
0:29:06.319396 INFO: performing precursor FDR with 40 features
0:29:06.319470 INFO: Decoy channel: -1
0:29:06.319496 INFO: competitive: True
0:29:06.320781 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:06.322582 INFO: Estimating optimal hyperparameters - samples: 1,560, batch_size: 128, learning_rate: 1.77e-04
0:29:06.323530 INFO: Using random state 753575 for train-test-split
0:29:06.440331 INFO: Test AUC: 0.523
0:29:06.440408 INFO: Train AUC: 0.581
0:29:06.440438 INFO: AUC difference: 10.04%
0:29:06.440462 WARNING: AUC difference > 5%. This may indicate overfitting.
0:29:06.677251 INFO: Resetting torch num_threads to 100
0:29:06.678729 PROGRESS: === Extracted 1950 precursors and 9160 fragments ===
0:29:06.679104 INFO: === FDR correction performed with classifier version -1 ===
0:29:06.679570 PROGRESS: ============================= Precursor FDR =============================
0:29:06.679656 PROGRESS: Total precursors accumulated: 0
0:29:06.679725 PROGRESS: Target precursors: 0 (0.00%)
0:29:06.679776 PROGRESS: Decoy precursors: 0 (0.00%)
0:29:06.679823 PROGRESS: 
0:29:06.679868 PROGRESS: Precursor Summary:
0:29:06.679976 PROGRESS: 
0:29:06.680034 PROGRESS: Protein Summary:
0:29:06.680107 PROGRESS: =========================================================================
0:29:06.680295 INFO: Target number of precursors not reached yet.
0:29:06.766909 INFO: Starting optimization step 1.
0:29:06.767159 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:29:06.767236 INFO: Using rust extraction backend
0:29:06.767294 PROGRESS: Extracting batch of 3942 precursors
0:29:06.775601 INFO: === Search parameters used ===
0:29:06.775723 INFO: rt_error       : 805.6019897460938
0:29:06.775775 INFO: mobility_error : 0.1
0:29:06.775823 INFO: num_candidates : 1
0:29:06.775866 INFO: ms1_error      : 30
0:29:06.775907 INFO: ms2_error      : 30
0:29:06.775946 INFO: fwhm_rt        : 5
0:29:06.775986 INFO: quant_window   : 3
0:29:06.776024 INFO: ==============================================
0:29:06.822584 INFO: performing precursor FDR with 40 features
0:29:06.822676 INFO: Decoy channel: -1
0:29:06.822700 INFO: competitive: True
0:29:06.827004 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:06.829401 INFO: Estimating optimal hyperparameters - samples: 4,682, batch_size: 128, learning_rate: 1.77e-04
0:29:06.829481 INFO: Using random state 583725 for train-test-split
0:29:07.231451 INFO: Test AUC: 0.569
0:29:07.231543 INFO: Train AUC: 0.574
0:29:07.231571 INFO: AUC difference: 0.80%
0:29:07.473978 INFO: Resetting torch num_threads to 100
0:29:07.476761 PROGRESS: === Extracted 5853 precursors and 27433 fragments ===
0:29:07.477127 INFO: === FDR correction performed with classifier version -1 ===
0:29:07.477609 PROGRESS: ============================= Precursor FDR =============================
0:29:07.477690 PROGRESS: Total precursors accumulated: 11
0:29:07.477746 PROGRESS: Target precursors: 11 (100.00%)
0:29:07.477796 PROGRESS: Decoy precursors: 0 (0.00%)
0:29:07.477840 PROGRESS: 
0:29:07.477916 PROGRESS: Precursor Summary:
0:29:07.478971 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
0:29:07.479051 PROGRESS: 
0:29:07.479110 PROGRESS: Protein Summary:
0:29:07.480275 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
0:29:07.480356 PROGRESS: =========================================================================
0:29:07.480600 INFO: Target number of precursors not reached yet.
0:29:07.570454 INFO: Starting optimization step 2.
0:29:07.570689 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:29:07.570764 INFO: Using rust extraction backend
0:29:07.570822 PROGRESS: Extracting batch of 7890 precursors
0:29:07.587471 INFO: === Search parameters used ===
0:29:07.587625 INFO: rt_error       : 805.6019897460938
0:29:07.587677 INFO: mobility_error : 0.1
0:29:07.587724 INFO: num_candidates : 1
0:29:07.587767 INFO: ms1_error      : 30
0:29:07.587808 INFO: ms2_error      : 30
0:29:07.587848 INFO: fwhm_rt        : 5
0:29:07.587887 INFO: quant_window   : 3
0:29:07.587925 INFO: ==============================================
0:29:07.668307 INFO: performing precursor FDR with 40 features
0:29:07.668417 INFO: Decoy channel: -1
0:29:07.668441 INFO: competitive: True
0:29:07.675465 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:07.679427 INFO: Estimating optimal hyperparameters - samples: 10,932, batch_size: 128, learning_rate: 1.77e-04
0:29:07.679569 INFO: Using random state 905395 for train-test-split
0:29:08.794886 INFO: Test AUC: 0.561
0:29:08.794992 INFO: Train AUC: 0.591
0:29:08.795020 INFO: AUC difference: 5.10%
0:29:08.795040 WARNING: AUC difference > 5%. This may indicate overfitting.
0:29:09.042373 INFO: Resetting torch num_threads to 100
0:29:09.046229 PROGRESS: === Extracted 13666 precursors and 64360 fragments ===
0:29:09.046616 INFO: === FDR correction performed with classifier version -1 ===
0:29:09.047113 PROGRESS: ============================= Precursor FDR =============================
0:29:09.047202 PROGRESS: Total precursors accumulated: 26
0:29:09.047274 PROGRESS: Target precursors: 26 (100.00%)
0:29:09.047325 PROGRESS: Decoy precursors: 0 (0.00%)
0:29:09.047369 PROGRESS: 
0:29:09.047413 PROGRESS: Precursor Summary:
0:29:09.048476 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:29:09.048561 PROGRESS: 
0:29:09.048623 PROGRESS: Protein Summary:
0:29:09.049797 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:29:09.049893 PROGRESS: =========================================================================
0:29:09.050215 INFO: Target number of precursors not reached yet.
0:29:09.149822 INFO: Starting optimization step 3.
0:29:09.150079 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:29:09.150156 INFO: Using rust extraction backend
0:29:09.150214 PROGRESS: Extracting batch of 15788 precursors
0:29:09.178464 INFO: === Search parameters used ===
0:29:09.178634 INFO: rt_error       : 805.6019897460938
0:29:09.178686 INFO: mobility_error : 0.1
0:29:09.178731 INFO: num_candidates : 1
0:29:09.178773 INFO: ms1_error      : 30
0:29:09.178815 INFO: ms2_error      : 30
0:29:09.178855 INFO: fwhm_rt        : 5
0:29:09.178895 INFO: quant_window   : 3
0:29:09.178952 INFO: ==============================================
0:29:09.313716 INFO: performing precursor FDR with 40 features
0:29:09.313832 INFO: Decoy channel: -1
0:29:09.313871 INFO: competitive: True
0:29:09.324521 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:09.332334 INFO: Estimating optimal hyperparameters - samples: 23,428, batch_size: 128, learning_rate: 1.77e-04
0:29:09.332502 INFO: Using random state 436396 for train-test-split
0:29:11.713954 INFO: Test AUC: 0.565
0:29:11.714078 INFO: Train AUC: 0.608
0:29:11.714108 INFO: AUC difference: 7.11%
0:29:11.714131 WARNING: AUC difference > 5%. This may indicate overfitting.
0:29:11.963993 INFO: Resetting torch num_threads to 100
0:29:11.970037 PROGRESS: === Extracted 29285 precursors and 138052 fragments ===
0:29:11.970506 INFO: === FDR correction performed with classifier version -1 ===
0:29:11.971040 PROGRESS: ============================= Precursor FDR =============================
0:29:11.971134 PROGRESS: Total precursors accumulated: 68
0:29:11.971195 PROGRESS: Target precursors: 68 (100.00%)
0:29:11.971248 PROGRESS: Decoy precursors: 0 (0.00%)
0:29:11.971297 PROGRESS: 
0:29:11.971343 PROGRESS: Precursor Summary:
0:29:11.972411 PROGRESS: Channel   0:	 0.050 FDR:    68; 0.010 FDR:    68; 0.001 FDR:    68
0:29:11.972495 PROGRESS: 
0:29:11.972552 PROGRESS: Protein Summary:
0:29:11.973752 PROGRESS: Channel   0:	 0.050 FDR:    67; 0.010 FDR:    67; 0.001 FDR:    67
0:29:11.973840 PROGRESS: =========================================================================
0:29:11.974337 INFO: Target number of precursors not reached yet.
0:29:12.092863 INFO: Starting optimization step 4.
0:29:12.093122 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:29:12.093204 INFO: Using rust extraction backend
0:29:12.093267 PROGRESS: Extracting batch of 31512 precursors
0:29:12.148180 INFO: === Search parameters used ===
0:29:12.148408 INFO: rt_error       : 805.6019897460938
0:29:12.148476 INFO: mobility_error : 0.1
0:29:12.148584 INFO: num_candidates : 1
0:29:12.148630 INFO: ms1_error      : 30
0:29:12.148673 INFO: ms2_error      : 30
0:29:12.148715 INFO: fwhm_rt        : 5
0:29:12.148758 INFO: quant_window   : 3
0:29:12.148799 INFO: ==============================================
0:29:12.369161 INFO: performing precursor FDR with 40 features
0:29:12.369275 INFO: Decoy channel: -1
0:29:12.369300 INFO: competitive: True
0:29:12.391549 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:12.405154 INFO: Estimating optimal hyperparameters - samples: 48,373, batch_size: 198, learning_rate: 2.20e-04
0:29:12.405366 INFO: Using random state 325038 for train-test-split
0:29:16.088347 INFO: Test AUC: 0.580
0:29:16.088475 INFO: Train AUC: 0.608
0:29:16.088506 INFO: AUC difference: 4.60%
0:29:16.344002 INFO: Resetting torch num_threads to 100
0:29:16.354119 PROGRESS: === Extracted 60467 precursors and 285178 fragments ===
0:29:16.354643 INFO: === FDR correction performed with classifier version -1 ===
0:29:16.355162 PROGRESS: ============================= Precursor FDR =============================
0:29:16.355254 PROGRESS: Total precursors accumulated: 146
0:29:16.355329 PROGRESS: Target precursors: 145 (99.32%)
0:29:16.355382 PROGRESS: Decoy precursors: 1 (0.68%)
0:29:16.355428 PROGRESS: 
0:29:16.355476 PROGRESS: Precursor Summary:
0:29:16.356477 PROGRESS: Channel   0:	 0.050 FDR:   145; 0.010 FDR:   145; 0.001 FDR:   115
0:29:16.356565 PROGRESS: 
0:29:16.356623 PROGRESS: Protein Summary:
0:29:16.357737 PROGRESS: Channel   0:	 0.050 FDR:   142; 0.010 FDR:   142; 0.001 FDR:   112
0:29:16.357823 PROGRESS: =========================================================================
0:29:16.358776 INFO: Target number of precursors not reached yet.
0:29:16.519392 INFO: Starting optimization step 5.
0:29:16.519674 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:29:16.519753 INFO: Using rust extraction backend
0:29:16.519812 PROGRESS: Extracting batch of 63110 precursors
0:29:16.627695 INFO: === Search parameters used ===
0:29:16.627955 INFO: rt_error       : 805.6019897460938
0:29:16.628008 INFO: mobility_error : 0.1
0:29:16.628054 INFO: num_candidates : 1
0:29:16.628098 INFO: ms1_error      : 30
0:29:16.628141 INFO: ms2_error      : 30
0:29:16.628182 INFO: fwhm_rt        : 5
0:29:16.628222 INFO: quant_window   : 3
0:29:16.628262 INFO: ==============================================
0:29:17.002305 INFO: performing precursor FDR with 40 features
0:29:17.002429 INFO: Decoy channel: -1
0:29:17.002453 INFO: competitive: True
0:29:17.055996 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:17.088953 INFO: Estimating optimal hyperparameters - samples: 98,338, batch_size: 402, learning_rate: 3.13e-04
0:29:17.089235 INFO: Using random state 410686 for train-test-split
0:29:21.773006 INFO: Test AUC: 0.578
0:29:21.773134 INFO: Train AUC: 0.613
0:29:21.773167 INFO: AUC difference: 5.65%
0:29:21.773190 WARNING: AUC difference > 5%. This may indicate overfitting.
0:29:22.049767 INFO: Resetting torch num_threads to 100
0:29:22.075525 PROGRESS: === Extracted 122923 precursors and 578562 fragments ===
0:29:22.076088 INFO: === FDR correction performed with classifier version -1 ===
0:29:22.076682 PROGRESS: ============================= Precursor FDR =============================
0:29:22.076779 PROGRESS: Total precursors accumulated: 346
0:29:22.076840 PROGRESS: Target precursors: 343 (99.13%)
0:29:22.076893 PROGRESS: Decoy precursors: 3 (0.87%)
0:29:22.076941 PROGRESS: 
0:29:22.076988 PROGRESS: Precursor Summary:
0:29:22.078092 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   343; 0.001 FDR:   264
0:29:22.078199 PROGRESS: 
0:29:22.078257 PROGRESS: Protein Summary:
0:29:22.079510 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   253
0:29:22.079600 PROGRESS: =========================================================================
0:29:22.081113 INFO: Target number of precursors not reached yet.
0:29:22.322217 INFO: Starting optimization step 6.
0:29:22.322489 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:29:22.322571 INFO: Using rust extraction backend
0:29:22.322636 PROGRESS: Extracting batch of 126235 precursors
0:29:22.537213 INFO: === Search parameters used ===
0:29:22.537469 INFO: rt_error       : 805.6019897460938
0:29:22.537527 INFO: mobility_error : 0.1
0:29:22.537577 INFO: num_candidates : 1
0:29:22.537622 INFO: ms1_error      : 30
0:29:22.537666 INFO: ms2_error      : 30
0:29:22.537709 INFO: fwhm_rt        : 5
0:29:22.537751 INFO: quant_window   : 3
0:29:22.537794 INFO: ==============================================
0:29:23.243588 INFO: performing precursor FDR with 40 features
0:29:23.243715 INFO: Decoy channel: -1
0:29:23.243742 INFO: competitive: True
0:29:23.361665 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:23.441978 INFO: Estimating optimal hyperparameters - samples: 198,298, batch_size: 812, learning_rate: 4.45e-04
0:29:23.442407 INFO: Using random state 379053 for train-test-split
0:29:29.749310 INFO: Test AUC: 0.586
0:29:29.749445 INFO: Train AUC: 0.610
0:29:29.749476 INFO: AUC difference: 3.83%
0:29:30.559251 INFO: Resetting torch num_threads to 100
0:29:30.606646 PROGRESS: === Extracted 247873 precursors and 1166298 fragments ===
0:29:30.607303 INFO: === FDR correction performed with classifier version -1 ===
0:29:30.608037 PROGRESS: ============================= Precursor FDR =============================
0:29:30.608127 PROGRESS: Total precursors accumulated: 947
0:29:30.608195 PROGRESS: Target precursors: 938 (99.05%)
0:29:30.608248 PROGRESS: Decoy precursors: 9 (0.95%)
0:29:30.608295 PROGRESS: 
0:29:30.608341 PROGRESS: Precursor Summary:
0:29:30.609557 PROGRESS: Channel   0:	 0.050 FDR:   938; 0.010 FDR:   938; 0.001 FDR:   440
0:29:30.609647 PROGRESS: 
0:29:30.609701 PROGRESS: Protein Summary:
0:29:30.611193 PROGRESS: Channel   0:	 0.050 FDR:   830; 0.010 FDR:   830; 0.001 FDR:   409
0:29:30.611285 PROGRESS: =========================================================================
0:29:30.614872 INFO: Target number of precursors not reached yet.
0:29:31.004683 INFO: Starting optimization step 7.
0:29:31.004963 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:29:31.005050 INFO: Using rust extraction backend
0:29:31.005120 PROGRESS: Extracting batch of 252313 precursors
0:29:31.429734 INFO: === Search parameters used ===
0:29:31.430005 INFO: rt_error       : 805.6019897460938
0:29:31.430062 INFO: mobility_error : 0.1
0:29:31.430111 INFO: num_candidates : 1
0:29:31.430156 INFO: ms1_error      : 30
0:29:31.430201 INFO: ms2_error      : 30
0:29:31.430245 INFO: fwhm_rt        : 5
0:29:31.430305 INFO: quant_window   : 3
0:29:31.430351 INFO: ==============================================
0:29:32.758985 INFO: performing precursor FDR with 40 features
0:29:32.759104 INFO: Decoy channel: -1
0:29:32.759130 INFO: competitive: True
0:29:32.998779 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:33.190663 INFO: Estimating optimal hyperparameters - samples: 398,084, batch_size: 1,630, learning_rate: 6.31e-04
0:29:33.191250 INFO: Using random state 390847 for train-test-split
0:29:43.563040 INFO: Test AUC: 0.591
0:29:43.563172 INFO: Train AUC: 0.607
0:29:43.563203 INFO: AUC difference: 2.59%
0:29:43.953713 INFO: Resetting torch num_threads to 100
0:29:44.037651 PROGRESS: === Extracted 497606 precursors and 2343103 fragments ===
0:29:44.038338 INFO: === FDR correction performed with classifier version -1 ===
0:29:44.039182 PROGRESS: ============================= Precursor FDR =============================
0:29:44.039270 PROGRESS: Total precursors accumulated: 1,646
0:29:44.039330 PROGRESS: Target precursors: 1,630 (99.03%)
0:29:44.039381 PROGRESS: Decoy precursors: 16 (0.97%)
0:29:44.039428 PROGRESS: 
0:29:44.039474 PROGRESS: Precursor Summary:
0:29:44.040871 PROGRESS: Channel   0:	 0.050 FDR: 1,630; 0.010 FDR: 1,630; 0.001 FDR: 1,132
0:29:44.040965 PROGRESS: 
0:29:44.041023 PROGRESS: Protein Summary:
0:29:44.042885 PROGRESS: Channel   0:	 0.050 FDR: 1,316; 0.010 FDR: 1,316; 0.001 FDR:   937
0:29:44.042981 PROGRESS: =========================================================================
0:29:44.050019 INFO: Target number of precursors reached.
0:29:44.321154 INFO: fragments_df: keeping 5000 of 2343103 [sum(precursor_idx_mask)=17517 sum(mass_error_mask)=2343103 stop_rank=5000
0:29:45.025204 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:45.285813 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:45.996087 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:29:45.996530 INFO: Using score_cutoff 12.935032365989684 (fac=0.99, q=1)
0:29:45.996844 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:29:45.996919 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:29:45.996975 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.935032365989684
0:29:45.997028 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:46.308056 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:46.971237 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:29:46.971487 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:29:46.971601 INFO: Starting optimization step 8.
0:29:46.971663 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:29:46.971724 INFO: Using rust extraction backend
0:29:46.971778 PROGRESS: Extracting batch of 502760 precursors
0:29:47.809534 INFO: === Search parameters used ===
0:29:47.809803 INFO: rt_error       : 805.6019897460938
0:29:47.809874 INFO: mobility_error : 0.1
0:29:47.809931 INFO: num_candidates : 3
0:29:47.809978 INFO: ms1_error      : 30
0:29:47.810023 INFO: ms2_error      : 30
0:29:47.810068 INFO: fwhm_rt        : 3.0
0:29:47.810111 INFO: quant_window   : 3
0:29:47.810153 INFO: ==============================================
0:29:53.099531 INFO: performing precursor FDR with 40 features
0:29:53.099684 INFO: Decoy channel: -1
0:29:53.099711 INFO: competitive: True
0:29:53.484270 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:54.111288 INFO: Estimating optimal hyperparameters - samples: 1,194,637, batch_size: 4,096, learning_rate: 1.00e-03
0:29:54.113836 INFO: Using random state 64982 for train-test-split
0:30:16.717412 INFO: Test AUC: 0.601
0:30:16.717624 INFO: Train AUC: 0.607
0:30:16.717659 INFO: AUC difference: 0.98%
0:30:17.405003 INFO: Resetting torch num_threads to 100
0:30:17.470235 PROGRESS: === Extracted 1493297 precursors and 6890878 fragments ===
0:30:17.470778 INFO: === FDR correction performed with classifier version 7 ===
0:30:17.471569 PROGRESS: ============================= Precursor FDR =============================
0:30:17.471657 PROGRESS: Total precursors accumulated: 2,148
0:30:17.471720 PROGRESS: Target precursors: 2,127 (99.02%)
0:30:17.471772 PROGRESS: Decoy precursors: 21 (0.98%)
0:30:17.471819 PROGRESS: 
0:30:17.471864 PROGRESS: Precursor Summary:
0:30:17.473382 PROGRESS: Channel   0:	 0.050 FDR: 2,127; 0.010 FDR: 2,127; 0.001 FDR: 1,540
0:30:17.473468 PROGRESS: 
0:30:17.473528 PROGRESS: Protein Summary:
0:30:17.475566 PROGRESS: Channel   0:	 0.050 FDR: 1,671; 0.010 FDR: 1,671; 0.001 FDR: 1,248
0:30:17.475666 PROGRESS: =========================================================================
0:30:17.504207 INFO: Target number of precursors reached.
0:30:18.223688 INFO: fragments_df: keeping 5000 of 6890878 [sum(precursor_idx_mask)=47830 sum(mass_error_mask)=6890878 stop_rank=5000
0:30:18.730049 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:19.035378 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:19.746342 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:19.746785 INFO: Using score_cutoff 13.389859425544739 (fac=0.99, q=1)
0:30:19.747103 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:19.747179 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:19.747241 INFO: Updating optimization_manager: score_cutoff        : 12.935032365989684 -> 13.389859425544739
0:30:19.747301 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:19.897867 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:20.252875 INFO: === checking if optimization conditions were reached ===
0:30:20.253198 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 5 ===
0:30:20.256095 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.417354945146739
0:30:20.256217 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.4174.
0:30:20.256295 INFO: ==============================================
0:30:20.256393 INFO: Starting optimization step 9.
0:30:20.256469 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:30:20.256565 INFO: Using rust extraction backend
0:30:20.256648 PROGRESS: Extracting batch of 250447 precursors
0:30:20.681865 INFO: === Search parameters used ===
0:30:20.682135 INFO: rt_error       : 805.6019897460938
0:30:20.682194 INFO: mobility_error : 0.1
0:30:20.682246 INFO: num_candidates : 3
0:30:20.682294 INFO: ms1_error      : 30
0:30:20.682340 INFO: ms2_error      : 7.417354945146739
0:30:20.682385 INFO: fwhm_rt        : 3.0
0:30:20.682446 INFO: quant_window   : 3
0:30:20.682494 INFO: ==============================================
0:30:23.260866 INFO: performing precursor FDR with 40 features
0:30:23.260989 INFO: Decoy channel: -1
0:30:23.261015 INFO: competitive: True
0:30:23.459295 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:23.769152 INFO: Estimating optimal hyperparameters - samples: 600,842, batch_size: 2,461, learning_rate: 7.75e-04
0:30:23.770264 INFO: Using random state 64982 for train-test-split
0:30:36.811486 INFO: Test AUC: 0.600
0:30:36.811623 INFO: Train AUC: 0.609
0:30:36.811656 INFO: AUC difference: 1.39%
0:30:37.275002 INFO: Resetting torch num_threads to 100
0:30:37.311646 PROGRESS: === Extracted 751053 precursors and 4190977 fragments ===
0:30:37.312139 INFO: === FDR correction performed with classifier version 7 ===
0:30:37.312802 PROGRESS: ============================= Precursor FDR =============================
0:30:37.312890 PROGRESS: Total precursors accumulated: 1,560
0:30:37.312950 PROGRESS: Target precursors: 1,545 (99.04%)
0:30:37.313002 PROGRESS: Decoy precursors: 15 (0.96%)
0:30:37.313049 PROGRESS: 
0:30:37.313096 PROGRESS: Precursor Summary:
0:30:37.314463 PROGRESS: Channel   0:	 0.050 FDR: 1,545; 0.010 FDR: 1,545; 0.001 FDR: 1,018
0:30:37.314558 PROGRESS: 
0:30:37.314616 PROGRESS: Protein Summary:
0:30:37.316374 PROGRESS: Channel   0:	 0.050 FDR: 1,319; 0.010 FDR: 1,319; 0.001 FDR:   893
0:30:37.316465 PROGRESS: =========================================================================
0:30:37.330946 INFO: Target number of precursors reached.
0:30:37.788866 INFO: fragments_df: keeping 5000 of 4190977 [sum(precursor_idx_mask)=36876 sum(mass_error_mask)=4190977 stop_rank=5000
0:30:38.193669 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:38.436624 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:39.160015 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:39.160445 INFO: Using score_cutoff 10.943173299407958 (fac=0.99, q=1)
0:30:39.160758 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:39.160835 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:39.160889 INFO: Updating optimization_manager: score_cutoff        : 13.389859425544739 -> 10.943173299407958
0:30:39.160944 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:39.311791 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:39.638004 INFO: === checking if optimization conditions were reached ===
0:30:39.638305 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 5 ===
0:30:39.641397 INFO: Updating optimization_manager: ms2_error           : 7.417354945146739 -> 7.449072592997001
0:30:39.641557 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.4491.
0:30:39.641637 INFO: ==============================================
0:30:39.641719 INFO: Starting optimization step 10.
0:30:39.641796 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:30:39.641886 INFO: Using rust extraction backend
0:30:39.641961 PROGRESS: Extracting batch of 250447 precursors
0:30:40.066229 INFO: === Search parameters used ===
0:30:40.066489 INFO: rt_error       : 805.6019897460938
0:30:40.066547 INFO: mobility_error : 0.1
0:30:40.066595 INFO: num_candidates : 3
0:30:40.066639 INFO: ms1_error      : 30
0:30:40.066683 INFO: ms2_error      : 7.449072592997001
0:30:40.066746 INFO: fwhm_rt        : 3.0
0:30:40.066791 INFO: quant_window   : 3
0:30:40.066832 INFO: ==============================================
0:30:42.472201 INFO: performing precursor FDR with 40 features
0:30:42.472324 INFO: Decoy channel: -1
0:30:42.472350 INFO: competitive: True
0:30:42.658065 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:42.946847 INFO: Estimating optimal hyperparameters - samples: 600,821, batch_size: 2,460, learning_rate: 7.75e-04
0:30:42.947950 INFO: Using random state 64982 for train-test-split
0:30:55.624834 INFO: Test AUC: 0.601
0:30:55.624973 INFO: Train AUC: 0.611
0:30:55.625006 INFO: AUC difference: 1.67%
0:30:56.083289 INFO: Resetting torch num_threads to 100
0:30:56.112174 PROGRESS: === Extracted 751027 precursors and 4189237 fragments ===
0:30:56.112642 INFO: === FDR correction performed with classifier version 7 ===
0:30:56.113281 PROGRESS: ============================= Precursor FDR =============================
0:30:56.113368 PROGRESS: Total precursors accumulated: 1,532
0:30:56.113429 PROGRESS: Target precursors: 1,517 (99.02%)
0:30:56.113481 PROGRESS: Decoy precursors: 15 (0.98%)
0:30:56.113528 PROGRESS: 
0:30:56.113576 PROGRESS: Precursor Summary:
0:30:56.114932 PROGRESS: Channel   0:	 0.050 FDR: 1,517; 0.010 FDR: 1,517; 0.001 FDR: 1,095
0:30:56.115022 PROGRESS: 
0:30:56.115080 PROGRESS: Protein Summary:
0:30:56.116825 PROGRESS: Channel   0:	 0.050 FDR: 1,306; 0.010 FDR: 1,306; 0.001 FDR:   956
0:30:56.116915 PROGRESS: =========================================================================
0:30:56.130398 INFO: Target number of precursors reached.
0:30:56.593722 INFO: fragments_df: keeping 5000 of 4189237 [sum(precursor_idx_mask)=36315 sum(mass_error_mask)=4189237 stop_rank=5000
0:30:56.998681 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:57.242280 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:57.951704 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:57.952144 INFO: Using score_cutoff 10.763804948043823 (fac=0.99, q=1)
0:30:57.952444 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:57.952521 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:57.952578 INFO: Updating optimization_manager: score_cutoff        : 10.943173299407958 -> 10.763804948043823
0:30:57.952633 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:58.103858 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:58.441034 INFO: === checking if optimization conditions were reached ===
0:30:58.441337 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 5 ===
0:30:58.444420 INFO: Updating optimization_manager: ms2_error           : 7.449072592997001 -> 7.487722209933946
0:30:58.444554 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 7.4877.
0:30:58.444633 INFO: ==============================================
0:30:58.444717 INFO: Starting optimization step 11.
0:30:58.444788 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:30:58.444862 INFO: Using rust extraction backend
0:30:58.444933 PROGRESS: Extracting batch of 250447 precursors
0:30:58.869136 INFO: === Search parameters used ===
0:30:58.869411 INFO: rt_error       : 805.6019897460938
0:30:58.869473 INFO: mobility_error : 0.1
0:30:58.869524 INFO: num_candidates : 3
0:30:58.869588 INFO: ms1_error      : 30
0:30:58.869634 INFO: ms2_error      : 7.487722209933946
0:30:58.869683 INFO: fwhm_rt        : 3.0
0:30:58.869724 INFO: quant_window   : 3
0:30:58.869771 INFO: ==============================================
0:31:01.305007 INFO: performing precursor FDR with 40 features
0:31:01.305969 INFO: Decoy channel: -1
0:31:01.306000 INFO: competitive: True
0:31:01.492982 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:01.781978 INFO: Estimating optimal hyperparameters - samples: 600,803, batch_size: 2,460, learning_rate: 7.75e-04
0:31:01.783075 INFO: Using random state 64982 for train-test-split
0:31:13.980800 INFO: Test AUC: 0.604
0:31:13.980939 INFO: Train AUC: 0.610
0:31:13.980972 INFO: AUC difference: 0.99%
0:31:14.451713 INFO: Resetting torch num_threads to 100
0:31:14.480238 PROGRESS: === Extracted 751004 precursors and 4186677 fragments ===
0:31:14.480717 INFO: === FDR correction performed with classifier version 7 ===
0:31:14.481363 PROGRESS: ============================= Precursor FDR =============================
0:31:14.481451 PROGRESS: Total precursors accumulated: 1,446
0:31:14.481513 PROGRESS: Target precursors: 1,432 (99.03%)
0:31:14.481581 PROGRESS: Decoy precursors: 14 (0.97%)
0:31:14.481629 PROGRESS: 
0:31:14.481673 PROGRESS: Precursor Summary:
0:31:14.483008 PROGRESS: Channel   0:	 0.050 FDR: 1,432; 0.010 FDR: 1,432; 0.001 FDR: 1,081
0:31:14.483100 PROGRESS: 
0:31:14.483157 PROGRESS: Protein Summary:
0:31:14.484871 PROGRESS: Channel   0:	 0.050 FDR: 1,225; 0.010 FDR: 1,225; 0.001 FDR:   943
0:31:14.484960 PROGRESS: =========================================================================
0:31:14.498414 INFO: Target number of precursors reached.
0:31:14.962984 INFO: fragments_df: keeping 5000 of 4186677 [sum(precursor_idx_mask)=34477 sum(mass_error_mask)=4186677 stop_rank=5000
0:31:15.391130 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:15.613836 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:16.324424 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:16.324866 INFO: Using score_cutoff 11.787093237304688 (fac=0.99, q=1)
0:31:16.325175 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:16.325251 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:16.325306 INFO: Updating optimization_manager: score_cutoff        : 10.763804948043823 -> 11.787093237304688
0:31:16.325358 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:16.476613 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:16.806698 INFO: === checking if optimization conditions were reached ===
0:31:16.807013 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 5 ===
0:31:16.810212 INFO: Updating optimization_manager: ms2_error           : 7.487722209933946 -> 7.476614924477974
0:31:16.810389 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 7.4766.
0:31:16.810467 INFO: ==============================================
0:31:16.810551 INFO: Starting optimization step 12.
0:31:16.810622 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:31:16.810696 INFO: Using rust extraction backend
0:31:16.810765 PROGRESS: Extracting batch of 250447 precursors
0:31:17.234218 INFO: === Search parameters used ===
0:31:17.234522 INFO: rt_error       : 805.6019897460938
0:31:17.234583 INFO: mobility_error : 0.1
0:31:17.234631 INFO: num_candidates : 3
0:31:17.234673 INFO: ms1_error      : 30
0:31:17.234714 INFO: ms2_error      : 7.476614924477974
0:31:17.234754 INFO: fwhm_rt        : 3.0
0:31:17.234792 INFO: quant_window   : 3
0:31:17.234830 INFO: ==============================================
0:31:19.710718 INFO: performing precursor FDR with 40 features
0:31:19.710850 INFO: Decoy channel: -1
0:31:19.710878 INFO: competitive: True
0:31:19.938078 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:20.242323 INFO: Estimating optimal hyperparameters - samples: 600,800, batch_size: 2,460, learning_rate: 7.75e-04
0:31:20.243459 INFO: Using random state 64982 for train-test-split
0:31:36.500579 INFO: Test AUC: 0.603
0:31:36.500787 INFO: Train AUC: 0.610
0:31:36.500820 INFO: AUC difference: 1.29%
0:31:36.977455 INFO: Resetting torch num_threads to 100
0:31:37.016222 PROGRESS: === Extracted 751001 precursors and 4186937 fragments ===
0:31:37.016815 INFO: === FDR correction performed with classifier version 7 ===
0:31:37.017509 PROGRESS: ============================= Precursor FDR =============================
0:31:37.017600 PROGRESS: Total precursors accumulated: 1,381
0:31:37.017666 PROGRESS: Target precursors: 1,368 (99.06%)
0:31:37.017720 PROGRESS: Decoy precursors: 13 (0.94%)
0:31:37.017768 PROGRESS: 
0:31:37.017815 PROGRESS: Precursor Summary:
0:31:37.019176 PROGRESS: Channel   0:	 0.050 FDR: 1,368; 0.010 FDR: 1,368; 0.001 FDR: 1,047
0:31:37.019266 PROGRESS: 
0:31:37.019326 PROGRESS: Protein Summary:
0:31:37.021059 PROGRESS: Channel   0:	 0.050 FDR: 1,177; 0.010 FDR: 1,177; 0.001 FDR:   917
0:31:37.021155 PROGRESS: =========================================================================
0:31:37.041664 INFO: Target number of precursors reached.
0:31:37.501328 INFO: fragments_df: keeping 5000 of 4186937 [sum(precursor_idx_mask)=33024 sum(mass_error_mask)=4186937 stop_rank=5000
0:31:38.125879 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:38.319308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:38.973881 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:38.974448 INFO: Using score_cutoff 11.72018422794342 (fac=0.99, q=1)
0:31:38.974797 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:38.974874 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:38.974930 INFO: Updating optimization_manager: score_cutoff        : 11.787093237304688 -> 11.72018422794342
0:31:38.974990 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:39.129297 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:39.492035 INFO: === checking if optimization conditions were reached ===
0:31:39.492429 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 5 ===
0:31:39.493711 INFO: Updating optimization_manager: ms2_error           : 7.476614924477974 -> 7.417354945146739
0:31:39.493864 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:31:39.493971 INFO: Updating optimization_manager: score_cutoff        : 11.72018422794342 -> 10.943173299407958
0:31:39.494092 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:39.494179 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:39.494266 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.4174 found after 5 searches.
0:31:39.494332 INFO: ==============================================
0:31:39.494425 PROGRESS: Optimization finished for ms2_error.
0:31:40.071493 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:40.225917 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:40.589693 INFO: Starting optimization step 0.
0:31:40.590023 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:31:40.590137 INFO: Using rust extraction backend
0:31:40.590223 PROGRESS: Extracting batch of 250447 precursors
0:31:41.049243 INFO: === Search parameters used ===
0:31:41.049575 INFO: rt_error       : 805.6019897460938
0:31:41.049636 INFO: mobility_error : 0.1
0:31:41.049687 INFO: num_candidates : 3
0:31:41.049734 INFO: ms1_error      : 30
0:31:41.049778 INFO: ms2_error      : 7.417354945146739
0:31:41.049822 INFO: fwhm_rt        : 3.0
0:31:41.049875 INFO: quant_window   : 3
0:31:41.049920 INFO: ==============================================
0:31:43.823461 INFO: performing precursor FDR with 40 features
0:31:43.823606 INFO: Decoy channel: -1
0:31:43.823633 INFO: competitive: True
0:31:44.089010 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:44.442474 INFO: Estimating optimal hyperparameters - samples: 600,827, batch_size: 2,460, learning_rate: 7.75e-04
0:31:44.444283 INFO: Using random state 774838 for train-test-split
0:31:58.703231 INFO: Test AUC: 0.603
0:31:58.703376 INFO: Train AUC: 0.617
0:31:58.703409 INFO: AUC difference: 2.20%
0:31:59.187439 INFO: Resetting torch num_threads to 100
0:31:59.214599 PROGRESS: === Extracted 751034 precursors and 4189818 fragments ===
0:31:59.215109 INFO: === FDR correction performed with classifier version 9 ===
0:31:59.215773 PROGRESS: ============================= Precursor FDR =============================
0:31:59.215862 PROGRESS: Total precursors accumulated: 1,582
0:31:59.215934 PROGRESS: Target precursors: 1,567 (99.05%)
0:31:59.215990 PROGRESS: Decoy precursors: 15 (0.95%)
0:31:59.216039 PROGRESS: 
0:31:59.216085 PROGRESS: Precursor Summary:
0:31:59.217460 PROGRESS: Channel   0:	 0.050 FDR: 1,567; 0.010 FDR: 1,567; 0.001 FDR: 1,188
0:31:59.217547 PROGRESS: 
0:31:59.217603 PROGRESS: Protein Summary:
0:31:59.219432 PROGRESS: Channel   0:	 0.050 FDR: 1,359; 0.010 FDR: 1,359; 0.001 FDR: 1,037
0:31:59.219528 PROGRESS: =========================================================================
0:31:59.234769 INFO: Target number of precursors reached.
0:31:59.686642 INFO: fragments_df: keeping 5000 of 4189818 [sum(precursor_idx_mask)=36407 sum(mass_error_mask)=4189818 stop_rank=5000
0:32:00.113226 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:00.351257 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:01.060334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:01.060768 INFO: Using score_cutoff 7.931379831790925 (fac=0.99, q=1)
0:32:01.061082 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:01.061156 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:01.061208 INFO: Updating optimization_manager: score_cutoff        : 10.943173299407958 -> 7.931379831790925
0:32:01.061258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:01.211664 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:01.540496 INFO: === checking if optimization conditions were reached ===
0:32:01.540812 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:32:01.543927 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 776.3435265952985
0:32:01.544045 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 776.3435.
0:32:01.544121 INFO: ==============================================
0:32:01.544203 INFO: Starting optimization step 1.
0:32:01.544270 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:32:01.544341 INFO: Using rust extraction backend
0:32:01.544410 PROGRESS: Extracting batch of 250447 precursors
0:32:01.967859 INFO: === Search parameters used ===
0:32:01.968137 INFO: rt_error       : 776.3435265952985
0:32:01.968198 INFO: mobility_error : 0.1
0:32:01.968248 INFO: num_candidates : 3
0:32:01.968294 INFO: ms1_error      : 30
0:32:01.968338 INFO: ms2_error      : 7.417354945146739
0:32:01.968387 INFO: fwhm_rt        : 3.0
0:32:01.968434 INFO: quant_window   : 3
0:32:01.968478 INFO: ==============================================
0:32:04.425864 INFO: performing precursor FDR with 40 features
0:32:04.425992 INFO: Decoy channel: -1
0:32:04.426020 INFO: competitive: True
0:32:04.611773 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:04.918937 INFO: Estimating optimal hyperparameters - samples: 600,846, batch_size: 2,461, learning_rate: 7.75e-04
0:32:04.919978 INFO: Using random state 774838 for train-test-split
0:32:19.574619 INFO: Test AUC: 0.604
0:32:19.574756 INFO: Train AUC: 0.617
0:32:19.574791 INFO: AUC difference: 2.09%
0:32:20.049347 INFO: Resetting torch num_threads to 100
0:32:20.110656 PROGRESS: === Extracted 751058 precursors and 4192109 fragments ===
0:32:20.111133 INFO: === FDR correction performed with classifier version 9 ===
0:32:20.111786 PROGRESS: ============================= Precursor FDR =============================
0:32:20.111890 PROGRESS: Total precursors accumulated: 1,549
0:32:20.111952 PROGRESS: Target precursors: 1,534 (99.03%)
0:32:20.112003 PROGRESS: Decoy precursors: 15 (0.97%)
0:32:20.112051 PROGRESS: 
0:32:20.112100 PROGRESS: Precursor Summary:
0:32:20.113471 PROGRESS: Channel   0:	 0.050 FDR: 1,534; 0.010 FDR: 1,534; 0.001 FDR: 1,250
0:32:20.113564 PROGRESS: 
0:32:20.113621 PROGRESS: Protein Summary:
0:32:20.115431 PROGRESS: Channel   0:	 0.050 FDR: 1,317; 0.010 FDR: 1,317; 0.001 FDR: 1,089
0:32:20.115530 PROGRESS: =========================================================================
0:32:20.133068 INFO: Target number of precursors reached.
0:32:20.607939 INFO: fragments_df: keeping 5000 of 4192109 [sum(precursor_idx_mask)=36462 sum(mass_error_mask)=4192109 stop_rank=5000
0:32:21.037002 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:21.276774 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:21.985326 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:21.985763 INFO: Using score_cutoff 9.87082005929947 (fac=0.99, q=1)
0:32:21.986087 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:21.986167 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:21.986220 INFO: Updating optimization_manager: score_cutoff        : 7.931379831790925 -> 9.87082005929947
0:32:21.986278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:22.137406 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:22.486465 INFO: === checking if optimization conditions were reached ===
0:32:22.486772 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:32:22.489946 INFO: Updating optimization_manager: rt_error            : 776.3435265952985 -> 732.9936958338001
0:32:22.490064 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 732.9937.
0:32:22.490139 INFO: ==============================================
0:32:22.490223 INFO: Starting optimization step 2.
0:32:22.490290 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:32:22.490359 INFO: Using rust extraction backend
0:32:22.490425 PROGRESS: Extracting batch of 250447 precursors
0:32:22.912681 INFO: === Search parameters used ===
0:32:22.913073 INFO: rt_error       : 732.9936958338001
0:32:22.913131 INFO: mobility_error : 0.1
0:32:22.913178 INFO: num_candidates : 3
0:32:22.913224 INFO: ms1_error      : 30
0:32:22.913276 INFO: ms2_error      : 7.417354945146739
0:32:22.913317 INFO: fwhm_rt        : 3.0
0:32:22.913358 INFO: quant_window   : 3
0:32:22.913396 INFO: ==============================================
0:32:25.300778 INFO: performing precursor FDR with 40 features
0:32:25.300903 INFO: Decoy channel: -1
0:32:25.300931 INFO: competitive: True
0:32:25.492356 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:25.796098 INFO: Estimating optimal hyperparameters - samples: 600,843, batch_size: 2,461, learning_rate: 7.75e-04
0:32:25.797528 INFO: Using random state 774838 for train-test-split
0:32:42.139960 INFO: Test AUC: 0.604
0:32:42.140125 INFO: Train AUC: 0.616
0:32:42.140161 INFO: AUC difference: 1.95%
0:32:42.625106 INFO: Resetting torch num_threads to 100
0:32:42.801099 PROGRESS: === Extracted 751054 precursors and 4191875 fragments ===
0:32:42.801790 INFO: === FDR correction performed with classifier version 9 ===
0:32:42.802536 PROGRESS: ============================= Precursor FDR =============================
0:32:42.802629 PROGRESS: Total precursors accumulated: 1,628
0:32:42.802692 PROGRESS: Target precursors: 1,612 (99.02%)
0:32:42.802744 PROGRESS: Decoy precursors: 16 (0.98%)
0:32:42.802791 PROGRESS: 
0:32:42.802836 PROGRESS: Precursor Summary:
0:32:42.804235 PROGRESS: Channel   0:	 0.050 FDR: 1,612; 0.010 FDR: 1,612; 0.001 FDR: 1,231
0:32:42.804326 PROGRESS: 
0:32:42.804381 PROGRESS: Protein Summary:
0:32:42.806253 PROGRESS: Channel   0:	 0.050 FDR: 1,379; 0.010 FDR: 1,379; 0.001 FDR: 1,070
0:32:42.806350 PROGRESS: =========================================================================
0:32:42.826724 INFO: Target number of precursors reached.
0:32:43.284357 INFO: fragments_df: keeping 5000 of 4191875 [sum(precursor_idx_mask)=38242 sum(mass_error_mask)=4191875 stop_rank=5000
0:32:43.918605 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:44.830854 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:45.542590 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:45.543053 INFO: Using score_cutoff 9.765004792785644 (fac=0.99, q=1)
0:32:45.543367 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:45.543447 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:45.543513 INFO: Updating optimization_manager: score_cutoff        : 9.87082005929947 -> 9.765004792785644
0:32:45.543571 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:45.693656 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:46.034598 INFO: === checking if optimization conditions were reached ===
0:32:46.034942 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:32:46.038387 INFO: Updating optimization_manager: rt_error            : 732.9936958338001 -> 755.036041522222
0:32:46.038516 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 755.0360.
0:32:46.038594 INFO: ==============================================
0:32:46.038678 INFO: Starting optimization step 3.
0:32:46.038748 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:32:46.038821 INFO: Using rust extraction backend
0:32:46.038889 PROGRESS: Extracting batch of 250447 precursors
0:32:46.460534 INFO: === Search parameters used ===
0:32:46.460825 INFO: rt_error       : 755.036041522222
0:32:46.460882 INFO: mobility_error : 0.1
0:32:46.460930 INFO: num_candidates : 3
0:32:46.460974 INFO: ms1_error      : 30
0:32:46.461017 INFO: ms2_error      : 7.417354945146739
0:32:46.461061 INFO: fwhm_rt        : 3.0
0:32:46.461103 INFO: quant_window   : 3
0:32:46.461161 INFO: ==============================================
0:32:48.880208 INFO: performing precursor FDR with 40 features
0:32:48.880342 INFO: Decoy channel: -1
0:32:48.880368 INFO: competitive: True
0:32:49.081054 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:49.386906 INFO: Estimating optimal hyperparameters - samples: 600,845, batch_size: 2,461, learning_rate: 7.75e-04
0:32:49.388078 INFO: Using random state 774838 for train-test-split
0:33:05.740259 INFO: Test AUC: 0.605
0:33:05.740422 INFO: Train AUC: 0.616
0:33:05.740457 INFO: AUC difference: 1.75%
0:33:06.203367 INFO: Resetting torch num_threads to 100
0:33:06.229968 PROGRESS: === Extracted 751057 precursors and 4191436 fragments ===
0:33:06.230477 INFO: === FDR correction performed with classifier version 9 ===
0:33:06.231150 PROGRESS: ============================= Precursor FDR =============================
0:33:06.231239 PROGRESS: Total precursors accumulated: 1,671
0:33:06.231300 PROGRESS: Target precursors: 1,655 (99.04%)
0:33:06.231369 PROGRESS: Decoy precursors: 16 (0.96%)
0:33:06.231417 PROGRESS: 
0:33:06.231464 PROGRESS: Precursor Summary:
0:33:06.232888 PROGRESS: Channel   0:	 0.050 FDR: 1,655; 0.010 FDR: 1,655; 0.001 FDR: 1,286
0:33:06.232983 PROGRESS: 
0:33:06.233039 PROGRESS: Protein Summary:
0:33:06.234906 PROGRESS: Channel   0:	 0.050 FDR: 1,430; 0.010 FDR: 1,430; 0.001 FDR: 1,117
0:33:06.235011 PROGRESS: =========================================================================
0:33:06.249800 INFO: Target number of precursors reached.
0:33:06.706245 INFO: fragments_df: keeping 5000 of 4191436 [sum(precursor_idx_mask)=38452 sum(mass_error_mask)=4191436 stop_rank=5000
0:33:07.120591 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:07.376847 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:08.088691 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:33:08.089163 INFO: Using score_cutoff 8.68832535381317 (fac=0.99, q=1)
0:33:08.089479 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:08.089557 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:08.089611 INFO: Updating optimization_manager: score_cutoff        : 9.765004792785644 -> 8.68832535381317
0:33:08.089665 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:08.238530 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:08.580064 INFO: === checking if optimization conditions were reached ===
0:33:08.580442 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:33:08.583927 INFO: Updating optimization_manager: rt_error            : 755.036041522222 -> 859.8721679315069
0:33:08.584060 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 859.8722.
0:33:08.584136 INFO: ==============================================
0:33:08.584218 INFO: Starting optimization step 4.
0:33:08.584287 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:33:08.584366 INFO: Using rust extraction backend
0:33:08.584455 PROGRESS: Extracting batch of 250447 precursors
0:33:09.006361 INFO: === Search parameters used ===
0:33:09.006656 INFO: rt_error       : 859.8721679315069
0:33:09.006709 INFO: mobility_error : 0.1
0:33:09.006755 INFO: num_candidates : 3
0:33:09.006797 INFO: ms1_error      : 30
0:33:09.006838 INFO: ms2_error      : 7.417354945146739
0:33:09.006897 INFO: fwhm_rt        : 3.0
0:33:09.006947 INFO: quant_window   : 3
0:33:09.006988 INFO: ==============================================
0:33:11.524150 INFO: performing precursor FDR with 40 features
0:33:11.524284 INFO: Decoy channel: -1
0:33:11.524311 INFO: competitive: True
0:33:11.716002 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:12.024113 INFO: Estimating optimal hyperparameters - samples: 600,836, batch_size: 2,461, learning_rate: 7.75e-04
0:33:12.025109 INFO: Using random state 774838 for train-test-split
0:33:25.449528 INFO: Test AUC: 0.605
0:33:25.449686 INFO: Train AUC: 0.617
0:33:25.449720 INFO: AUC difference: 1.85%
0:33:25.912574 INFO: Resetting torch num_threads to 100
0:33:25.940338 PROGRESS: === Extracted 751046 precursors and 4192008 fragments ===
0:33:25.940867 INFO: === FDR correction performed with classifier version 9 ===
0:33:25.941538 PROGRESS: ============================= Precursor FDR =============================
0:33:25.941627 PROGRESS: Total precursors accumulated: 1,661
0:33:25.941688 PROGRESS: Target precursors: 1,645 (99.04%)
0:33:25.941740 PROGRESS: Decoy precursors: 16 (0.96%)
0:33:25.941788 PROGRESS: 
0:33:25.941833 PROGRESS: Precursor Summary:
0:33:25.943239 PROGRESS: Channel   0:	 0.050 FDR: 1,645; 0.010 FDR: 1,645; 0.001 FDR: 1,161
0:33:25.943331 PROGRESS: 
0:33:25.943388 PROGRESS: Protein Summary:
0:33:25.945194 PROGRESS: Channel   0:	 0.050 FDR: 1,424; 0.010 FDR: 1,424; 0.001 FDR: 1,011
0:33:25.945288 PROGRESS: =========================================================================
0:33:25.960637 INFO: Target number of precursors reached.
0:33:26.425572 INFO: fragments_df: keeping 5000 of 4192008 [sum(precursor_idx_mask)=38115 sum(mass_error_mask)=4192008 stop_rank=5000
0:33:26.857884 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:27.104037 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:27.813634 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:33:27.814120 INFO: Using score_cutoff 7.866377158927917 (fac=0.99, q=1)
0:33:27.814428 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:27.814506 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:27.814561 INFO: Updating optimization_manager: score_cutoff        : 8.68832535381317 -> 7.866377158927917
0:33:27.814616 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:27.964804 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:28.305041 INFO: === checking if optimization conditions were reached ===
0:33:28.305377 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:33:28.308811 INFO: Updating optimization_manager: rt_error            : 859.8721679315069 -> 831.081833902955
0:33:28.308934 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 831.0818.
0:33:28.309012 INFO: ==============================================
0:33:28.309096 INFO: Starting optimization step 5.
0:33:28.309170 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:33:28.309244 INFO: Using rust extraction backend
0:33:28.309314 PROGRESS: Extracting batch of 250447 precursors
0:33:28.731230 INFO: === Search parameters used ===
0:33:28.731519 INFO: rt_error       : 831.081833902955
0:33:28.731579 INFO: mobility_error : 0.1
0:33:28.731627 INFO: num_candidates : 3
0:33:28.731689 INFO: ms1_error      : 30
0:33:28.731734 INFO: ms2_error      : 7.417354945146739
0:33:28.731777 INFO: fwhm_rt        : 3.0
0:33:28.731819 INFO: quant_window   : 3
0:33:28.731860 INFO: ==============================================
0:33:31.208692 INFO: performing precursor FDR with 40 features
0:33:31.208824 INFO: Decoy channel: -1
0:33:31.208850 INFO: competitive: True
0:33:31.402608 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:31.712885 INFO: Estimating optimal hyperparameters - samples: 600,840, batch_size: 2,461, learning_rate: 7.75e-04
0:33:31.714090 INFO: Using random state 774838 for train-test-split
0:33:49.034115 INFO: Test AUC: 0.603
0:33:49.034293 INFO: Train AUC: 0.616
0:33:49.034328 INFO: AUC difference: 2.09%
0:33:49.512901 INFO: Resetting torch num_threads to 100
0:33:49.552762 PROGRESS: === Extracted 751050 precursors and 4191893 fragments ===
0:33:49.553315 INFO: === FDR correction performed with classifier version 9 ===
0:33:49.554051 PROGRESS: ============================= Precursor FDR =============================
0:33:49.554145 PROGRESS: Total precursors accumulated: 1,566
0:33:49.554209 PROGRESS: Target precursors: 1,551 (99.04%)
0:33:49.554267 PROGRESS: Decoy precursors: 15 (0.96%)
0:33:49.554316 PROGRESS: 
0:33:49.554364 PROGRESS: Precursor Summary:
0:33:49.555769 PROGRESS: Channel   0:	 0.050 FDR: 1,551; 0.010 FDR: 1,551; 0.001 FDR: 1,128
0:33:49.555863 PROGRESS: 
0:33:49.555921 PROGRESS: Protein Summary:
0:33:49.557747 PROGRESS: Channel   0:	 0.050 FDR: 1,314; 0.010 FDR: 1,314; 0.001 FDR:   986
0:33:49.557840 PROGRESS: =========================================================================
0:33:49.577803 INFO: Target number of precursors reached.
0:33:50.054739 INFO: fragments_df: keeping 5000 of 4191893 [sum(precursor_idx_mask)=36948 sum(mass_error_mask)=4191893 stop_rank=5000
0:33:50.496188 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:50.759923 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:51.471638 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:33:51.472124 INFO: Using score_cutoff 10.903342080116271 (fac=0.99, q=1)
0:33:51.472444 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:51.472523 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:51.472581 INFO: Updating optimization_manager: score_cutoff        : 7.866377158927917 -> 10.903342080116271
0:33:51.472637 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:51.623733 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:51.958272 INFO: === checking if optimization conditions were reached ===
0:33:51.958635 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:33:51.959837 INFO: Updating optimization_manager: rt_error            : 831.081833902955 -> 755.036041522222
0:33:51.960020 INFO: Updating optimization_manager: classifier_version  : 9 -> 16
0:33:51.960142 INFO: Updating optimization_manager: score_cutoff        : 10.903342080116271 -> 8.68832535381317
0:33:51.960258 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:51.960366 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:51.960475 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 755.0360 found after 6 searches.
0:33:51.960550 INFO: ==============================================
0:33:51.960644 PROGRESS: Optimization finished for rt_error.
0:33:52.364467 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:52.515412 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:52.848644 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:33:52.848970 PROGRESS: ==============================================
0:33:52.849073 PROGRESS: ms2_error      : 7.4174
0:33:52.849144 PROGRESS: rt_error       : 755.0360
0:33:52.849203 PROGRESS: ==============================================
0:33:52.850300 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:00.448223 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:16.508872 INFO: Using rust extraction backend
0:34:16.509195 PROGRESS: Extracting batch of 11997144 precursors
0:34:32.507802 INFO: === Search parameters used ===
0:34:32.508270 INFO: rt_error       : 755.036041522222
0:34:32.508334 INFO: mobility_error : 0.1
0:34:32.508384 INFO: num_candidates : 3
0:34:32.508435 INFO: ms1_error      : 30
0:34:32.508477 INFO: ms2_error      : 7.417354945146739
0:34:32.508518 INFO: fwhm_rt        : 3.0
0:34:32.508558 INFO: quant_window   : 3
0:34:32.508598 INFO: ==============================================
0:35:06.034187 INFO: Removed 6132730 precursors with score below cutoff 8.68832535381317
0:35:29.212136 INFO: performing precursor FDR with 40 features
0:35:29.212276 INFO: Decoy channel: -1
0:35:29.212323 INFO: competitive: True
0:35:32.364410 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:44.380878 INFO: Estimating optimal hyperparameters - samples: 23,886,397, batch_size: 4,096, learning_rate: 1.00e-03
0:35:44.452814 INFO: Using random state 9397 for train-test-split
0:43:22.863806 INFO: Test AUC: 0.624
0:43:22.864104 INFO: Train AUC: 0.624
0:43:22.864145 INFO: AUC difference: 0.06%
0:43:29.297974 INFO: Resetting torch num_threads to 100
0:43:31.282679 PROGRESS: ============================= Precursor FDR =============================
0:43:31.283008 PROGRESS: Total precursors accumulated: 93,528
0:43:31.283082 PROGRESS: Target precursors: 92,602 (99.01%)
0:43:31.283139 PROGRESS: Decoy precursors: 926 (0.99%)
0:43:31.283188 PROGRESS: 
0:43:31.283236 PROGRESS: Precursor Summary:
0:43:31.309214 PROGRESS: Channel   0:	 0.050 FDR: 92,602; 0.010 FDR: 92,602; 0.001 FDR: 59,098
0:43:31.309464 PROGRESS: 
0:43:31.309536 PROGRESS: Protein Summary:
0:43:31.345950 PROGRESS: Channel   0:	 0.050 FDR: 13,362; 0.010 FDR: 13,362; 0.001 FDR: 9,432
0:43:31.346209 PROGRESS: =========================================================================
0:43:31.504146 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:43:31.676438 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:43:31.910331 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:43:32.410555 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
0:43:32.410709 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant
0:43:32.410825 INFO: Initializing TimingManager
0:43:32.411497 INFO: Initializing RawFileManager
0:43:42.198303 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.
0:43:42.206661 INFO: Determining DIA cycle
0:43:42.223237 INFO: Found cycle with start 0.00 min and length 300.
0:43:42.385518 INFO: RT (min)            : 0.0 - 26.9
0:43:42.385605 INFO: RT duration (sec)   : 1611.2
0:43:42.385634 INFO: RT duration (min)   : 26.9
0:43:42.385662 INFO: Cycle len (scans)   : 300
0:43:42.385683 INFO: Cycle len (sec)     : 1.65
0:43:42.385704 INFO: Number of cycles    : 977
0:43:42.385723 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:43:42.385749 INFO: Creating DIA data object took: 9.974156618118286
0:43:43.059801 INFO: Creating DIA data NG object took: 0.6739366054534912
0:43:44.292639 INFO: Initializing CalibrationManager
0:43:44.292927 INFO: Setting up calibration estimators ..
0:43:44.292990 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:43:44.293075 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'}' ..
0:43:44.293176 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:43:44.293229 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:43:44.293304 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}}' ..
0:43:44.293362 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:43:44.293408 INFO: Done setting up calibration estimators.
0:43:44.293604 INFO: Initializing OptimizationManager
0:43:44.293739 INFO: initial parameter: ms1_error = 30
0:43:44.293792 INFO: initial parameter: ms2_error = 30
0:43:44.293839 INFO: initial parameter: rt_error = 805.6004638671875
0:43:44.293901 INFO: initial parameter: mobility_error = 0.1
0:43:44.293943 INFO: initial parameter: num_candidates = 1
0:43:44.293983 INFO: initial parameter: fwhm_rt = 5
0:43:44.294023 INFO: initial parameter: fwhm_mobility = 0.01
0:43:44.294062 INFO: initial parameter: score_cutoff = 0
0:43:44.294101 INFO: initial parameter: classifier_version = -1
0:43:44.294167 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:43:44.294392 INFO: FDRManager: loading saved state not requested, will be initialized.
0:43:44.294420 INFO: Initializing FDRManager
0:43:44.294455 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:43:45.713927 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:43:46.591374 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:43:46.591745 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:43:46.591847 PROGRESS: Starting initial search for precursors.
0:43:46.591933 INFO: Starting optimization step 0.
0:43:46.591995 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:43:46.592057 INFO: Using rust extraction backend
0:43:46.592115 PROGRESS: Extracting batch of 1970 precursors
0:43:46.596884 INFO: === Search parameters used ===
0:43:46.596991 INFO: rt_error       : 805.6004638671875
0:43:46.597041 INFO: mobility_error : 0.1
0:43:46.597084 INFO: num_candidates : 1
0:43:46.597125 INFO: ms1_error      : 30
0:43:46.597164 INFO: ms2_error      : 30
0:43:46.597204 INFO: fwhm_rt        : 5
0:43:46.597242 INFO: quant_window   : 3
0:43:46.597280 INFO: ==============================================
0:43:46.625179 INFO: performing precursor FDR with 40 features
0:43:46.625248 INFO: Decoy channel: -1
0:43:46.625272 INFO: competitive: True
0:43:46.626552 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:46.628451 INFO: Estimating optimal hyperparameters - samples: 1,563, batch_size: 128, learning_rate: 1.77e-04
0:43:46.629242 INFO: Using random state 763055 for train-test-split
0:43:46.780170 INFO: Test AUC: 0.520
0:43:46.780252 INFO: Train AUC: 0.566
0:43:46.780280 INFO: AUC difference: 8.12%
0:43:46.780301 WARNING: AUC difference > 5%. This may indicate overfitting.
0:43:47.020376 INFO: Resetting torch num_threads to 100
0:43:47.022392 PROGRESS: === Extracted 1954 precursors and 9184 fragments ===
0:43:47.022817 INFO: === FDR correction performed with classifier version -1 ===
0:43:47.023310 PROGRESS: ============================= Precursor FDR =============================
0:43:47.023395 PROGRESS: Total precursors accumulated: 4
0:43:47.023452 PROGRESS: Target precursors: 4 (100.00%)
0:43:47.023499 PROGRESS: Decoy precursors: 0 (0.00%)
0:43:47.023542 PROGRESS: 
0:43:47.023584 PROGRESS: Precursor Summary:
0:43:47.024667 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:43:47.024751 PROGRESS: 
0:43:47.024805 PROGRESS: Protein Summary:
0:43:47.026005 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:43:47.026093 PROGRESS: =========================================================================
0:43:47.026520 INFO: Target number of precursors not reached yet.
0:43:47.112502 INFO: Starting optimization step 1.
0:43:47.112741 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:43:47.112815 INFO: Using rust extraction backend
0:43:47.112892 PROGRESS: Extracting batch of 3942 precursors
0:43:47.121131 INFO: === Search parameters used ===
0:43:47.121256 INFO: rt_error       : 805.6004638671875
0:43:47.121308 INFO: mobility_error : 0.1
0:43:47.121354 INFO: num_candidates : 1
0:43:47.121397 INFO: ms1_error      : 30
0:43:47.121438 INFO: ms2_error      : 30
0:43:47.121478 INFO: fwhm_rt        : 5
0:43:47.121517 INFO: quant_window   : 3
0:43:47.121556 INFO: ==============================================
0:43:47.166489 INFO: performing precursor FDR with 40 features
0:43:47.166582 INFO: Decoy channel: -1
0:43:47.166606 INFO: competitive: True
0:43:47.170691 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:47.172908 INFO: Estimating optimal hyperparameters - samples: 4,692, batch_size: 128, learning_rate: 1.77e-04
0:43:47.172984 INFO: Using random state 182388 for train-test-split
0:43:47.627691 INFO: Test AUC: 0.547
0:43:47.627801 INFO: Train AUC: 0.581
0:43:47.627829 INFO: AUC difference: 5.82%
0:43:47.627849 WARNING: AUC difference > 5%. This may indicate overfitting.
0:43:47.871387 INFO: Resetting torch num_threads to 100
0:43:47.874202 PROGRESS: === Extracted 5865 precursors and 27716 fragments ===
0:43:47.874588 INFO: === FDR correction performed with classifier version -1 ===
0:43:47.875080 PROGRESS: ============================= Precursor FDR =============================
0:43:47.875161 PROGRESS: Total precursors accumulated: 2
0:43:47.875218 PROGRESS: Target precursors: 2 (100.00%)
0:43:47.875265 PROGRESS: Decoy precursors: 0 (0.00%)
0:43:47.875308 PROGRESS: 
0:43:47.875350 PROGRESS: Precursor Summary:
0:43:47.876404 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:43:47.876486 PROGRESS: 
0:43:47.876539 PROGRESS: Protein Summary:
0:43:47.877689 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:43:47.877770 PROGRESS: =========================================================================
0:43:47.878054 INFO: Target number of precursors not reached yet.
0:43:47.968144 INFO: Starting optimization step 2.
0:43:47.968386 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:43:47.968472 INFO: Using rust extraction backend
0:43:47.968537 PROGRESS: Extracting batch of 7890 precursors
0:43:47.983423 INFO: === Search parameters used ===
0:43:47.983561 INFO: rt_error       : 805.6004638671875
0:43:47.983616 INFO: mobility_error : 0.1
0:43:47.983665 INFO: num_candidates : 1
0:43:47.983712 INFO: ms1_error      : 30
0:43:47.983756 INFO: ms2_error      : 30
0:43:47.983800 INFO: fwhm_rt        : 5
0:43:47.983843 INFO: quant_window   : 3
0:43:47.983890 INFO: ==============================================
0:43:48.055012 INFO: performing precursor FDR with 40 features
0:43:48.055120 INFO: Decoy channel: -1
0:43:48.055146 INFO: competitive: True
0:43:48.061316 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:48.064954 INFO: Estimating optimal hyperparameters - samples: 10,939, batch_size: 128, learning_rate: 1.77e-04
0:43:48.065068 INFO: Using random state 75841 for train-test-split
0:43:49.154269 INFO: Test AUC: 0.541
0:43:49.154376 INFO: Train AUC: 0.593
0:43:49.154404 INFO: AUC difference: 8.78%
0:43:49.154426 WARNING: AUC difference > 5%. This may indicate overfitting.
0:43:49.402759 INFO: Resetting torch num_threads to 100
0:43:49.406538 PROGRESS: === Extracted 13674 precursors and 64527 fragments ===
0:43:49.406921 INFO: === FDR correction performed with classifier version -1 ===
0:43:49.407425 PROGRESS: ============================= Precursor FDR =============================
0:43:49.407511 PROGRESS: Total precursors accumulated: 8
0:43:49.407578 PROGRESS: Target precursors: 8 (100.00%)
0:43:49.407630 PROGRESS: Decoy precursors: 0 (0.00%)
0:43:49.407676 PROGRESS: 
0:43:49.407722 PROGRESS: Precursor Summary:
0:43:49.408783 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:43:49.408865 PROGRESS: 
0:43:49.408921 PROGRESS: Protein Summary:
0:43:49.410112 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:43:49.410207 PROGRESS: =========================================================================
0:43:49.410536 INFO: Target number of precursors not reached yet.
0:43:49.511539 INFO: Starting optimization step 3.
0:43:49.511792 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:43:49.511867 INFO: Using rust extraction backend
0:43:49.511925 PROGRESS: Extracting batch of 15788 precursors
0:43:49.540033 INFO: === Search parameters used ===
0:43:49.540212 INFO: rt_error       : 805.6004638671875
0:43:49.540264 INFO: mobility_error : 0.1
0:43:49.540308 INFO: num_candidates : 1
0:43:49.540353 INFO: ms1_error      : 30
0:43:49.540395 INFO: ms2_error      : 30
0:43:49.540456 INFO: fwhm_rt        : 5
0:43:49.540500 INFO: quant_window   : 3
0:43:49.540542 INFO: ==============================================
0:43:49.674241 INFO: performing precursor FDR with 40 features
0:43:49.674360 INFO: Decoy channel: -1
0:43:49.674383 INFO: competitive: True
0:43:49.685049 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:49.691378 INFO: Estimating optimal hyperparameters - samples: 23,435, batch_size: 128, learning_rate: 1.77e-04
0:43:49.691540 INFO: Using random state 718436 for train-test-split
0:43:52.056267 INFO: Test AUC: 0.575
0:43:52.056357 INFO: Train AUC: 0.598
0:43:52.056384 INFO: AUC difference: 3.92%
0:43:52.309167 INFO: Resetting torch num_threads to 100
0:43:52.315006 PROGRESS: === Extracted 29294 precursors and 138622 fragments ===
0:43:52.315457 INFO: === FDR correction performed with classifier version -1 ===
0:43:52.315970 PROGRESS: ============================= Precursor FDR =============================
0:43:52.316050 PROGRESS: Total precursors accumulated: 0
0:43:52.316107 PROGRESS: Target precursors: 0 (0.00%)
0:43:52.316155 PROGRESS: Decoy precursors: 0 (0.00%)
0:43:52.316199 PROGRESS: 
0:43:52.316242 PROGRESS: Precursor Summary:
0:43:52.316353 PROGRESS: 
0:43:52.316409 PROGRESS: Protein Summary:
0:43:52.316481 PROGRESS: =========================================================================
0:43:52.316928 INFO: Target number of precursors not reached yet.
0:43:52.434361 INFO: Starting optimization step 4.
0:43:52.434622 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:43:52.434698 INFO: Using rust extraction backend
0:43:52.434760 PROGRESS: Extracting batch of 31512 precursors
0:43:52.489643 INFO: === Search parameters used ===
0:43:52.489891 INFO: rt_error       : 805.6004638671875
0:43:52.489964 INFO: mobility_error : 0.1
0:43:52.490015 INFO: num_candidates : 1
0:43:52.490062 INFO: ms1_error      : 30
0:43:52.490105 INFO: ms2_error      : 30
0:43:52.490145 INFO: fwhm_rt        : 5
0:43:52.490184 INFO: quant_window   : 3
0:43:52.490223 INFO: ==============================================
0:43:52.711987 INFO: performing precursor FDR with 40 features
0:43:52.712110 INFO: Decoy channel: -1
0:43:52.712134 INFO: competitive: True
0:43:52.733545 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:52.747329 INFO: Estimating optimal hyperparameters - samples: 48,396, batch_size: 198, learning_rate: 2.20e-04
0:43:52.747533 INFO: Using random state 195380 for train-test-split
0:43:56.379875 INFO: Test AUC: 0.571
0:43:56.380003 INFO: Train AUC: 0.614
0:43:56.380033 INFO: AUC difference: 6.96%
0:43:56.380056 WARNING: AUC difference > 5%. This may indicate overfitting.
0:43:56.635745 INFO: Resetting torch num_threads to 100
0:43:56.645783 PROGRESS: === Extracted 60496 precursors and 285845 fragments ===
0:43:56.646312 INFO: === FDR correction performed with classifier version -1 ===
0:43:56.646867 PROGRESS: ============================= Precursor FDR =============================
0:43:56.646959 PROGRESS: Total precursors accumulated: 52
0:43:56.647020 PROGRESS: Target precursors: 52 (100.00%)
0:43:56.647073 PROGRESS: Decoy precursors: 0 (0.00%)
0:43:56.647123 PROGRESS: 
0:43:56.647170 PROGRESS: Precursor Summary:
0:43:56.648243 PROGRESS: Channel   0:	 0.050 FDR:    52; 0.010 FDR:    52; 0.001 FDR:    52
0:43:56.648328 PROGRESS: 
0:43:56.648398 PROGRESS: Protein Summary:
0:43:56.649572 PROGRESS: Channel   0:	 0.050 FDR:    51; 0.010 FDR:    51; 0.001 FDR:    51
0:43:56.649657 PROGRESS: =========================================================================
0:43:56.650563 INFO: Target number of precursors not reached yet.
0:43:56.808543 INFO: Starting optimization step 5.
0:43:56.808824 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:43:56.808903 INFO: Using rust extraction backend
0:43:56.808967 PROGRESS: Extracting batch of 63110 precursors
0:43:56.917505 INFO: === Search parameters used ===
0:43:56.917791 INFO: rt_error       : 805.6004638671875
0:43:56.917857 INFO: mobility_error : 0.1
0:43:56.917909 INFO: num_candidates : 1
0:43:56.917952 INFO: ms1_error      : 30
0:43:56.917994 INFO: ms2_error      : 30
0:43:56.918035 INFO: fwhm_rt        : 5
0:43:56.918073 INFO: quant_window   : 3
0:43:56.918112 INFO: ==============================================
0:43:57.310099 INFO: performing precursor FDR with 40 features
0:43:57.310212 INFO: Decoy channel: -1
0:43:57.310237 INFO: competitive: True
0:43:57.358107 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:57.388019 INFO: Estimating optimal hyperparameters - samples: 98,373, batch_size: 402, learning_rate: 3.13e-04
0:43:57.388331 INFO: Using random state 494653 for train-test-split
0:44:02.029381 INFO: Test AUC: 0.588
0:44:02.029510 INFO: Train AUC: 0.608
0:44:02.029540 INFO: AUC difference: 3.28%
0:44:02.305667 INFO: Resetting torch num_threads to 100
0:44:02.327310 PROGRESS: === Extracted 122967 precursors and 581846 fragments ===
0:44:02.327938 INFO: === FDR correction performed with classifier version -1 ===
0:44:02.328530 PROGRESS: ============================= Precursor FDR =============================
0:44:02.328622 PROGRESS: Total precursors accumulated: 356
0:44:02.328683 PROGRESS: Target precursors: 353 (99.16%)
0:44:02.328736 PROGRESS: Decoy precursors: 3 (0.84%)
0:44:02.328784 PROGRESS: 
0:44:02.328832 PROGRESS: Precursor Summary:
0:44:02.329883 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   353; 0.001 FDR:   155
0:44:02.329989 PROGRESS: 
0:44:02.330047 PROGRESS: Protein Summary:
0:44:02.331255 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   333; 0.001 FDR:   153
0:44:02.331346 PROGRESS: =========================================================================
0:44:02.333203 INFO: Target number of precursors not reached yet.
0:44:02.574087 INFO: Starting optimization step 6.
0:44:02.574354 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:44:02.574435 INFO: Using rust extraction backend
0:44:02.574498 PROGRESS: Extracting batch of 126235 precursors
0:44:02.787562 INFO: === Search parameters used ===
0:44:02.787830 INFO: rt_error       : 805.6004638671875
0:44:02.787889 INFO: mobility_error : 0.1
0:44:02.787941 INFO: num_candidates : 1
0:44:02.787989 INFO: ms1_error      : 30
0:44:02.788035 INFO: ms2_error      : 30
0:44:02.788079 INFO: fwhm_rt        : 5
0:44:02.788121 INFO: quant_window   : 3
0:44:02.788163 INFO: ==============================================
0:44:03.473729 INFO: performing precursor FDR with 40 features
0:44:03.473866 INFO: Decoy channel: -1
0:44:03.473895 INFO: competitive: True
0:44:03.571486 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:03.649797 INFO: Estimating optimal hyperparameters - samples: 198,366, batch_size: 812, learning_rate: 4.45e-04
0:44:03.650172 INFO: Using random state 359611 for train-test-split
0:44:09.936002 INFO: Test AUC: 0.590
0:44:09.936126 INFO: Train AUC: 0.608
0:44:09.936158 INFO: AUC difference: 2.95%
0:44:10.249476 INFO: Resetting torch num_threads to 100
0:44:10.291661 PROGRESS: === Extracted 247958 precursors and 1173602 fragments ===
0:44:10.292322 INFO: === FDR correction performed with classifier version -1 ===
0:44:10.293022 PROGRESS: ============================= Precursor FDR =============================
0:44:10.293127 PROGRESS: Total precursors accumulated: 869
0:44:10.293188 PROGRESS: Target precursors: 861 (99.08%)
0:44:10.293239 PROGRESS: Decoy precursors: 8 (0.92%)
0:44:10.293291 PROGRESS: 
0:44:10.293337 PROGRESS: Precursor Summary:
0:44:10.294523 PROGRESS: Channel   0:	 0.050 FDR:   861; 0.010 FDR:   861; 0.001 FDR:   257
0:44:10.294611 PROGRESS: 
0:44:10.294666 PROGRESS: Protein Summary:
0:44:10.296082 PROGRESS: Channel   0:	 0.050 FDR:   770; 0.010 FDR:   770; 0.001 FDR:   242
0:44:10.296168 PROGRESS: =========================================================================
0:44:10.300003 INFO: Target number of precursors not reached yet.
0:44:10.694798 INFO: Starting optimization step 7.
0:44:10.695080 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:44:10.695160 INFO: Using rust extraction backend
0:44:10.695223 PROGRESS: Extracting batch of 252313 precursors
0:44:11.119672 INFO: === Search parameters used ===
0:44:11.119944 INFO: rt_error       : 805.6004638671875
0:44:11.120002 INFO: mobility_error : 0.1
0:44:11.120049 INFO: num_candidates : 1
0:44:11.120093 INFO: ms1_error      : 30
0:44:11.120135 INFO: ms2_error      : 30
0:44:11.120175 INFO: fwhm_rt        : 5
0:44:11.120233 INFO: quant_window   : 3
0:44:11.120275 INFO: ==============================================
0:44:12.416018 INFO: performing precursor FDR with 40 features
0:44:12.416139 INFO: Decoy channel: -1
0:44:12.416165 INFO: competitive: True
0:44:12.608802 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:12.798930 INFO: Estimating optimal hyperparameters - samples: 398,132, batch_size: 1,630, learning_rate: 6.31e-04
0:44:12.799504 INFO: Using random state 84581 for train-test-split
0:44:22.865643 INFO: Test AUC: 0.591
0:44:22.865796 INFO: Train AUC: 0.608
0:44:22.865830 INFO: AUC difference: 2.90%
0:44:23.249933 INFO: Resetting torch num_threads to 100
0:44:23.340487 PROGRESS: === Extracted 497665 precursors and 2356925 fragments ===
0:44:23.341134 INFO: === FDR correction performed with classifier version -1 ===
0:44:23.342064 PROGRESS: ============================= Precursor FDR =============================
0:44:23.342161 PROGRESS: Total precursors accumulated: 2,011
0:44:23.342222 PROGRESS: Target precursors: 1,992 (99.06%)
0:44:23.342274 PROGRESS: Decoy precursors: 19 (0.94%)
0:44:23.342341 PROGRESS: 
0:44:23.342389 PROGRESS: Precursor Summary:
0:44:23.343780 PROGRESS: Channel   0:	 0.050 FDR: 1,992; 0.010 FDR: 1,992; 0.001 FDR:   109
0:44:23.343871 PROGRESS: 
0:44:23.343930 PROGRESS: Protein Summary:
0:44:23.345684 PROGRESS: Channel   0:	 0.050 FDR: 1,586; 0.010 FDR: 1,586; 0.001 FDR:   104
0:44:23.345780 PROGRESS: =========================================================================
0:44:23.352710 INFO: Target number of precursors reached.
0:44:23.624669 INFO: fragments_df: keeping 5000 of 2356925 [sum(precursor_idx_mask)=21203 sum(mass_error_mask)=2356925 stop_rank=5000
0:44:24.296491 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:24.588469 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:25.300842 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:44:25.301293 INFO: Using score_cutoff 12.625525819301604 (fac=0.99, q=1)
0:44:25.301629 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:44:25.301709 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:44:25.301765 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.625525819301604
0:44:25.301827 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:25.604816 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:26.254849 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:44:26.255069 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:44:26.255168 INFO: Starting optimization step 8.
0:44:26.255233 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:44:26.255299 INFO: Using rust extraction backend
0:44:26.255357 PROGRESS: Extracting batch of 502760 precursors
0:44:27.093416 INFO: === Search parameters used ===
0:44:27.093685 INFO: rt_error       : 805.6004638671875
0:44:27.093745 INFO: mobility_error : 0.1
0:44:27.093828 INFO: num_candidates : 3
0:44:27.093890 INFO: ms1_error      : 30
0:44:27.093936 INFO: ms2_error      : 30
0:44:27.093977 INFO: fwhm_rt        : 3.0
0:44:27.094017 INFO: quant_window   : 3
0:44:27.094057 INFO: ==============================================
0:44:32.228277 INFO: performing precursor FDR with 40 features
0:44:32.228405 INFO: Decoy channel: -1
0:44:32.228431 INFO: competitive: True
0:44:32.609779 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:33.247816 INFO: Estimating optimal hyperparameters - samples: 1,194,790, batch_size: 4,096, learning_rate: 1.00e-03
0:44:33.250217 INFO: Using random state 64166 for train-test-split
0:44:55.699360 INFO: Test AUC: 0.601
0:44:55.699502 INFO: Train AUC: 0.606
0:44:55.699534 INFO: AUC difference: 0.84%
0:44:56.372216 INFO: Resetting torch num_threads to 100
0:44:56.428674 PROGRESS: === Extracted 1493488 precursors and 6919103 fragments ===
0:44:56.429156 INFO: === FDR correction performed with classifier version 7 ===
0:44:56.429975 PROGRESS: ============================= Precursor FDR =============================
0:44:56.430066 PROGRESS: Total precursors accumulated: 2,461
0:44:56.430127 PROGRESS: Target precursors: 2,437 (99.02%)
0:44:56.430179 PROGRESS: Decoy precursors: 24 (0.98%)
0:44:56.430243 PROGRESS: 
0:44:56.430290 PROGRESS: Precursor Summary:
0:44:56.431835 PROGRESS: Channel   0:	 0.050 FDR: 2,437; 0.010 FDR: 2,437; 0.001 FDR: 1,455
0:44:56.431923 PROGRESS: 
0:44:56.431979 PROGRESS: Protein Summary:
0:44:56.434112 PROGRESS: Channel   0:	 0.050 FDR: 1,903; 0.010 FDR: 1,903; 0.001 FDR: 1,191
0:44:56.434206 PROGRESS: =========================================================================
0:44:56.464839 INFO: Target number of precursors reached.
0:44:57.220582 INFO: fragments_df: keeping 5000 of 6919103 [sum(precursor_idx_mask)=53337 sum(mass_error_mask)=6919103 stop_rank=5000
0:44:57.662535 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:58.012898 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:58.722506 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:58.722963 INFO: Using score_cutoff 11.982064934921265 (fac=0.99, q=1)
0:44:58.723267 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:58.723352 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:58.723408 INFO: Updating optimization_manager: score_cutoff        : 12.625525819301604 -> 11.982064934921265
0:44:58.723461 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:58.874689 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:59.211067 INFO: === checking if optimization conditions were reached ===
0:44:59.211384 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 5 ===
0:44:59.214329 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.508769952736491
0:44:59.214500 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.5088.
0:44:59.214582 INFO: ==============================================
0:44:59.214674 INFO: Starting optimization step 9.
0:44:59.214749 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:44:59.214825 INFO: Using rust extraction backend
0:44:59.214895 PROGRESS: Extracting batch of 250447 precursors
0:44:59.639035 INFO: === Search parameters used ===
0:44:59.639307 INFO: rt_error       : 805.6004638671875
0:44:59.639364 INFO: mobility_error : 0.1
0:44:59.639413 INFO: num_candidates : 3
0:44:59.639458 INFO: ms1_error      : 30
0:44:59.639500 INFO: ms2_error      : 7.508769952736491
0:44:59.639541 INFO: fwhm_rt        : 3.0
0:44:59.639583 INFO: quant_window   : 3
0:44:59.639641 INFO: ==============================================
0:45:02.025668 INFO: performing precursor FDR with 40 features
0:45:02.025799 INFO: Decoy channel: -1
0:45:02.025825 INFO: competitive: True
0:45:02.214089 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:02.507621 INFO: Estimating optimal hyperparameters - samples: 600,786, batch_size: 2,460, learning_rate: 7.75e-04
0:45:02.508767 INFO: Using random state 64166 for train-test-split
0:45:15.079762 INFO: Test AUC: 0.601
0:45:15.079903 INFO: Train AUC: 0.610
0:45:15.079936 INFO: AUC difference: 1.61%
0:45:16.268342 INFO: Resetting torch num_threads to 100
0:45:16.294394 PROGRESS: === Extracted 750983 precursors and 4202851 fragments ===
0:45:16.294870 INFO: === FDR correction performed with classifier version 7 ===
0:45:16.295549 PROGRESS: ============================= Precursor FDR =============================
0:45:16.295636 PROGRESS: Total precursors accumulated: 1,651
0:45:16.295695 PROGRESS: Target precursors: 1,635 (99.03%)
0:45:16.295746 PROGRESS: Decoy precursors: 16 (0.97%)
0:45:16.295793 PROGRESS: 
0:45:16.295839 PROGRESS: Precursor Summary:
0:45:16.297251 PROGRESS: Channel   0:	 0.050 FDR: 1,635; 0.010 FDR: 1,635; 0.001 FDR: 1,334
0:45:16.297339 PROGRESS: 
0:45:16.297394 PROGRESS: Protein Summary:
0:45:16.299246 PROGRESS: Channel   0:	 0.050 FDR: 1,404; 0.010 FDR: 1,404; 0.001 FDR: 1,145
0:45:16.299339 PROGRESS: =========================================================================
0:45:16.313787 INFO: Target number of precursors reached.
0:45:16.770687 INFO: fragments_df: keeping 5000 of 4202851 [sum(precursor_idx_mask)=37916 sum(mass_error_mask)=4202851 stop_rank=5000
0:45:17.181581 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:17.431019 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:18.144427 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:18.144863 INFO: Using score_cutoff 6.856759103679657 (fac=0.99, q=1)
0:45:18.145177 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:18.145255 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:18.145310 INFO: Updating optimization_manager: score_cutoff        : 11.982064934921265 -> 6.856759103679657
0:45:18.145364 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:18.295452 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:18.627607 INFO: === checking if optimization conditions were reached ===
0:45:18.627920 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 5 ===
0:45:18.631033 INFO: Updating optimization_manager: ms2_error           : 7.508769952736491 -> 7.530149623983008
0:45:18.631175 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.5301.
0:45:18.631252 INFO: ==============================================
0:45:18.631336 INFO: Starting optimization step 10.
0:45:18.631409 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:18.631486 INFO: Using rust extraction backend
0:45:18.631556 PROGRESS: Extracting batch of 250447 precursors
0:45:19.055442 INFO: === Search parameters used ===
0:45:19.055723 INFO: rt_error       : 805.6004638671875
0:45:19.055784 INFO: mobility_error : 0.1
0:45:19.055835 INFO: num_candidates : 3
0:45:19.055880 INFO: ms1_error      : 30
0:45:19.055923 INFO: ms2_error      : 7.530149623983008
0:45:19.055998 INFO: fwhm_rt        : 3.0
0:45:19.056044 INFO: quant_window   : 3
0:45:19.056087 INFO: ==============================================
0:45:21.474152 INFO: performing precursor FDR with 40 features
0:45:21.474274 INFO: Decoy channel: -1
0:45:21.474300 INFO: competitive: True
0:45:21.669386 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:21.973300 INFO: Estimating optimal hyperparameters - samples: 600,772, batch_size: 2,460, learning_rate: 7.75e-04
0:45:21.974441 INFO: Using random state 64166 for train-test-split
0:45:34.446233 INFO: Test AUC: 0.602
0:45:34.446369 INFO: Train AUC: 0.611
0:45:34.446401 INFO: AUC difference: 1.47%
0:45:34.909664 INFO: Resetting torch num_threads to 100
0:45:34.936287 PROGRESS: === Extracted 750965 precursors and 4201296 fragments ===
0:45:34.936767 INFO: === FDR correction performed with classifier version 7 ===
0:45:34.937444 PROGRESS: ============================= Precursor FDR =============================
0:45:34.937547 PROGRESS: Total precursors accumulated: 1,674
0:45:34.937608 PROGRESS: Target precursors: 1,658 (99.04%)
0:45:34.937660 PROGRESS: Decoy precursors: 16 (0.96%)
0:45:34.937707 PROGRESS: 
0:45:34.937752 PROGRESS: Precursor Summary:
0:45:34.939168 PROGRESS: Channel   0:	 0.050 FDR: 1,658; 0.010 FDR: 1,658; 0.001 FDR: 1,199
0:45:34.939263 PROGRESS: 
0:45:34.939320 PROGRESS: Protein Summary:
0:45:34.941142 PROGRESS: Channel   0:	 0.050 FDR: 1,409; 0.010 FDR: 1,409; 0.001 FDR: 1,042
0:45:34.941233 PROGRESS: =========================================================================
0:45:34.955955 INFO: Target number of precursors reached.
0:45:35.399088 INFO: fragments_df: keeping 5000 of 4201296 [sum(precursor_idx_mask)=39469 sum(mass_error_mask)=4201296 stop_rank=5000
0:45:35.810225 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:36.066045 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:36.778689 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:36.779120 INFO: Using score_cutoff 10.855095677661897 (fac=0.99, q=1)
0:45:36.779425 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:36.779501 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:36.779556 INFO: Updating optimization_manager: score_cutoff        : 6.856759103679657 -> 10.855095677661897
0:45:36.779609 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:36.930875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:37.259633 INFO: === checking if optimization conditions were reached ===
0:45:37.259942 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 5 ===
0:45:37.263025 INFO: Updating optimization_manager: ms2_error           : 7.530149623983008 -> 7.482599320007754
0:45:37.263146 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 7.4826.
0:45:37.263220 INFO: ==============================================
0:45:37.263302 INFO: Starting optimization step 11.
0:45:37.263373 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:37.263445 INFO: Using rust extraction backend
0:45:37.263514 PROGRESS: Extracting batch of 250447 precursors
0:45:37.686406 INFO: === Search parameters used ===
0:45:37.686676 INFO: rt_error       : 805.6004638671875
0:45:37.686733 INFO: mobility_error : 0.1
0:45:37.686780 INFO: num_candidates : 3
0:45:37.686855 INFO: ms1_error      : 30
0:45:37.686900 INFO: ms2_error      : 7.482599320007754
0:45:37.686940 INFO: fwhm_rt        : 3.0
0:45:37.686982 INFO: quant_window   : 3
0:45:37.687022 INFO: ==============================================
0:45:40.083519 INFO: performing precursor FDR with 40 features
0:45:40.083671 INFO: Decoy channel: -1
0:45:40.083698 INFO: competitive: True
0:45:40.272988 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:40.577682 INFO: Estimating optimal hyperparameters - samples: 600,803, batch_size: 2,460, learning_rate: 7.75e-04
0:45:40.578691 INFO: Using random state 64166 for train-test-split
0:45:53.669020 INFO: Test AUC: 0.596
0:45:53.669166 INFO: Train AUC: 0.612
0:45:53.669199 INFO: AUC difference: 2.61%
0:45:54.137603 INFO: Resetting torch num_threads to 100
0:45:54.167653 PROGRESS: === Extracted 751004 precursors and 4204531 fragments ===
0:45:54.168147 INFO: === FDR correction performed with classifier version 7 ===
0:45:54.168805 PROGRESS: ============================= Precursor FDR =============================
0:45:54.168892 PROGRESS: Total precursors accumulated: 1,482
0:45:54.168952 PROGRESS: Target precursors: 1,468 (99.06%)
0:45:54.169004 PROGRESS: Decoy precursors: 14 (0.94%)
0:45:54.169052 PROGRESS: 
0:45:54.169099 PROGRESS: Precursor Summary:
0:45:54.170470 PROGRESS: Channel   0:	 0.050 FDR: 1,468; 0.010 FDR: 1,468; 0.001 FDR: 1,116
0:45:54.170567 PROGRESS: 
0:45:54.170628 PROGRESS: Protein Summary:
0:45:54.172373 PROGRESS: Channel   0:	 0.050 FDR: 1,249; 0.010 FDR: 1,249; 0.001 FDR:   964
0:45:54.172481 PROGRESS: =========================================================================
0:45:54.186914 INFO: Target number of precursors reached.
0:45:54.649678 INFO: fragments_df: keeping 5000 of 4204531 [sum(precursor_idx_mask)=35678 sum(mass_error_mask)=4204531 stop_rank=5000
0:45:55.157949 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:55.360296 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:56.007571 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:56.008016 INFO: Using score_cutoff 12.123099799633025 (fac=0.99, q=1)
0:45:56.008326 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:56.008404 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:56.008460 INFO: Updating optimization_manager: score_cutoff        : 10.855095677661897 -> 12.123099799633025
0:45:56.008515 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:56.160339 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:56.492773 INFO: === checking if optimization conditions were reached ===
0:45:56.493119 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 5 ===
0:45:56.496210 INFO: Updating optimization_manager: ms2_error           : 7.482599320007754 -> 7.436181072758187
0:45:56.496328 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 7.4362.
0:45:56.496405 INFO: ==============================================
0:45:56.496491 INFO: Starting optimization step 12.
0:45:56.496562 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:56.496639 INFO: Using rust extraction backend
0:45:56.496709 PROGRESS: Extracting batch of 250447 precursors
0:45:56.920125 INFO: === Search parameters used ===
0:45:56.920406 INFO: rt_error       : 805.6004638671875
0:45:56.920466 INFO: mobility_error : 0.1
0:45:56.920514 INFO: num_candidates : 3
0:45:56.920560 INFO: ms1_error      : 30
0:45:56.920603 INFO: ms2_error      : 7.436181072758187
0:45:56.920645 INFO: fwhm_rt        : 3.0
0:45:56.920685 INFO: quant_window   : 3
0:45:56.920724 INFO: ==============================================
0:45:59.367041 INFO: performing precursor FDR with 40 features
0:45:59.367168 INFO: Decoy channel: -1
0:45:59.367194 INFO: competitive: True
0:45:59.556317 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:59.861541 INFO: Estimating optimal hyperparameters - samples: 600,827, batch_size: 2,460, learning_rate: 7.75e-04
0:45:59.862571 INFO: Using random state 64166 for train-test-split
0:46:12.366060 INFO: Test AUC: 0.599
0:46:12.366203 INFO: Train AUC: 0.610
0:46:12.366236 INFO: AUC difference: 1.84%
0:46:12.824579 INFO: Resetting torch num_threads to 100
0:46:12.854150 PROGRESS: === Extracted 751034 precursors and 4207742 fragments ===
0:46:12.854627 INFO: === FDR correction performed with classifier version 7 ===
0:46:12.855276 PROGRESS: ============================= Precursor FDR =============================
0:46:12.855363 PROGRESS: Total precursors accumulated: 1,490
0:46:12.855423 PROGRESS: Target precursors: 1,476 (99.06%)
0:46:12.855474 PROGRESS: Decoy precursors: 14 (0.94%)
0:46:12.855523 PROGRESS: 
0:46:12.855570 PROGRESS: Precursor Summary:
0:46:12.856938 PROGRESS: Channel   0:	 0.050 FDR: 1,476; 0.010 FDR: 1,476; 0.001 FDR: 1,224
0:46:12.857027 PROGRESS: 
0:46:12.857085 PROGRESS: Protein Summary:
0:46:12.858877 PROGRESS: Channel   0:	 0.050 FDR: 1,277; 0.010 FDR: 1,277; 0.001 FDR: 1,059
0:46:12.858971 PROGRESS: =========================================================================
0:46:12.873724 INFO: Target number of precursors reached.
0:46:13.338966 INFO: fragments_df: keeping 5000 of 4207742 [sum(precursor_idx_mask)=34589 sum(mass_error_mask)=4207742 stop_rank=5000
0:46:13.750793 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:13.954065 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:14.599721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:14.600166 INFO: Using score_cutoff 7.485724686384201 (fac=0.99, q=1)
0:46:14.600467 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:14.600544 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:14.600598 INFO: Updating optimization_manager: score_cutoff        : 12.123099799633025 -> 7.485724686384201
0:46:14.600653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:14.750999 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:15.097520 INFO: === checking if optimization conditions were reached ===
0:46:15.097834 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 5 ===
0:46:15.098936 INFO: Updating optimization_manager: ms2_error           : 7.436181072758187 -> 7.530149623983008
0:46:15.099087 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
0:46:15.099204 INFO: Updating optimization_manager: score_cutoff        : 7.485724686384201 -> 10.855095677661897
0:46:15.099313 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:15.099418 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:15.099523 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.5301 found after 5 searches.
0:46:15.099615 INFO: ==============================================
0:46:15.099699 PROGRESS: Optimization finished for ms2_error.
0:46:15.497989 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:15.648286 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:15.992951 INFO: Starting optimization step 0.
0:46:15.993257 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:15.993371 INFO: Using rust extraction backend
0:46:15.993448 PROGRESS: Extracting batch of 250447 precursors
0:46:16.415898 INFO: === Search parameters used ===
0:46:16.416171 INFO: rt_error       : 805.6004638671875
0:46:16.416230 INFO: mobility_error : 0.1
0:46:16.416281 INFO: num_candidates : 3
0:46:16.416327 INFO: ms1_error      : 30
0:46:16.416371 INFO: ms2_error      : 7.530149623983008
0:46:16.416413 INFO: fwhm_rt        : 3.0
0:46:16.416455 INFO: quant_window   : 3
0:46:16.416496 INFO: ==============================================
0:46:18.814602 INFO: performing precursor FDR with 40 features
0:46:18.814722 INFO: Decoy channel: -1
0:46:18.814747 INFO: competitive: True
0:46:19.002756 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:19.305821 INFO: Estimating optimal hyperparameters - samples: 600,774, batch_size: 2,460, learning_rate: 7.75e-04
0:46:19.306933 INFO: Using random state 785393 for train-test-split
0:46:32.624877 INFO: Test AUC: 0.604
0:46:32.625010 INFO: Train AUC: 0.616
0:46:32.625041 INFO: AUC difference: 1.93%
0:46:33.083720 INFO: Resetting torch num_threads to 100
0:46:33.110472 PROGRESS: === Extracted 750968 precursors and 4200531 fragments ===
0:46:33.110922 INFO: === FDR correction performed with classifier version 10 ===
0:46:33.111612 PROGRESS: ============================= Precursor FDR =============================
0:46:33.111707 PROGRESS: Total precursors accumulated: 1,756
0:46:33.111780 PROGRESS: Target precursors: 1,739 (99.03%)
0:46:33.111835 PROGRESS: Decoy precursors: 17 (0.97%)
0:46:33.111883 PROGRESS: 
0:46:33.111928 PROGRESS: Precursor Summary:
0:46:33.113330 PROGRESS: Channel   0:	 0.050 FDR: 1,739; 0.010 FDR: 1,739; 0.001 FDR: 1,246
0:46:33.113419 PROGRESS: 
0:46:33.113475 PROGRESS: Protein Summary:
0:46:33.115326 PROGRESS: Channel   0:	 0.050 FDR: 1,462; 0.010 FDR: 1,462; 0.001 FDR: 1,077
0:46:33.115421 PROGRESS: =========================================================================
0:46:33.129935 INFO: Target number of precursors reached.
0:46:33.584857 INFO: fragments_df: keeping 5000 of 4200531 [sum(precursor_idx_mask)=41722 sum(mass_error_mask)=4200531 stop_rank=5000
0:46:33.995990 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:34.255969 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:34.966359 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:34.966803 INFO: Using score_cutoff 11.981047532272338 (fac=0.99, q=1)
0:46:34.967104 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:34.967181 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:34.967234 INFO: Updating optimization_manager: score_cutoff        : 10.855095677661897 -> 11.981047532272338
0:46:34.967287 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:35.118356 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:35.460921 INFO: === checking if optimization conditions were reached ===
0:46:35.461235 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:46:35.464471 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 546.6086809876618
0:46:35.464664 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 546.6087.
0:46:35.464740 INFO: ==============================================
0:46:35.464822 INFO: Starting optimization step 1.
0:46:35.464889 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:35.464961 INFO: Using rust extraction backend
0:46:35.465026 PROGRESS: Extracting batch of 250447 precursors
0:46:35.887086 INFO: === Search parameters used ===
0:46:35.887353 INFO: rt_error       : 546.6086809876618
0:46:35.887411 INFO: mobility_error : 0.1
0:46:35.887465 INFO: num_candidates : 3
0:46:35.887510 INFO: ms1_error      : 30
0:46:35.887550 INFO: ms2_error      : 7.530149623983008
0:46:35.887589 INFO: fwhm_rt        : 3.0
0:46:35.887627 INFO: quant_window   : 3
0:46:35.887664 INFO: ==============================================
0:46:38.249410 INFO: performing precursor FDR with 40 features
0:46:38.249540 INFO: Decoy channel: -1
0:46:38.249566 INFO: competitive: True
0:46:38.440516 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:38.747365 INFO: Estimating optimal hyperparameters - samples: 600,629, batch_size: 2,460, learning_rate: 7.75e-04
0:46:38.748446 INFO: Using random state 785393 for train-test-split
0:46:50.860996 INFO: Test AUC: 0.602
0:46:50.861137 INFO: Train AUC: 0.616
0:46:50.861168 INFO: AUC difference: 2.17%
0:46:51.327387 INFO: Resetting torch num_threads to 100
0:46:51.353577 PROGRESS: === Extracted 750787 precursors and 4162987 fragments ===
0:46:51.354067 INFO: === FDR correction performed with classifier version 10 ===
0:46:51.354753 PROGRESS: ============================= Precursor FDR =============================
0:46:51.354841 PROGRESS: Total precursors accumulated: 1,722
0:46:51.354900 PROGRESS: Target precursors: 1,705 (99.01%)
0:46:51.354951 PROGRESS: Decoy precursors: 17 (0.99%)
0:46:51.354998 PROGRESS: 
0:46:51.355043 PROGRESS: Precursor Summary:
0:46:51.356449 PROGRESS: Channel   0:	 0.050 FDR: 1,705; 0.010 FDR: 1,705; 0.001 FDR: 1,406
0:46:51.356536 PROGRESS: 
0:46:51.356592 PROGRESS: Protein Summary:
0:46:51.358459 PROGRESS: Channel   0:	 0.050 FDR: 1,446; 0.010 FDR: 1,446; 0.001 FDR: 1,201
0:46:51.358551 PROGRESS: =========================================================================
0:46:51.373141 INFO: Target number of precursors reached.
0:46:51.830159 INFO: fragments_df: keeping 5000 of 4162987 [sum(precursor_idx_mask)=40374 sum(mass_error_mask)=4162987 stop_rank=5000
0:46:52.241596 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:52.497166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:53.207491 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:53.207935 INFO: Using score_cutoff 8.602970502090454 (fac=0.99, q=1)
0:46:53.208237 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:53.208316 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:53.208372 INFO: Updating optimization_manager: score_cutoff        : 11.981047532272338 -> 8.602970502090454
0:46:53.208435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:53.359113 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:53.687362 INFO: === checking if optimization conditions were reached ===
0:46:53.687667 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:46:53.691028 INFO: Updating optimization_manager: rt_error            : 546.6086809876618 -> 587.9926755747327
0:46:53.691187 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 587.9927.
0:46:53.691263 INFO: ==============================================
0:46:53.691345 INFO: Starting optimization step 2.
0:46:53.691415 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:53.691488 INFO: Using rust extraction backend
0:46:53.691556 PROGRESS: Extracting batch of 250447 precursors
0:46:54.116107 INFO: === Search parameters used ===
0:46:54.116374 INFO: rt_error       : 587.9926755747327
0:46:54.116431 INFO: mobility_error : 0.1
0:46:54.116479 INFO: num_candidates : 3
0:46:54.116522 INFO: ms1_error      : 30
0:46:54.116563 INFO: ms2_error      : 7.530149623983008
0:46:54.116603 INFO: fwhm_rt        : 3.0
0:46:54.116641 INFO: quant_window   : 3
0:46:54.116679 INFO: ==============================================
0:46:56.432120 INFO: performing precursor FDR with 40 features
0:46:56.432238 INFO: Decoy channel: -1
0:46:56.432263 INFO: competitive: True
0:46:56.624959 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:56.929494 INFO: Estimating optimal hyperparameters - samples: 600,731, batch_size: 2,460, learning_rate: 7.75e-04
0:46:56.930466 INFO: Using random state 785393 for train-test-split
0:47:08.828070 INFO: Test AUC: 0.603
0:47:08.828212 INFO: Train AUC: 0.616
0:47:08.828245 INFO: AUC difference: 2.06%
0:47:09.294125 INFO: Resetting torch num_threads to 100
0:47:09.320606 PROGRESS: === Extracted 750914 precursors and 4189809 fragments ===
0:47:09.321100 INFO: === FDR correction performed with classifier version 10 ===
0:47:09.321765 PROGRESS: ============================= Precursor FDR =============================
0:47:09.321866 PROGRESS: Total precursors accumulated: 1,741
0:47:09.321931 PROGRESS: Target precursors: 1,724 (99.02%)
0:47:09.321982 PROGRESS: Decoy precursors: 17 (0.98%)
0:47:09.322030 PROGRESS: 
0:47:09.322077 PROGRESS: Precursor Summary:
0:47:09.323416 PROGRESS: Channel   0:	 0.050 FDR: 1,724; 0.010 FDR: 1,724; 0.001 FDR:   440
0:47:09.323504 PROGRESS: 
0:47:09.323560 PROGRESS: Protein Summary:
0:47:09.325267 PROGRESS: Channel   0:	 0.050 FDR: 1,449; 0.010 FDR: 1,449; 0.001 FDR:   410
0:47:09.325358 PROGRESS: =========================================================================
0:47:09.339891 INFO: Target number of precursors reached.
0:47:09.784015 INFO: fragments_df: keeping 5000 of 4189809 [sum(precursor_idx_mask)=41446 sum(mass_error_mask)=4189809 stop_rank=5000
0:47:10.195873 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:10.420293 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:11.106645 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:11.107085 INFO: Using score_cutoff 11.934664819622041 (fac=0.99, q=1)
0:47:11.107383 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:11.107467 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:11.107527 INFO: Updating optimization_manager: score_cutoff        : 8.602970502090454 -> 11.934664819622041
0:47:11.107584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:11.257602 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:11.586771 INFO: === checking if optimization conditions were reached ===
0:47:11.587087 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:47:11.590488 INFO: Updating optimization_manager: rt_error            : 587.9926755747327 -> 688.985283339252
0:47:11.590611 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 688.9853.
0:47:11.590687 INFO: ==============================================
0:47:11.590788 INFO: Starting optimization step 3.
0:47:11.590858 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:47:11.590930 INFO: Using rust extraction backend
0:47:11.590998 PROGRESS: Extracting batch of 250447 precursors
0:47:12.013333 INFO: === Search parameters used ===
0:47:12.013597 INFO: rt_error       : 688.985283339252
0:47:12.013652 INFO: mobility_error : 0.1
0:47:12.013698 INFO: num_candidates : 3
0:47:12.013740 INFO: ms1_error      : 30
0:47:12.013780 INFO: ms2_error      : 7.530149623983008
0:47:12.013820 INFO: fwhm_rt        : 3.0
0:47:12.013871 INFO: quant_window   : 3
0:47:12.013932 INFO: ==============================================
0:47:14.356760 INFO: performing precursor FDR with 40 features
0:47:14.356884 INFO: Decoy channel: -1
0:47:14.356910 INFO: competitive: True
0:47:14.538646 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:14.828325 INFO: Estimating optimal hyperparameters - samples: 600,749, batch_size: 2,460, learning_rate: 7.75e-04
0:47:14.829230 INFO: Using random state 785393 for train-test-split
0:47:28.359308 INFO: Test AUC: 0.606
0:47:28.359447 INFO: Train AUC: 0.615
0:47:28.359479 INFO: AUC difference: 1.45%
0:47:28.819739 INFO: Resetting torch num_threads to 100
0:47:28.845720 PROGRESS: === Extracted 750937 precursors and 4195083 fragments ===
0:47:28.846235 INFO: === FDR correction performed with classifier version 10 ===
0:47:28.846920 PROGRESS: ============================= Precursor FDR =============================
0:47:28.847010 PROGRESS: Total precursors accumulated: 1,793
0:47:28.847071 PROGRESS: Target precursors: 1,776 (99.05%)
0:47:28.847124 PROGRESS: Decoy precursors: 17 (0.95%)
0:47:28.847172 PROGRESS: 
0:47:28.847223 PROGRESS: Precursor Summary:
0:47:28.848638 PROGRESS: Channel   0:	 0.050 FDR: 1,776; 0.010 FDR: 1,776; 0.001 FDR: 1,235
0:47:28.848732 PROGRESS: 
0:47:28.848789 PROGRESS: Protein Summary:
0:47:28.850649 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR: 1,073
0:47:28.850741 PROGRESS: =========================================================================
0:47:28.865057 INFO: Target number of precursors reached.
0:47:29.325036 INFO: fragments_df: keeping 5000 of 4195083 [sum(precursor_idx_mask)=41602 sum(mass_error_mask)=4195083 stop_rank=5000
0:47:29.733001 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:29.999038 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:30.709977 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:30.710422 INFO: Using score_cutoff 8.378360381126404 (fac=0.99, q=1)
0:47:30.710743 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:30.710824 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:30.710880 INFO: Updating optimization_manager: score_cutoff        : 11.934664819622041 -> 8.378360381126404
0:47:30.710935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:30.862653 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:31.193545 INFO: === checking if optimization conditions were reached ===
0:47:31.193860 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:47:31.197264 INFO: Updating optimization_manager: rt_error            : 688.985283339252 -> 718.1673023076576
0:47:31.197390 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 718.1673.
0:47:31.197466 INFO: ==============================================
0:47:31.197550 INFO: Starting optimization step 4.
0:47:31.197622 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:47:31.197695 INFO: Using rust extraction backend
0:47:31.197766 PROGRESS: Extracting batch of 250447 precursors
0:47:31.620819 INFO: === Search parameters used ===
0:47:31.621085 INFO: rt_error       : 718.1673023076576
0:47:31.621143 INFO: mobility_error : 0.1
0:47:31.621191 INFO: num_candidates : 3
0:47:31.621238 INFO: ms1_error      : 30
0:47:31.621285 INFO: ms2_error      : 7.530149623983008
0:47:31.621353 INFO: fwhm_rt        : 3.0
0:47:31.621398 INFO: quant_window   : 3
0:47:31.621439 INFO: ==============================================
0:47:33.957096 INFO: performing precursor FDR with 40 features
0:47:33.957211 INFO: Decoy channel: -1
0:47:33.957237 INFO: competitive: True
0:47:34.139078 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:34.426086 INFO: Estimating optimal hyperparameters - samples: 600,779, batch_size: 2,460, learning_rate: 7.75e-04
0:47:34.427199 INFO: Using random state 785393 for train-test-split
0:47:46.940201 INFO: Test AUC: 0.605
0:47:46.940339 INFO: Train AUC: 0.616
0:47:46.940373 INFO: AUC difference: 1.78%
0:47:47.402018 INFO: Resetting torch num_threads to 100
0:47:47.428461 PROGRESS: === Extracted 750974 precursors and 4200728 fragments ===
0:47:47.428928 INFO: === FDR correction performed with classifier version 10 ===
0:47:47.429602 PROGRESS: ============================= Precursor FDR =============================
0:47:47.429689 PROGRESS: Total precursors accumulated: 1,763
0:47:47.429749 PROGRESS: Target precursors: 1,746 (99.04%)
0:47:47.429800 PROGRESS: Decoy precursors: 17 (0.96%)
0:47:47.429862 PROGRESS: 
0:47:47.429917 PROGRESS: Precursor Summary:
0:47:47.431320 PROGRESS: Channel   0:	 0.050 FDR: 1,746; 0.010 FDR: 1,746; 0.001 FDR: 1,331
0:47:47.431407 PROGRESS: 
0:47:47.431464 PROGRESS: Protein Summary:
0:47:47.433310 PROGRESS: Channel   0:	 0.050 FDR: 1,468; 0.010 FDR: 1,468; 0.001 FDR: 1,137
0:47:47.433414 PROGRESS: =========================================================================
0:47:47.447723 INFO: Target number of precursors reached.
0:47:47.898808 INFO: fragments_df: keeping 5000 of 4200728 [sum(precursor_idx_mask)=41519 sum(mass_error_mask)=4200728 stop_rank=5000
0:47:48.303942 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:48.569708 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:49.280744 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:49.281184 INFO: Using score_cutoff 11.134743354320525 (fac=0.99, q=1)
0:47:49.281487 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:49.281564 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:49.281623 INFO: Updating optimization_manager: score_cutoff        : 8.378360381126404 -> 11.134743354320525
0:47:49.281678 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:49.432768 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:49.760972 INFO: === checking if optimization conditions were reached ===
0:47:49.761284 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:47:49.762344 INFO: Updating optimization_manager: rt_error            : 718.1673023076576 -> 688.985283339252
0:47:49.762500 INFO: Updating optimization_manager: classifier_version  : 10 -> 16
0:47:49.762616 INFO: Updating optimization_manager: score_cutoff        : 11.134743354320525 -> 8.378360381126404
0:47:49.762721 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:49.762825 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:49.762931 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 688.9853 found after 5 searches.
0:47:49.763004 INFO: ==============================================
0:47:49.763087 PROGRESS: Optimization finished for rt_error.
0:47:50.159148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:50.310005 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:50.638871 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:50.639167 PROGRESS: ==============================================
0:47:50.639251 PROGRESS: ms2_error      : 7.5301
0:47:50.639317 PROGRESS: rt_error       : 688.9853
0:47:50.639377 PROGRESS: ==============================================
0:47:50.640376 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:58.301136 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:14.188001 INFO: Using rust extraction backend
0:48:14.188297 PROGRESS: Extracting batch of 11997144 precursors
0:48:30.162344 INFO: === Search parameters used ===
0:48:30.162625 INFO: rt_error       : 688.985283339252
0:48:30.162685 INFO: mobility_error : 0.1
0:48:30.162735 INFO: num_candidates : 3
0:48:30.162785 INFO: ms1_error      : 30
0:48:30.162834 INFO: ms2_error      : 7.530149623983008
0:48:30.162881 INFO: fwhm_rt        : 3.0
0:48:30.162925 INFO: quant_window   : 3
0:48:30.162969 INFO: ==============================================
0:48:59.366670 INFO: Removed 5410944 precursors with score below cutoff 8.378360381126404
0:49:23.284261 INFO: performing precursor FDR with 40 features
0:49:23.284390 INFO: Decoy channel: -1
0:49:23.284417 INFO: competitive: True
0:49:26.444255 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:38.634581 INFO: Estimating optimal hyperparameters - samples: 24,463,644, batch_size: 4,096, learning_rate: 1.00e-03
0:49:38.707667 INFO: Using random state 438794 for train-test-split
0:59:21.408453 INFO: Test AUC: 0.624
0:59:21.409071 INFO: Train AUC: 0.624
0:59:21.409125 INFO: AUC difference: 0.08%
0:59:28.200474 INFO: Resetting torch num_threads to 100
0:59:31.431528 PROGRESS: ============================= Precursor FDR =============================
0:59:31.431967 PROGRESS: Total precursors accumulated: 93,654
0:59:31.432042 PROGRESS: Target precursors: 92,727 (99.01%)
0:59:31.432097 PROGRESS: Decoy precursors: 927 (0.99%)
0:59:31.432146 PROGRESS: 
0:59:31.432192 PROGRESS: Precursor Summary:
0:59:31.460216 PROGRESS: Channel   0:	 0.050 FDR: 92,727; 0.010 FDR: 92,727; 0.001 FDR: 53,089
0:59:31.460474 PROGRESS: 
0:59:31.460536 PROGRESS: Protein Summary:
0:59:31.498995 PROGRESS: Channel   0:	 0.050 FDR: 13,562; 0.010 FDR: 13,562; 0.001 FDR: 8,741
0:59:31.499247 PROGRESS: =========================================================================
0:59:31.724850 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
0:59:31.901489 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
0:59:32.150888 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:59:32.812269 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
0:59:32.812469 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant
0:59:32.812658 INFO: Initializing TimingManager
0:59:32.813407 INFO: Initializing RawFileManager
0:59:44.462838 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.
0:59:44.470651 INFO: Determining DIA cycle
0:59:44.488154 INFO: Found cycle with start 0.00 min and length 300.
0:59:44.660171 INFO: RT (min)            : 0.0 - 26.9
0:59:44.660281 INFO: RT duration (sec)   : 1611.2
0:59:44.660311 INFO: RT duration (min)   : 26.9
0:59:44.660337 INFO: Cycle len (scans)   : 300
0:59:44.660357 INFO: Cycle len (sec)     : 1.65
0:59:44.660378 INFO: Number of cycles    : 977
0:59:44.660398 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:59:44.660429 INFO: Creating DIA data object took: 11.846923351287842
0:59:45.329431 INFO: Creating DIA data NG object took: 0.6688673496246338
0:59:46.617723 INFO: Initializing CalibrationManager
0:59:46.618073 INFO: Setting up calibration estimators ..
0:59:46.618142 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:59:46.618237 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'}' ..
0:59:46.618367 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:59:46.618422 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:59:46.618486 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}}' ..
0:59:46.618545 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:59:46.618594 INFO: Done setting up calibration estimators.
0:59:46.618804 INFO: Initializing OptimizationManager
0:59:46.618948 INFO: initial parameter: ms1_error = 30
0:59:46.619001 INFO: initial parameter: ms2_error = 30
0:59:46.619050 INFO: initial parameter: rt_error = 805.5982666015625
0:59:46.619095 INFO: initial parameter: mobility_error = 0.1
0:59:46.619138 INFO: initial parameter: num_candidates = 1
0:59:46.619178 INFO: initial parameter: fwhm_rt = 5
0:59:46.619220 INFO: initial parameter: fwhm_mobility = 0.01
0:59:46.619261 INFO: initial parameter: score_cutoff = 0
0:59:46.619302 INFO: initial parameter: classifier_version = -1
0:59:46.619375 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:59:46.619696 INFO: FDRManager: loading saved state not requested, will be initialized.
0:59:46.619730 INFO: Initializing FDRManager
0:59:46.619772 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:59:48.235426 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:59:49.216272 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:59:49.216680 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
0:59:49.216801 PROGRESS: Starting initial search for precursors.
0:59:49.216907 INFO: Starting optimization step 0.
0:59:49.216982 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:59:49.217065 INFO: Using rust extraction backend
0:59:49.217148 PROGRESS: Extracting batch of 1970 precursors
0:59:49.222033 INFO: === Search parameters used ===
0:59:49.222139 INFO: rt_error       : 805.5982666015625
0:59:49.222191 INFO: mobility_error : 0.1
0:59:49.222238 INFO: num_candidates : 1
0:59:49.222283 INFO: ms1_error      : 30
0:59:49.222326 INFO: ms2_error      : 30
0:59:49.222368 INFO: fwhm_rt        : 5
0:59:49.222410 INFO: quant_window   : 3
0:59:49.222451 INFO: ==============================================
0:59:49.252687 INFO: performing precursor FDR with 40 features
0:59:49.252771 INFO: Decoy channel: -1
0:59:49.252797 INFO: competitive: True
0:59:49.254144 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:49.256148 INFO: Estimating optimal hyperparameters - samples: 1,564, batch_size: 128, learning_rate: 1.77e-04
0:59:49.257025 INFO: Using random state 836565 for train-test-split
0:59:49.415713 INFO: Test AUC: 0.482
0:59:49.415811 INFO: Train AUC: 0.535
0:59:49.415841 INFO: AUC difference: 9.94%
0:59:49.415864 WARNING: AUC difference > 5%. This may indicate overfitting.
0:59:49.660476 INFO: Resetting torch num_threads to 100
0:59:49.662256 PROGRESS: === Extracted 1955 precursors and 9268 fragments ===
0:59:49.662639 INFO: === FDR correction performed with classifier version -1 ===
0:59:49.663130 PROGRESS: ============================= Precursor FDR =============================
0:59:49.663216 PROGRESS: Total precursors accumulated: 7
0:59:49.663276 PROGRESS: Target precursors: 7 (100.00%)
0:59:49.663327 PROGRESS: Decoy precursors: 0 (0.00%)
0:59:49.663374 PROGRESS: 
0:59:49.663419 PROGRESS: Precursor Summary:
0:59:49.664478 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:59:49.664562 PROGRESS: 
0:59:49.664618 PROGRESS: Protein Summary:
0:59:49.665780 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:59:49.665879 PROGRESS: =========================================================================
0:59:49.666147 INFO: Target number of precursors not reached yet.
0:59:49.752299 INFO: Starting optimization step 1.
0:59:49.752542 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:59:49.752622 INFO: Using rust extraction backend
0:59:49.752687 PROGRESS: Extracting batch of 3942 precursors
0:59:49.760953 INFO: === Search parameters used ===
0:59:49.761093 INFO: rt_error       : 805.5982666015625
0:59:49.761144 INFO: mobility_error : 0.1
0:59:49.761190 INFO: num_candidates : 1
0:59:49.761235 INFO: ms1_error      : 30
0:59:49.761276 INFO: ms2_error      : 30
0:59:49.761320 INFO: fwhm_rt        : 5
0:59:49.761366 INFO: quant_window   : 3
0:59:49.761410 INFO: ==============================================
0:59:49.808548 INFO: performing precursor FDR with 40 features
0:59:49.808669 INFO: Decoy channel: -1
0:59:49.808695 INFO: competitive: True
0:59:49.813237 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:49.815651 INFO: Estimating optimal hyperparameters - samples: 4,690, batch_size: 128, learning_rate: 1.77e-04
0:59:49.815742 INFO: Using random state 944200 for train-test-split
0:59:50.281107 INFO: Test AUC: 0.509
0:59:50.281214 INFO: Train AUC: 0.565
0:59:50.281242 INFO: AUC difference: 9.91%
0:59:50.281263 WARNING: AUC difference > 5%. This may indicate overfitting.
0:59:50.522336 INFO: Resetting torch num_threads to 100
0:59:50.525481 PROGRESS: === Extracted 5863 precursors and 27754 fragments ===
0:59:50.525913 INFO: === FDR correction performed with classifier version -1 ===
0:59:50.526415 PROGRESS: ============================= Precursor FDR =============================
0:59:50.526498 PROGRESS: Total precursors accumulated: 4
0:59:50.526555 PROGRESS: Target precursors: 4 (100.00%)
0:59:50.526603 PROGRESS: Decoy precursors: 0 (0.00%)
0:59:50.526648 PROGRESS: 
0:59:50.526692 PROGRESS: Precursor Summary:
0:59:50.527776 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:59:50.527860 PROGRESS: 
0:59:50.527914 PROGRESS: Protein Summary:
0:59:50.529087 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:59:50.529168 PROGRESS: =========================================================================
0:59:50.529480 INFO: Target number of precursors not reached yet.
0:59:50.619837 INFO: Starting optimization step 2.
0:59:50.620104 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:59:50.620184 INFO: Using rust extraction backend
0:59:50.620247 PROGRESS: Extracting batch of 7890 precursors
0:59:50.635250 INFO: === Search parameters used ===
0:59:50.635424 INFO: rt_error       : 805.5982666015625
0:59:50.635476 INFO: mobility_error : 0.1
0:59:50.635521 INFO: num_candidates : 1
0:59:50.635563 INFO: ms1_error      : 30
0:59:50.635606 INFO: ms2_error      : 30
0:59:50.635648 INFO: fwhm_rt        : 5
0:59:50.635689 INFO: quant_window   : 3
0:59:50.635729 INFO: ==============================================
0:59:50.720456 INFO: performing precursor FDR with 40 features
0:59:50.720586 INFO: Decoy channel: -1
0:59:50.720616 INFO: competitive: True
0:59:50.727344 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:50.731522 INFO: Estimating optimal hyperparameters - samples: 10,966, batch_size: 128, learning_rate: 1.77e-04
0:59:50.731658 INFO: Using random state 758849 for train-test-split
0:59:51.918893 INFO: Test AUC: 0.541
0:59:51.919022 INFO: Train AUC: 0.573
0:59:51.919050 INFO: AUC difference: 5.46%
0:59:51.919070 WARNING: AUC difference > 5%. This may indicate overfitting.
0:59:52.191295 INFO: Resetting torch num_threads to 100
0:59:52.195907 PROGRESS: === Extracted 13708 precursors and 64977 fragments ===
0:59:52.196384 INFO: === FDR correction performed with classifier version -1 ===
0:59:52.196950 PROGRESS: ============================= Precursor FDR =============================
0:59:52.197037 PROGRESS: Total precursors accumulated: 32
0:59:52.197094 PROGRESS: Target precursors: 32 (100.00%)
0:59:52.197141 PROGRESS: Decoy precursors: 0 (0.00%)
0:59:52.197184 PROGRESS: 
0:59:52.197226 PROGRESS: Precursor Summary:
0:59:52.198413 PROGRESS: Channel   0:	 0.050 FDR:    32; 0.010 FDR:    32; 0.001 FDR:    32
0:59:52.198525 PROGRESS: 
0:59:52.198582 PROGRESS: Protein Summary:
0:59:52.199857 PROGRESS: Channel   0:	 0.050 FDR:    32; 0.010 FDR:    32; 0.001 FDR:    32
0:59:52.199945 PROGRESS: =========================================================================
0:59:52.200378 INFO: Target number of precursors not reached yet.
0:59:52.303711 INFO: Starting optimization step 3.
0:59:52.303975 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:59:52.304060 INFO: Using rust extraction backend
0:59:52.304143 PROGRESS: Extracting batch of 15788 precursors
0:59:52.332494 INFO: === Search parameters used ===
0:59:52.332715 INFO: rt_error       : 805.5982666015625
0:59:52.332775 INFO: mobility_error : 0.1
0:59:52.332824 INFO: num_candidates : 1
0:59:52.332868 INFO: ms1_error      : 30
0:59:52.332929 INFO: ms2_error      : 30
0:59:52.332992 INFO: fwhm_rt        : 5
0:59:52.333033 INFO: quant_window   : 3
0:59:52.333072 INFO: ==============================================
0:59:52.471066 INFO: performing precursor FDR with 40 features
0:59:52.471200 INFO: Decoy channel: -1
0:59:52.471224 INFO: competitive: True
0:59:52.482818 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:52.489711 INFO: Estimating optimal hyperparameters - samples: 23,485, batch_size: 128, learning_rate: 1.77e-04
0:59:52.489909 INFO: Using random state 984302 for train-test-split
0:59:54.941316 INFO: Test AUC: 0.574
0:59:54.941460 INFO: Train AUC: 0.593
0:59:54.941491 INFO: AUC difference: 3.14%
0:59:55.198411 INFO: Resetting torch num_threads to 100
0:59:55.206598 PROGRESS: === Extracted 29357 precursors and 139556 fragments ===
0:59:55.207179 INFO: === FDR correction performed with classifier version -1 ===
0:59:55.207786 PROGRESS: ============================= Precursor FDR =============================
0:59:55.207876 PROGRESS: Total precursors accumulated: 45
0:59:55.207937 PROGRESS: Target precursors: 45 (100.00%)
0:59:55.207991 PROGRESS: Decoy precursors: 0 (0.00%)
0:59:55.208039 PROGRESS: 
0:59:55.208086 PROGRESS: Precursor Summary:
0:59:55.209181 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    45; 0.001 FDR:    45
0:59:55.209271 PROGRESS: 
0:59:55.209328 PROGRESS: Protein Summary:
0:59:55.210542 PROGRESS: Channel   0:	 0.050 FDR:    44; 0.010 FDR:    44; 0.001 FDR:    44
0:59:55.210631 PROGRESS: =========================================================================
0:59:55.211244 INFO: Target number of precursors not reached yet.
0:59:55.331626 INFO: Starting optimization step 4.
0:59:55.331898 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:59:55.331984 INFO: Using rust extraction backend
0:59:55.332053 PROGRESS: Extracting batch of 31512 precursors
0:59:55.386661 INFO: === Search parameters used ===
0:59:55.386901 INFO: rt_error       : 805.5982666015625
0:59:55.386957 INFO: mobility_error : 0.1
0:59:55.387005 INFO: num_candidates : 1
0:59:55.387050 INFO: ms1_error      : 30
0:59:55.387093 INFO: ms2_error      : 30
0:59:55.387136 INFO: fwhm_rt        : 5
0:59:55.387177 INFO: quant_window   : 3
0:59:55.387236 INFO: ==============================================
0:59:55.618288 INFO: performing precursor FDR with 40 features
0:59:55.618421 INFO: Decoy channel: -1
0:59:55.618446 INFO: competitive: True
0:59:55.643713 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:55.659509 INFO: Estimating optimal hyperparameters - samples: 48,488, batch_size: 198, learning_rate: 2.20e-04
0:59:55.659756 INFO: Using random state 5995 for train-test-split
0:59:59.732193 INFO: Test AUC: 0.573
0:59:59.732342 INFO: Train AUC: 0.605
0:59:59.732373 INFO: AUC difference: 5.29%
0:59:59.732397 WARNING: AUC difference > 5%. This may indicate overfitting.
1:00:00.000974 INFO: Resetting torch num_threads to 100
1:00:00.013933 PROGRESS: === Extracted 60611 precursors and 288042 fragments ===
1:00:00.014590 INFO: === FDR correction performed with classifier version -1 ===
1:00:00.015158 PROGRESS: ============================= Precursor FDR =============================
1:00:00.015257 PROGRESS: Total precursors accumulated: 132
1:00:00.015318 PROGRESS: Target precursors: 131 (99.24%)
1:00:00.015373 PROGRESS: Decoy precursors: 1 (0.76%)
1:00:00.015420 PROGRESS: 
1:00:00.015465 PROGRESS: Precursor Summary:
1:00:00.016479 PROGRESS: Channel   0:	 0.050 FDR:   131; 0.010 FDR:   131; 0.001 FDR:   119
1:00:00.016567 PROGRESS: 
1:00:00.016625 PROGRESS: Protein Summary:
1:00:00.017741 PROGRESS: Channel   0:	 0.050 FDR:   126; 0.010 FDR:   126; 0.001 FDR:   115
1:00:00.017828 PROGRESS: =========================================================================
1:00:00.018884 INFO: Target number of precursors not reached yet.
1:00:00.210496 INFO: Starting optimization step 5.
1:00:00.210754 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:00:00.210842 INFO: Using rust extraction backend
1:00:00.210909 PROGRESS: Extracting batch of 63110 precursors
1:00:00.324470 INFO: === Search parameters used ===
1:00:00.324762 INFO: rt_error       : 805.5982666015625
1:00:00.324819 INFO: mobility_error : 0.1
1:00:00.324867 INFO: num_candidates : 1
1:00:00.324910 INFO: ms1_error      : 30
1:00:00.324951 INFO: ms2_error      : 30
1:00:00.324992 INFO: fwhm_rt        : 5
1:00:00.325033 INFO: quant_window   : 3
1:00:00.325076 INFO: ==============================================
1:00:00.731871 INFO: performing precursor FDR with 40 features
1:00:00.731993 INFO: Decoy channel: -1
1:00:00.732019 INFO: competitive: True
1:00:00.785259 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:00.826454 INFO: Estimating optimal hyperparameters - samples: 98,540, batch_size: 403, learning_rate: 3.14e-04
1:00:00.826818 INFO: Using random state 250260 for train-test-split
1:00:06.685454 INFO: Test AUC: 0.585
1:00:06.685617 INFO: Train AUC: 0.602
1:00:06.685648 INFO: AUC difference: 2.85%
1:00:08.077268 INFO: Resetting torch num_threads to 100
1:00:08.103923 PROGRESS: === Extracted 123175 precursors and 584730 fragments ===
1:00:08.104645 INFO: === FDR correction performed with classifier version -1 ===
1:00:08.105360 PROGRESS: ============================= Precursor FDR =============================
1:00:08.105468 PROGRESS: Total precursors accumulated: 313
1:00:08.105531 PROGRESS: Target precursors: 310 (99.04%)
1:00:08.105585 PROGRESS: Decoy precursors: 3 (0.96%)
1:00:08.105633 PROGRESS: 
1:00:08.105695 PROGRESS: Precursor Summary:
1:00:08.106819 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   310; 0.001 FDR:   262
1:00:08.106920 PROGRESS: 
1:00:08.106974 PROGRESS: Protein Summary:
1:00:08.108229 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   252
1:00:08.108325 PROGRESS: =========================================================================
1:00:08.110594 INFO: Target number of precursors not reached yet.
1:00:08.363721 INFO: Starting optimization step 6.
1:00:08.364030 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:00:08.364114 INFO: Using rust extraction backend
1:00:08.364178 PROGRESS: Extracting batch of 126235 precursors
1:00:08.580399 INFO: === Search parameters used ===
1:00:08.581218 INFO: rt_error       : 805.5982666015625
1:00:08.581308 INFO: mobility_error : 0.1
1:00:08.581365 INFO: num_candidates : 1
1:00:08.581414 INFO: ms1_error      : 30
1:00:08.581457 INFO: ms2_error      : 30
1:00:08.581497 INFO: fwhm_rt        : 5
1:00:08.581535 INFO: quant_window   : 3
1:00:08.581573 INFO: ==============================================
1:00:09.325221 INFO: performing precursor FDR with 40 features
1:00:09.325374 INFO: Decoy channel: -1
1:00:09.325401 INFO: competitive: True
1:00:09.459420 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:09.573901 INFO: Estimating optimal hyperparameters - samples: 198,626, batch_size: 813, learning_rate: 4.46e-04
1:00:09.574336 INFO: Using random state 479680 for train-test-split
1:00:17.897215 INFO: Test AUC: 0.584
1:00:17.897366 INFO: Train AUC: 0.606
1:00:17.897397 INFO: AUC difference: 3.49%
1:00:18.220673 INFO: Resetting torch num_threads to 100
1:00:18.276745 PROGRESS: === Extracted 248283 precursors and 1179178 fragments ===
1:00:18.277564 INFO: === FDR correction performed with classifier version -1 ===
1:00:18.278418 PROGRESS: ============================= Precursor FDR =============================
1:00:18.278517 PROGRESS: Total precursors accumulated: 810
1:00:18.278580 PROGRESS: Target precursors: 802 (99.01%)
1:00:18.278638 PROGRESS: Decoy precursors: 8 (0.99%)
1:00:18.278685 PROGRESS: 
1:00:18.278731 PROGRESS: Precursor Summary:
1:00:18.279954 PROGRESS: Channel   0:	 0.050 FDR:   802; 0.010 FDR:   802; 0.001 FDR:   609
1:00:18.280043 PROGRESS: 
1:00:18.280109 PROGRESS: Protein Summary:
1:00:18.281596 PROGRESS: Channel   0:	 0.050 FDR:   729; 0.010 FDR:   729; 0.001 FDR:   556
1:00:18.281681 PROGRESS: =========================================================================
1:00:18.287272 INFO: Target number of precursors not reached yet.
1:00:18.706602 INFO: Starting optimization step 7.
1:00:18.706914 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:00:18.706997 INFO: Using rust extraction backend
1:00:18.707061 PROGRESS: Extracting batch of 252313 precursors
1:00:19.132967 INFO: === Search parameters used ===
1:00:19.133272 INFO: rt_error       : 805.5982666015625
1:00:19.133331 INFO: mobility_error : 0.1
1:00:19.133382 INFO: num_candidates : 1
1:00:19.133428 INFO: ms1_error      : 30
1:00:19.133486 INFO: ms2_error      : 30
1:00:19.133530 INFO: fwhm_rt        : 5
1:00:19.133570 INFO: quant_window   : 3
1:00:19.133610 INFO: ==============================================
1:00:20.523293 INFO: performing precursor FDR with 40 features
1:00:20.523434 INFO: Decoy channel: -1
1:00:20.523471 INFO: competitive: True
1:00:20.808766 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:21.040322 INFO: Estimating optimal hyperparameters - samples: 398,593, batch_size: 1,632, learning_rate: 6.31e-04
1:00:21.041030 INFO: Using random state 115374 for train-test-split
1:00:33.858308 INFO: Test AUC: 0.590
1:00:33.858452 INFO: Train AUC: 0.604
1:00:33.858486 INFO: AUC difference: 2.27%
1:00:34.255540 INFO: Resetting torch num_threads to 100
1:00:34.375049 PROGRESS: === Extracted 498242 precursors and 2367022 fragments ===
1:00:34.375814 INFO: === FDR correction performed with classifier version -1 ===
1:00:34.376768 PROGRESS: ============================= Precursor FDR =============================
1:00:34.376859 PROGRESS: Total precursors accumulated: 1,662
1:00:34.376921 PROGRESS: Target precursors: 1,646 (99.04%)
1:00:34.376974 PROGRESS: Decoy precursors: 16 (0.96%)
1:00:34.377025 PROGRESS: 
1:00:34.377072 PROGRESS: Precursor Summary:
1:00:34.378515 PROGRESS: Channel   0:	 0.050 FDR: 1,646; 0.010 FDR: 1,646; 0.001 FDR: 1,071
1:00:34.378608 PROGRESS: 
1:00:34.378677 PROGRESS: Protein Summary:
1:00:34.380529 PROGRESS: Channel   0:	 0.050 FDR: 1,325; 0.010 FDR: 1,325; 0.001 FDR:   880
1:00:34.380623 PROGRESS: =========================================================================
1:00:34.390780 INFO: Target number of precursors reached.
1:00:34.661670 INFO: fragments_df: keeping 5000 of 2367022 [sum(precursor_idx_mask)=17696 sum(mass_error_mask)=2367022 stop_rank=5000
1:00:35.441309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:00:35.703118 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:00:36.420331 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:00:36.420853 INFO: Using score_cutoff 12.959970693111421 (fac=0.99, q=1)
1:00:36.421197 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:00:36.421277 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:00:36.421334 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.959970693111421
1:00:36.421393 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:36.731468 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:37.409566 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:00:37.409863 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:00:37.409991 INFO: Starting optimization step 8.
1:00:37.410058 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:00:37.410127 INFO: Using rust extraction backend
1:00:37.410190 PROGRESS: Extracting batch of 502760 precursors
1:00:38.251894 INFO: === Search parameters used ===
1:00:38.252195 INFO: rt_error       : 805.5982666015625
1:00:38.252258 INFO: mobility_error : 0.1
1:00:38.252309 INFO: num_candidates : 3
1:00:38.252355 INFO: ms1_error      : 30
1:00:38.252399 INFO: ms2_error      : 30
1:00:38.252444 INFO: fwhm_rt        : 3.0
1:00:38.252509 INFO: quant_window   : 3
1:00:38.252554 INFO: ==============================================
1:00:43.669329 INFO: performing precursor FDR with 40 features
1:00:43.669480 INFO: Decoy channel: -1
1:00:43.669507 INFO: competitive: True
1:00:44.131394 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:44.792100 INFO: Estimating optimal hyperparameters - samples: 1,196,744, batch_size: 4,096, learning_rate: 1.00e-03
1:00:44.794216 INFO: Using random state 498336 for train-test-split
1:01:15.033942 INFO: Test AUC: 0.601
1:01:15.034396 INFO: Train AUC: 0.605
1:01:15.034438 INFO: AUC difference: 0.69%
1:01:15.757711 INFO: Resetting torch num_threads to 100
1:01:15.827786 PROGRESS: === Extracted 1495930 precursors and 6960246 fragments ===
1:01:15.828562 INFO: === FDR correction performed with classifier version 7 ===
1:01:15.829561 PROGRESS: ============================= Precursor FDR =============================
1:01:15.829672 PROGRESS: Total precursors accumulated: 1,954
1:01:15.829749 PROGRESS: Target precursors: 1,935 (99.03%)
1:01:15.829806 PROGRESS: Decoy precursors: 19 (0.97%)
1:01:15.829878 PROGRESS: 
1:01:15.829936 PROGRESS: Precursor Summary:
1:01:15.831642 PROGRESS: Channel   0:	 0.050 FDR: 1,935; 0.010 FDR: 1,935; 0.001 FDR: 1,523
1:01:15.831742 PROGRESS: 
1:01:15.831807 PROGRESS: Protein Summary:
1:01:15.833905 PROGRESS: Channel   0:	 0.050 FDR: 1,563; 0.010 FDR: 1,563; 0.001 FDR: 1,231
1:01:15.834013 PROGRESS: =========================================================================
1:01:15.877083 INFO: Target number of precursors reached.
1:01:16.619633 INFO: fragments_df: keeping 5000 of 6960246 [sum(precursor_idx_mask)=42506 sum(mass_error_mask)=6960246 stop_rank=5000
1:01:17.488692 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:01:17.778691 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:01:18.493270 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:01:18.493799 INFO: Using score_cutoff 12.338632141685485 (fac=0.99, q=1)
1:01:18.494171 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:01:18.494254 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:01:18.494310 INFO: Updating optimization_manager: score_cutoff        : 12.959970693111421 -> 12.338632141685485
1:01:18.494379 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:18.800081 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:19.502139 INFO: === checking if optimization conditions were reached ===
1:01:19.502446 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 5 ===
1:01:19.505093 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.5221597911183915
1:01:19.505230 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.5222.
1:01:19.505299 INFO: ==============================================
1:01:19.505383 INFO: Starting optimization step 9.
1:01:19.505446 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:01:19.505546 INFO: Using rust extraction backend
1:01:19.505633 PROGRESS: Extracting batch of 502760 precursors
1:01:20.348595 INFO: === Search parameters used ===
1:01:20.348876 INFO: rt_error       : 805.5982666015625
1:01:20.348937 INFO: mobility_error : 0.1
1:01:20.348987 INFO: num_candidates : 3
1:01:20.349033 INFO: ms1_error      : 30
1:01:20.349095 INFO: ms2_error      : 7.5221597911183915
1:01:20.349141 INFO: fwhm_rt        : 3.0
1:01:20.349190 INFO: quant_window   : 3
1:01:20.349231 INFO: ==============================================
1:01:25.484382 INFO: performing precursor FDR with 40 features
1:01:25.484518 INFO: Decoy channel: -1
1:01:25.484544 INFO: competitive: True
1:01:25.899396 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:26.630144 INFO: Estimating optimal hyperparameters - samples: 1,206,127, batch_size: 4,096, learning_rate: 1.00e-03
1:01:26.634338 INFO: Using random state 498336 for train-test-split
1:01:55.778252 INFO: Test AUC: 0.605
1:01:55.778698 INFO: Train AUC: 0.610
1:01:55.778735 INFO: AUC difference: 0.79%
1:01:56.502280 INFO: Resetting torch num_threads to 100
1:01:56.577801 PROGRESS: === Extracted 1507659 precursors and 8483802 fragments ===
1:01:56.578516 INFO: === FDR correction performed with classifier version 7 ===
1:01:56.579679 PROGRESS: ============================= Precursor FDR =============================
1:01:56.579785 PROGRESS: Total precursors accumulated: 2,779
1:01:56.579852 PROGRESS: Target precursors: 2,752 (99.03%)
1:01:56.579906 PROGRESS: Decoy precursors: 27 (0.97%)
1:01:56.579954 PROGRESS: 
1:01:56.580001 PROGRESS: Precursor Summary:
1:01:56.581957 PROGRESS: Channel   0:	 0.050 FDR: 2,752; 0.010 FDR: 2,752; 0.001 FDR: 1,606
1:01:56.582062 PROGRESS: 
1:01:56.582123 PROGRESS: Protein Summary:
1:01:56.584536 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,056; 0.001 FDR: 1,275
1:01:56.584638 PROGRESS: =========================================================================
1:01:56.632997 INFO: Target number of precursors reached.
1:01:57.527587 INFO: fragments_df: keeping 5000 of 8483802 [sum(precursor_idx_mask)=67313 sum(mass_error_mask)=8483802 stop_rank=5000
1:01:58.129874 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:01:58.536383 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:01:59.252292 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:01:59.252791 INFO: Using score_cutoff 12.332873752212524 (fac=0.99, q=1)
1:01:59.253168 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:01:59.253248 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:01:59.253303 INFO: Updating optimization_manager: score_cutoff        : 12.338632141685485 -> 12.332873752212524
1:01:59.253362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:59.402927 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:59.744980 INFO: === checking if optimization conditions were reached ===
1:01:59.745309 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 5 ===
1:01:59.748812 INFO: Updating optimization_manager: ms2_error           : 7.5221597911183915 -> 7.5718712441575216
1:01:59.748931 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.5719.
1:01:59.749009 INFO: ==============================================
1:01:59.749122 INFO: Starting optimization step 10.
1:01:59.749199 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:01:59.749307 INFO: Using rust extraction backend
1:01:59.749414 PROGRESS: Extracting batch of 250447 precursors
1:02:00.174833 INFO: === Search parameters used ===
1:02:00.175086 INFO: rt_error       : 805.5982666015625
1:02:00.175146 INFO: mobility_error : 0.1
1:02:00.175208 INFO: num_candidates : 3
1:02:00.175255 INFO: ms1_error      : 30
1:02:00.175298 INFO: ms2_error      : 7.5718712441575216
1:02:00.175340 INFO: fwhm_rt        : 3.0
1:02:00.175381 INFO: quant_window   : 3
1:02:00.175423 INFO: ==============================================
1:02:02.740526 INFO: performing precursor FDR with 40 features
1:02:02.740649 INFO: Decoy channel: -1
1:02:02.740677 INFO: competitive: True
1:02:02.971637 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:03.291473 INFO: Estimating optimal hyperparameters - samples: 600,835, batch_size: 2,461, learning_rate: 7.75e-04
1:02:03.292435 INFO: Using random state 498336 for train-test-split
1:02:20.273513 INFO: Test AUC: 0.601
1:02:20.273749 INFO: Train AUC: 0.609
1:02:20.273784 INFO: AUC difference: 1.39%
1:02:20.749494 INFO: Resetting torch num_threads to 100
1:02:20.782009 PROGRESS: === Extracted 751044 precursors and 4221828 fragments ===
1:02:20.782599 INFO: === FDR correction performed with classifier version 7 ===
1:02:20.783332 PROGRESS: ============================= Precursor FDR =============================
1:02:20.783424 PROGRESS: Total precursors accumulated: 1,414
1:02:20.783489 PROGRESS: Target precursors: 1,400 (99.01%)
1:02:20.783543 PROGRESS: Decoy precursors: 14 (0.99%)
1:02:20.783592 PROGRESS: 
1:02:20.783639 PROGRESS: Precursor Summary:
1:02:20.784981 PROGRESS: Channel   0:	 0.050 FDR: 1,400; 0.010 FDR: 1,364; 0.001 FDR: 1,087
1:02:20.785073 PROGRESS: 
1:02:20.785132 PROGRESS: Protein Summary:
1:02:20.786894 PROGRESS: Channel   0:	 0.050 FDR: 1,192; 0.010 FDR: 1,169; 0.001 FDR:   952
1:02:20.786990 PROGRESS: =========================================================================
1:02:20.801136 INFO: Target number of precursors reached.
1:02:21.273271 INFO: fragments_df: keeping 5000 of 4221828 [sum(precursor_idx_mask)=33120 sum(mass_error_mask)=4221828 stop_rank=5000
1:02:21.825460 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:02:22.022816 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:02:22.679115 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:02:22.679618 INFO: Using score_cutoff 12.070704233551025 (fac=0.99, q=1)
1:02:22.679983 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:02:22.680063 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:02:22.680123 INFO: Updating optimization_manager: score_cutoff        : 12.332873752212524 -> 12.070704233551025
1:02:22.680183 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:02:22.836779 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:02:23.219401 INFO: === checking if optimization conditions were reached ===
1:02:23.219759 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 5 ===
1:02:23.222637 INFO: Updating optimization_manager: ms2_error           : 7.5718712441575216 -> 7.436575624071253
1:02:23.222750 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 7.4366.
1:02:23.222820 INFO: ==============================================
1:02:23.222905 INFO: Starting optimization step 11.
1:02:23.222973 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:02:23.223046 INFO: Using rust extraction backend
1:02:23.223113 PROGRESS: Extracting batch of 250447 precursors
1:02:23.663172 INFO: === Search parameters used ===
1:02:23.663491 INFO: rt_error       : 805.5982666015625
1:02:23.663551 INFO: mobility_error : 0.1
1:02:23.663602 INFO: num_candidates : 3
1:02:23.663650 INFO: ms1_error      : 30
1:02:23.663696 INFO: ms2_error      : 7.436575624071253
1:02:23.663739 INFO: fwhm_rt        : 3.0
1:02:23.663782 INFO: quant_window   : 3
1:02:23.663825 INFO: ==============================================
1:02:26.312280 INFO: performing precursor FDR with 40 features
1:02:26.312418 INFO: Decoy channel: -1
1:02:26.312445 INFO: competitive: True
1:02:26.523298 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:26.837696 INFO: Estimating optimal hyperparameters - samples: 600,876, batch_size: 2,461, learning_rate: 7.75e-04
1:02:26.839113 INFO: Using random state 498336 for train-test-split
1:02:43.511141 INFO: Test AUC: 0.599
1:02:43.511293 INFO: Train AUC: 0.610
1:02:43.511326 INFO: AUC difference: 1.78%
1:02:43.979530 INFO: Resetting torch num_threads to 100
1:02:44.008236 PROGRESS: === Extracted 751096 precursors and 4233963 fragments ===
1:02:44.008767 INFO: === FDR correction performed with classifier version 7 ===
1:02:44.009438 PROGRESS: ============================= Precursor FDR =============================
1:02:44.009529 PROGRESS: Total precursors accumulated: 1,361
1:02:44.009592 PROGRESS: Target precursors: 1,348 (99.04%)
1:02:44.009663 PROGRESS: Decoy precursors: 13 (0.96%)
1:02:44.009716 PROGRESS: 
1:02:44.009764 PROGRESS: Precursor Summary:
1:02:44.011082 PROGRESS: Channel   0:	 0.050 FDR: 1,348; 0.010 FDR: 1,348; 0.001 FDR:   877
1:02:44.011198 PROGRESS: 
1:02:44.011257 PROGRESS: Protein Summary:
1:02:44.012956 PROGRESS: Channel   0:	 0.050 FDR: 1,155; 0.010 FDR: 1,155; 0.001 FDR:   785
1:02:44.013045 PROGRESS: =========================================================================
1:02:44.026200 INFO: Target number of precursors reached.
1:02:44.491144 INFO: fragments_df: keeping 5000 of 4233963 [sum(precursor_idx_mask)=32706 sum(mass_error_mask)=4233963 stop_rank=5000
1:02:45.037444 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:02:45.227608 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:02:45.885481 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:02:45.886001 INFO: Using score_cutoff 11.725142224788666 (fac=0.99, q=1)
1:02:45.886329 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:02:45.886408 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:02:45.886467 INFO: Updating optimization_manager: score_cutoff        : 12.070704233551025 -> 11.725142224788666
1:02:45.886529 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:02:46.040569 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:02:46.384901 INFO: === checking if optimization conditions were reached ===
1:02:46.385219 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 5 ===
1:02:46.387978 INFO: Updating optimization_manager: ms2_error           : 7.436575624071253 -> 7.399536526372681
1:02:46.388087 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 7.3995.
1:02:46.388158 INFO: ==============================================
1:02:46.388229 INFO: Starting optimization step 12.
1:02:46.388293 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:02:46.388360 INFO: Using rust extraction backend
1:02:46.388435 PROGRESS: Extracting batch of 250447 precursors
1:02:46.822669 INFO: === Search parameters used ===
1:02:46.822989 INFO: rt_error       : 805.5982666015625
1:02:46.823049 INFO: mobility_error : 0.1
1:02:46.823102 INFO: num_candidates : 3
1:02:46.823155 INFO: ms1_error      : 30
1:02:46.823200 INFO: ms2_error      : 7.399536526372681
1:02:46.823243 INFO: fwhm_rt        : 3.0
1:02:46.823286 INFO: quant_window   : 3
1:02:46.823329 INFO: ==============================================
1:02:49.449330 INFO: performing precursor FDR with 40 features
1:02:49.449472 INFO: Decoy channel: -1
1:02:49.449499 INFO: competitive: True
1:02:49.662443 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:49.956873 INFO: Estimating optimal hyperparameters - samples: 600,889, batch_size: 2,461, learning_rate: 7.75e-04
1:02:49.958423 INFO: Using random state 498336 for train-test-split
1:03:07.121396 INFO: Test AUC: 0.602
1:03:07.121549 INFO: Train AUC: 0.608
1:03:07.121585 INFO: AUC difference: 0.99%
1:03:07.600860 INFO: Resetting torch num_threads to 100
1:03:07.636039 PROGRESS: === Extracted 751112 precursors and 4237142 fragments ===
1:03:07.636591 INFO: === FDR correction performed with classifier version 7 ===
1:03:07.637239 PROGRESS: ============================= Precursor FDR =============================
1:03:07.637329 PROGRESS: Total precursors accumulated: 1,344
1:03:07.637390 PROGRESS: Target precursors: 1,331 (99.03%)
1:03:07.637455 PROGRESS: Decoy precursors: 13 (0.97%)
1:03:07.637505 PROGRESS: 
1:03:07.637552 PROGRESS: Precursor Summary:
1:03:07.638823 PROGRESS: Channel   0:	 0.050 FDR: 1,331; 0.010 FDR: 1,331; 0.001 FDR:   317
1:03:07.638913 PROGRESS: 
1:03:07.638969 PROGRESS: Protein Summary:
1:03:07.640549 PROGRESS: Channel   0:	 0.050 FDR: 1,152; 0.010 FDR: 1,152; 0.001 FDR:   296
1:03:07.640645 PROGRESS: =========================================================================
1:03:07.653513 INFO: Target number of precursors reached.
1:03:08.134362 INFO: fragments_df: keeping 5000 of 4237142 [sum(precursor_idx_mask)=32035 sum(mass_error_mask)=4237142 stop_rank=5000
1:03:08.729141 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:03:08.921839 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:03:09.584405 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:03:09.584903 INFO: Using score_cutoff 9.125741383552551 (fac=0.99, q=1)
1:03:09.585217 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:03:09.585291 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:03:09.585343 INFO: Updating optimization_manager: score_cutoff        : 11.725142224788666 -> 9.125741383552551
1:03:09.585397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:09.738529 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:10.078342 INFO: === checking if optimization conditions were reached ===
1:03:10.078674 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 5 ===
1:03:10.079862 INFO: Updating optimization_manager: ms2_error           : 7.399536526372681 -> 7.5221597911183915
1:03:10.079992 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
1:03:10.080093 INFO: Updating optimization_manager: score_cutoff        : 9.125741383552551 -> 12.332873752212524
1:03:10.080188 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:03:10.080283 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:03:10.080372 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.5222 found after 5 searches.
1:03:10.080431 INFO: ==============================================
1:03:10.080529 PROGRESS: Optimization finished for ms2_error.
1:03:10.621190 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:10.774879 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:11.116657 INFO: Starting optimization step 0.
1:03:11.116981 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:03:11.117083 INFO: Using rust extraction backend
1:03:11.117151 PROGRESS: Extracting batch of 250447 precursors
1:03:11.549248 INFO: === Search parameters used ===
1:03:11.549735 INFO: rt_error       : 805.5982666015625
1:03:11.549926 INFO: mobility_error : 0.1
1:03:11.550059 INFO: num_candidates : 3
1:03:11.550173 INFO: ms1_error      : 30
1:03:11.550256 INFO: ms2_error      : 7.5221597911183915
1:03:11.550297 INFO: fwhm_rt        : 3.0
1:03:11.550337 INFO: quant_window   : 3
1:03:11.550377 INFO: ==============================================
1:03:14.112797 INFO: performing precursor FDR with 40 features
1:03:14.112930 INFO: Decoy channel: -1
1:03:14.112957 INFO: competitive: True
1:03:14.336268 INFO: Setting torch num_threads to 2 for FDR classification task
1:03:14.647890 INFO: Estimating optimal hyperparameters - samples: 600,837, batch_size: 2,461, learning_rate: 7.75e-04
1:03:14.649140 INFO: Using random state 139146 for train-test-split
1:03:31.302693 INFO: Test AUC: 0.608
1:03:31.302842 INFO: Train AUC: 0.616
1:03:31.302875 INFO: AUC difference: 1.25%
1:03:31.775864 INFO: Resetting torch num_threads to 100
1:03:31.805691 PROGRESS: === Extracted 751047 precursors and 4226631 fragments ===
1:03:31.806231 INFO: === FDR correction performed with classifier version 9 ===
1:03:31.806925 PROGRESS: ============================= Precursor FDR =============================
1:03:31.807013 PROGRESS: Total precursors accumulated: 1,525
1:03:31.807072 PROGRESS: Target precursors: 1,510 (99.02%)
1:03:31.807122 PROGRESS: Decoy precursors: 15 (0.98%)
1:03:31.807172 PROGRESS: 
1:03:31.807216 PROGRESS: Precursor Summary:
1:03:31.808578 PROGRESS: Channel   0:	 0.050 FDR: 1,510; 0.010 FDR: 1,510; 0.001 FDR: 1,181
1:03:31.808673 PROGRESS: 
1:03:31.808730 PROGRESS: Protein Summary:
1:03:31.810557 PROGRESS: Channel   0:	 0.050 FDR: 1,292; 0.010 FDR: 1,292; 0.001 FDR: 1,023
1:03:31.810651 PROGRESS: =========================================================================
1:03:31.822921 INFO: Target number of precursors reached.
1:03:32.301573 INFO: fragments_df: keeping 5000 of 4226631 [sum(precursor_idx_mask)=35990 sum(mass_error_mask)=4226631 stop_rank=5000
1:03:32.838876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:03:33.057156 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:03:33.713265 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:03:33.713760 INFO: Using score_cutoff 8.922914102554321 (fac=0.99, q=1)
1:03:33.714094 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:03:33.714177 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:03:33.714233 INFO: Updating optimization_manager: score_cutoff        : 12.332873752212524 -> 8.922914102554321
1:03:33.714299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:33.866740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:34.190217 INFO: === checking if optimization conditions were reached ===
1:03:34.190513 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:03:34.193369 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 766.238493288751
1:03:34.193476 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 766.2385.
1:03:34.193542 INFO: ==============================================
1:03:34.193614 INFO: Starting optimization step 1.
1:03:34.193676 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:03:34.193740 INFO: Using rust extraction backend
1:03:34.193800 PROGRESS: Extracting batch of 250447 precursors
1:03:34.626087 INFO: === Search parameters used ===
1:03:34.626398 INFO: rt_error       : 766.238493288751
1:03:34.626458 INFO: mobility_error : 0.1
1:03:34.626507 INFO: num_candidates : 3
1:03:34.626553 INFO: ms1_error      : 30
1:03:34.626599 INFO: ms2_error      : 7.5221597911183915
1:03:34.626644 INFO: fwhm_rt        : 3.0
1:03:34.626691 INFO: quant_window   : 3
1:03:34.626735 INFO: ==============================================
1:03:37.227732 INFO: performing precursor FDR with 40 features
1:03:37.227873 INFO: Decoy channel: -1
1:03:37.227900 INFO: competitive: True
1:03:37.431551 INFO: Setting torch num_threads to 2 for FDR classification task
1:03:37.742890 INFO: Estimating optimal hyperparameters - samples: 600,840, batch_size: 2,461, learning_rate: 7.75e-04
1:03:37.744497 INFO: Using random state 139146 for train-test-split
1:03:54.585087 INFO: Test AUC: 0.606
1:03:54.585228 INFO: Train AUC: 0.615
1:03:54.585262 INFO: AUC difference: 1.50%
1:03:55.052828 INFO: Resetting torch num_threads to 100
1:03:55.082930 PROGRESS: === Extracted 751051 precursors and 4226784 fragments ===
1:03:55.083460 INFO: === FDR correction performed with classifier version 9 ===
1:03:55.084193 PROGRESS: ============================= Precursor FDR =============================
1:03:55.084296 PROGRESS: Total precursors accumulated: 1,537
1:03:55.084360 PROGRESS: Target precursors: 1,522 (99.02%)
1:03:55.084415 PROGRESS: Decoy precursors: 15 (0.98%)
1:03:55.084465 PROGRESS: 
1:03:55.084513 PROGRESS: Precursor Summary:
1:03:55.085960 PROGRESS: Channel   0:	 0.050 FDR: 1,522; 0.010 FDR: 1,522; 0.001 FDR: 1,186
1:03:55.086062 PROGRESS: 
1:03:55.086121 PROGRESS: Protein Summary:
1:03:55.087957 PROGRESS: Channel   0:	 0.050 FDR: 1,293; 0.010 FDR: 1,293; 0.001 FDR: 1,030
1:03:55.088054 PROGRESS: =========================================================================
1:03:55.101135 INFO: Target number of precursors reached.
1:03:55.584549 INFO: fragments_df: keeping 5000 of 4226784 [sum(precursor_idx_mask)=36391 sum(mass_error_mask)=4226784 stop_rank=5000
1:03:56.128606 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:03:56.336439 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:03:56.993667 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:03:56.994171 INFO: Using score_cutoff 9.187244657707215 (fac=0.99, q=1)
1:03:56.994545 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:03:56.994639 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:03:56.994697 INFO: Updating optimization_manager: score_cutoff        : 8.922914102554321 -> 9.187244657707215
1:03:56.994770 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:57.148389 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:57.484760 INFO: === checking if optimization conditions were reached ===
1:03:57.485091 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:03:57.488057 INFO: Updating optimization_manager: rt_error            : 766.238493288751 -> 596.8358754070143
1:03:57.488163 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 596.8359.
1:03:57.488228 INFO: ==============================================
1:03:57.488297 INFO: Starting optimization step 2.
1:03:57.488356 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:03:57.488420 INFO: Using rust extraction backend
1:03:57.488479 PROGRESS: Extracting batch of 250447 precursors
1:03:57.921085 INFO: === Search parameters used ===
1:03:57.921388 INFO: rt_error       : 596.8358754070143
1:03:57.921446 INFO: mobility_error : 0.1
1:03:57.921494 INFO: num_candidates : 3
1:03:57.921538 INFO: ms1_error      : 30
1:03:57.921580 INFO: ms2_error      : 7.5221597911183915
1:03:57.921652 INFO: fwhm_rt        : 3.0
1:03:57.921711 INFO: quant_window   : 3
1:03:57.921757 INFO: ==============================================
1:04:00.419440 INFO: performing precursor FDR with 40 features
1:04:00.419589 INFO: Decoy channel: -1
1:04:00.419616 INFO: competitive: True
1:04:00.621929 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:00.921356 INFO: Estimating optimal hyperparameters - samples: 600,788, batch_size: 2,460, learning_rate: 7.75e-04
1:04:00.922523 INFO: Using random state 139146 for train-test-split
1:04:17.218726 INFO: Test AUC: 0.609
1:04:17.218874 INFO: Train AUC: 0.615
1:04:17.218908 INFO: AUC difference: 0.97%
1:04:17.690495 INFO: Resetting torch num_threads to 100
1:04:17.720268 PROGRESS: === Extracted 750985 precursors and 4211546 fragments ===
1:04:17.720791 INFO: === FDR correction performed with classifier version 9 ===
1:04:17.721473 PROGRESS: ============================= Precursor FDR =============================
1:04:17.721565 PROGRESS: Total precursors accumulated: 1,489
1:04:17.721627 PROGRESS: Target precursors: 1,475 (99.06%)
1:04:17.721682 PROGRESS: Decoy precursors: 14 (0.94%)
1:04:17.721731 PROGRESS: 
1:04:17.721778 PROGRESS: Precursor Summary:
1:04:17.723173 PROGRESS: Channel   0:	 0.050 FDR: 1,475; 0.010 FDR: 1,475; 0.001 FDR: 1,134
1:04:17.723266 PROGRESS: 
1:04:17.723323 PROGRESS: Protein Summary:
1:04:17.725101 PROGRESS: Channel   0:	 0.050 FDR: 1,263; 0.010 FDR: 1,263; 0.001 FDR:   990
1:04:17.725195 PROGRESS: =========================================================================
1:04:17.737677 INFO: Target number of precursors reached.
1:04:18.213568 INFO: fragments_df: keeping 5000 of 4211546 [sum(precursor_idx_mask)=35334 sum(mass_error_mask)=4211546 stop_rank=5000
1:04:18.757309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:04:18.960061 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:04:19.615736 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:04:19.616251 INFO: Using score_cutoff 8.904002026176453 (fac=0.99, q=1)
1:04:19.616579 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:04:19.616656 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:04:19.616711 INFO: Updating optimization_manager: score_cutoff        : 9.187244657707215 -> 8.904002026176453
1:04:19.616768 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:04:19.769501 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:04:20.102361 INFO: === checking if optimization conditions were reached ===
1:04:20.102671 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:04:20.105653 INFO: Updating optimization_manager: rt_error            : 596.8358754070143 -> 643.1528901626891
1:04:20.105757 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 643.1529.
1:04:20.105825 INFO: ==============================================
1:04:20.105911 INFO: Starting optimization step 3.
1:04:20.105975 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:04:20.106039 INFO: Using rust extraction backend
1:04:20.106100 PROGRESS: Extracting batch of 250447 precursors
1:04:20.540803 INFO: === Search parameters used ===
1:04:20.541115 INFO: rt_error       : 643.1528901626891
1:04:20.541176 INFO: mobility_error : 0.1
1:04:20.541246 INFO: num_candidates : 3
1:04:20.541296 INFO: ms1_error      : 30
1:04:20.541356 INFO: ms2_error      : 7.5221597911183915
1:04:20.541399 INFO: fwhm_rt        : 3.0
1:04:20.541439 INFO: quant_window   : 3
1:04:20.541480 INFO: ==============================================
1:04:23.097945 INFO: performing precursor FDR with 40 features
1:04:23.098085 INFO: Decoy channel: -1
1:04:23.098109 INFO: competitive: True
1:04:23.307024 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:23.623117 INFO: Estimating optimal hyperparameters - samples: 600,818, batch_size: 2,460, learning_rate: 7.75e-04
1:04:23.624382 INFO: Using random state 139146 for train-test-split
1:04:39.766109 INFO: Test AUC: 0.607
1:04:39.766342 INFO: Train AUC: 0.616
1:04:39.766376 INFO: AUC difference: 1.40%
1:04:40.234905 INFO: Resetting torch num_threads to 100
1:04:40.263808 PROGRESS: === Extracted 751023 precursors and 4220649 fragments ===
1:04:40.264374 INFO: === FDR correction performed with classifier version 9 ===
1:04:40.265064 PROGRESS: ============================= Precursor FDR =============================
1:04:40.265155 PROGRESS: Total precursors accumulated: 1,443
1:04:40.265218 PROGRESS: Target precursors: 1,429 (99.03%)
1:04:40.265271 PROGRESS: Decoy precursors: 14 (0.97%)
1:04:40.265320 PROGRESS: 
1:04:40.265367 PROGRESS: Precursor Summary:
1:04:40.266716 PROGRESS: Channel   0:	 0.050 FDR: 1,429; 0.010 FDR: 1,429; 0.001 FDR:   895
1:04:40.266820 PROGRESS: 
1:04:40.266879 PROGRESS: Protein Summary:
1:04:40.268604 PROGRESS: Channel   0:	 0.050 FDR: 1,219; 0.010 FDR: 1,219; 0.001 FDR:   805
1:04:40.268695 PROGRESS: =========================================================================
1:04:40.281832 INFO: Target number of precursors reached.
1:04:40.756696 INFO: fragments_df: keeping 5000 of 4220649 [sum(precursor_idx_mask)=34544 sum(mass_error_mask)=4220649 stop_rank=5000
1:04:41.306672 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:04:41.505537 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:04:42.158328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:04:42.158803 INFO: Using score_cutoff 10.65736480407715 (fac=0.99, q=1)
1:04:42.159125 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:04:42.159204 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:04:42.159260 INFO: Updating optimization_manager: score_cutoff        : 8.904002026176453 -> 10.65736480407715
1:04:42.159317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:04:42.315269 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:04:42.658530 INFO: === checking if optimization conditions were reached ===
1:04:42.658874 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:04:42.661986 INFO: Updating optimization_manager: rt_error            : 643.1528901626891 -> 568.7257787042518
1:04:42.662132 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 568.7258.
1:04:42.662201 INFO: ==============================================
1:04:42.662282 INFO: Starting optimization step 4.
1:04:42.662372 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:04:42.662459 INFO: Using rust extraction backend
1:04:42.662528 PROGRESS: Extracting batch of 250447 precursors
1:04:43.097761 INFO: === Search parameters used ===
1:04:43.098068 INFO: rt_error       : 568.7257787042518
1:04:43.098136 INFO: mobility_error : 0.1
1:04:43.098196 INFO: num_candidates : 3
1:04:43.098242 INFO: ms1_error      : 30
1:04:43.098285 INFO: ms2_error      : 7.5221597911183915
1:04:43.098325 INFO: fwhm_rt        : 3.0
1:04:43.098363 INFO: quant_window   : 3
1:04:43.098401 INFO: ==============================================
1:04:45.674181 INFO: performing precursor FDR with 40 features
1:04:45.674326 INFO: Decoy channel: -1
1:04:45.674355 INFO: competitive: True
1:04:45.888117 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:46.201673 INFO: Estimating optimal hyperparameters - samples: 600,752, batch_size: 2,460, learning_rate: 7.75e-04
1:04:46.203196 INFO: Using random state 139146 for train-test-split
1:05:02.356663 INFO: Test AUC: 0.608
1:05:02.356810 INFO: Train AUC: 0.616
1:05:02.356843 INFO: AUC difference: 1.31%
1:05:02.824573 INFO: Resetting torch num_threads to 100
1:05:02.854586 PROGRESS: === Extracted 750940 precursors and 4202211 fragments ===
1:05:02.855087 INFO: === FDR correction performed with classifier version 9 ===
1:05:02.855773 PROGRESS: ============================= Precursor FDR =============================
1:05:02.855864 PROGRESS: Total precursors accumulated: 1,485
1:05:02.855926 PROGRESS: Target precursors: 1,471 (99.06%)
1:05:02.855978 PROGRESS: Decoy precursors: 14 (0.94%)
1:05:02.856025 PROGRESS: 
1:05:02.856071 PROGRESS: Precursor Summary:
1:05:02.857352 PROGRESS: Channel   0:	 0.050 FDR: 1,471; 0.010 FDR: 1,471; 0.001 FDR:   108
1:05:02.857445 PROGRESS: 
1:05:02.857501 PROGRESS: Protein Summary:
1:05:02.859132 PROGRESS: Channel   0:	 0.050 FDR: 1,260; 0.010 FDR: 1,260; 0.001 FDR:   105
1:05:02.859225 PROGRESS: =========================================================================
1:05:02.871986 INFO: Target number of precursors reached.
1:05:03.347027 INFO: fragments_df: keeping 5000 of 4202211 [sum(precursor_idx_mask)=34951 sum(mass_error_mask)=4202211 stop_rank=5000
1:05:03.905442 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:04.108441 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:04.760312 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:04.760783 INFO: Using score_cutoff 8.480999842643739 (fac=0.99, q=1)
1:05:04.761101 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:04.761179 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:04.761235 INFO: Updating optimization_manager: score_cutoff        : 10.65736480407715 -> 8.480999842643739
1:05:04.761292 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:04.913687 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:05.231385 INFO: === checking if optimization conditions were reached ===
1:05:05.231690 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:05:05.234672 INFO: Updating optimization_manager: rt_error            : 568.7257787042518 -> 660.9921359531917
1:05:05.234792 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 660.9921.
1:05:05.234859 INFO: ==============================================
1:05:05.234930 INFO: Starting optimization step 5.
1:05:05.234990 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:05:05.235054 INFO: Using rust extraction backend
1:05:05.235115 PROGRESS: Extracting batch of 250447 precursors
1:05:05.672217 INFO: === Search parameters used ===
1:05:05.672540 INFO: rt_error       : 660.9921359531917
1:05:05.672601 INFO: mobility_error : 0.1
1:05:05.672652 INFO: num_candidates : 3
1:05:05.672699 INFO: ms1_error      : 30
1:05:05.672743 INFO: ms2_error      : 7.5221597911183915
1:05:05.672785 INFO: fwhm_rt        : 3.0
1:05:05.672827 INFO: quant_window   : 3
1:05:05.672870 INFO: ==============================================
1:05:08.276869 INFO: performing precursor FDR with 40 features
1:05:08.277015 INFO: Decoy channel: -1
1:05:08.277041 INFO: competitive: True
1:05:08.481065 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:08.793965 INFO: Estimating optimal hyperparameters - samples: 600,820, batch_size: 2,460, learning_rate: 7.75e-04
1:05:08.795462 INFO: Using random state 139146 for train-test-split
1:05:24.999712 INFO: Test AUC: 0.608
1:05:24.999857 INFO: Train AUC: 0.616
1:05:24.999892 INFO: AUC difference: 1.33%
1:05:25.470045 INFO: Resetting torch num_threads to 100
1:05:25.499927 PROGRESS: === Extracted 751025 precursors and 4221369 fragments ===
1:05:25.500451 INFO: === FDR correction performed with classifier version 9 ===
1:05:25.501119 PROGRESS: ============================= Precursor FDR =============================
1:05:25.501209 PROGRESS: Total precursors accumulated: 1,438
1:05:25.501271 PROGRESS: Target precursors: 1,424 (99.03%)
1:05:25.501324 PROGRESS: Decoy precursors: 14 (0.97%)
1:05:25.501372 PROGRESS: 
1:05:25.501419 PROGRESS: Precursor Summary:
1:05:25.502792 PROGRESS: Channel   0:	 0.050 FDR: 1,424; 0.010 FDR: 1,424; 0.001 FDR: 1,001
1:05:25.502887 PROGRESS: 
1:05:25.502946 PROGRESS: Protein Summary:
1:05:25.504658 PROGRESS: Channel   0:	 0.050 FDR: 1,232; 0.010 FDR: 1,232; 0.001 FDR:   888
1:05:25.504751 PROGRESS: =========================================================================
1:05:25.518024 INFO: Target number of precursors reached.
1:05:25.989631 INFO: fragments_df: keeping 5000 of 4221369 [sum(precursor_idx_mask)=33726 sum(mass_error_mask)=4221369 stop_rank=5000
1:05:26.535316 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:26.733503 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:27.384680 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:27.385162 INFO: Using score_cutoff 6.648132103586197 (fac=0.99, q=1)
1:05:27.385478 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:27.385555 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:27.385611 INFO: Updating optimization_manager: score_cutoff        : 8.480999842643739 -> 6.648132103586197
1:05:27.385668 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:27.538603 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:27.870816 INFO: === checking if optimization conditions were reached ===
1:05:27.871120 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:05:27.874037 INFO: Updating optimization_manager: rt_error            : 660.9921359531917 -> 576.5520458335606
1:05:27.874143 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 576.5520.
1:05:27.874209 INFO: ==============================================
1:05:27.874279 INFO: Starting optimization step 6.
1:05:27.874338 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:05:27.874400 INFO: Using rust extraction backend
1:05:27.874469 PROGRESS: Extracting batch of 250447 precursors
1:05:28.306025 INFO: === Search parameters used ===
1:05:28.306331 INFO: rt_error       : 576.5520458335606
1:05:28.306390 INFO: mobility_error : 0.1
1:05:28.306437 INFO: num_candidates : 3
1:05:28.306482 INFO: ms1_error      : 30
1:05:28.306525 INFO: ms2_error      : 7.5221597911183915
1:05:28.306567 INFO: fwhm_rt        : 3.0
1:05:28.306608 INFO: quant_window   : 3
1:05:28.306651 INFO: ==============================================
1:05:30.828006 INFO: performing precursor FDR with 40 features
1:05:30.828156 INFO: Decoy channel: -1
1:05:30.828184 INFO: competitive: True
1:05:31.035581 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:31.347111 INFO: Estimating optimal hyperparameters - samples: 600,848, batch_size: 2,461, learning_rate: 7.75e-04
1:05:31.348745 INFO: Using random state 139146 for train-test-split
1:05:48.331282 INFO: Test AUC: 0.607
1:05:48.331429 INFO: Train AUC: 0.616
1:05:48.331464 INFO: AUC difference: 1.31%
1:05:48.806123 INFO: Resetting torch num_threads to 100
1:05:48.837238 PROGRESS: === Extracted 751060 precursors and 4222550 fragments ===
1:05:48.837755 INFO: === FDR correction performed with classifier version 9 ===
1:05:48.838475 PROGRESS: ============================= Precursor FDR =============================
1:05:48.838567 PROGRESS: Total precursors accumulated: 1,559
1:05:48.838628 PROGRESS: Target precursors: 1,544 (99.04%)
1:05:48.838679 PROGRESS: Decoy precursors: 15 (0.96%)
1:05:48.838727 PROGRESS: 
1:05:48.838773 PROGRESS: Precursor Summary:
1:05:48.840162 PROGRESS: Channel   0:	 0.050 FDR: 1,544; 0.010 FDR: 1,544; 0.001 FDR: 1,131
1:05:48.840255 PROGRESS: 
1:05:48.840311 PROGRESS: Protein Summary:
1:05:48.842111 PROGRESS: Channel   0:	 0.050 FDR: 1,311; 0.010 FDR: 1,311; 0.001 FDR:   988
1:05:48.842218 PROGRESS: =========================================================================
1:05:48.857111 INFO: Target number of precursors reached.
1:05:49.332977 INFO: fragments_df: keeping 5000 of 4222550 [sum(precursor_idx_mask)=36688 sum(mass_error_mask)=4222550 stop_rank=5000
1:05:49.887562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:50.102118 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:50.771343 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:50.771845 INFO: Using score_cutoff 7.656484414958953 (fac=0.99, q=1)
1:05:50.772210 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:50.772290 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:50.772343 INFO: Updating optimization_manager: score_cutoff        : 6.648132103586197 -> 7.656484414958953
1:05:50.772398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:50.927994 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:51.261284 INFO: === checking if optimization conditions were reached ===
1:05:51.261598 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:05:51.264885 INFO: Updating optimization_manager: rt_error            : 576.5520458335606 -> 675.3927037835149
1:05:51.265039 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 675.3927.
1:05:51.265110 INFO: ==============================================
1:05:51.265183 INFO: Starting optimization step 7.
1:05:51.265245 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:05:51.265324 INFO: Using rust extraction backend
1:05:51.265387 PROGRESS: Extracting batch of 250447 precursors
1:05:51.713387 INFO: === Search parameters used ===
1:05:51.713669 INFO: rt_error       : 675.3927037835149
1:05:51.713735 INFO: mobility_error : 0.1
1:05:51.713788 INFO: num_candidates : 3
1:05:51.713837 INFO: ms1_error      : 30
1:05:51.713904 INFO: ms2_error      : 7.5221597911183915
1:05:51.713951 INFO: fwhm_rt        : 3.0
1:05:51.713995 INFO: quant_window   : 3
1:05:51.714047 INFO: ==============================================
1:05:54.335341 INFO: performing precursor FDR with 40 features
1:05:54.335491 INFO: Decoy channel: -1
1:05:54.335518 INFO: competitive: True
1:05:54.532422 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:54.837423 INFO: Estimating optimal hyperparameters - samples: 600,841, batch_size: 2,461, learning_rate: 7.75e-04
1:05:54.839133 INFO: Using random state 139146 for train-test-split
1:06:12.118265 INFO: Test AUC: 0.608
1:06:12.118439 INFO: Train AUC: 0.616
1:06:12.118476 INFO: AUC difference: 1.24%
1:06:13.931874 INFO: Resetting torch num_threads to 100
1:06:13.962643 PROGRESS: === Extracted 751052 precursors and 4227171 fragments ===
1:06:13.963157 INFO: === FDR correction performed with classifier version 9 ===
1:06:13.963869 PROGRESS: ============================= Precursor FDR =============================
1:06:13.963961 PROGRESS: Total precursors accumulated: 1,567
1:06:13.964023 PROGRESS: Target precursors: 1,552 (99.04%)
1:06:13.964077 PROGRESS: Decoy precursors: 15 (0.96%)
1:06:13.964129 PROGRESS: 
1:06:13.964188 PROGRESS: Precursor Summary:
1:06:13.965618 PROGRESS: Channel   0:	 0.050 FDR: 1,552; 0.010 FDR: 1,552; 0.001 FDR: 1,134
1:06:13.965711 PROGRESS: 
1:06:13.965773 PROGRESS: Protein Summary:
1:06:13.967629 PROGRESS: Channel   0:	 0.050 FDR: 1,319; 0.010 FDR: 1,319; 0.001 FDR:   992
1:06:13.967724 PROGRESS: =========================================================================
1:06:13.981334 INFO: Target number of precursors reached.
1:06:14.466416 INFO: fragments_df: keeping 5000 of 4227171 [sum(precursor_idx_mask)=37022 sum(mass_error_mask)=4227171 stop_rank=5000
1:06:15.012763 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:06:15.229941 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:06:15.885517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:06:15.886012 INFO: Using score_cutoff 9.135186979579926 (fac=0.99, q=1)
1:06:15.886339 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:15.886412 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:15.886464 INFO: Updating optimization_manager: score_cutoff        : 7.656484414958953 -> 9.135186979579926
1:06:15.886516 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:16.040400 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:16.389547 INFO: === checking if optimization conditions were reached ===
1:06:16.389869 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:06:16.392934 INFO: Updating optimization_manager: rt_error            : 675.3927037835149 -> 679.6511318459204
1:06:16.393037 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 679.6511.
1:06:16.393101 INFO: ==============================================
1:06:16.393196 INFO: Starting optimization step 8.
1:06:16.393257 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:06:16.393321 INFO: Using rust extraction backend
1:06:16.393381 PROGRESS: Extracting batch of 250447 precursors
1:06:16.825574 INFO: === Search parameters used ===
1:06:16.825889 INFO: rt_error       : 679.6511318459204
1:06:16.825949 INFO: mobility_error : 0.1
1:06:16.825995 INFO: num_candidates : 3
1:06:16.826041 INFO: ms1_error      : 30
1:06:16.826091 INFO: ms2_error      : 7.5221597911183915
1:06:16.826132 INFO: fwhm_rt        : 3.0
1:06:16.826171 INFO: quant_window   : 3
1:06:16.826212 INFO: ==============================================
1:06:19.381809 INFO: performing precursor FDR with 40 features
1:06:19.381965 INFO: Decoy channel: -1
1:06:19.381992 INFO: competitive: True
1:06:19.586445 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:19.897356 INFO: Estimating optimal hyperparameters - samples: 600,836, batch_size: 2,461, learning_rate: 7.75e-04
1:06:19.898970 INFO: Using random state 139146 for train-test-split
1:06:37.324940 INFO: Test AUC: 0.609
1:06:37.325119 INFO: Train AUC: 0.616
1:06:37.325152 INFO: AUC difference: 1.13%
1:06:37.802890 INFO: Resetting torch num_threads to 100
1:06:37.833153 PROGRESS: === Extracted 751045 precursors and 4225556 fragments ===
1:06:37.833696 INFO: === FDR correction performed with classifier version 9 ===
1:06:37.834439 PROGRESS: ============================= Precursor FDR =============================
1:06:37.834537 PROGRESS: Total precursors accumulated: 1,523
1:06:37.834601 PROGRESS: Target precursors: 1,508 (99.02%)
1:06:37.834656 PROGRESS: Decoy precursors: 15 (0.98%)
1:06:37.834707 PROGRESS: 
1:06:37.834756 PROGRESS: Precursor Summary:
1:06:37.836126 PROGRESS: Channel   0:	 0.050 FDR: 1,508; 0.010 FDR: 1,508; 0.001 FDR:   855
1:06:37.836231 PROGRESS: 
1:06:37.836289 PROGRESS: Protein Summary:
1:06:37.838056 PROGRESS: Channel   0:	 0.050 FDR: 1,289; 0.010 FDR: 1,289; 0.001 FDR:   771
1:06:37.838150 PROGRESS: =========================================================================
1:06:37.852078 INFO: Target number of precursors reached.
1:06:38.315010 INFO: fragments_df: keeping 5000 of 4225556 [sum(precursor_idx_mask)=35881 sum(mass_error_mask)=4225556 stop_rank=5000
1:06:38.873412 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:06:39.081442 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:06:39.734055 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:06:39.734540 INFO: Using score_cutoff 8.445199420452118 (fac=0.99, q=1)
1:06:39.734879 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:39.734959 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:39.735016 INFO: Updating optimization_manager: score_cutoff        : 9.135186979579926 -> 8.445199420452118
1:06:39.735074 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:39.888738 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:40.235361 INFO: === checking if optimization conditions were reached ===
1:06:40.235684 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
1:06:40.236704 INFO: Updating optimization_manager: rt_error            : 679.6511318459204 -> 675.3927037835149
1:06:40.236877 INFO: Updating optimization_manager: classifier_version  : 9 -> 20
1:06:40.236983 INFO: Updating optimization_manager: score_cutoff        : 8.445199420452118 -> 9.135186979579926
1:06:40.237078 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:40.237170 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:40.237264 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 675.3927 found after 9 searches.
1:06:40.237329 INFO: ==============================================
1:06:40.237410 PROGRESS: Optimization finished for rt_error.
1:06:40.774897 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:40.931394 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:41.276539 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:06:41.276852 PROGRESS: ==============================================
1:06:41.276926 PROGRESS: ms2_error      : 7.5222
1:06:41.276984 PROGRESS: rt_error       : 675.3927
1:06:41.277032 PROGRESS: ==============================================
1:06:41.278970 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:48.954785 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:05.049397 INFO: Using rust extraction backend
1:07:05.050183 PROGRESS: Extracting batch of 11997144 precursors
1:07:21.316295 INFO: === Search parameters used ===
1:07:21.316664 INFO: rt_error       : 675.3927037835149
1:07:21.316741 INFO: mobility_error : 0.1
1:07:21.316800 INFO: num_candidates : 3
1:07:21.316848 INFO: ms1_error      : 30
1:07:21.316899 INFO: ms2_error      : 7.5221597911183915
1:07:21.316966 INFO: fwhm_rt        : 3.0
1:07:21.317029 INFO: quant_window   : 3
1:07:21.317082 INFO: ==============================================
1:07:51.109165 INFO: Removed 6604920 precursors with score below cutoff 9.135186979579926
1:08:14.690570 INFO: performing precursor FDR with 40 features
1:08:14.690910 INFO: Decoy channel: -1
1:08:14.690945 INFO: competitive: True
1:08:17.756509 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:29.683139 INFO: Estimating optimal hyperparameters - samples: 23,508,757, batch_size: 4,096, learning_rate: 1.00e-03
1:08:29.755007 INFO: Using random state 308492 for train-test-split
1:18:29.842927 INFO: Test AUC: 0.623
1:18:29.843234 INFO: Train AUC: 0.623
1:18:29.843278 INFO: AUC difference: 0.04%
1:18:36.128957 INFO: Resetting torch num_threads to 100
1:18:38.321023 PROGRESS: ============================= Precursor FDR =============================
1:18:38.321379 PROGRESS: Total precursors accumulated: 91,684
1:18:38.321460 PROGRESS: Target precursors: 90,777 (99.01%)
1:18:38.321520 PROGRESS: Decoy precursors: 907 (0.99%)
1:18:38.321571 PROGRESS: 
1:18:38.321619 PROGRESS: Precursor Summary:
1:18:38.341090 PROGRESS: Channel   0:	 0.050 FDR: 90,777; 0.010 FDR: 90,777; 0.001 FDR:     1
1:18:38.341326 PROGRESS: 
1:18:38.341405 PROGRESS: Protein Summary:
1:18:38.369228 PROGRESS: Channel   0:	 0.050 FDR: 13,417; 0.010 FDR: 13,417; 0.001 FDR:     1
1:18:38.369460 PROGRESS: =========================================================================
1:18:38.517941 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
1:18:38.686403 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
1:18:38.929674 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:18:39.486653 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
1:18:39.486838 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant
1:18:39.486962 INFO: Initializing TimingManager
1:18:39.487660 INFO: Initializing RawFileManager
1:18:50.298870 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.
1:18:50.307857 INFO: Determining DIA cycle
1:18:50.324189 INFO: Found cycle with start 0.00 min and length 300.
1:18:50.522774 INFO: RT (min)            : 0.0 - 26.9
1:18:50.522877 INFO: RT duration (sec)   : 1611.2
1:18:50.522907 INFO: RT duration (min)   : 26.9
1:18:50.522939 INFO: Cycle len (scans)   : 300
1:18:50.522960 INFO: Cycle len (sec)     : 1.65
1:18:50.522987 INFO: Number of cycles    : 977
1:18:50.523008 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:18:50.523056 INFO: Creating DIA data object took: 11.035300254821777
1:18:51.230192 INFO: Creating DIA data NG object took: 0.7069888114929199
1:18:52.594808 INFO: Initializing CalibrationManager
1:18:52.595111 INFO: Setting up calibration estimators ..
1:18:52.595178 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:18:52.595309 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'}' ..
1:18:52.595438 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:18:52.595495 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:18:52.595569 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}}' ..
1:18:52.595623 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:18:52.595671 INFO: Done setting up calibration estimators.
1:18:52.595947 INFO: Initializing OptimizationManager
1:18:52.596119 INFO: initial parameter: ms1_error = 30
1:18:52.596177 INFO: initial parameter: ms2_error = 30
1:18:52.596228 INFO: initial parameter: rt_error = 805.6002197265625
1:18:52.596276 INFO: initial parameter: mobility_error = 0.1
1:18:52.596320 INFO: initial parameter: num_candidates = 1
1:18:52.596362 INFO: initial parameter: fwhm_rt = 5
1:18:52.596405 INFO: initial parameter: fwhm_mobility = 0.01
1:18:52.596446 INFO: initial parameter: score_cutoff = 0
1:18:52.596486 INFO: initial parameter: classifier_version = -1
1:18:52.596560 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:18:52.596936 INFO: FDRManager: loading saved state not requested, will be initialized.
1:18:52.596974 INFO: Initializing FDRManager
1:18:52.597030 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:18:54.031583 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:18:54.935765 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:18:54.936156 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
1:18:54.936275 PROGRESS: Starting initial search for precursors.
1:18:54.936370 INFO: Starting optimization step 0.
1:18:54.936438 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:18:54.936512 INFO: Using rust extraction backend
1:18:54.936582 PROGRESS: Extracting batch of 1970 precursors
1:18:54.941648 INFO: === Search parameters used ===
1:18:54.941758 INFO: rt_error       : 805.6002197265625
1:18:54.941809 INFO: mobility_error : 0.1
1:18:54.941864 INFO: num_candidates : 1
1:18:54.941910 INFO: ms1_error      : 30
1:18:54.941967 INFO: ms2_error      : 30
1:18:54.942009 INFO: fwhm_rt        : 5
1:18:54.942048 INFO: quant_window   : 3
1:18:54.942087 INFO: ==============================================
1:18:54.981070 INFO: performing precursor FDR with 40 features
1:18:54.981151 INFO: Decoy channel: -1
1:18:54.981175 INFO: competitive: True
1:18:54.982577 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:54.984899 INFO: Estimating optimal hyperparameters - samples: 1,559, batch_size: 128, learning_rate: 1.77e-04
1:18:54.985855 INFO: Using random state 254436 for train-test-split
1:18:55.157886 INFO: Test AUC: 0.514
1:18:55.157973 INFO: Train AUC: 0.541
1:18:55.158001 INFO: AUC difference: 5.07%
1:18:55.158022 WARNING: AUC difference > 5%. This may indicate overfitting.
1:18:55.404997 INFO: Resetting torch num_threads to 100
1:18:55.406667 PROGRESS: === Extracted 1949 precursors and 9162 fragments ===
1:18:55.407053 INFO: === FDR correction performed with classifier version -1 ===
1:18:55.407544 PROGRESS: ============================= Precursor FDR =============================
1:18:55.407627 PROGRESS: Total precursors accumulated: 4
1:18:55.407683 PROGRESS: Target precursors: 4 (100.00%)
1:18:55.407731 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:55.407775 PROGRESS: 
1:18:55.407817 PROGRESS: Precursor Summary:
1:18:55.408890 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
1:18:55.408970 PROGRESS: 
1:18:55.409023 PROGRESS: Protein Summary:
1:18:55.410204 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
1:18:55.410293 PROGRESS: =========================================================================
1:18:55.410522 INFO: Target number of precursors not reached yet.
1:18:55.494940 INFO: Starting optimization step 1.
1:18:55.495176 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:18:55.495284 INFO: Using rust extraction backend
1:18:55.495347 PROGRESS: Extracting batch of 3942 precursors
1:18:55.503901 INFO: === Search parameters used ===
1:18:55.504043 INFO: rt_error       : 805.6002197265625
1:18:55.504097 INFO: mobility_error : 0.1
1:18:55.504143 INFO: num_candidates : 1
1:18:55.504186 INFO: ms1_error      : 30
1:18:55.504227 INFO: ms2_error      : 30
1:18:55.504268 INFO: fwhm_rt        : 5
1:18:55.504309 INFO: quant_window   : 3
1:18:55.504349 INFO: ==============================================
1:18:55.559555 INFO: performing precursor FDR with 40 features
1:18:55.559654 INFO: Decoy channel: -1
1:18:55.559680 INFO: competitive: True
1:18:55.564092 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:55.566439 INFO: Estimating optimal hyperparameters - samples: 4,680, batch_size: 128, learning_rate: 1.77e-04
1:18:55.566527 INFO: Using random state 644706 for train-test-split
1:18:56.104298 INFO: Test AUC: 0.534
1:18:56.104390 INFO: Train AUC: 0.558
1:18:56.104419 INFO: AUC difference: 4.29%
1:18:56.349746 INFO: Resetting torch num_threads to 100
1:18:56.352862 PROGRESS: === Extracted 5850 precursors and 27466 fragments ===
1:18:56.353253 INFO: === FDR correction performed with classifier version -1 ===
1:18:56.353746 PROGRESS: ============================= Precursor FDR =============================
1:18:56.353831 PROGRESS: Total precursors accumulated: 2
1:18:56.353903 PROGRESS: Target precursors: 2 (100.00%)
1:18:56.353958 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:56.354006 PROGRESS: 
1:18:56.354053 PROGRESS: Precursor Summary:
1:18:56.355133 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:18:56.355214 PROGRESS: 
1:18:56.355267 PROGRESS: Protein Summary:
1:18:56.356423 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:18:56.356506 PROGRESS: =========================================================================
1:18:56.356790 INFO: Target number of precursors not reached yet.
1:18:56.446956 INFO: Starting optimization step 2.
1:18:56.447198 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:18:56.447276 INFO: Using rust extraction backend
1:18:56.447337 PROGRESS: Extracting batch of 7890 precursors
1:18:56.462681 INFO: === Search parameters used ===
1:18:56.462827 INFO: rt_error       : 805.6002197265625
1:18:56.462878 INFO: mobility_error : 0.1
1:18:56.462922 INFO: num_candidates : 1
1:18:56.462964 INFO: ms1_error      : 30
1:18:56.463003 INFO: ms2_error      : 30
1:18:56.463043 INFO: fwhm_rt        : 5
1:18:56.463082 INFO: quant_window   : 3
1:18:56.463120 INFO: ==============================================
1:18:56.549001 INFO: performing precursor FDR with 40 features
1:18:56.549108 INFO: Decoy channel: -1
1:18:56.549133 INFO: competitive: True
1:18:56.555641 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:56.559598 INFO: Estimating optimal hyperparameters - samples: 10,936, batch_size: 128, learning_rate: 1.77e-04
1:18:56.559723 INFO: Using random state 748111 for train-test-split
1:18:57.765226 INFO: Test AUC: 0.553
1:18:57.765337 INFO: Train AUC: 0.575
1:18:57.765366 INFO: AUC difference: 3.83%
1:18:58.019957 INFO: Resetting torch num_threads to 100
1:18:58.024434 PROGRESS: === Extracted 13671 precursors and 64473 fragments ===
1:18:58.024849 INFO: === FDR correction performed with classifier version -1 ===
1:18:58.025360 PROGRESS: ============================= Precursor FDR =============================
1:18:58.025444 PROGRESS: Total precursors accumulated: 16
1:18:58.025500 PROGRESS: Target precursors: 16 (100.00%)
1:18:58.025548 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:58.025592 PROGRESS: 
1:18:58.025634 PROGRESS: Precursor Summary:
1:18:58.026703 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
1:18:58.026795 PROGRESS: 
1:18:58.026849 PROGRESS: Protein Summary:
1:18:58.028015 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
1:18:58.028098 PROGRESS: =========================================================================
1:18:58.028468 INFO: Target number of precursors not reached yet.
1:18:58.127930 INFO: Starting optimization step 3.
1:18:58.128177 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:18:58.128253 INFO: Using rust extraction backend
1:18:58.128312 PROGRESS: Extracting batch of 15788 precursors
1:18:58.157142 INFO: === Search parameters used ===
1:18:58.157339 INFO: rt_error       : 805.6002197265625
1:18:58.157391 INFO: mobility_error : 0.1
1:18:58.157437 INFO: num_candidates : 1
1:18:58.157480 INFO: ms1_error      : 30
1:18:58.157521 INFO: ms2_error      : 30
1:18:58.157575 INFO: fwhm_rt        : 5
1:18:58.157617 INFO: quant_window   : 3
1:18:58.157657 INFO: ==============================================
1:18:58.302374 INFO: performing precursor FDR with 40 features
1:18:58.302490 INFO: Decoy channel: -1
1:18:58.302514 INFO: competitive: True
1:18:58.315334 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:58.323329 INFO: Estimating optimal hyperparameters - samples: 23,450, batch_size: 128, learning_rate: 1.77e-04
1:18:58.323535 INFO: Using random state 339475 for train-test-split
1:19:01.031590 INFO: Test AUC: 0.568
1:19:01.031704 INFO: Train AUC: 0.597
1:19:01.031736 INFO: AUC difference: 4.96%
1:19:01.292478 INFO: Resetting torch num_threads to 100
1:19:01.299696 PROGRESS: === Extracted 29313 precursors and 138582 fragments ===
1:19:01.300205 INFO: === FDR correction performed with classifier version -1 ===
1:19:01.300759 PROGRESS: ============================= Precursor FDR =============================
1:19:01.300848 PROGRESS: Total precursors accumulated: 46
1:19:01.300919 PROGRESS: Target precursors: 46 (100.00%)
1:19:01.300972 PROGRESS: Decoy precursors: 0 (0.00%)
1:19:01.301021 PROGRESS: 
1:19:01.301071 PROGRESS: Precursor Summary:
1:19:01.302168 PROGRESS: Channel   0:	 0.050 FDR:    46; 0.010 FDR:    46; 0.001 FDR:    46
1:19:01.302258 PROGRESS: 
1:19:01.302314 PROGRESS: Protein Summary:
1:19:01.303522 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    45; 0.001 FDR:    45
1:19:01.303609 PROGRESS: =========================================================================
1:19:01.304134 INFO: Target number of precursors not reached yet.
1:19:01.425111 INFO: Starting optimization step 4.
1:19:01.425381 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:19:01.425466 INFO: Using rust extraction backend
1:19:01.425534 PROGRESS: Extracting batch of 31512 precursors
1:19:01.481465 INFO: === Search parameters used ===
1:19:01.481721 INFO: rt_error       : 805.6002197265625
1:19:01.481775 INFO: mobility_error : 0.1
1:19:01.481822 INFO: num_candidates : 1
1:19:01.481878 INFO: ms1_error      : 30
1:19:01.481925 INFO: ms2_error      : 30
1:19:01.481968 INFO: fwhm_rt        : 5
1:19:01.482009 INFO: quant_window   : 3
1:19:01.482050 INFO: ==============================================
1:19:01.715848 INFO: performing precursor FDR with 40 features
1:19:01.715970 INFO: Decoy channel: -1
1:19:01.715994 INFO: competitive: True
1:19:01.740903 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:01.757897 INFO: Estimating optimal hyperparameters - samples: 48,440, batch_size: 198, learning_rate: 2.20e-04
1:19:01.758130 INFO: Using random state 431483 for train-test-split
1:19:05.932274 INFO: Test AUC: 0.588
1:19:05.932400 INFO: Train AUC: 0.604
1:19:05.932432 INFO: AUC difference: 2.71%
1:19:06.196872 INFO: Resetting torch num_threads to 100
1:19:06.209353 PROGRESS: === Extracted 60550 precursors and 286398 fragments ===
1:19:06.210021 INFO: === FDR correction performed with classifier version -1 ===
1:19:06.210602 PROGRESS: ============================= Precursor FDR =============================
1:19:06.210692 PROGRESS: Total precursors accumulated: 138
1:19:06.210755 PROGRESS: Target precursors: 137 (99.28%)
1:19:06.210809 PROGRESS: Decoy precursors: 1 (0.72%)
1:19:06.210859 PROGRESS: 
1:19:06.210907 PROGRESS: Precursor Summary:
1:19:06.211960 PROGRESS: Channel   0:	 0.050 FDR:   137; 0.010 FDR:   137; 0.001 FDR:    92
1:19:06.212051 PROGRESS: 
1:19:06.212111 PROGRESS: Protein Summary:
1:19:06.213279 PROGRESS: Channel   0:	 0.050 FDR:   132; 0.010 FDR:   132; 0.001 FDR:    89
1:19:06.213378 PROGRESS: =========================================================================
1:19:06.214372 INFO: Target number of precursors not reached yet.
1:19:06.377123 INFO: Starting optimization step 5.
1:19:06.377403 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:19:06.377487 INFO: Using rust extraction backend
1:19:06.377554 PROGRESS: Extracting batch of 63110 precursors
1:19:06.488249 INFO: === Search parameters used ===
1:19:06.488547 INFO: rt_error       : 805.6002197265625
1:19:06.488610 INFO: mobility_error : 0.1
1:19:06.488660 INFO: num_candidates : 1
1:19:06.488708 INFO: ms1_error      : 30
1:19:06.488751 INFO: ms2_error      : 30
1:19:06.488794 INFO: fwhm_rt        : 5
1:19:06.488835 INFO: quant_window   : 3
1:19:06.488877 INFO: ==============================================
1:19:06.889057 INFO: performing precursor FDR with 40 features
1:19:06.889189 INFO: Decoy channel: -1
1:19:06.889216 INFO: competitive: True
1:19:06.942374 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:06.976778 INFO: Estimating optimal hyperparameters - samples: 98,460, batch_size: 403, learning_rate: 3.14e-04
1:19:06.977076 INFO: Using random state 280043 for train-test-split
1:19:12.247040 INFO: Test AUC: 0.581
1:19:12.247162 INFO: Train AUC: 0.608
1:19:12.247193 INFO: AUC difference: 4.38%
1:19:12.533009 INFO: Resetting torch num_threads to 100
1:19:12.557841 PROGRESS: === Extracted 123076 precursors and 582518 fragments ===
1:19:12.558556 INFO: === FDR correction performed with classifier version -1 ===
1:19:12.559210 PROGRESS: ============================= Precursor FDR =============================
1:19:12.559306 PROGRESS: Total precursors accumulated: 391
1:19:12.559378 PROGRESS: Target precursors: 388 (99.23%)
1:19:12.559431 PROGRESS: Decoy precursors: 3 (0.77%)
1:19:12.559478 PROGRESS: 
1:19:12.559530 PROGRESS: Precursor Summary:
1:19:12.560642 PROGRESS: Channel   0:	 0.050 FDR:   388; 0.010 FDR:   388; 0.001 FDR:   272
1:19:12.560729 PROGRESS: 
1:19:12.560784 PROGRESS: Protein Summary:
1:19:12.562088 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   368; 0.001 FDR:   263
1:19:12.562181 PROGRESS: =========================================================================
1:19:12.564173 INFO: Target number of precursors not reached yet.
1:19:12.813186 INFO: Starting optimization step 6.
1:19:12.813485 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:19:12.813571 INFO: Using rust extraction backend
1:19:12.813636 PROGRESS: Extracting batch of 126235 precursors
1:19:13.033797 INFO: === Search parameters used ===
1:19:13.034094 INFO: rt_error       : 805.6002197265625
1:19:13.034151 INFO: mobility_error : 0.1
1:19:13.034197 INFO: num_candidates : 1
1:19:13.034240 INFO: ms1_error      : 30
1:19:13.034281 INFO: ms2_error      : 30
1:19:13.034320 INFO: fwhm_rt        : 5
1:19:13.034359 INFO: quant_window   : 3
1:19:13.034398 INFO: ==============================================
1:19:13.763710 INFO: performing precursor FDR with 40 features
1:19:13.763835 INFO: Decoy channel: -1
1:19:13.763860 INFO: competitive: True
1:19:13.869485 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:13.974721 INFO: Estimating optimal hyperparameters - samples: 198,567, batch_size: 813, learning_rate: 4.46e-04
1:19:13.975225 INFO: Using random state 998750 for train-test-split
1:19:21.587104 INFO: Test AUC: 0.586
1:19:21.587229 INFO: Train AUC: 0.607
1:19:21.587262 INFO: AUC difference: 3.35%
1:19:21.913120 INFO: Resetting torch num_threads to 100
1:19:21.959836 PROGRESS: === Extracted 248209 precursors and 1174722 fragments ===
1:19:21.960534 INFO: === FDR correction performed with classifier version -1 ===
1:19:21.961294 PROGRESS: ============================= Precursor FDR =============================
1:19:21.961385 PROGRESS: Total precursors accumulated: 993
1:19:21.961448 PROGRESS: Target precursors: 984 (99.09%)
1:19:21.961499 PROGRESS: Decoy precursors: 9 (0.91%)
1:19:21.961546 PROGRESS: 
1:19:21.961591 PROGRESS: Precursor Summary:
1:19:21.962850 PROGRESS: Channel   0:	 0.050 FDR:   984; 0.010 FDR:   984; 0.001 FDR:   493
1:19:21.962940 PROGRESS: 
1:19:21.962998 PROGRESS: Protein Summary:
1:19:21.964531 PROGRESS: Channel   0:	 0.050 FDR:   877; 0.010 FDR:   877; 0.001 FDR:   457
1:19:21.964618 PROGRESS: =========================================================================
1:19:21.968163 INFO: Target number of precursors not reached yet.
1:19:22.391482 INFO: Starting optimization step 7.
1:19:22.391768 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:19:22.391868 INFO: Using rust extraction backend
1:19:22.391936 PROGRESS: Extracting batch of 252313 precursors
1:19:22.831699 INFO: === Search parameters used ===
1:19:22.831999 INFO: rt_error       : 805.6002197265625
1:19:22.832057 INFO: mobility_error : 0.1
1:19:22.832107 INFO: num_candidates : 1
1:19:22.832152 INFO: ms1_error      : 30
1:19:22.832203 INFO: ms2_error      : 30
1:19:22.832246 INFO: fwhm_rt        : 5
1:19:22.832287 INFO: quant_window   : 3
1:19:22.832327 INFO: ==============================================
1:19:24.243883 INFO: performing precursor FDR with 40 features
1:19:24.244013 INFO: Decoy channel: -1
1:19:24.244040 INFO: competitive: True
1:19:24.441579 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:24.729087 INFO: Estimating optimal hyperparameters - samples: 398,507, batch_size: 1,632, learning_rate: 6.31e-04
1:19:24.729791 INFO: Using random state 557102 for train-test-split
1:19:36.965510 INFO: Test AUC: 0.590
1:19:36.965778 INFO: Train AUC: 0.605
1:19:36.965813 INFO: AUC difference: 2.36%
1:19:37.368119 INFO: Resetting torch num_threads to 100
1:19:37.474023 PROGRESS: === Extracted 498134 precursors and 2357810 fragments ===
1:19:37.474960 INFO: === FDR correction performed with classifier version -1 ===
1:19:37.476065 PROGRESS: ============================= Precursor FDR =============================
1:19:37.476162 PROGRESS: Total precursors accumulated: 2,161
1:19:37.476233 PROGRESS: Target precursors: 2,140 (99.03%)
1:19:37.476290 PROGRESS: Decoy precursors: 21 (0.97%)
1:19:37.476339 PROGRESS: 
1:19:37.476388 PROGRESS: Precursor Summary:
1:19:37.477892 PROGRESS: Channel   0:	 0.050 FDR: 2,140; 0.010 FDR: 2,140; 0.001 FDR:     2
1:19:37.477986 PROGRESS: 
1:19:37.478048 PROGRESS: Protein Summary:
1:19:37.479917 PROGRESS: Channel   0:	 0.050 FDR: 1,671; 0.010 FDR: 1,671; 0.001 FDR:     2
1:19:37.480018 PROGRESS: =========================================================================
1:19:37.487415 INFO: Target number of precursors reached.
1:19:37.769919 INFO: fragments_df: keeping 5000 of 2357810 [sum(precursor_idx_mask)=22742 sum(mass_error_mask)=2357810 stop_rank=5000
1:19:38.223062 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:19:38.500338 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:19:39.151119 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:19:39.151595 INFO: Using score_cutoff 12.086065106391906 (fac=0.99, q=1)
1:19:39.151974 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:19:39.152055 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:19:39.152117 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.086065106391906
1:19:39.152191 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:19:39.304736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:19:39.664018 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:19:39.664322 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:19:39.664450 INFO: Starting optimization step 8.
1:19:39.664523 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:19:39.664615 INFO: Using rust extraction backend
1:19:39.664690 PROGRESS: Extracting batch of 250447 precursors
1:19:40.090853 INFO: === Search parameters used ===
1:19:40.091158 INFO: rt_error       : 805.6002197265625
1:19:40.091217 INFO: mobility_error : 0.1
1:19:40.091266 INFO: num_candidates : 3
1:19:40.091313 INFO: ms1_error      : 30
1:19:40.091357 INFO: ms2_error      : 30
1:19:40.091398 INFO: fwhm_rt        : 3.0
1:19:40.091450 INFO: quant_window   : 3
1:19:40.091493 INFO: ==============================================
1:19:42.764392 INFO: performing precursor FDR with 40 features
1:19:42.764518 INFO: Decoy channel: -1
1:19:42.764544 INFO: competitive: True
1:19:42.974117 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:43.291447 INFO: Estimating optimal hyperparameters - samples: 596,063, batch_size: 2,441, learning_rate: 7.72e-04
1:19:43.292934 INFO: Using random state 161177 for train-test-split
1:19:59.300980 INFO: Test AUC: 0.599
1:19:59.301252 INFO: Train AUC: 0.606
1:19:59.301289 INFO: AUC difference: 1.03%
1:19:59.775484 INFO: Resetting torch num_threads to 100
1:19:59.803972 PROGRESS: === Extracted 745079 precursors and 3454614 fragments ===
1:19:59.804583 INFO: === FDR correction performed with classifier version 7 ===
1:19:59.805227 PROGRESS: ============================= Precursor FDR =============================
1:19:59.805317 PROGRESS: Total precursors accumulated: 1,113
1:19:59.805382 PROGRESS: Target precursors: 1,102 (99.01%)
1:19:59.805435 PROGRESS: Decoy precursors: 11 (0.99%)
1:19:59.805483 PROGRESS: 
1:19:59.805531 PROGRESS: Precursor Summary:
1:19:59.806781 PROGRESS: Channel   0:	 0.050 FDR: 1,102; 0.010 FDR: 1,102; 0.001 FDR:   385
1:19:59.806872 PROGRESS: 
1:19:59.806931 PROGRESS: Protein Summary:
1:19:59.808477 PROGRESS: Channel   0:	 0.050 FDR:   967; 0.010 FDR:   967; 0.001 FDR:   357
1:19:59.808579 PROGRESS: =========================================================================
1:19:59.823890 INFO: Target number of precursors reached.
1:20:00.201915 INFO: fragments_df: keeping 5000 of 3454614 [sum(precursor_idx_mask)=24692 sum(mass_error_mask)=3454614 stop_rank=5000
1:20:00.752498 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:00.924313 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:01.569588 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:01.570068 INFO: Using score_cutoff 12.659798947906493 (fac=0.99, q=1)
1:20:01.570432 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:01.570509 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:01.570565 INFO: Updating optimization_manager: score_cutoff        : 12.086065106391906 -> 12.659798947906493
1:20:01.570625 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:01.724217 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:02.079076 INFO: === checking if optimization conditions were reached ===
1:20:02.079431 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 5 ===
1:20:02.082071 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.207590060615828
1:20:02.082176 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.2076.
1:20:02.082240 INFO: ==============================================
1:20:02.082320 INFO: Starting optimization step 9.
1:20:02.082381 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:02.082468 INFO: Using rust extraction backend
1:20:02.082541 PROGRESS: Extracting batch of 250447 precursors
1:20:02.508077 INFO: === Search parameters used ===
1:20:02.508358 INFO: rt_error       : 805.6002197265625
1:20:02.508415 INFO: mobility_error : 0.1
1:20:02.508463 INFO: num_candidates : 3
1:20:02.508506 INFO: ms1_error      : 30
1:20:02.508559 INFO: ms2_error      : 7.207590060615828
1:20:02.508630 INFO: fwhm_rt        : 3.0
1:20:02.508674 INFO: quant_window   : 3
1:20:02.508713 INFO: ==============================================
1:20:05.122673 INFO: performing precursor FDR with 40 features
1:20:05.122799 INFO: Decoy channel: -1
1:20:05.122824 INFO: competitive: True
1:20:05.318161 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:05.614427 INFO: Estimating optimal hyperparameters - samples: 600,968, batch_size: 2,461, learning_rate: 7.75e-04
1:20:05.615915 INFO: Using random state 161177 for train-test-split
1:20:22.375157 INFO: Test AUC: 0.601
1:20:22.375290 INFO: Train AUC: 0.612
1:20:22.375324 INFO: AUC difference: 1.82%
1:20:22.844661 INFO: Resetting torch num_threads to 100
1:20:22.895875 PROGRESS: === Extracted 751211 precursors and 4239350 fragments ===
1:20:22.896371 INFO: === FDR correction performed with classifier version 7 ===
1:20:22.897063 PROGRESS: ============================= Precursor FDR =============================
1:20:22.897156 PROGRESS: Total precursors accumulated: 1,592
1:20:22.897217 PROGRESS: Target precursors: 1,577 (99.06%)
1:20:22.897269 PROGRESS: Decoy precursors: 15 (0.94%)
1:20:22.897317 PROGRESS: 
1:20:22.897363 PROGRESS: Precursor Summary:
1:20:22.898674 PROGRESS: Channel   0:	 0.050 FDR: 1,577; 0.010 FDR: 1,577; 0.001 FDR:   100
1:20:22.898767 PROGRESS: 
1:20:22.898823 PROGRESS: Protein Summary:
1:20:22.900472 PROGRESS: Channel   0:	 0.050 FDR: 1,339; 0.010 FDR: 1,339; 0.001 FDR:    98
1:20:22.900565 PROGRESS: =========================================================================
1:20:22.915261 INFO: Target number of precursors reached.
1:20:23.387194 INFO: fragments_df: keeping 5000 of 4239350 [sum(precursor_idx_mask)=37518 sum(mass_error_mask)=4239350 stop_rank=5000
1:20:23.861362 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:24.082079 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:24.729561 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:24.730056 INFO: Using score_cutoff 9.246413551712035 (fac=0.99, q=1)
1:20:24.730368 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:24.730444 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:24.730504 INFO: Updating optimization_manager: score_cutoff        : 12.659798947906493 -> 9.246413551712035
1:20:24.730555 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:24.881924 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:25.213773 INFO: === checking if optimization conditions were reached ===
1:20:25.214068 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 5 ===
1:20:25.216705 INFO: Updating optimization_manager: ms2_error           : 7.207590060615828 -> 7.4540134741190895
1:20:25.216801 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.4540.
1:20:25.216864 INFO: ==============================================
1:20:25.216933 INFO: Starting optimization step 10.
1:20:25.216995 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:25.217056 INFO: Using rust extraction backend
1:20:25.217114 PROGRESS: Extracting batch of 250447 precursors
1:20:25.647835 INFO: === Search parameters used ===
1:20:25.648117 INFO: rt_error       : 805.6002197265625
1:20:25.648172 INFO: mobility_error : 0.1
1:20:25.648230 INFO: num_candidates : 3
1:20:25.648274 INFO: ms1_error      : 30
1:20:25.648314 INFO: ms2_error      : 7.4540134741190895
1:20:25.648354 INFO: fwhm_rt        : 3.0
1:20:25.648393 INFO: quant_window   : 3
1:20:25.648430 INFO: ==============================================
1:20:28.331176 INFO: performing precursor FDR with 40 features
1:20:28.331306 INFO: Decoy channel: -1
1:20:28.331333 INFO: competitive: True
1:20:28.535540 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:28.852580 INFO: Estimating optimal hyperparameters - samples: 600,858, batch_size: 2,461, learning_rate: 7.75e-04
1:20:28.853869 INFO: Using random state 161177 for train-test-split
1:20:45.668972 INFO: Test AUC: 0.603
1:20:45.669116 INFO: Train AUC: 0.611
1:20:45.669148 INFO: AUC difference: 1.37%
1:20:46.138211 INFO: Resetting torch num_threads to 100
1:20:46.165195 PROGRESS: === Extracted 751073 precursors and 4219786 fragments ===
1:20:46.165676 INFO: === FDR correction performed with classifier version 7 ===
1:20:46.166368 PROGRESS: ============================= Precursor FDR =============================
1:20:46.166483 PROGRESS: Total precursors accumulated: 1,583
1:20:46.166545 PROGRESS: Target precursors: 1,568 (99.05%)
1:20:46.166598 PROGRESS: Decoy precursors: 15 (0.95%)
1:20:46.166647 PROGRESS: 
1:20:46.166693 PROGRESS: Precursor Summary:
1:20:46.168014 PROGRESS: Channel   0:	 0.050 FDR: 1,568; 0.010 FDR: 1,568; 0.001 FDR:   594
1:20:46.168106 PROGRESS: 
1:20:46.168162 PROGRESS: Protein Summary:
1:20:46.169901 PROGRESS: Channel   0:	 0.050 FDR: 1,325; 0.010 FDR: 1,325; 0.001 FDR:   546
1:20:46.169998 PROGRESS: =========================================================================
1:20:46.184741 INFO: Target number of precursors reached.
1:20:46.666795 INFO: fragments_df: keeping 5000 of 4219786 [sum(precursor_idx_mask)=37783 sum(mass_error_mask)=4219786 stop_rank=5000
1:20:47.122644 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:47.328857 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:47.975913 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:47.976377 INFO: Using score_cutoff 11.94274228477478 (fac=0.99, q=1)
1:20:47.976684 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:47.976759 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:47.976812 INFO: Updating optimization_manager: score_cutoff        : 9.246413551712035 -> 11.94274228477478
1:20:47.976865 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:48.129637 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:48.459322 INFO: === checking if optimization conditions were reached ===
1:20:48.459606 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 5 ===
1:20:48.462338 INFO: Updating optimization_manager: ms2_error           : 7.4540134741190895 -> 7.395923408588301
1:20:48.462445 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 7.3959.
1:20:48.462512 INFO: ==============================================
1:20:48.462582 INFO: Starting optimization step 11.
1:20:48.462643 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:48.462706 INFO: Using rust extraction backend
1:20:48.462764 PROGRESS: Extracting batch of 250447 precursors
1:20:48.894936 INFO: === Search parameters used ===
1:20:48.895240 INFO: rt_error       : 805.6002197265625
1:20:48.895298 INFO: mobility_error : 0.1
1:20:48.895347 INFO: num_candidates : 3
1:20:48.895393 INFO: ms1_error      : 30
1:20:48.895437 INFO: ms2_error      : 7.395923408588301
1:20:48.895480 INFO: fwhm_rt        : 3.0
1:20:48.895522 INFO: quant_window   : 3
1:20:48.895564 INFO: ==============================================
1:20:51.515378 INFO: performing precursor FDR with 40 features
1:20:51.515512 INFO: Decoy channel: -1
1:20:51.515538 INFO: competitive: True
1:20:51.720889 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:52.054526 INFO: Estimating optimal hyperparameters - samples: 600,888, batch_size: 2,461, learning_rate: 7.75e-04
1:20:52.055935 INFO: Using random state 161177 for train-test-split
1:21:09.244524 INFO: Test AUC: 0.604
1:21:09.244686 INFO: Train AUC: 0.610
1:21:09.244720 INFO: AUC difference: 0.93%
1:21:09.704613 INFO: Resetting torch num_threads to 100
1:21:09.734976 PROGRESS: === Extracted 751110 precursors and 4223412 fragments ===
1:21:09.735481 INFO: === FDR correction performed with classifier version 7 ===
1:21:09.736160 PROGRESS: ============================= Precursor FDR =============================
1:21:09.736249 PROGRESS: Total precursors accumulated: 1,556
1:21:09.736310 PROGRESS: Target precursors: 1,541 (99.04%)
1:21:09.736362 PROGRESS: Decoy precursors: 15 (0.96%)
1:21:09.736410 PROGRESS: 
1:21:09.736456 PROGRESS: Precursor Summary:
1:21:09.737814 PROGRESS: Channel   0:	 0.050 FDR: 1,541; 0.010 FDR: 1,541; 0.001 FDR:   765
1:21:09.737915 PROGRESS: 
1:21:09.737973 PROGRESS: Protein Summary:
1:21:09.739716 PROGRESS: Channel   0:	 0.050 FDR: 1,313; 0.010 FDR: 1,313; 0.001 FDR:   694
1:21:09.739810 PROGRESS: =========================================================================
1:21:09.753878 INFO: Target number of precursors reached.
1:21:10.223624 INFO: fragments_df: keeping 5000 of 4223412 [sum(precursor_idx_mask)=37310 sum(mass_error_mask)=4223412 stop_rank=5000
1:21:10.643069 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:10.847778 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:11.495541 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:11.495991 INFO: Using score_cutoff 11.993618648529052 (fac=0.99, q=1)
1:21:11.496292 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:11.496368 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:11.496423 INFO: Updating optimization_manager: score_cutoff        : 11.94274228477478 -> 11.993618648529052
1:21:11.496475 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:11.647721 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:11.996792 INFO: === checking if optimization conditions were reached ===
1:21:11.997093 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 5 ===
1:21:11.999740 INFO: Updating optimization_manager: ms2_error           : 7.395923408588301 -> 7.4043457305115705
1:21:11.999845 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 7.4043.
1:21:11.999910 INFO: ==============================================
1:21:11.999979 INFO: Starting optimization step 12.
1:21:12.000050 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:21:12.000108 INFO: Using rust extraction backend
1:21:12.000167 PROGRESS: Extracting batch of 250447 precursors
1:21:12.434417 INFO: === Search parameters used ===
1:21:12.434826 INFO: rt_error       : 805.6002197265625
1:21:12.434965 INFO: mobility_error : 0.1
1:21:12.435081 INFO: num_candidates : 3
1:21:12.435184 INFO: ms1_error      : 30
1:21:12.435291 INFO: ms2_error      : 7.4043457305115705
1:21:12.435389 INFO: fwhm_rt        : 3.0
1:21:12.435482 INFO: quant_window   : 3
1:21:12.435573 INFO: ==============================================
1:21:14.951092 INFO: performing precursor FDR with 40 features
1:21:14.951228 INFO: Decoy channel: -1
1:21:14.951257 INFO: competitive: True
1:21:15.143279 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:15.444527 INFO: Estimating optimal hyperparameters - samples: 600,881, batch_size: 2,461, learning_rate: 7.75e-04
1:21:15.446261 INFO: Using random state 161177 for train-test-split
1:21:32.712921 INFO: Test AUC: 0.605
1:21:32.713174 INFO: Train AUC: 0.610
1:21:32.713209 INFO: AUC difference: 0.86%
1:21:33.183731 INFO: Resetting torch num_threads to 100
1:21:33.377441 PROGRESS: === Extracted 751102 precursors and 4222269 fragments ===
1:21:33.378062 INFO: === FDR correction performed with classifier version 7 ===
1:21:33.378787 PROGRESS: ============================= Precursor FDR =============================
1:21:33.378884 PROGRESS: Total precursors accumulated: 1,591
1:21:33.378947 PROGRESS: Target precursors: 1,576 (99.06%)
1:21:33.379000 PROGRESS: Decoy precursors: 15 (0.94%)
1:21:33.379049 PROGRESS: 
1:21:33.379095 PROGRESS: Precursor Summary:
1:21:33.380480 PROGRESS: Channel   0:	 0.050 FDR: 1,576; 0.010 FDR: 1,576; 0.001 FDR:   914
1:21:33.380570 PROGRESS: 
1:21:33.380626 PROGRESS: Protein Summary:
1:21:33.382404 PROGRESS: Channel   0:	 0.050 FDR: 1,341; 0.010 FDR: 1,341; 0.001 FDR:   821
1:21:33.382509 PROGRESS: =========================================================================
1:21:33.399733 INFO: Target number of precursors reached.
1:21:33.871696 INFO: fragments_df: keeping 5000 of 4222269 [sum(precursor_idx_mask)=37956 sum(mass_error_mask)=4222269 stop_rank=5000
1:21:34.999698 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:35.242929 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:35.957081 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:35.957641 INFO: Using score_cutoff 11.419123492240905 (fac=0.99, q=1)
1:21:35.958016 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:35.958098 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:35.958152 INFO: Updating optimization_manager: score_cutoff        : 11.993618648529052 -> 11.419123492240905
1:21:35.958221 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:36.109163 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:36.467147 INFO: === checking if optimization conditions were reached ===
1:21:36.467590 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 5 ===
1:21:36.469298 INFO: Updating optimization_manager: ms2_error           : 7.4043457305115705 -> 7.207590060615828
1:21:36.469497 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
1:21:36.469623 INFO: Updating optimization_manager: score_cutoff        : 11.419123492240905 -> 9.246413551712035
1:21:36.469754 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:36.469896 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:36.470026 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.2076 found after 5 searches.
1:21:36.470107 INFO: ==============================================
1:21:36.470247 PROGRESS: Optimization finished for ms2_error.
1:21:37.036122 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:37.187204 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:37.540607 INFO: Starting optimization step 0.
1:21:37.540968 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:21:37.541129 INFO: Using rust extraction backend
1:21:37.541264 PROGRESS: Extracting batch of 250447 precursors
1:21:37.970573 INFO: === Search parameters used ===
1:21:37.970879 INFO: rt_error       : 805.6002197265625
1:21:37.970943 INFO: mobility_error : 0.1
1:21:37.971005 INFO: num_candidates : 3
1:21:37.971051 INFO: ms1_error      : 30
1:21:37.971093 INFO: ms2_error      : 7.207590060615828
1:21:37.971135 INFO: fwhm_rt        : 3.0
1:21:37.971179 INFO: quant_window   : 3
1:21:37.971223 INFO: ==============================================
1:21:40.566340 INFO: performing precursor FDR with 40 features
1:21:40.566531 INFO: Decoy channel: -1
1:21:40.566557 INFO: competitive: True
1:21:40.779183 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:41.099370 INFO: Estimating optimal hyperparameters - samples: 600,972, batch_size: 2,461, learning_rate: 7.75e-04
1:21:41.100695 INFO: Using random state 396989 for train-test-split
1:21:57.910469 INFO: Test AUC: 0.606
1:21:57.910665 INFO: Train AUC: 0.616
1:21:57.910698 INFO: AUC difference: 1.66%
1:21:58.379592 INFO: Resetting torch num_threads to 100
1:21:58.405587 PROGRESS: === Extracted 751215 precursors and 4239927 fragments ===
1:21:58.406191 INFO: === FDR correction performed with classifier version 9 ===
1:21:58.406895 PROGRESS: ============================= Precursor FDR =============================
1:21:58.406985 PROGRESS: Total precursors accumulated: 1,686
1:21:58.407048 PROGRESS: Target precursors: 1,670 (99.05%)
1:21:58.407104 PROGRESS: Decoy precursors: 16 (0.95%)
1:21:58.407152 PROGRESS: 
1:21:58.407197 PROGRESS: Precursor Summary:
1:21:58.408574 PROGRESS: Channel   0:	 0.050 FDR: 1,670; 0.010 FDR: 1,670; 0.001 FDR:   633
1:21:58.408664 PROGRESS: 
1:21:58.408723 PROGRESS: Protein Summary:
1:21:58.410464 PROGRESS: Channel   0:	 0.050 FDR: 1,393; 0.010 FDR: 1,393; 0.001 FDR:   578
1:21:58.410561 PROGRESS: =========================================================================
1:21:58.425574 INFO: Target number of precursors reached.
1:21:58.889158 INFO: fragments_df: keeping 5000 of 4239927 [sum(precursor_idx_mask)=40160 sum(mass_error_mask)=4239927 stop_rank=5000
1:21:59.385106 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:59.601932 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:00.252945 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:00.253440 INFO: Using score_cutoff 11.966078646469116 (fac=0.99, q=1)
1:22:00.253786 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:00.253883 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:00.253944 INFO: Updating optimization_manager: score_cutoff        : 9.246413551712035 -> 11.966078646469116
1:22:00.254011 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:00.402443 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:00.749621 INFO: === checking if optimization conditions were reached ===
1:22:00.750033 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:22:00.752974 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 463.1038082416403
1:22:00.753083 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 463.1038.
1:22:00.753152 INFO: ==============================================
1:22:00.753229 INFO: Starting optimization step 1.
1:22:00.753292 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:00.753364 INFO: Using rust extraction backend
1:22:00.753428 PROGRESS: Extracting batch of 250447 precursors
1:22:01.191950 INFO: === Search parameters used ===
1:22:01.192263 INFO: rt_error       : 463.1038082416403
1:22:01.192321 INFO: mobility_error : 0.1
1:22:01.192372 INFO: num_candidates : 3
1:22:01.192418 INFO: ms1_error      : 30
1:22:01.192476 INFO: ms2_error      : 7.207590060615828
1:22:01.192534 INFO: fwhm_rt        : 3.0
1:22:01.192576 INFO: quant_window   : 3
1:22:01.192616 INFO: ==============================================
1:22:03.748367 INFO: performing precursor FDR with 40 features
1:22:03.748515 INFO: Decoy channel: -1
1:22:03.748542 INFO: competitive: True
1:22:03.964450 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:04.283728 INFO: Estimating optimal hyperparameters - samples: 600,766, batch_size: 2,460, learning_rate: 7.75e-04
1:22:04.285390 INFO: Using random state 396989 for train-test-split
1:22:20.617516 INFO: Test AUC: 0.604
1:22:20.617786 INFO: Train AUC: 0.615
1:22:20.617822 INFO: AUC difference: 1.83%
1:22:21.103652 INFO: Resetting torch num_threads to 100
1:22:21.130983 PROGRESS: === Extracted 750958 precursors and 4141000 fragments ===
1:22:21.131636 INFO: === FDR correction performed with classifier version 9 ===
1:22:21.132355 PROGRESS: ============================= Precursor FDR =============================
1:22:21.132445 PROGRESS: Total precursors accumulated: 1,705
1:22:21.132520 PROGRESS: Target precursors: 1,689 (99.06%)
1:22:21.132577 PROGRESS: Decoy precursors: 16 (0.94%)
1:22:21.132626 PROGRESS: 
1:22:21.132672 PROGRESS: Precursor Summary:
1:22:21.134119 PROGRESS: Channel   0:	 0.050 FDR: 1,689; 0.010 FDR: 1,689; 0.001 FDR:   857
1:22:21.134214 PROGRESS: 
1:22:21.134280 PROGRESS: Protein Summary:
1:22:21.136083 PROGRESS: Channel   0:	 0.050 FDR: 1,431; 0.010 FDR: 1,431; 0.001 FDR:   772
1:22:21.136204 PROGRESS: =========================================================================
1:22:21.153658 INFO: Target number of precursors reached.
1:22:21.616931 INFO: fragments_df: keeping 5000 of 4141000 [sum(precursor_idx_mask)=39836 sum(mass_error_mask)=4141000 stop_rank=5000
1:22:22.197268 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:22.454183 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:23.169003 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:23.169495 INFO: Using score_cutoff 10.024887685775758 (fac=0.99, q=1)
1:22:23.169855 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:23.169946 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:23.170006 INFO: Updating optimization_manager: score_cutoff        : 11.966078646469116 -> 10.024887685775758
1:22:23.170064 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:23.318019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:23.687575 INFO: === checking if optimization conditions were reached ===
1:22:23.687953 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:22:23.691477 INFO: Updating optimization_manager: rt_error            : 463.1038082416403 -> 504.4943658459695
1:22:23.691598 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 504.4944.
1:22:23.691677 INFO: ==============================================
1:22:23.691793 INFO: Starting optimization step 2.
1:22:23.691871 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:23.692003 INFO: Using rust extraction backend
1:22:23.692102 PROGRESS: Extracting batch of 250447 precursors
1:22:24.118505 INFO: === Search parameters used ===
1:22:24.118795 INFO: rt_error       : 504.4943658459695
1:22:24.118854 INFO: mobility_error : 0.1
1:22:24.118906 INFO: num_candidates : 3
1:22:24.118954 INFO: ms1_error      : 30
1:22:24.119002 INFO: ms2_error      : 7.207590060615828
1:22:24.119050 INFO: fwhm_rt        : 3.0
1:22:24.119108 INFO: quant_window   : 3
1:22:24.119152 INFO: ==============================================
1:22:26.573412 INFO: performing precursor FDR with 40 features
1:22:26.573548 INFO: Decoy channel: -1
1:22:26.573574 INFO: competitive: True
1:22:26.775137 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:27.084111 INFO: Estimating optimal hyperparameters - samples: 600,874, batch_size: 2,461, learning_rate: 7.75e-04
1:22:27.085290 INFO: Using random state 396989 for train-test-split
1:22:40.906004 INFO: Test AUC: 0.607
1:22:40.906149 INFO: Train AUC: 0.616
1:22:40.906183 INFO: AUC difference: 1.41%
1:22:41.360571 INFO: Resetting torch num_threads to 100
1:22:41.390393 PROGRESS: === Extracted 751093 precursors and 4187359 fragments ===
1:22:41.390911 INFO: === FDR correction performed with classifier version 9 ===
1:22:41.391571 PROGRESS: ============================= Precursor FDR =============================
1:22:41.391660 PROGRESS: Total precursors accumulated: 1,559
1:22:41.391720 PROGRESS: Target precursors: 1,544 (99.04%)
1:22:41.391772 PROGRESS: Decoy precursors: 15 (0.96%)
1:22:41.391822 PROGRESS: 
1:22:41.391869 PROGRESS: Precursor Summary:
1:22:41.393147 PROGRESS: Channel   0:	 0.050 FDR: 1,544; 0.010 FDR: 1,544; 0.001 FDR:   190
1:22:41.393237 PROGRESS: 
1:22:41.393294 PROGRESS: Protein Summary:
1:22:41.394930 PROGRESS: Channel   0:	 0.050 FDR: 1,301; 0.010 FDR: 1,301; 0.001 FDR:   184
1:22:41.395023 PROGRESS: =========================================================================
1:22:41.408144 INFO: Target number of precursors reached.
1:22:41.882133 INFO: fragments_df: keeping 5000 of 4187359 [sum(precursor_idx_mask)=37513 sum(mass_error_mask)=4187359 stop_rank=5000
1:22:42.427079 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:42.663595 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:44.772028 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:44.772578 INFO: Using score_cutoff 12.00428671388626 (fac=0.99, q=1)
1:22:44.772941 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:44.773020 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:44.773075 INFO: Updating optimization_manager: score_cutoff        : 10.024887685775758 -> 12.00428671388626
1:22:44.773129 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:44.922263 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:45.276781 INFO: === checking if optimization conditions were reached ===
1:22:45.277104 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:22:45.280812 INFO: Updating optimization_manager: rt_error            : 504.4943658459695 -> 559.9108426738572
1:22:45.280991 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 559.9108.
1:22:45.281074 INFO: ==============================================
1:22:45.281161 INFO: Starting optimization step 3.
1:22:45.281232 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:45.281310 INFO: Using rust extraction backend
1:22:45.281382 PROGRESS: Extracting batch of 250447 precursors
1:22:45.703602 INFO: === Search parameters used ===
1:22:45.703889 INFO: rt_error       : 559.9108426738572
1:22:45.703946 INFO: mobility_error : 0.1
1:22:45.703996 INFO: num_candidates : 3
1:22:45.704043 INFO: ms1_error      : 30
1:22:45.704256 INFO: ms2_error      : 7.207590060615828
1:22:45.704304 INFO: fwhm_rt        : 3.0
1:22:45.704357 INFO: quant_window   : 3
1:22:45.704398 INFO: ==============================================
1:22:48.147530 INFO: performing precursor FDR with 40 features
1:22:48.147678 INFO: Decoy channel: -1
1:22:48.147706 INFO: competitive: True
1:22:48.349035 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:48.651113 INFO: Estimating optimal hyperparameters - samples: 600,892, batch_size: 2,461, learning_rate: 7.75e-04
1:22:48.652317 INFO: Using random state 396989 for train-test-split
1:23:03.824430 INFO: Test AUC: 0.606
1:23:03.824606 INFO: Train AUC: 0.616
1:23:03.824640 INFO: AUC difference: 1.62%
1:23:04.287267 INFO: Resetting torch num_threads to 100
1:23:04.313198 PROGRESS: === Extracted 751115 precursors and 4199827 fragments ===
1:23:04.313741 INFO: === FDR correction performed with classifier version 9 ===
1:23:04.314459 PROGRESS: ============================= Precursor FDR =============================
1:23:04.314555 PROGRESS: Total precursors accumulated: 1,683
1:23:04.314634 PROGRESS: Target precursors: 1,667 (99.05%)
1:23:04.314688 PROGRESS: Decoy precursors: 16 (0.95%)
1:23:04.314736 PROGRESS: 
1:23:04.314782 PROGRESS: Precursor Summary:
1:23:04.316196 PROGRESS: Channel   0:	 0.050 FDR: 1,667; 0.010 FDR: 1,667; 0.001 FDR:   820
1:23:04.316294 PROGRESS: 
1:23:04.316352 PROGRESS: Protein Summary:
1:23:04.318152 PROGRESS: Channel   0:	 0.050 FDR: 1,421; 0.010 FDR: 1,421; 0.001 FDR:   742
1:23:04.318248 PROGRESS: =========================================================================
1:23:04.332001 INFO: Target number of precursors reached.
1:23:04.796972 INFO: fragments_df: keeping 5000 of 4199827 [sum(precursor_idx_mask)=39408 sum(mass_error_mask)=4199827 stop_rank=5000
1:23:05.280787 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:05.532524 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:06.252820 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:06.253305 INFO: Using score_cutoff 9.043449559593201 (fac=0.99, q=1)
1:23:06.253650 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:06.253729 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:06.253784 INFO: Updating optimization_manager: score_cutoff        : 12.00428671388626 -> 9.043449559593201
1:23:06.253837 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:06.403573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:06.754688 INFO: === checking if optimization conditions were reached ===
1:23:06.755065 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:23:06.758810 INFO: Updating optimization_manager: rt_error            : 559.9108426738572 -> 603.7420765006923
1:23:06.758982 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 603.7421.
1:23:06.759063 INFO: ==============================================
1:23:06.759157 INFO: Starting optimization step 4.
1:23:06.759230 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:06.759309 INFO: Using rust extraction backend
1:23:06.759381 PROGRESS: Extracting batch of 250447 precursors
1:23:07.181642 INFO: === Search parameters used ===
1:23:07.181941 INFO: rt_error       : 603.7420765006923
1:23:07.181999 INFO: mobility_error : 0.1
1:23:07.182064 INFO: num_candidates : 3
1:23:07.182108 INFO: ms1_error      : 30
1:23:07.182148 INFO: ms2_error      : 7.207590060615828
1:23:07.182188 INFO: fwhm_rt        : 3.0
1:23:07.182227 INFO: quant_window   : 3
1:23:07.182264 INFO: ==============================================
1:23:09.627894 INFO: performing precursor FDR with 40 features
1:23:09.628030 INFO: Decoy channel: -1
1:23:09.628057 INFO: competitive: True
1:23:09.824158 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:10.129036 INFO: Estimating optimal hyperparameters - samples: 600,967, batch_size: 2,461, learning_rate: 7.75e-04
1:23:10.130481 INFO: Using random state 396989 for train-test-split
1:23:23.764577 INFO: Test AUC: 0.608
1:23:23.764727 INFO: Train AUC: 0.614
1:23:23.764761 INFO: AUC difference: 1.02%
1:23:24.225159 INFO: Resetting torch num_threads to 100
1:23:24.251804 PROGRESS: === Extracted 751209 precursors and 4231241 fragments ===
1:23:24.252324 INFO: === FDR correction performed with classifier version 9 ===
1:23:24.253005 PROGRESS: ============================= Precursor FDR =============================
1:23:24.253097 PROGRESS: Total precursors accumulated: 1,697
1:23:24.253159 PROGRESS: Target precursors: 1,681 (99.06%)
1:23:24.253212 PROGRESS: Decoy precursors: 16 (0.94%)
1:23:24.253262 PROGRESS: 
1:23:24.253310 PROGRESS: Precursor Summary:
1:23:24.254772 PROGRESS: Channel   0:	 0.050 FDR: 1,681; 0.010 FDR: 1,681; 0.001 FDR:   692
1:23:24.254870 PROGRESS: 
1:23:24.254929 PROGRESS: Protein Summary:
1:23:24.256746 PROGRESS: Channel   0:	 0.050 FDR: 1,411; 0.010 FDR: 1,411; 0.001 FDR:   633
1:23:24.256838 PROGRESS: =========================================================================
1:23:24.271834 INFO: Target number of precursors reached.
1:23:24.755117 INFO: fragments_df: keeping 5000 of 4231241 [sum(precursor_idx_mask)=40515 sum(mass_error_mask)=4231241 stop_rank=5000
1:23:25.237036 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:25.489575 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:26.207304 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:26.207796 INFO: Using score_cutoff 11.82268027496338 (fac=0.99, q=1)
1:23:26.208116 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:26.208202 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:26.208260 INFO: Updating optimization_manager: score_cutoff        : 9.043449559593201 -> 11.82268027496338
1:23:26.208316 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:26.360691 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:26.727684 INFO: === checking if optimization conditions were reached ===
1:23:26.728031 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:23:26.731717 INFO: Updating optimization_manager: rt_error            : 603.7420765006923 -> 576.9137578284867
1:23:26.731902 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 576.9138.
1:23:26.732010 INFO: ==============================================
1:23:26.732098 INFO: Starting optimization step 5.
1:23:26.732169 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:26.732246 INFO: Using rust extraction backend
1:23:26.732316 PROGRESS: Extracting batch of 250447 precursors
1:23:27.154233 INFO: === Search parameters used ===
1:23:27.154546 INFO: rt_error       : 576.9137578284867
1:23:27.154607 INFO: mobility_error : 0.1
1:23:27.154659 INFO: num_candidates : 3
1:23:27.154705 INFO: ms1_error      : 30
1:23:27.154749 INFO: ms2_error      : 7.207590060615828
1:23:27.154791 INFO: fwhm_rt        : 3.0
1:23:27.154832 INFO: quant_window   : 3
1:23:27.154872 INFO: ==============================================
1:23:29.626903 INFO: performing precursor FDR with 40 features
1:23:29.627036 INFO: Decoy channel: -1
1:23:29.627062 INFO: competitive: True
1:23:29.829073 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:30.137898 INFO: Estimating optimal hyperparameters - samples: 600,916, batch_size: 2,461, learning_rate: 7.75e-04
1:23:30.138867 INFO: Using random state 396989 for train-test-split
1:23:43.825505 INFO: Test AUC: 0.606
1:23:43.825658 INFO: Train AUC: 0.614
1:23:43.825690 INFO: AUC difference: 1.38%
1:23:44.293516 INFO: Resetting torch num_threads to 100
1:23:44.319276 PROGRESS: === Extracted 751145 precursors and 4210151 fragments ===
1:23:44.319797 INFO: === FDR correction performed with classifier version 9 ===
1:23:44.320467 PROGRESS: ============================= Precursor FDR =============================
1:23:44.320555 PROGRESS: Total precursors accumulated: 1,654
1:23:44.320615 PROGRESS: Target precursors: 1,638 (99.03%)
1:23:44.320667 PROGRESS: Decoy precursors: 16 (0.97%)
1:23:44.320716 PROGRESS: 
1:23:44.320764 PROGRESS: Precursor Summary:
1:23:44.322149 PROGRESS: Channel   0:	 0.050 FDR: 1,638; 0.010 FDR: 1,638; 0.001 FDR:   732
1:23:44.322242 PROGRESS: 
1:23:44.322302 PROGRESS: Protein Summary:
1:23:44.324059 PROGRESS: Channel   0:	 0.050 FDR: 1,382; 0.010 FDR: 1,382; 0.001 FDR:   665
1:23:44.324151 PROGRESS: =========================================================================
1:23:44.338012 INFO: Target number of precursors reached.
1:23:44.808029 INFO: fragments_df: keeping 5000 of 4210151 [sum(precursor_idx_mask)=39583 sum(mass_error_mask)=4210151 stop_rank=5000
1:23:45.393453 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:45.643318 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:46.365166 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:46.365662 INFO: Using score_cutoff 11.892315037822723 (fac=0.99, q=1)
1:23:46.366036 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:46.366120 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:46.366174 INFO: Updating optimization_manager: score_cutoff        : 11.82268027496338 -> 11.892315037822723
1:23:46.366227 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:46.520389 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:46.874200 INFO: === checking if optimization conditions were reached ===
1:23:46.874573 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:23:46.875844 INFO: Updating optimization_manager: rt_error            : 576.9137578284867 -> 463.1038082416403
1:23:46.875995 INFO: Updating optimization_manager: classifier_version  : 9 -> 14
1:23:46.876113 INFO: Updating optimization_manager: score_cutoff        : 11.892315037822723 -> 10.024887685775758
1:23:46.876226 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:46.876345 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:46.876457 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 463.1038 found after 6 searches.
1:23:46.876547 INFO: ==============================================
1:23:46.876639 PROGRESS: Optimization finished for rt_error.
1:23:47.392506 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:47.541428 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:47.891121 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:23:47.891455 PROGRESS: ==============================================
1:23:47.891576 PROGRESS: ms2_error      : 7.2076
1:23:47.891648 PROGRESS: rt_error       : 463.1038
1:23:47.891708 PROGRESS: ==============================================
1:23:47.893056 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:55.392994 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:11.626084 INFO: Using rust extraction backend
1:24:11.626983 PROGRESS: Extracting batch of 11997144 precursors
1:24:27.658405 INFO: === Search parameters used ===
1:24:27.658757 INFO: rt_error       : 463.1038082416403
1:24:27.658830 INFO: mobility_error : 0.1
1:24:27.658888 INFO: num_candidates : 3
1:24:27.658950 INFO: ms1_error      : 30
1:24:27.659014 INFO: ms2_error      : 7.207590060615828
1:24:27.659063 INFO: fwhm_rt        : 3.0
1:24:27.659113 INFO: quant_window   : 3
1:24:27.659170 INFO: ==============================================
1:24:52.965590 INFO: Removed 10300215 precursors with score below cutoff 10.024887685775758
1:25:13.147458 INFO: performing precursor FDR with 40 features
1:25:13.147684 INFO: Decoy channel: -1
1:25:13.147718 INFO: competitive: True
1:25:15.965492 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:26.375915 INFO: Estimating optimal hyperparameters - samples: 20,547,093, batch_size: 4,096, learning_rate: 1.00e-03
1:25:26.438399 INFO: Using random state 112375 for train-test-split
1:36:18.980430 INFO: Test AUC: 0.622
1:36:18.981082 INFO: Train AUC: 0.622
1:36:18.981170 INFO: AUC difference: 0.12%
1:36:27.390834 INFO: Resetting torch num_threads to 100
1:36:31.595802 PROGRESS: ============================= Precursor FDR =============================
1:36:31.596561 PROGRESS: Total precursors accumulated: 96,062
1:36:31.596734 PROGRESS: Target precursors: 95,111 (99.01%)
1:36:31.596806 PROGRESS: Decoy precursors: 951 (0.99%)
1:36:31.596866 PROGRESS: 
1:36:31.596917 PROGRESS: Precursor Summary:
1:36:31.682011 PROGRESS: Channel   0:	 0.050 FDR: 95,111; 0.010 FDR: 95,111; 0.001 FDR: 62,446
1:36:31.682551 PROGRESS: 
1:36:31.682678 PROGRESS: Protein Summary:
1:36:31.799842 PROGRESS: Channel   0:	 0.050 FDR: 14,415; 0.010 FDR: 14,415; 0.001 FDR: 9,396
1:36:31.800428 PROGRESS: =========================================================================
1:36:32.028619 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
1:36:32.339051 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
1:36:32.868265 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:36:34.698988 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
1:36:34.699393 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant
1:36:34.699696 INFO: Initializing TimingManager
1:36:34.701885 INFO: Initializing RawFileManager
1:36:59.557789 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.
1:36:59.571553 INFO: Determining DIA cycle
1:36:59.589708 INFO: Found cycle with start 0.00 min and length 300.
1:37:00.173341 INFO: RT (min)            : 0.0 - 26.9
1:37:00.173554 INFO: RT duration (sec)   : 1611.2
1:37:00.173585 INFO: RT duration (min)   : 26.9
1:37:00.173633 INFO: Cycle len (scans)   : 300
1:37:00.173657 INFO: Cycle len (sec)     : 1.65
1:37:00.173692 INFO: Number of cycles    : 978
1:37:00.173717 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:37:00.173794 INFO: Creating DIA data object took: 25.471683502197266
1:37:02.112817 INFO: Creating DIA data NG object took: 1.938749074935913
1:37:05.297711 INFO: Initializing CalibrationManager
1:37:05.298462 INFO: Setting up calibration estimators ..
1:37:05.298558 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:37:05.298748 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1:37:05.298948 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:37:05.299006 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:37:05.299111 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1:37:05.299175 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:37:05.299230 INFO: Done setting up calibration estimators.
1:37:05.299919 INFO: Initializing OptimizationManager
1:37:05.300244 INFO: initial parameter: ms1_error = 30
1:37:05.300304 INFO: initial parameter: ms2_error = 30
1:37:05.300362 INFO: initial parameter: rt_error = 805.611083984375
1:37:05.300413 INFO: initial parameter: mobility_error = 0.1
1:37:05.300457 INFO: initial parameter: num_candidates = 1
1:37:05.300500 INFO: initial parameter: fwhm_rt = 5
1:37:05.300545 INFO: initial parameter: fwhm_mobility = 0.01
1:37:05.300588 INFO: initial parameter: score_cutoff = 0
1:37:05.300632 INFO: initial parameter: classifier_version = -1
1:37:05.300720 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:37:05.301389 INFO: FDRManager: loading saved state not requested, will be initialized.
1:37:05.301448 INFO: Initializing FDRManager
1:37:05.301539 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:37:09.263604 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:37:14.697564 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:37:14.698530 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
1:37:14.698743 PROGRESS: Starting initial search for precursors.
1:37:14.698881 INFO: Starting optimization step 0.
1:37:14.698964 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:37:14.699044 INFO: Using rust extraction backend
1:37:14.699144 PROGRESS: Extracting batch of 1970 precursors
1:37:14.712065 INFO: === Search parameters used ===
1:37:14.712854 INFO: rt_error       : 805.611083984375
1:37:14.712911 INFO: mobility_error : 0.1
1:37:14.712961 INFO: num_candidates : 1
1:37:14.713018 INFO: ms1_error      : 30
1:37:14.713060 INFO: ms2_error      : 30
1:37:14.713101 INFO: fwhm_rt        : 5
1:37:14.713143 INFO: quant_window   : 3
1:37:14.713183 INFO: ==============================================
1:37:14.833738 INFO: performing precursor FDR with 40 features
1:37:14.834046 INFO: Decoy channel: -1
1:37:14.834072 INFO: competitive: True
1:37:14.838409 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:14.843335 INFO: Estimating optimal hyperparameters - samples: 1,556, batch_size: 128, learning_rate: 1.77e-04
1:37:14.845482 INFO: Using random state 817984 for train-test-split
1:37:15.054903 INFO: Test AUC: 0.463
1:37:15.055176 INFO: Train AUC: 0.555
1:37:15.055208 INFO: AUC difference: 16.62%
1:37:15.055231 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:15.521581 INFO: Resetting torch num_threads to 100
1:37:15.526800 PROGRESS: === Extracted 1945 precursors and 9159 fragments ===
1:37:15.528380 INFO: === FDR correction performed with classifier version -1 ===
1:37:15.529796 PROGRESS: ============================= Precursor FDR =============================
1:37:15.530056 PROGRESS: Total precursors accumulated: 0
1:37:15.530159 PROGRESS: Target precursors: 0 (0.00%)
1:37:15.530214 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:15.530263 PROGRESS: 
1:37:15.530313 PROGRESS: Precursor Summary:
1:37:15.530632 PROGRESS: 
1:37:15.530740 PROGRESS: Protein Summary:
1:37:15.530858 PROGRESS: =========================================================================
1:37:15.532024 INFO: Target number of precursors not reached yet.
1:37:15.643044 INFO: Starting optimization step 1.
1:37:15.644098 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:37:15.644298 INFO: Using rust extraction backend
1:37:15.644408 PROGRESS: Extracting batch of 3942 precursors
1:37:15.666718 INFO: === Search parameters used ===
1:37:15.667962 INFO: rt_error       : 805.611083984375
1:37:15.668029 INFO: mobility_error : 0.1
1:37:15.668086 INFO: num_candidates : 1
1:37:15.668139 INFO: ms1_error      : 30
1:37:15.668192 INFO: ms2_error      : 30
1:37:15.668245 INFO: fwhm_rt        : 5
1:37:15.668289 INFO: quant_window   : 3
1:37:15.668336 INFO: ==============================================
1:37:15.840609 INFO: performing precursor FDR with 40 features
1:37:15.841008 INFO: Decoy channel: -1
1:37:15.841045 INFO: competitive: True
1:37:15.855834 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:15.864658 INFO: Estimating optimal hyperparameters - samples: 4,680, batch_size: 128, learning_rate: 1.77e-04
1:37:15.864971 INFO: Using random state 112444 for train-test-split
1:37:16.356582 INFO: Test AUC: 0.533
1:37:16.356941 INFO: Train AUC: 0.557
1:37:16.356978 INFO: AUC difference: 4.23%
1:37:16.845362 INFO: Resetting torch num_threads to 100
1:37:16.856400 PROGRESS: === Extracted 5851 precursors and 27624 fragments ===
1:37:16.857841 INFO: === FDR correction performed with classifier version -1 ===
1:37:16.858952 PROGRESS: ============================= Precursor FDR =============================
1:37:16.859115 PROGRESS: Total precursors accumulated: 6
1:37:16.859178 PROGRESS: Target precursors: 6 (100.00%)
1:37:16.859231 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:16.859280 PROGRESS: 
1:37:16.859328 PROGRESS: Precursor Summary:
1:37:16.860683 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:37:16.860789 PROGRESS: 
1:37:16.860866 PROGRESS: Protein Summary:
1:37:16.862356 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:37:16.862476 PROGRESS: =========================================================================
1:37:16.863439 INFO: Target number of precursors not reached yet.
1:37:16.977180 INFO: Starting optimization step 2.
1:37:16.977948 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:37:16.978112 INFO: Using rust extraction backend
1:37:16.978207 PROGRESS: Extracting batch of 7890 precursors
1:37:17.013372 INFO: === Search parameters used ===
1:37:17.014182 INFO: rt_error       : 805.611083984375
1:37:17.014263 INFO: mobility_error : 0.1
1:37:17.014316 INFO: num_candidates : 1
1:37:17.014362 INFO: ms1_error      : 30
1:37:17.014409 INFO: ms2_error      : 30
1:37:17.014452 INFO: fwhm_rt        : 5
1:37:17.014493 INFO: quant_window   : 3
1:37:17.014534 INFO: ==============================================
1:37:17.354939 INFO: performing precursor FDR with 40 features
1:37:17.355370 INFO: Decoy channel: -1
1:37:17.355406 INFO: competitive: True
1:37:17.381464 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:17.393968 INFO: Estimating optimal hyperparameters - samples: 10,932, batch_size: 128, learning_rate: 1.77e-04
1:37:17.394407 INFO: Using random state 96683 for train-test-split
1:37:19.058792 INFO: Test AUC: 0.526
1:37:19.059081 INFO: Train AUC: 0.579
1:37:19.059123 INFO: AUC difference: 9.14%
1:37:19.059150 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:19.570345 INFO: Resetting torch num_threads to 100
1:37:19.592176 PROGRESS: === Extracted 13666 precursors and 64644 fragments ===
1:37:19.594397 INFO: === FDR correction performed with classifier version -1 ===
1:37:19.597295 PROGRESS: ============================= Precursor FDR =============================
1:37:19.598000 PROGRESS: Total precursors accumulated: 25
1:37:19.598242 PROGRESS: Target precursors: 25 (100.00%)
1:37:19.598396 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:19.598483 PROGRESS: 
1:37:19.598537 PROGRESS: Precursor Summary:
1:37:19.602450 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:    25; 0.001 FDR:    25
1:37:19.603257 PROGRESS: 
1:37:19.603419 PROGRESS: Protein Summary:
1:37:19.607297 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:    25; 0.001 FDR:    25
1:37:19.608094 PROGRESS: =========================================================================
1:37:19.610984 INFO: Target number of precursors not reached yet.
1:37:19.805505 INFO: Starting optimization step 3.
1:37:19.807456 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:37:19.807614 INFO: Using rust extraction backend
1:37:19.807765 PROGRESS: Extracting batch of 15788 precursors
1:37:19.879530 INFO: === Search parameters used ===
1:37:19.880404 INFO: rt_error       : 805.611083984375
1:37:19.880467 INFO: mobility_error : 0.1
1:37:19.880516 INFO: num_candidates : 1
1:37:19.880567 INFO: ms1_error      : 30
1:37:19.880624 INFO: ms2_error      : 30
1:37:19.880668 INFO: fwhm_rt        : 5
1:37:19.880709 INFO: quant_window   : 3
1:37:19.880753 INFO: ==============================================
1:37:20.291159 INFO: performing precursor FDR with 40 features
1:37:20.291542 INFO: Decoy channel: -1
1:37:20.291575 INFO: competitive: True
1:37:20.344920 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:20.376258 INFO: Estimating optimal hyperparameters - samples: 23,438, batch_size: 128, learning_rate: 1.77e-04
1:37:20.376793 INFO: Using random state 397478 for train-test-split
1:37:24.115413 INFO: Test AUC: 0.561
1:37:24.115823 INFO: Train AUC: 0.594
1:37:24.115893 INFO: AUC difference: 5.68%
1:37:24.115920 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:24.702738 INFO: Resetting torch num_threads to 100
1:37:24.745646 PROGRESS: === Extracted 29298 precursors and 138904 fragments ===
1:37:24.747640 INFO: === FDR correction performed with classifier version -1 ===
1:37:24.750199 PROGRESS: ============================= Precursor FDR =============================
1:37:24.750653 PROGRESS: Total precursors accumulated: 83
1:37:24.750807 PROGRESS: Target precursors: 83 (100.00%)
1:37:24.750890 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:24.750944 PROGRESS: 
1:37:24.751006 PROGRESS: Precursor Summary:
1:37:24.754386 PROGRESS: Channel   0:	 0.050 FDR:    83; 0.010 FDR:    83; 0.001 FDR:    83
1:37:24.754794 PROGRESS: 
1:37:24.754917 PROGRESS: Protein Summary:
1:37:24.757825 PROGRESS: Channel   0:	 0.050 FDR:    82; 0.010 FDR:    82; 0.001 FDR:    82
1:37:24.758235 PROGRESS: =========================================================================
1:37:24.761920 INFO: Target number of precursors not reached yet.
1:37:25.030591 INFO: Starting optimization step 4.
1:37:25.031445 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:37:25.031674 INFO: Using rust extraction backend
1:37:25.031826 PROGRESS: Extracting batch of 31512 precursors
1:37:25.188467 INFO: === Search parameters used ===
1:37:25.189131 INFO: rt_error       : 805.611083984375
1:37:25.189201 INFO: mobility_error : 0.1
1:37:25.189302 INFO: num_candidates : 1
1:37:25.189356 INFO: ms1_error      : 30
1:37:25.189404 INFO: ms2_error      : 30
1:37:25.189449 INFO: fwhm_rt        : 5
1:37:25.189494 INFO: quant_window   : 3
1:37:25.189538 INFO: ==============================================
1:37:25.894521 INFO: performing precursor FDR with 40 features
1:37:25.894866 INFO: Decoy channel: -1
1:37:25.894900 INFO: competitive: True
1:37:26.000591 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:26.065206 INFO: Estimating optimal hyperparameters - samples: 48,396, batch_size: 198, learning_rate: 2.20e-04
1:37:26.065834 INFO: Using random state 675471 for train-test-split
1:37:31.838492 INFO: Test AUC: 0.577
1:37:31.838874 INFO: Train AUC: 0.604
1:37:31.838913 INFO: AUC difference: 4.49%
1:37:32.299326 INFO: Resetting torch num_threads to 100
1:37:32.359685 PROGRESS: === Extracted 60495 precursors and 286357 fragments ===
1:37:32.361597 INFO: === FDR correction performed with classifier version -1 ===
1:37:32.363857 PROGRESS: ============================= Precursor FDR =============================
1:37:32.364210 PROGRESS: Total precursors accumulated: 115
1:37:32.364331 PROGRESS: Target precursors: 114 (99.13%)
1:37:32.364399 PROGRESS: Decoy precursors: 1 (0.87%)
1:37:32.364458 PROGRESS: 
1:37:32.364512 PROGRESS: Precursor Summary:
1:37:32.367231 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:   114; 0.001 FDR:     0
1:37:32.367564 PROGRESS: 
1:37:32.367651 PROGRESS: Protein Summary:
1:37:32.370348 PROGRESS: Channel   0:	 0.050 FDR:   110; 0.010 FDR:   110; 0.001 FDR:     0
1:37:32.370661 PROGRESS: =========================================================================
1:37:32.375849 INFO: Target number of precursors not reached yet.
1:37:32.747936 INFO: Starting optimization step 5.
1:37:32.748874 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:37:32.749145 INFO: Using rust extraction backend
1:37:32.749284 PROGRESS: Extracting batch of 63110 precursors
1:37:33.222899 INFO: === Search parameters used ===
1:37:33.223844 INFO: rt_error       : 805.611083984375
1:37:33.223999 INFO: mobility_error : 0.1
1:37:33.224063 INFO: num_candidates : 1
1:37:33.224120 INFO: ms1_error      : 30
1:37:33.224170 INFO: ms2_error      : 30
1:37:33.224214 INFO: fwhm_rt        : 5
1:37:33.224259 INFO: quant_window   : 3
1:37:33.224314 INFO: ==============================================
1:37:34.341551 INFO: performing precursor FDR with 40 features
1:37:34.341820 INFO: Decoy channel: -1
1:37:34.341861 INFO: competitive: True
1:37:34.544944 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:34.725441 INFO: Estimating optimal hyperparameters - samples: 98,420, batch_size: 403, learning_rate: 3.14e-04
1:37:34.726629 INFO: Using random state 498506 for train-test-split
1:37:42.793475 INFO: Test AUC: 0.580
1:37:42.794000 INFO: Train AUC: 0.608
1:37:42.794051 INFO: AUC difference: 4.60%
1:37:43.249969 INFO: Resetting torch num_threads to 100
1:37:43.353455 PROGRESS: === Extracted 123025 precursors and 581480 fragments ===
1:37:43.355465 INFO: === FDR correction performed with classifier version -1 ===
1:37:43.358122 PROGRESS: ============================= Precursor FDR =============================
1:37:43.358668 PROGRESS: Total precursors accumulated: 431
1:37:43.358799 PROGRESS: Target precursors: 427 (99.07%)
1:37:43.358871 PROGRESS: Decoy precursors: 4 (0.93%)
1:37:43.358924 PROGRESS: 
1:37:43.358977 PROGRESS: Precursor Summary:
1:37:43.362640 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   427; 0.001 FDR:     1
1:37:43.362983 PROGRESS: 
1:37:43.363078 PROGRESS: Protein Summary:
1:37:43.366492 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   402; 0.001 FDR:     1
1:37:43.366880 PROGRESS: =========================================================================
1:37:43.375357 INFO: Target number of precursors not reached yet.
1:37:44.000637 INFO: Starting optimization step 6.
1:37:44.001483 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:37:44.001714 INFO: Using rust extraction backend
1:37:44.001832 PROGRESS: Extracting batch of 126235 precursors
1:37:44.599804 INFO: === Search parameters used ===
1:37:44.600666 INFO: rt_error       : 805.611083984375
1:37:44.600735 INFO: mobility_error : 0.1
1:37:44.600784 INFO: num_candidates : 1
1:37:44.600828 INFO: ms1_error      : 30
1:37:44.600869 INFO: ms2_error      : 30
1:37:44.600914 INFO: fwhm_rt        : 5
1:37:44.600955 INFO: quant_window   : 3
1:37:44.600996 INFO: ==============================================
1:37:46.733194 INFO: performing precursor FDR with 40 features
1:37:46.733521 INFO: Decoy channel: -1
1:37:46.733551 INFO: competitive: True
1:37:47.016425 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:47.318459 INFO: Estimating optimal hyperparameters - samples: 198,477, batch_size: 812, learning_rate: 4.45e-04
1:37:47.319406 INFO: Using random state 515164 for train-test-split
1:38:00.308566 INFO: Test AUC: 0.584
1:38:00.308973 INFO: Train AUC: 0.609
1:38:00.309018 INFO: AUC difference: 4.01%
1:38:00.824920 INFO: Resetting torch num_threads to 100
1:38:01.007792 PROGRESS: === Extracted 248097 precursors and 1173344 fragments ===
1:38:01.009605 INFO: === FDR correction performed with classifier version -1 ===
1:38:01.011551 PROGRESS: ============================= Precursor FDR =============================
1:38:01.011788 PROGRESS: Total precursors accumulated: 958
1:38:01.011950 PROGRESS: Target precursors: 949 (99.06%)
1:38:01.012024 PROGRESS: Decoy precursors: 9 (0.94%)
1:38:01.012084 PROGRESS: 
1:38:01.012145 PROGRESS: Precursor Summary:
1:38:01.014453 PROGRESS: Channel   0:	 0.050 FDR:   949; 0.010 FDR:   949; 0.001 FDR:   179
1:38:01.014611 PROGRESS: 
1:38:01.014680 PROGRESS: Protein Summary:
1:38:01.016713 PROGRESS: Channel   0:	 0.050 FDR:   843; 0.010 FDR:   843; 0.001 FDR:   171
1:38:01.016848 PROGRESS: =========================================================================
1:38:01.030008 INFO: Target number of precursors not reached yet.
1:38:02.142679 INFO: Starting optimization step 7.
1:38:02.143428 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:38:02.143662 INFO: Using rust extraction backend
1:38:02.143793 PROGRESS: Extracting batch of 252313 precursors
1:38:03.469376 INFO: === Search parameters used ===
1:38:03.470411 INFO: rt_error       : 805.611083984375
1:38:03.470542 INFO: mobility_error : 0.1
1:38:03.470613 INFO: num_candidates : 1
1:38:03.470667 INFO: ms1_error      : 30
1:38:03.470719 INFO: ms2_error      : 30
1:38:03.470766 INFO: fwhm_rt        : 5
1:38:03.470814 INFO: quant_window   : 3
1:38:03.470905 INFO: ==============================================
1:38:07.629253 INFO: performing precursor FDR with 40 features
1:38:07.629578 INFO: Decoy channel: -1
1:38:07.629609 INFO: competitive: True
1:38:08.325229 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:09.083323 INFO: Estimating optimal hyperparameters - samples: 398,420, batch_size: 1,631, learning_rate: 6.31e-04
1:38:09.086398 INFO: Using random state 772193 for train-test-split
1:38:31.853716 INFO: Test AUC: 0.592
1:38:31.854110 INFO: Train AUC: 0.606
1:38:31.854156 INFO: AUC difference: 2.35%
1:38:32.570169 INFO: Resetting torch num_threads to 100
1:38:32.908795 PROGRESS: === Extracted 498026 precursors and 2354323 fragments ===
1:38:32.910587 INFO: === FDR correction performed with classifier version -1 ===
1:38:32.913203 PROGRESS: ============================= Precursor FDR =============================
1:38:32.913489 PROGRESS: Total precursors accumulated: 2,122
1:38:32.913560 PROGRESS: Target precursors: 2,101 (99.01%)
1:38:32.913616 PROGRESS: Decoy precursors: 21 (0.99%)
1:38:32.913670 PROGRESS: 
1:38:32.913751 PROGRESS: Precursor Summary:
1:38:32.916426 PROGRESS: Channel   0:	 0.050 FDR: 2,101; 0.010 FDR: 2,101; 0.001 FDR: 1,578
1:38:32.916597 PROGRESS: 
1:38:32.916661 PROGRESS: Protein Summary:
1:38:32.919707 PROGRESS: Channel   0:	 0.050 FDR: 1,657; 0.010 FDR: 1,657; 0.001 FDR: 1,284
1:38:32.919901 PROGRESS: =========================================================================
1:38:32.943793 INFO: Target number of precursors reached.
1:38:33.290534 INFO: fragments_df: keeping 5000 of 2354323 [sum(precursor_idx_mask)=22257 sum(mass_error_mask)=2354323 stop_rank=5000
1:38:34.473622 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:35.007121 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:35.906536 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:38:35.908875 INFO: Using score_cutoff 12.01645525932312 (fac=0.99, q=1)
1:38:35.910371 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:38:35.910496 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:38:35.910556 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.01645525932312
1:38:35.910665 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:36.170444 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:36.688699 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:38:36.689656 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:38:36.690026 INFO: Starting optimization step 8.
1:38:36.690226 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:36.690468 INFO: Using rust extraction backend
1:38:36.690618 PROGRESS: Extracting batch of 250447 precursors
1:38:37.819922 INFO: === Search parameters used ===
1:38:37.820747 INFO: rt_error       : 805.611083984375
1:38:37.820845 INFO: mobility_error : 0.1
1:38:37.820905 INFO: num_candidates : 3
1:38:37.820952 INFO: ms1_error      : 30
1:38:37.820998 INFO: ms2_error      : 30
1:38:37.821046 INFO: fwhm_rt        : 3.0
1:38:37.821092 INFO: quant_window   : 3
1:38:37.821136 INFO: ==============================================
1:38:45.629749 INFO: performing precursor FDR with 40 features
1:38:45.630130 INFO: Decoy channel: -1
1:38:45.630167 INFO: competitive: True
1:38:46.472595 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:47.668370 INFO: Estimating optimal hyperparameters - samples: 595,998, batch_size: 2,441, learning_rate: 7.72e-04
1:38:47.677054 INFO: Using random state 857940 for train-test-split
1:39:17.311290 INFO: Test AUC: 0.595
1:39:17.311751 INFO: Train AUC: 0.606
1:39:17.311796 INFO: AUC difference: 1.87%
1:39:18.151571 INFO: Resetting torch num_threads to 100
1:39:18.224078 PROGRESS: === Extracted 744998 precursors and 3453648 fragments ===
1:39:18.225632 INFO: === FDR correction performed with classifier version 7 ===
1:39:18.227267 PROGRESS: ============================= Precursor FDR =============================
1:39:18.227429 PROGRESS: Total precursors accumulated: 1,129
1:39:18.227503 PROGRESS: Target precursors: 1,118 (99.03%)
1:39:18.227559 PROGRESS: Decoy precursors: 11 (0.97%)
1:39:18.227611 PROGRESS: 
1:39:18.227658 PROGRESS: Precursor Summary:
1:39:18.229688 PROGRESS: Channel   0:	 0.050 FDR: 1,118; 0.010 FDR: 1,118; 0.001 FDR:   771
1:39:18.229901 PROGRESS: 
1:39:18.229966 PROGRESS: Protein Summary:
1:39:18.232023 PROGRESS: Channel   0:	 0.050 FDR:   983; 0.010 FDR:   983; 0.001 FDR:   692
1:39:18.232167 PROGRESS: =========================================================================
1:39:18.282498 INFO: Target number of precursors reached.
1:39:18.694749 INFO: fragments_df: keeping 5000 of 3453648 [sum(precursor_idx_mask)=24729 sum(mass_error_mask)=3453648 stop_rank=5000
1:39:19.866095 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:20.276865 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:21.447281 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:21.448891 INFO: Using score_cutoff 12.406196070957183 (fac=0.99, q=1)
1:39:21.449627 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:21.449740 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:21.449872 INFO: Updating optimization_manager: score_cutoff        : 12.01645525932312 -> 12.406196070957183
1:39:21.449978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:21.709826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:22.330095 INFO: === checking if optimization conditions were reached ===
1:39:22.330897 PROGRESS: === Optimization of ms2_error has been performed 1 time(s); minimum number is 5 ===
1:39:22.337274 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.344998787232752
1:39:22.337804 PROGRESS: ❌ ms2_error      : optimization incomplete after 1 search(es). Will search with parameter 7.3450.
1:39:22.337970 INFO: ==============================================
1:39:22.338089 INFO: Starting optimization step 9.
1:39:22.338177 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:39:22.338316 INFO: Using rust extraction backend
1:39:22.338410 PROGRESS: Extracting batch of 250447 precursors
1:39:23.708117 INFO: === Search parameters used ===
1:39:23.708848 INFO: rt_error       : 805.611083984375
1:39:23.708969 INFO: mobility_error : 0.1
1:39:23.709028 INFO: num_candidates : 3
1:39:23.709079 INFO: ms1_error      : 30
1:39:23.709125 INFO: ms2_error      : 7.344998787232752
1:39:23.709176 INFO: fwhm_rt        : 3.0
1:39:23.709219 INFO: quant_window   : 3
1:39:23.709339 INFO: ==============================================
1:39:28.816119 INFO: performing precursor FDR with 40 features
1:39:28.816354 INFO: Decoy channel: -1
1:39:28.816381 INFO: competitive: True
1:39:29.220428 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:30.013050 INFO: Estimating optimal hyperparameters - samples: 600,915, batch_size: 2,461, learning_rate: 7.75e-04
1:39:30.016101 INFO: Using random state 857940 for train-test-split
1:39:57.263615 INFO: Test AUC: 0.600
1:39:57.264021 INFO: Train AUC: 0.610
1:39:57.264070 INFO: AUC difference: 1.64%
1:39:58.153594 INFO: Resetting torch num_threads to 100
1:39:58.230632 PROGRESS: === Extracted 751144 precursors and 4224023 fragments ===
1:39:58.232407 INFO: === FDR correction performed with classifier version 7 ===
1:39:58.234059 PROGRESS: ============================= Precursor FDR =============================
1:39:58.234210 PROGRESS: Total precursors accumulated: 1,416
1:39:58.234277 PROGRESS: Target precursors: 1,402 (99.01%)
1:39:58.234337 PROGRESS: Decoy precursors: 14 (0.99%)
1:39:58.234390 PROGRESS: 
1:39:58.234438 PROGRESS: Precursor Summary:
1:39:58.236402 PROGRESS: Channel   0:	 0.050 FDR: 1,402; 0.010 FDR: 1,402; 0.001 FDR: 1,116
1:39:58.236531 PROGRESS: 
1:39:58.236618 PROGRESS: Protein Summary:
1:39:58.238896 PROGRESS: Channel   0:	 0.050 FDR: 1,192; 0.010 FDR: 1,192; 0.001 FDR:   968
1:39:58.239029 PROGRESS: =========================================================================
1:39:58.291837 INFO: Target number of precursors reached.
1:39:58.793844 INFO: fragments_df: keeping 5000 of 4224023 [sum(precursor_idx_mask)=34089 sum(mass_error_mask)=4224023 stop_rank=5000
1:40:00.094335 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:40:00.637552 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:40:01.680996 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:40:01.682129 INFO: Using score_cutoff 12.370000517749787 (fac=0.99, q=1)
1:40:01.682667 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:40:01.682757 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:40:01.682820 INFO: Updating optimization_manager: score_cutoff        : 12.406196070957183 -> 12.370000517749787
1:40:01.682897 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:40:01.931027 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:40:02.550070 INFO: === checking if optimization conditions were reached ===
1:40:02.550997 PROGRESS: === Optimization of ms2_error has been performed 2 time(s); minimum number is 5 ===
1:40:02.558650 INFO: Updating optimization_manager: ms2_error           : 7.344998787232752 -> 7.436734766983846
1:40:02.559246 PROGRESS: ❌ ms2_error      : optimization incomplete after 2 search(es). Will search with parameter 7.4367.
1:40:02.559422 INFO: ==============================================
1:40:02.559577 INFO: Starting optimization step 10.
1:40:02.559683 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:40:02.559817 INFO: Using rust extraction backend
1:40:02.559932 PROGRESS: Extracting batch of 250447 precursors
1:40:03.684814 INFO: === Search parameters used ===
1:40:03.685552 INFO: rt_error       : 805.611083984375
1:40:03.685620 INFO: mobility_error : 0.1
1:40:03.685673 INFO: num_candidates : 3
1:40:03.685724 INFO: ms1_error      : 30
1:40:03.685768 INFO: ms2_error      : 7.436734766983846
1:40:03.685873 INFO: fwhm_rt        : 3.0
1:40:03.685928 INFO: quant_window   : 3
1:40:03.685969 INFO: ==============================================
1:40:07.699771 INFO: performing precursor FDR with 40 features
1:40:07.699964 INFO: Decoy channel: -1
1:40:07.699990 INFO: competitive: True
1:40:07.956265 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:08.381825 INFO: Estimating optimal hyperparameters - samples: 600,875, batch_size: 2,461, learning_rate: 7.75e-04
1:40:08.383967 INFO: Using random state 857940 for train-test-split
1:40:24.992771 INFO: Test AUC: 0.601
1:40:24.993117 INFO: Train AUC: 0.609
1:40:24.993158 INFO: AUC difference: 1.44%
1:40:25.749270 INFO: Resetting torch num_threads to 100
1:40:25.822187 PROGRESS: === Extracted 751094 precursors and 4216855 fragments ===
1:40:25.823422 INFO: === FDR correction performed with classifier version 7 ===
1:40:25.825277 PROGRESS: ============================= Precursor FDR =============================
1:40:25.825439 PROGRESS: Total precursors accumulated: 1,465
1:40:25.825511 PROGRESS: Target precursors: 1,451 (99.04%)
1:40:25.825567 PROGRESS: Decoy precursors: 14 (0.96%)
1:40:25.825619 PROGRESS: 
1:40:25.825669 PROGRESS: Precursor Summary:
1:40:25.827680 PROGRESS: Channel   0:	 0.050 FDR: 1,451; 0.010 FDR: 1,451; 0.001 FDR: 1,032
1:40:25.827827 PROGRESS: 
1:40:25.827891 PROGRESS: Protein Summary:
1:40:25.830227 PROGRESS: Channel   0:	 0.050 FDR: 1,223; 0.010 FDR: 1,223; 0.001 FDR:   898
1:40:25.830379 PROGRESS: =========================================================================
1:40:25.876800 INFO: Target number of precursors reached.
1:40:26.380202 INFO: fragments_df: keeping 5000 of 4216855 [sum(precursor_idx_mask)=35203 sum(mass_error_mask)=4216855 stop_rank=5000
1:40:27.601403 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:40:28.121586 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:40:29.300936 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:40:29.302226 INFO: Using score_cutoff 12.226773705482483 (fac=0.99, q=1)
1:40:29.302793 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:40:29.302900 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:40:29.302958 INFO: Updating optimization_manager: score_cutoff        : 12.370000517749787 -> 12.226773705482483
1:40:29.303032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:40:29.576513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:40:30.085830 INFO: === checking if optimization conditions were reached ===
1:40:30.086935 PROGRESS: === Optimization of ms2_error has been performed 3 time(s); minimum number is 5 ===
1:40:30.095859 INFO: Updating optimization_manager: ms2_error           : 7.436734766983846 -> 7.399321144056134
1:40:30.096813 PROGRESS: ❌ ms2_error      : optimization incomplete after 3 search(es). Will search with parameter 7.3993.
1:40:30.097203 INFO: ==============================================
1:40:30.097461 INFO: Starting optimization step 11.
1:40:30.097649 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:40:30.097810 INFO: Using rust extraction backend
1:40:30.097979 PROGRESS: Extracting batch of 250447 precursors
1:40:31.636793 INFO: === Search parameters used ===
1:40:31.637619 INFO: rt_error       : 805.611083984375
1:40:31.637687 INFO: mobility_error : 0.1
1:40:31.637742 INFO: num_candidates : 3
1:40:31.637845 INFO: ms1_error      : 30
1:40:31.637919 INFO: ms2_error      : 7.399321144056134
1:40:31.637962 INFO: fwhm_rt        : 3.0
1:40:31.638003 INFO: quant_window   : 3
1:40:31.638043 INFO: ==============================================
1:40:39.577124 INFO: performing precursor FDR with 40 features
1:40:39.577466 INFO: Decoy channel: -1
1:40:39.577497 INFO: competitive: True
1:40:40.293308 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:41.568974 INFO: Estimating optimal hyperparameters - samples: 600,891, batch_size: 2,461, learning_rate: 7.75e-04
1:40:41.574254 INFO: Using random state 857940 for train-test-split
1:41:17.576378 INFO: Test AUC: 0.600
1:41:17.576720 INFO: Train AUC: 0.610
1:41:17.576764 INFO: AUC difference: 1.65%
1:41:19.051786 INFO: Resetting torch num_threads to 100
1:41:19.219836 PROGRESS: === Extracted 751114 precursors and 4219585 fragments ===
1:41:19.222547 INFO: === FDR correction performed with classifier version 7 ===
1:41:19.227714 PROGRESS: ============================= Precursor FDR =============================
1:41:19.228534 PROGRESS: Total precursors accumulated: 1,489
1:41:19.228773 PROGRESS: Target precursors: 1,475 (99.06%)
1:41:19.228914 PROGRESS: Decoy precursors: 14 (0.94%)
1:41:19.228991 PROGRESS: 
1:41:19.229052 PROGRESS: Precursor Summary:
1:41:19.239887 PROGRESS: Channel   0:	 0.050 FDR: 1,475; 0.010 FDR: 1,475; 0.001 FDR:   952
1:41:19.240828 PROGRESS: 
1:41:19.241150 PROGRESS: Protein Summary:
1:41:19.254015 PROGRESS: Channel   0:	 0.050 FDR: 1,243; 0.010 FDR: 1,243; 0.001 FDR:   840
1:41:19.255043 PROGRESS: =========================================================================
1:41:19.344254 INFO: Target number of precursors reached.
1:41:20.785818 INFO: fragments_df: keeping 5000 of 4219585 [sum(precursor_idx_mask)=35702 sum(mass_error_mask)=4219585 stop_rank=5000
1:41:22.052397 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:41:22.404323 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:41:23.340283 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:41:23.341588 INFO: Using score_cutoff 11.78790241985321 (fac=0.99, q=1)
1:41:23.342072 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:41:23.342171 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:41:23.342235 INFO: Updating optimization_manager: score_cutoff        : 12.226773705482483 -> 11.78790241985321
1:41:23.342319 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:41:23.550857 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:41:24.150053 INFO: === checking if optimization conditions were reached ===
1:41:24.151473 PROGRESS: === Optimization of ms2_error has been performed 4 time(s); minimum number is 5 ===
1:41:24.159674 INFO: Updating optimization_manager: ms2_error           : 7.399321144056134 -> 7.435933660764805
1:41:24.160476 PROGRESS: ❌ ms2_error      : optimization incomplete after 4 search(es). Will search with parameter 7.4359.
1:41:24.160618 INFO: ==============================================
1:41:24.160728 INFO: Starting optimization step 12.
1:41:24.160813 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:41:24.160907 INFO: Using rust extraction backend
1:41:24.160980 PROGRESS: Extracting batch of 250447 precursors
1:41:25.184560 INFO: === Search parameters used ===
1:41:25.185441 INFO: rt_error       : 805.611083984375
1:41:25.185894 INFO: mobility_error : 0.1
1:41:25.185956 INFO: num_candidates : 3
1:41:25.186002 INFO: ms1_error      : 30
1:41:25.186063 INFO: ms2_error      : 7.435933660764805
1:41:25.186105 INFO: fwhm_rt        : 3.0
1:41:25.186146 INFO: quant_window   : 3
1:41:25.186186 INFO: ==============================================
1:41:32.941724 INFO: performing precursor FDR with 40 features
1:41:32.942088 INFO: Decoy channel: -1
1:41:32.942118 INFO: competitive: True
1:41:33.641706 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:34.808608 INFO: Estimating optimal hyperparameters - samples: 600,873, batch_size: 2,461, learning_rate: 7.75e-04
1:41:34.816227 INFO: Using random state 857940 for train-test-split
1:42:14.026295 INFO: Test AUC: 0.601
1:42:14.026605 INFO: Train AUC: 0.610
1:42:14.026642 INFO: AUC difference: 1.34%
1:42:14.816430 INFO: Resetting torch num_threads to 100
1:42:14.890444 PROGRESS: === Extracted 751092 precursors and 4216479 fragments ===
1:42:14.891676 INFO: === FDR correction performed with classifier version 7 ===
1:42:14.893611 PROGRESS: ============================= Precursor FDR =============================
1:42:14.893780 PROGRESS: Total precursors accumulated: 1,485
1:42:14.893879 PROGRESS: Target precursors: 1,471 (99.06%)
1:42:14.893944 PROGRESS: Decoy precursors: 14 (0.94%)
1:42:14.894004 PROGRESS: 
1:42:14.894057 PROGRESS: Precursor Summary:
1:42:14.896852 PROGRESS: Channel   0:	 0.050 FDR: 1,471; 0.010 FDR: 1,471; 0.001 FDR: 1,091
1:42:14.897119 PROGRESS: 
1:42:14.897200 PROGRESS: Protein Summary:
1:42:14.899737 PROGRESS: Channel   0:	 0.050 FDR: 1,253; 0.010 FDR: 1,253; 0.001 FDR:   950
1:42:14.899967 PROGRESS: =========================================================================
1:42:14.944734 INFO: Target number of precursors reached.
1:42:15.454826 INFO: fragments_df: keeping 5000 of 4216479 [sum(precursor_idx_mask)=35585 sum(mass_error_mask)=4216479 stop_rank=5000
1:42:16.596591 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:42:17.162274 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:42:18.184443 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:42:18.185919 INFO: Using score_cutoff 11.969174077033998 (fac=0.99, q=1)
1:42:18.186579 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:42:18.186664 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:42:18.186723 INFO: Updating optimization_manager: score_cutoff        : 11.78790241985321 -> 11.969174077033998
1:42:18.186791 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:42:18.402636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:42:19.142377 INFO: === checking if optimization conditions were reached ===
1:42:19.143620 PROGRESS: === Optimization of ms2_error has been performed 5 time(s); minimum number is 5 ===
1:42:19.147189 INFO: Updating optimization_manager: ms2_error           : 7.435933660764805 -> 7.399321144056134
1:42:19.147861 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
1:42:19.148164 INFO: Updating optimization_manager: score_cutoff        : 11.969174077033998 -> 11.78790241985321
1:42:19.148351 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:42:19.148491 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:42:19.148651 PROGRESS: ✅ ms2_error      : optimization just completed. Optimal parameter 7.3993 found after 5 searches.
1:42:19.148824 INFO: ==============================================
1:42:19.148968 PROGRESS: Optimization finished for ms2_error.
1:42:20.297195 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:42:20.510318 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:42:21.197827 INFO: Starting optimization step 0.
1:42:21.198856 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:42:21.199063 INFO: Using rust extraction backend
1:42:21.199162 PROGRESS: Extracting batch of 250447 precursors
1:42:22.266627 INFO: === Search parameters used ===
1:42:22.267732 INFO: rt_error       : 805.611083984375
1:42:22.267800 INFO: mobility_error : 0.1
1:42:22.267914 INFO: num_candidates : 3
1:42:22.267969 INFO: ms1_error      : 30
1:42:22.268018 INFO: ms2_error      : 7.399321144056134
1:42:22.268064 INFO: fwhm_rt        : 3.0
1:42:22.268110 INFO: quant_window   : 3
1:42:22.268152 INFO: ==============================================
1:42:30.464026 INFO: performing precursor FDR with 40 features
1:42:30.464586 INFO: Decoy channel: -1
1:42:30.464616 INFO: competitive: True
1:42:31.366086 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:32.528172 INFO: Estimating optimal hyperparameters - samples: 600,888, batch_size: 2,461, learning_rate: 7.75e-04
1:42:32.533393 INFO: Using random state 237603 for train-test-split
1:43:04.873783 INFO: Test AUC: 0.604
1:43:04.874207 INFO: Train AUC: 0.615
1:43:04.874313 INFO: AUC difference: 1.88%
1:43:05.623689 INFO: Resetting torch num_threads to 100
1:43:05.700117 PROGRESS: === Extracted 751110 precursors and 4219892 fragments ===
1:43:05.701617 INFO: === FDR correction performed with classifier version 11 ===
1:43:05.704546 PROGRESS: ============================= Precursor FDR =============================
1:43:05.704964 PROGRESS: Total precursors accumulated: 1,519
1:43:05.705064 PROGRESS: Target precursors: 1,504 (99.01%)
1:43:05.705172 PROGRESS: Decoy precursors: 15 (0.99%)
1:43:05.705226 PROGRESS: 
1:43:05.705274 PROGRESS: Precursor Summary:
1:43:05.709924 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR: 1,275
1:43:05.710313 PROGRESS: 
1:43:05.710389 PROGRESS: Protein Summary:
1:43:05.713514 PROGRESS: Channel   0:	 0.050 FDR: 1,271; 0.010 FDR: 1,271; 0.001 FDR: 1,092
1:43:05.713825 PROGRESS: =========================================================================
1:43:05.757295 INFO: Target number of precursors reached.
1:43:06.273854 INFO: fragments_df: keeping 5000 of 4219892 [sum(precursor_idx_mask)=36250 sum(mass_error_mask)=4219892 stop_rank=5000
1:43:07.457886 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:43:07.837385 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:43:08.733155 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:43:08.734398 INFO: Using score_cutoff 11.506816085243225 (fac=0.99, q=1)
1:43:08.734997 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:43:08.735103 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:43:08.735165 INFO: Updating optimization_manager: score_cutoff        : 11.78790241985321 -> 11.506816085243225
1:43:08.735227 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:43:08.950334 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:43:09.706501 INFO: === checking if optimization conditions were reached ===
1:43:09.707454 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:43:09.713142 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 747.5491721164951
1:43:09.713634 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 747.5492.
1:43:09.713811 INFO: ==============================================
1:43:09.713967 INFO: Starting optimization step 1.
1:43:09.714067 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:43:09.714173 INFO: Using rust extraction backend
1:43:09.714256 PROGRESS: Extracting batch of 250447 precursors
1:43:10.689900 INFO: === Search parameters used ===
1:43:10.690789 INFO: rt_error       : 747.5491721164951
1:43:10.690916 INFO: mobility_error : 0.1
1:43:10.690974 INFO: num_candidates : 3
1:43:10.691025 INFO: ms1_error      : 30
1:43:10.691071 INFO: ms2_error      : 7.399321144056134
1:43:10.691120 INFO: fwhm_rt        : 3.0
1:43:10.691167 INFO: quant_window   : 3
1:43:10.691211 INFO: ==============================================
1:43:16.652893 INFO: performing precursor FDR with 40 features
1:43:16.653250 INFO: Decoy channel: -1
1:43:16.653280 INFO: competitive: True
1:43:17.092310 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:17.875949 INFO: Estimating optimal hyperparameters - samples: 600,883, batch_size: 2,461, learning_rate: 7.75e-04
1:43:17.878750 INFO: Using random state 237603 for train-test-split
1:43:32.013952 INFO: Test AUC: 0.603
1:43:32.014089 INFO: Train AUC: 0.616
1:43:32.014129 INFO: AUC difference: 2.09%
1:43:32.475734 INFO: Resetting torch num_threads to 100
1:43:32.504130 PROGRESS: === Extracted 751104 precursors and 4219013 fragments ===
1:43:32.504605 INFO: === FDR correction performed with classifier version 11 ===
1:43:32.505273 PROGRESS: ============================= Precursor FDR =============================
1:43:32.505378 PROGRESS: Total precursors accumulated: 1,468
1:43:32.505439 PROGRESS: Target precursors: 1,454 (99.05%)
1:43:32.505496 PROGRESS: Decoy precursors: 14 (0.95%)
1:43:32.505543 PROGRESS: 
1:43:32.505588 PROGRESS: Precursor Summary:
1:43:32.506953 PROGRESS: Channel   0:	 0.050 FDR: 1,454; 0.010 FDR: 1,454; 0.001 FDR: 1,221
1:43:32.507049 PROGRESS: 
1:43:32.507105 PROGRESS: Protein Summary:
1:43:32.508845 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR: 1,046
1:43:32.508939 PROGRESS: =========================================================================
1:43:32.522714 INFO: Target number of precursors reached.
1:43:32.980906 INFO: fragments_df: keeping 5000 of 4219013 [sum(precursor_idx_mask)=35162 sum(mass_error_mask)=4219013 stop_rank=5000
1:43:33.391809 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:43:33.616407 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:43:34.328103 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:43:34.328537 INFO: Using score_cutoff 12.286109258651734 (fac=0.99, q=1)
1:43:34.328840 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:43:34.328918 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:43:34.328973 INFO: Updating optimization_manager: score_cutoff        : 11.506816085243225 -> 12.286109258651734
1:43:34.329027 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:43:34.481802 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:43:34.824195 INFO: === checking if optimization conditions were reached ===
1:43:34.824505 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:43:34.827834 INFO: Updating optimization_manager: rt_error            : 747.5491721164951 -> 312.9493436684986
1:43:34.827993 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 312.9493.
1:43:34.828073 INFO: ==============================================
1:43:34.828158 INFO: Starting optimization step 2.
1:43:34.828231 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:43:34.828306 INFO: Using rust extraction backend
1:43:34.828379 PROGRESS: Extracting batch of 250447 precursors
1:43:35.251041 INFO: === Search parameters used ===
1:43:35.251323 INFO: rt_error       : 312.9493436684986
1:43:35.251381 INFO: mobility_error : 0.1
1:43:35.251431 INFO: num_candidates : 3
1:43:35.251476 INFO: ms1_error      : 30
1:43:35.251522 INFO: ms2_error      : 7.399321144056134
1:43:35.251570 INFO: fwhm_rt        : 3.0
1:43:35.251614 INFO: quant_window   : 3
1:43:35.251656 INFO: ==============================================
1:43:37.565536 INFO: performing precursor FDR with 40 features
1:43:37.565665 INFO: Decoy channel: -1
1:43:37.565691 INFO: competitive: True
1:43:37.755037 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:38.056985 INFO: Estimating optimal hyperparameters - samples: 599,956, batch_size: 2,457, learning_rate: 7.75e-04
1:43:38.058161 INFO: Using random state 237603 for train-test-split
1:43:50.845280 INFO: Test AUC: 0.603
1:43:50.845456 INFO: Train AUC: 0.610
1:43:50.845488 INFO: AUC difference: 1.19%
1:43:51.306716 INFO: Resetting torch num_threads to 100
1:43:51.339188 PROGRESS: === Extracted 749945 precursors and 3891788 fragments ===
1:43:51.339705 INFO: === FDR correction performed with classifier version 11 ===
1:43:51.340358 PROGRESS: ============================= Precursor FDR =============================
1:43:51.340451 PROGRESS: Total precursors accumulated: 1,469
1:43:51.340510 PROGRESS: Target precursors: 1,455 (99.05%)
1:43:51.340562 PROGRESS: Decoy precursors: 14 (0.95%)
1:43:51.340608 PROGRESS: 
1:43:51.340652 PROGRESS: Precursor Summary:
1:43:51.342008 PROGRESS: Channel   0:	 0.050 FDR: 1,455; 0.010 FDR: 1,455; 0.001 FDR: 1,022
1:43:51.342097 PROGRESS: 
1:43:51.342152 PROGRESS: Protein Summary:
1:43:51.343865 PROGRESS: Channel   0:	 0.050 FDR: 1,229; 0.010 FDR: 1,229; 0.001 FDR:   896
1:43:51.343953 PROGRESS: =========================================================================
1:43:51.357674 INFO: Target number of precursors reached.
1:43:51.788111 INFO: fragments_df: keeping 5000 of 3891788 [sum(precursor_idx_mask)=35015 sum(mass_error_mask)=3891788 stop_rank=5000
1:43:52.192443 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:43:52.413976 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:43:53.125284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:43:53.125713 INFO: Using score_cutoff 11.9469493806839 (fac=0.99, q=1)
1:43:53.126032 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:43:53.126115 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:43:53.126179 INFO: Updating optimization_manager: score_cutoff        : 12.286109258651734 -> 11.9469493806839
1:43:53.126235 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:43:53.277050 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:43:53.617179 INFO: === checking if optimization conditions were reached ===
1:43:53.617482 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:43:53.620849 INFO: Updating optimization_manager: rt_error            : 312.9493436684986 -> 315.64238086999325
1:43:53.621006 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 315.6424.
1:43:53.621086 INFO: ==============================================
1:43:53.621173 INFO: Starting optimization step 3.
1:43:53.621246 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:43:53.621322 INFO: Using rust extraction backend
1:43:53.621395 PROGRESS: Extracting batch of 250447 precursors
1:43:54.043687 INFO: === Search parameters used ===
1:43:54.043960 INFO: rt_error       : 315.64238086999325
1:43:54.044018 INFO: mobility_error : 0.1
1:43:54.044067 INFO: num_candidates : 3
1:43:54.044112 INFO: ms1_error      : 30
1:43:54.044154 INFO: ms2_error      : 7.399321144056134
1:43:54.044196 INFO: fwhm_rt        : 3.0
1:43:54.044238 INFO: quant_window   : 3
1:43:54.044279 INFO: ==============================================
1:43:56.351398 INFO: performing precursor FDR with 40 features
1:43:56.351532 INFO: Decoy channel: -1
1:43:56.351578 INFO: competitive: True
1:43:56.540028 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:56.846598 INFO: Estimating optimal hyperparameters - samples: 600,023, batch_size: 2,457, learning_rate: 7.75e-04
1:43:56.847775 INFO: Using random state 237603 for train-test-split
1:44:09.950721 INFO: Test AUC: 0.601
1:44:09.950864 INFO: Train AUC: 0.611
1:44:09.950898 INFO: AUC difference: 1.59%
1:44:10.403552 INFO: Resetting torch num_threads to 100
1:44:10.428385 PROGRESS: === Extracted 750029 precursors and 3897923 fragments ===
1:44:10.428882 INFO: === FDR correction performed with classifier version 11 ===
1:44:10.429529 PROGRESS: ============================= Precursor FDR =============================
1:44:10.429616 PROGRESS: Total precursors accumulated: 1,652
1:44:10.429677 PROGRESS: Target precursors: 1,636 (99.03%)
1:44:10.429729 PROGRESS: Decoy precursors: 16 (0.97%)
1:44:10.429777 PROGRESS: 
1:44:10.429823 PROGRESS: Precursor Summary:
1:44:10.431244 PROGRESS: Channel   0:	 0.050 FDR: 1,636; 0.010 FDR: 1,636; 0.001 FDR: 1,342
1:44:10.431348 PROGRESS: 
1:44:10.431405 PROGRESS: Protein Summary:
1:44:10.433233 PROGRESS: Channel   0:	 0.050 FDR: 1,377; 0.010 FDR: 1,377; 0.001 FDR: 1,140
1:44:10.433340 PROGRESS: =========================================================================
1:44:10.446517 INFO: Target number of precursors reached.
1:44:10.864866 INFO: fragments_df: keeping 5000 of 3897923 [sum(precursor_idx_mask)=38942 sum(mass_error_mask)=3897923 stop_rank=5000
1:44:11.275035 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:44:11.517011 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:44:12.231817 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:44:12.232255 INFO: Using score_cutoff 11.358025942325591 (fac=0.99, q=1)
1:44:12.232559 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:44:12.232642 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:44:12.232699 INFO: Updating optimization_manager: score_cutoff        : 11.9469493806839 -> 11.358025942325591
1:44:12.232752 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:44:12.381834 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:44:12.721167 INFO: === checking if optimization conditions were reached ===
1:44:12.721468 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:44:12.724874 INFO: Updating optimization_manager: rt_error            : 315.64238086999325 -> 268.1942786134179
1:44:12.725032 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 268.1943.
1:44:12.725114 INFO: ==============================================
1:44:12.725200 INFO: Starting optimization step 4.
1:44:12.725273 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:44:12.725350 INFO: Using rust extraction backend
1:44:12.725421 PROGRESS: Extracting batch of 250447 precursors
1:44:13.147769 INFO: === Search parameters used ===
1:44:13.148008 INFO: rt_error       : 268.1942786134179
1:44:13.148066 INFO: mobility_error : 0.1
1:44:13.148117 INFO: num_candidates : 3
1:44:13.148196 INFO: ms1_error      : 30
1:44:13.148243 INFO: ms2_error      : 7.399321144056134
1:44:13.148288 INFO: fwhm_rt        : 3.0
1:44:13.148336 INFO: quant_window   : 3
1:44:13.148378 INFO: ==============================================
1:44:15.448945 INFO: performing precursor FDR with 40 features
1:44:15.449064 INFO: Decoy channel: -1
1:44:15.449089 INFO: competitive: True
1:44:15.642286 INFO: Setting torch num_threads to 2 for FDR classification task
1:44:15.950908 INFO: Estimating optimal hyperparameters - samples: 599,531, batch_size: 2,455, learning_rate: 7.74e-04
1:44:15.952020 INFO: Using random state 237603 for train-test-split
1:44:29.566373 INFO: Test AUC: 0.598
1:44:29.566543 INFO: Train AUC: 0.610
1:44:29.566580 INFO: AUC difference: 1.82%
1:44:30.039543 INFO: Resetting torch num_threads to 100
1:44:30.064961 PROGRESS: === Extracted 749414 precursors and 3768206 fragments ===
1:44:30.065455 INFO: === FDR correction performed with classifier version 11 ===
1:44:30.066166 PROGRESS: ============================= Precursor FDR =============================
1:44:30.066258 PROGRESS: Total precursors accumulated: 1,808
1:44:30.066319 PROGRESS: Target precursors: 1,791 (99.06%)
1:44:30.066372 PROGRESS: Decoy precursors: 17 (0.94%)
1:44:30.066447 PROGRESS: 
1:44:30.066496 PROGRESS: Precursor Summary:
1:44:30.067898 PROGRESS: Channel   0:	 0.050 FDR: 1,791; 0.010 FDR: 1,791; 0.001 FDR: 1,285
1:44:30.067990 PROGRESS: 
1:44:30.068047 PROGRESS: Protein Summary:
1:44:30.069921 PROGRESS: Channel   0:	 0.050 FDR: 1,496; 0.010 FDR: 1,496; 0.001 FDR: 1,097
1:44:30.070024 PROGRESS: =========================================================================
1:44:30.083700 INFO: Target number of precursors reached.
1:44:30.496626 INFO: fragments_df: keeping 5000 of 3768206 [sum(precursor_idx_mask)=41932 sum(mass_error_mask)=3768206 stop_rank=5000
1:44:30.906417 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:44:31.164789 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:44:31.881414 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:44:31.881902 INFO: Using score_cutoff 10.281095749855043 (fac=0.99, q=1)
1:44:31.882216 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:44:31.882292 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:44:31.882348 INFO: Updating optimization_manager: score_cutoff        : 11.358025942325591 -> 10.281095749855043
1:44:31.882403 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:44:32.037302 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:44:32.380390 INFO: === checking if optimization conditions were reached ===
1:44:32.380699 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:44:32.384272 INFO: Updating optimization_manager: rt_error            : 268.1942786134179 -> 294.55140711722345
1:44:32.384424 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 294.5514.
1:44:32.384501 INFO: ==============================================
1:44:32.384590 INFO: Starting optimization step 5.
1:44:32.384661 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:44:32.384763 INFO: Using rust extraction backend
1:44:32.384834 PROGRESS: Extracting batch of 250447 precursors
1:44:32.808417 INFO: === Search parameters used ===
1:44:32.808684 INFO: rt_error       : 294.55140711722345
1:44:32.808740 INFO: mobility_error : 0.1
1:44:32.808794 INFO: num_candidates : 3
1:44:32.808854 INFO: ms1_error      : 30
1:44:32.808897 INFO: ms2_error      : 7.399321144056134
1:44:32.808936 INFO: fwhm_rt        : 3.0
1:44:32.808975 INFO: quant_window   : 3
1:44:32.809012 INFO: ==============================================
1:44:35.078753 INFO: performing precursor FDR with 40 features
1:44:35.078878 INFO: Decoy channel: -1
1:44:35.078905 INFO: competitive: True
1:44:35.270068 INFO: Setting torch num_threads to 2 for FDR classification task
1:44:35.576716 INFO: Estimating optimal hyperparameters - samples: 599,735, batch_size: 2,456, learning_rate: 7.74e-04
1:44:35.577906 INFO: Using random state 237603 for train-test-split
1:44:48.501019 INFO: Test AUC: 0.598
1:44:48.501162 INFO: Train AUC: 0.609
1:44:48.501195 INFO: AUC difference: 1.88%
1:44:50.369334 INFO: Resetting torch num_threads to 100
1:44:50.396878 PROGRESS: === Extracted 749669 precursors and 3841373 fragments ===
1:44:50.397344 INFO: === FDR correction performed with classifier version 11 ===
1:44:50.398023 PROGRESS: ============================= Precursor FDR =============================
1:44:50.398114 PROGRESS: Total precursors accumulated: 1,598
1:44:50.398175 PROGRESS: Target precursors: 1,583 (99.06%)
1:44:50.398227 PROGRESS: Decoy precursors: 15 (0.94%)
1:44:50.398273 PROGRESS: 
1:44:50.398319 PROGRESS: Precursor Summary:
1:44:50.399695 PROGRESS: Channel   0:	 0.050 FDR: 1,583; 0.010 FDR: 1,583; 0.001 FDR: 1,096
1:44:50.399789 PROGRESS: 
1:44:50.399846 PROGRESS: Protein Summary:
1:44:50.401634 PROGRESS: Channel   0:	 0.050 FDR: 1,328; 0.010 FDR: 1,328; 0.001 FDR:   949
1:44:50.401729 PROGRESS: =========================================================================
1:44:50.415058 INFO: Target number of precursors reached.
1:44:50.835269 INFO: fragments_df: keeping 5000 of 3841373 [sum(precursor_idx_mask)=37736 sum(mass_error_mask)=3841373 stop_rank=5000
1:44:51.266151 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:44:51.502845 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:44:52.216096 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:44:52.216542 INFO: Using score_cutoff 11.544053248786927 (fac=0.99, q=1)
1:44:52.216842 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:44:52.216919 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:44:52.216974 INFO: Updating optimization_manager: score_cutoff        : 10.281095749855043 -> 11.544053248786927
1:44:52.217028 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:44:52.366056 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:44:52.719320 INFO: === checking if optimization conditions were reached ===
1:44:52.719634 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:44:52.723008 INFO: Updating optimization_manager: rt_error            : 294.55140711722345 -> 300.0081344471522
1:44:52.723155 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 300.0081.
1:44:52.723230 INFO: ==============================================
1:44:52.723311 INFO: Starting optimization step 6.
1:44:52.723381 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:44:52.723451 INFO: Using rust extraction backend
1:44:52.723516 PROGRESS: Extracting batch of 250447 precursors
1:44:53.144920 INFO: === Search parameters used ===
1:44:53.145191 INFO: rt_error       : 300.0081344471522
1:44:53.145264 INFO: mobility_error : 0.1
1:44:53.145314 INFO: num_candidates : 3
1:44:53.145357 INFO: ms1_error      : 30
1:44:53.145399 INFO: ms2_error      : 7.399321144056134
1:44:53.145439 INFO: fwhm_rt        : 3.0
1:44:53.145478 INFO: quant_window   : 3
1:44:53.145516 INFO: ==============================================
1:44:55.426781 INFO: performing precursor FDR with 40 features
1:44:55.426910 INFO: Decoy channel: -1
1:44:55.426938 INFO: competitive: True
1:44:55.616892 INFO: Setting torch num_threads to 2 for FDR classification task
1:44:55.925523 INFO: Estimating optimal hyperparameters - samples: 599,840, batch_size: 2,456, learning_rate: 7.74e-04
1:44:55.926654 INFO: Using random state 237603 for train-test-split
1:45:08.284239 INFO: Test AUC: 0.600
1:45:08.284404 INFO: Train AUC: 0.611
1:45:08.284436 INFO: AUC difference: 1.66%
1:45:08.741346 INFO: Resetting torch num_threads to 100
1:45:08.766452 PROGRESS: === Extracted 749801 precursors and 3850397 fragments ===
1:45:08.766954 INFO: === FDR correction performed with classifier version 11 ===
1:45:08.767660 PROGRESS: ============================= Precursor FDR =============================
1:45:08.767749 PROGRESS: Total precursors accumulated: 1,740
1:45:08.767809 PROGRESS: Target precursors: 1,723 (99.02%)
1:45:08.767862 PROGRESS: Decoy precursors: 17 (0.98%)
1:45:08.767909 PROGRESS: 
1:45:08.767956 PROGRESS: Precursor Summary:
1:45:08.769407 PROGRESS: Channel   0:	 0.050 FDR: 1,723; 0.010 FDR: 1,723; 0.001 FDR: 1,314
1:45:08.769499 PROGRESS: 
1:45:08.769556 PROGRESS: Protein Summary:
1:45:08.771458 PROGRESS: Channel   0:	 0.050 FDR: 1,439; 0.010 FDR: 1,439; 0.001 FDR: 1,116
1:45:08.771556 PROGRESS: =========================================================================
1:45:08.785041 INFO: Target number of precursors reached.
1:45:09.209161 INFO: fragments_df: keeping 5000 of 3850397 [sum(precursor_idx_mask)=40845 sum(mass_error_mask)=3850397 stop_rank=5000
1:45:09.617658 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:45:09.834379 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:45:10.483390 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:45:10.483836 INFO: Using score_cutoff 10.38766420211792 (fac=0.99, q=1)
1:45:10.484148 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:45:10.484227 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:45:10.484282 INFO: Updating optimization_manager: score_cutoff        : 11.544053248786927 -> 10.38766420211792
1:45:10.484334 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:45:10.633466 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:45:10.992053 INFO: === checking if optimization conditions were reached ===
1:45:10.992381 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:45:10.993477 INFO: Updating optimization_manager: rt_error            : 300.0081344471522 -> 268.1942786134179
1:45:10.993629 INFO: Updating optimization_manager: classifier_version  : 11 -> 17
1:45:10.993755 INFO: Updating optimization_manager: score_cutoff        : 10.38766420211792 -> 10.281095749855043
1:45:10.993922 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:45:10.994035 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:45:10.994143 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 268.1943 found after 7 searches.
1:45:10.994217 INFO: ==============================================
1:45:10.994316 PROGRESS: Optimization finished for rt_error.
1:45:11.390515 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:45:11.539819 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:45:11.890340 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:45:11.890669 PROGRESS: ==============================================
1:45:11.890782 PROGRESS: ms2_error      : 7.3993
1:45:11.890855 PROGRESS: rt_error       : 268.1943
1:45:11.890915 PROGRESS: ==============================================
1:45:11.892012 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:45:19.463573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:45:35.102024 INFO: Using rust extraction backend
1:45:35.102322 PROGRESS: Extracting batch of 11997144 precursors
1:45:51.096507 INFO: === Search parameters used ===
1:45:51.096784 INFO: rt_error       : 268.1942786134179
1:45:51.096851 INFO: mobility_error : 0.1
1:45:51.096903 INFO: num_candidates : 3
1:45:51.096950 INFO: ms1_error      : 30
1:45:51.096994 INFO: ms2_error      : 7.399321144056134
1:45:51.097039 INFO: fwhm_rt        : 3.0
1:45:51.097081 INFO: quant_window   : 3
1:45:51.097123 INFO: ==============================================
1:46:10.535077 INFO: Removed 14730021 precursors with score below cutoff 10.281095749855043
1:46:29.503544 INFO: performing precursor FDR with 40 features
1:46:29.503675 INFO: Decoy channel: -1
1:46:29.503702 INFO: competitive: True
1:46:31.733982 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:40.324179 INFO: Estimating optimal hyperparameters - samples: 16,969,798, batch_size: 4,096, learning_rate: 1.00e-03
1:46:40.376928 INFO: Using random state 841514 for train-test-split
1:52:12.325579 INFO: Test AUC: 0.619
1:52:12.325732 INFO: Train AUC: 0.620
1:52:12.325766 INFO: AUC difference: 0.18%
1:52:17.463754 INFO: Resetting torch num_threads to 100
1:52:19.180666 PROGRESS: ============================= Precursor FDR =============================
1:52:19.180936 PROGRESS: Total precursors accumulated: 96,258
1:52:19.181005 PROGRESS: Target precursors: 95,305 (99.01%)
1:52:19.181060 PROGRESS: Decoy precursors: 953 (0.99%)
1:52:19.181109 PROGRESS: 
1:52:19.181157 PROGRESS: Precursor Summary:
1:52:19.205370 PROGRESS: Channel   0:	 0.050 FDR: 95,305; 0.010 FDR: 95,305; 0.001 FDR: 65,865
1:52:19.205624 PROGRESS: 
1:52:19.205685 PROGRESS: Protein Summary:
1:52:19.242128 PROGRESS: Channel   0:	 0.050 FDR: 13,706; 0.010 FDR: 13,706; 0.001 FDR: 9,884
1:52:19.242376 PROGRESS: =========================================================================
1:52:19.365733 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
1:52:19.543472 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
1:52:19.839531 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:52:47.385779 PROGRESS: Processing search outputs
1:52:47.385967 PROGRESS: === Performing protein grouping and FDR ===
1:52:47.386005 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:52:47.440785 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:52:47.495816 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:52:47.559042 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:52:47.619770 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:52:47.684091 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:52:47.784729 INFO: Performing protein inference
1:52:48.611617 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1:53:40.087185 INFO: Performing protein FDR
1:53:47.315782 INFO: Normalizing q-values using 19,587 targets and 3,942 decoys
1:53:47.320684 INFO: Test AUC: 0.859
1:53:47.320743 INFO: Train AUC: 0.854
1:53:47.320782 INFO: AUC difference: 0.58%
1:53:47.969516 INFO: ================ Protein FDR =================
1:53:47.969666 INFO: Unique protein groups in output
1:53:47.969696 INFO:   1% protein FDR: 10,119
1:53:47.969718 INFO: 
1:53:47.969741 INFO: Unique precursor in output
1:53:47.969767 INFO:   1% protein FDR: 131,664
1:53:47.969788 INFO: ================================================
1:53:48.030089 PROGRESS: Building search statistics
1:53:48.122395 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
1:53:48.122593 INFO: Initializing OptimizationManager
1:53:48.122856 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
1:53:48.122932 INFO: Initializing CalibrationManager
1:53:48.123174 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
1:53:48.123249 INFO: Initializing RawFileManager
1:53:48.155365 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
1:53:48.155548 INFO: Initializing OptimizationManager
1:53:48.155758 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
1:53:48.155848 INFO: Initializing CalibrationManager
1:53:48.156056 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
1:53:48.156128 INFO: Initializing RawFileManager
1:53:48.188369 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
1:53:48.188563 INFO: Initializing OptimizationManager
1:53:48.188775 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
1:53:48.188847 INFO: Initializing CalibrationManager
1:53:48.189048 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
1:53:48.189117 INFO: Initializing RawFileManager
1:53:48.221563 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
1:53:48.221741 INFO: Initializing OptimizationManager
1:53:48.222023 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
1:53:48.222102 INFO: Initializing CalibrationManager
1:53:48.222300 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
1:53:48.222369 INFO: Initializing RawFileManager
1:53:48.255468 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
1:53:48.255656 INFO: Initializing OptimizationManager
1:53:48.255859 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
1:53:48.255937 INFO: Initializing CalibrationManager
1:53:48.256132 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
1:53:48.256197 INFO: Initializing RawFileManager
1:53:48.289356 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
1:53:48.289537 INFO: Initializing OptimizationManager
1:53:48.289746 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
1:53:48.289814 INFO: Initializing CalibrationManager
1:53:48.290029 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
1:53:48.290099 INFO: Initializing RawFileManager
1:53:48.293258 INFO: Writing stat output to disk
1:53:48.293327 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/stat.tsv to disk
1:53:48.302941 PROGRESS: Building internal statistics
1:53:48.303245 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
1:53:48.303288 INFO: Initializing TimingManager
1:53:48.303636 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
1:53:48.303676 INFO: Initializing TimingManager
1:53:48.303893 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
1:53:48.303929 INFO: Initializing TimingManager
1:53:48.304128 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
1:53:48.304161 INFO: Initializing TimingManager
1:53:48.304351 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
1:53:48.304395 INFO: Initializing TimingManager
1:53:48.304583 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
1:53:48.304616 INFO: Initializing TimingManager
1:53:48.305037 INFO: Writing internal output to disk
1:53:48.305079 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/internal.tsv to disk
1:53:48.369720 INFO: Performing label free quantification
1:53:48.369875 INFO: Accumulating fragment data
1:53:48.369942 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:53:48.587927 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:53:49.830650 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:53:51.145816 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:53:52.608162 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:53:54.141048 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:53:56.030163 INFO: Performing label free quantification on the precursor level
1:53:56.030324 INFO: Filtering fragments by quality
1:53:56.410796 INFO: Performing label-free quantification with directlfq normalization
1:53:56.987138 INFO: 131664 lfq-groups total
1:55:07.574692 INFO: using 100 processes
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1:55:08.648310 INFO: lfq-object 100
1:55:08.717792 INFO: lfq-object 400
1:55:08.756111 INFO: lfq-object 200
1:55:08.758483 INFO: lfq-object 3300
1:55:08.784493 INFO: lfq-object 700
1:55:08.836320 INFO: lfq-object 500
1:55:08.842759 INFO: lfq-object 1000
1:55:08.868875 INFO: lfq-object 300
1:55:08.894911 INFO: lfq-object 800
1:55:08.948994 INFO: lfq-object 600
1:55:08.957259 INFO: lfq-object 1100
1:55:09.013402 INFO: lfq-object 900
1:55:09.039199 INFO: lfq-object 1400
1:55:09.072021 INFO: lfq-object 1200
1:55:09.078424 INFO: lfq-object 1700
1:55:09.155803 INFO: lfq-object 1500
1:55:09.175329 INFO: lfq-object 2000
1:55:09.184325 INFO: lfq-object 1800
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1:55:09.273151 INFO: lfq-object 1600
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1:56:51.782802 INFO: Performing label free quantification on the peptide level
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1:59:32.407422 INFO: Performing label free quantification on the pg level
1:59:32.407886 INFO: Filtering fragments by quality
1:59:32.786926 INFO: Performing label-free quantification with directlfq normalization
1:59:33.002836 INFO: 10119 lfq-groups total
2:00:16.776137 INFO: using 100 processes
2:00:16.894679 INFO: lfq-object 0
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2:00:18.084662 INFO: lfq-object 200
2:00:18.302007 INFO: lfq-object 100
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2:00:18.848929 INFO: lfq-object 800
2:00:18.906751 INFO: lfq-object 2900
2:00:18.930204 INFO: lfq-object 3100
2:00:18.962248 INFO: lfq-object 3000
2:00:18.999971 INFO: lfq-object 3200
2:00:19.101645 INFO: lfq-object 1400
2:00:19.106036 INFO: lfq-object 2800
2:00:19.133801 INFO: lfq-object 1600
2:00:19.162816 INFO: lfq-object 3400
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2:00:19.331664 INFO: lfq-object 1900
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2:00:19.355550 INFO: lfq-object 1800
2:00:19.372512 INFO: lfq-object 2000
2:00:19.377407 INFO: lfq-object 3900
2:00:19.407363 INFO: lfq-object 1500
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2:00:19.491037 INFO: lfq-object 4000
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2:00:19.821402 INFO: lfq-object 2500
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2:00:20.005267 INFO: lfq-object 5000
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2:00:20.995548 INFO: lfq-object 7000
2:00:21.018459 INFO: lfq-object 6700
2:00:21.032311 INFO: lfq-object 7100
2:00:21.049993 INFO: lfq-object 6600
2:00:21.164001 INFO: lfq-object 7200
2:00:21.173938 INFO: lfq-object 7300
2:00:21.183184 INFO: lfq-object 7400
2:00:21.249104 INFO: lfq-object 7600
2:00:21.275102 INFO: lfq-object 7700
2:00:21.280375 INFO: lfq-object 7500
2:00:21.352554 INFO: lfq-object 7800
2:00:21.438506 INFO: lfq-object 7900
2:00:21.510576 INFO: lfq-object 8000
2:00:21.560484 INFO: lfq-object 8200
2:00:21.565793 INFO: lfq-object 8100
2:00:21.629529 INFO: lfq-object 8300
2:00:21.676969 INFO: lfq-object 8400
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2:00:21.968078 INFO: lfq-object 8700
2:00:22.020018 INFO: lfq-object 8600
2:00:22.050175 INFO: lfq-object 8800
2:00:22.095755 INFO: lfq-object 8900
2:00:22.189177 INFO: lfq-object 9000
2:00:22.203889 INFO: lfq-object 9100
2:00:22.269773 INFO: lfq-object 9200
2:00:22.295592 INFO: lfq-object 9300
2:00:22.357955 INFO: lfq-object 9400
2:00:22.453901 INFO: lfq-object 9700
2:00:22.459213 INFO: lfq-object 9500
2:00:22.459476 INFO: lfq-object 9600
2:00:22.581466 INFO: lfq-object 9900
2:00:22.649488 INFO: lfq-object 9800
2:00:22.741864 INFO: lfq-object 10100
2:00:22.771458 INFO: lfq-object 10000
2:00:25.772395 INFO: Writing psm output to disk
2:00:25.859649 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/precursors.parquet to disk
2:00:26.620133 INFO: Writing precursor output to disk
2:00:26.623502 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/precursor.matrix.parquet to disk
2:00:26.712543 INFO: Writing peptide output to disk
2:00:26.717816 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/peptide.matrix.parquet to disk
2:00:26.799283 INFO: Writing pg output to disk
2:00:26.802732 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/pg.matrix.parquet to disk
2:00:26.876431 PROGRESS: Building MBR spectral library
2:00:26.876613 INFO: Running MbrLibraryBuilder
2:00:28.835551 INFO: MBR spectral library contains 131,664 precursors, 10,119 proteins
2:00:28.835688 INFO: Writing MBR spectral library to disk
2:00:30.302094 PROGRESS: =================== Search step 'library' finished ===================
2:00:31.546016 INFO: =================== Running step 'mbr' ===================
2:00:31.548872 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 7.4697575}})
2:00:31.549027 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
2:00:31.561760 INFO: loading additional config provided via CLI
2:00:31.561822 INFO: loading additional config provided via CLI parameters
2:00:31.562234 INFO: Updating config with 'user defined'
2:00:31.562298 INFO: Updating config with 'user defined (cli)'
2:00:31.562379 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/AstralAlphaDIA/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': 0, 'target_ms2_tolerance': 0, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': False}}, {'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': 30.0, 'target_ms2_tolerance': 7.4697575}, 'quant_directory': None, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': '/home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf', 'output_directory': '/home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1'}]
2:00:31.562610 INFO: Updating config with 'user defined'
2:00:31.562655 INFO: Updating config with 'user defined (cli)'
2:00:31.562674 INFO: Updating config with 'multistep search'
2:00:31.562719 INFO: ├──version: None
2:00:31.562747 INFO: ├──workflow_name: None
2:00:31.562768 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1 [multistep search, default: None][0m
2:00:31.562788 INFO: [32;20m├──library_path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf [multistep search, default: None][0m
2:00:31.562806 INFO: ├──raw_paths:
2:00:31.562825 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
2:00:31.562843 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
2:00:31.562860 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
2:00:31.562876 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
2:00:31.562893 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
2:00:31.562910 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
2:00:31.562926 INFO: ├──fasta_paths:
2:00:31.562943 INFO: ├──quant_directory: None
2:00:31.562959 INFO: ├──general
2:00:31.562978 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
2:00:31.563001 INFO: │   ├──transfer_step_enabled: False
2:00:31.563021 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
2:00:31.563040 INFO: │   ├──reuse_calibration: False
2:00:31.563058 INFO: │   ├──reuse_quant: False
2:00:31.563076 INFO: │   ├──log_level: INFO
2:00:31.563093 INFO: │   ├──use_gpu: True
2:00:31.563111 INFO: │   ├──save_figures: True
2:00:31.563128 INFO: │   ├──save_library: True
2:00:31.563146 INFO: │   ├──save_flat_library: False
2:00:31.563164 INFO: │   ├──input_library_type: base
2:00:31.563181 INFO: │   ├──save_mbr_library: True
2:00:31.563198 INFO: │   ├──random_state: None
2:00:31.563216 INFO: │   └──fail_fast: False
2:00:31.563233 INFO: ├──library_loading
2:00:31.563251 INFO: │   └──drop_decoys: False
2:00:31.563267 INFO: ├──library_prediction
2:00:31.563284 INFO: │   ├──enabled: False
2:00:31.563301 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
2:00:31.563319 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
2:00:31.563339 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
2:00:31.563358 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
2:00:31.563375 INFO: │   ├──missed_cleavages: 1
2:00:31.563392 INFO: │   ├──precursor_len:
2:00:31.563410 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
2:00:31.563427 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
2:00:31.563444 INFO: │   ├──precursor_charge:
2:00:31.563461 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
2:00:31.563477 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
2:00:31.563494 INFO: │   ├──precursor_mz:
2:00:31.563512 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
2:00:31.563530 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
2:00:31.563548 INFO: │   ├──fragment_mz:
2:00:31.563565 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
2:00:31.563582 INFO: │   │   - 2000.0
2:00:31.563600 INFO: │   ├──nce: 25.0
2:00:31.563619 INFO: │   ├──fragment_types:
2:00:31.563637 INFO: │   │   - b
2:00:31.563654 INFO: │   │   - y
2:00:31.563672 INFO: │   ├──max_fragment_charge: 2
2:00:31.563692 INFO: │   ├──instrument: Lumos
2:00:31.563709 INFO: │   ├──peptdeep_model_path: None
2:00:31.563727 INFO: │   ├──peptdeep_model_type: generic
2:00:31.563744 INFO: │   ├──predict_charge: False
2:00:31.563762 INFO: │   └──min_charge_probability: 0.1
2:00:31.563781 INFO: ├──custom_modifications:
2:00:31.563799 INFO: │   ├──name: Dimethyl:d12@K
2:00:31.563817 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:00:31.563834 INFO: │   ├──name: Dimethyl:d12@Any_N-term
2:00:31.563851 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:00:31.563868 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
2:00:31.563885 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:00:31.563902 INFO: │   ├──name: mTRAQ:d12@K
2:00:31.563918 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
2:00:31.563938 INFO: │   ├──name: mTRAQ:d12@Any_N-term
2:00:31.563956 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:00:31.563973 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
2:00:31.563990 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:00:31.564007 INFO: │   ├──name: Label:13C(12)@K
2:00:31.564023 INFO: │   └──composition: C(12)
2:00:31.564040 INFO: ├──search
2:00:31.564058 INFO: │   ├──extraction_backend: rust
2:00:31.564076 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
2:00:31.564095 INFO: │   [32;20m├──target_ms2_tolerance: 7.4697575 [multistep search, default: 10][0m
2:00:31.564116 INFO: │   ├──target_rt_tolerance: 0.0
2:00:31.564133 INFO: │   ├──target_mobility_tolerance: 0.0
2:00:31.564151 INFO: │   ├──quant_window: 3
2:00:31.564168 INFO: │   ├──target_num_candidates: 3
2:00:31.564185 INFO: │   ├──channel_filter: 
2:00:31.564202 INFO: │   ├──compete_for_fragments: True
2:00:31.564219 INFO: │   ├──top_k_fragments_selection: 12
2:00:31.564237 INFO: │   ├──top_k_fragments_scoring: 12
2:00:31.564255 INFO: │   ├──min_fragment_intensity: 0.01
2:00:31.564272 INFO: │   ├──optimized_peak_group_score: False
2:00:31.564289 INFO: │   ├──exclude_shared_ions: True
2:00:31.564307 INFO: │   ├──quant_all: True
2:00:31.564324 INFO: │   └──experimental_xic: True
2:00:31.564341 INFO: ├──calibration
2:00:31.564359 INFO: │   ├──batch_size: 1000
2:00:31.564376 INFO: │   ├──optimization_lock_target: 1000
2:00:31.564394 INFO: │   ├──max_steps: 20
2:00:31.564410 INFO: │   ├──min_steps: 5
2:00:31.564428 INFO: │   ├──max_skips: 1
2:00:31.564445 INFO: │   ├──max_fragments: 5000
2:00:31.564462 INFO: │   └──min_correlation: 0.7
2:00:31.564479 INFO: ├──search_initial
2:00:31.564497 INFO: │   ├──num_candidates: 1
2:00:31.564514 INFO: │   ├──ms1_tolerance: 30
2:00:31.564532 INFO: │   ├──ms2_tolerance: 30
2:00:31.564550 INFO: │   ├──mobility_tolerance: 0.1
2:00:31.564568 INFO: │   └──rt_tolerance: 0.5
2:00:31.564585 INFO: ├──library_multiplexing
2:00:31.564603 INFO: │   ├──enabled: False
2:00:31.564620 INFO: │   ├──input_channel: 0
2:00:31.564637 INFO: │   └──multiplex_mapping:
2:00:31.564654 INFO: ├──multiplexing
2:00:31.564671 INFO: │   ├──enabled: False
2:00:31.564688 INFO: │   ├──target_channels: 4,8
2:00:31.564705 INFO: │   ├──decoy_channel: 12
2:00:31.564722 INFO: │   ├──reference_channel: 0
2:00:31.564739 INFO: │   └──competitive_scoring: True
2:00:31.564756 INFO: ├──fdr
2:00:31.564774 INFO: │   ├──fdr: 0.01
2:00:31.564791 INFO: │   ├──group_level: proteins
2:00:31.564810 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
2:00:31.564829 INFO: │   ├──competitive_scoring: True
2:00:31.564847 INFO: │   ├──keep_decoys: False
2:00:31.564864 INFO: │   ├──keep_decoys_in_mbr_library: False
2:00:31.564885 INFO: │   ├──channel_wise_fdr: False
2:00:31.564903 INFO: │   └──enable_nn_hyperparameter_tuning: True
2:00:31.564920 INFO: ├──search_output
2:00:31.564937 INFO: │   ├──file_format: parquet
2:00:31.564954 INFO: │   ├──precursor_level_lfq: True
2:00:31.564971 INFO: │   ├──peptide_level_lfq: True
2:00:31.564989 INFO: │   ├──save_fragment_quant_matrix: False
2:00:31.565007 INFO: │   ├──min_k_fragments: 12
2:00:31.565024 INFO: │   ├──min_correlation: 0.9
2:00:31.565041 INFO: │   ├──num_samples_quadratic: 50
2:00:31.565058 INFO: │   ├──min_nonnan: 3
2:00:31.565075 INFO: │   ├──normalization_method: directlfq
2:00:31.565093 INFO: │   [32;20m└──normalize_directlfq: False [user defined, default: True][0m
2:00:31.565109 INFO: ├──optimization
2:00:31.565126 INFO: │   ├──order_of_optimization: None
2:00:31.565143 INFO: │   ├──ms2_error
2:00:31.565161 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:00:31.565178 INFO: │   │   ├──targeted_update_factor: 1.0
2:00:31.565196 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:00:31.565213 INFO: │   │   ├──automatic_update_factor: 1.1
2:00:31.565230 INFO: │   │   ├──try_narrower_values: True
2:00:31.565248 INFO: │   │   ├──maximal_decrease: 0.5
2:00:31.565265 INFO: │   │   ├──favour_narrower_optimum: False
2:00:31.565282 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:00:31.565301 INFO: │   ├──ms1_error
2:00:31.565319 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:00:31.565336 INFO: │   │   ├──targeted_update_factor: 1.0
2:00:31.565354 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:00:31.565371 INFO: │   │   ├──automatic_update_factor: 1.1
2:00:31.565388 INFO: │   │   ├──try_narrower_values: False
2:00:31.565405 INFO: │   │   ├──maximal_decrease: 0.2
2:00:31.565421 INFO: │   │   ├──favour_narrower_optimum: False
2:00:31.565439 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:00:31.565455 INFO: │   ├──mobility_error
2:00:31.565473 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:00:31.565490 INFO: │   │   ├──targeted_update_factor: 1.0
2:00:31.565508 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:00:31.565525 INFO: │   │   ├──automatic_update_factor: 1.1
2:00:31.565542 INFO: │   │   ├──try_narrower_values: False
2:00:31.565560 INFO: │   │   ├──maximal_decrease: 0.2
2:00:31.565577 INFO: │   │   ├──favour_narrower_optimum: False
2:00:31.565595 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:00:31.565611 INFO: │   └──rt_error
2:00:31.565629 INFO: │       ├──targeted_update_percentile_range: 0.95
2:00:31.565646 INFO: │       ├──targeted_update_factor: 1.0
2:00:31.565664 INFO: │       ├──automatic_update_percentile_range: 0.999
2:00:31.565681 INFO: │       ├──automatic_update_factor: 1.5
2:00:31.565698 INFO: │       ├──try_narrower_values: True
2:00:31.565716 INFO: │       ├──maximal_decrease: 0.1
2:00:31.565733 INFO: │       ├──favour_narrower_optimum: False
2:00:31.565752 INFO: │       └──maximum_decrease_from_maximum: 0.5
2:00:31.565769 INFO: ├──optimization_manager
2:00:31.565788 INFO: │   ├──fwhm_rt: 5
2:00:31.565806 INFO: │   ├──fwhm_mobility: 0.01
2:00:31.565823 INFO: │   └──score_cutoff: 0
2:00:31.565839 INFO: ├──transfer_library
2:00:31.565873 INFO: │   ├──enabled: False
2:00:31.565890 INFO: │   ├──fragment_types:
2:00:31.565907 INFO: │   │   - b
2:00:31.565924 INFO: │   │   - y
2:00:31.565942 INFO: │   ├──max_charge: 2
2:00:31.565960 INFO: │   ├──top_k_samples: 3
2:00:31.565978 INFO: │   ├──norm_delta_max: True
2:00:31.565996 INFO: │   ├──precursor_correlation_cutoff: 0.5
2:00:31.566019 INFO: │   └──fragment_correlation_ratio: 0.75
2:00:31.566037 INFO: └──transfer_learning
2:00:31.566056 INFO:     ├──enabled: False
2:00:31.566074 INFO:     ├──batch_size: 2000
2:00:31.566091 INFO:     ├──max_lr: 0.0001
2:00:31.566108 INFO:     ├──train_fraction: 0.7
2:00:31.566126 INFO:     ├──validation_fraction: 0.2
2:00:31.566143 INFO:     ├──test_fraction: 0.1
2:00:31.566160 INFO:     ├──test_interval: 1
2:00:31.566177 INFO:     ├──lr_patience: 3
2:00:31.566195 INFO:     ├──epochs: 51
2:00:31.566212 INFO:     ├──warmup_epochs: 5
2:00:31.566229 INFO:     ├──nce: 25
2:00:31.566247 INFO:     └──instrument: Lumos
2:00:31.571549 INFO: Moved existing config file /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/frozen_config.yaml to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/frozen_config.0.bkp.yaml
2:00:31.572174 INFO: Registering 7 custom modifications
2:00:31.593284 INFO: Searching 6 files:
2:00:31.593359 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
2:00:31.593381 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
2:00:31.593400 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
2:00:31.593416 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
2:00:31.593432 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
2:00:31.593448 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
2:00:31.593464 INFO: Using 0 fasta files:
2:00:31.593490 INFO: Using library: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:00:31.593509 INFO: Saving output to: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1
2:00:31.593534 PROGRESS: Loading spectral library
2:00:31.593565 PROGRESS: Loading library (type: base) from disk..
2:00:31.593592 INFO: Running DynamicLoader
2:00:31.593651 INFO: Loading .hdf library from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:00:32.222009 INFO: Running PrecursorInitializer
2:00:32.222406 INFO: Channel column already present, skipping initialization
2:00:32.222443 INFO: Elution group indices already present, skipping initialization
2:00:32.222464 INFO: Precursor indices already present, skipping initialization
2:00:32.222596 INFO: Running AnnotateFasta
2:00:32.235681 INFO: Running IsotopeGenerator
2:00:32.235919 INFO: Isotope information already present, skipping isotope generation
2:00:32.235950 INFO: Running RTNormalization
2:00:32.239829 INFO: Saving library to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/speclib.hdf
2:00:33.154377 INFO: Running DecoyGenerator
2:00:40.690437 INFO: Running FlattenLibrary
2:00:41.849375 INFO: Running InitFlatColumns
2:00:41.855152 INFO: Running LogFlatLibraryStats
2:00:41.855264 INFO: ============ Library Stats ============
2:00:41.855293 INFO: Number of precursors: 263,292
2:00:41.902436 INFO: 	thereof targets:131,664
2:00:41.902563 INFO: 	thereof decoys: 131,628
2:00:41.904574 INFO: Number of elution groups: 131,664
2:00:41.904634 INFO: 	average size: 2.00
2:00:41.922701 INFO: Number of proteins: 10,119
2:00:41.923744 INFO: Number of channels: 1 ([0])
2:00:41.923827 INFO: Isotopes Distribution for 4 isotopes
2:00:41.923852 INFO: =======================================
2:00:41.923919 PROGRESS: =================== Starting Search Workflows for step mbr ===================
2:00:41.923971 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
2:00:41.924008 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant
2:00:41.924090 INFO: Initializing TimingManager
2:00:41.924594 INFO: Initializing RawFileManager
2:00:52.212933 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.
2:00:52.220899 INFO: Determining DIA cycle
2:00:52.237394 INFO: Found cycle with start 0.00 min and length 300.
2:00:52.402302 INFO: RT (min)            : 0.0 - 26.9
2:00:52.402390 INFO: RT duration (sec)   : 1611.2
2:00:52.402419 INFO: RT duration (min)   : 26.9
2:00:52.402441 INFO: Cycle len (scans)   : 300
2:00:52.402461 INFO: Cycle len (sec)     : 1.65
2:00:52.402480 INFO: Number of cycles    : 977
2:00:52.402500 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:00:52.402530 INFO: Creating DIA data object took: 10.47784686088562
2:00:53.078085 INFO: Creating DIA data NG object took: 0.6754364967346191
2:00:53.109267 INFO: Initializing CalibrationManager
2:00:53.109565 INFO: Setting up calibration estimators ..
2:00:53.109625 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:00:53.109691 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'}' ..
2:00:53.109760 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:00:53.109832 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:00:53.109917 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}}' ..
2:00:53.109968 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:00:53.110020 INFO: Done setting up calibration estimators.
2:00:53.110225 INFO: Initializing OptimizationManager
2:00:53.110345 INFO: initial parameter: ms1_error = 30
2:00:53.110394 INFO: initial parameter: ms2_error = 30
2:00:53.110437 INFO: initial parameter: rt_error = 805.5992431640625
2:00:53.110480 INFO: initial parameter: mobility_error = 0.1
2:00:53.110519 INFO: initial parameter: num_candidates = 1
2:00:53.110559 INFO: initial parameter: fwhm_rt = 5
2:00:53.110598 INFO: initial parameter: fwhm_mobility = 0.01
2:00:53.110637 INFO: initial parameter: score_cutoff = 0
2:00:53.110674 INFO: initial parameter: classifier_version = -1
2:00:53.110740 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:00:53.110976 INFO: FDRManager: loading saved state not requested, will be initialized.
2:00:53.111006 INFO: Initializing FDRManager
2:00:53.111037 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:00:53.148579 PROGRESS: Initializing spectral library: 131,664 target precursors potentially observable (0 removed)
2:00:53.173130 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:00:53.173497 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
2:00:53.173604 PROGRESS: Starting initial search for precursors.
2:00:53.173686 INFO: Starting optimization step 0.
2:00:53.173745 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:00:53.173798 INFO: Using rust extraction backend
2:00:53.173874 PROGRESS: Extracting batch of 1977 precursors
2:00:53.178802 INFO: === Search parameters used ===
2:00:53.178917 INFO: rt_error       : 805.5992431640625
2:00:53.178967 INFO: mobility_error : 0.1
2:00:53.179010 INFO: num_candidates : 1
2:00:53.179051 INFO: ms1_error      : 30
2:00:53.179090 INFO: ms2_error      : 30
2:00:53.179129 INFO: fwhm_rt        : 5
2:00:53.179167 INFO: quant_window   : 3
2:00:53.179205 INFO: ==============================================
2:00:53.221969 INFO: performing precursor FDR with 40 features
2:00:53.222044 INFO: Decoy channel: -1
2:00:53.222067 INFO: competitive: True
2:00:53.223368 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:53.225253 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
2:00:53.226062 INFO: Using random state 116775 for train-test-split
2:00:53.346553 INFO: Test AUC: 0.763
2:00:53.346637 INFO: Train AUC: 0.751
2:00:53.346664 INFO: AUC difference: 1.65%
2:00:53.617556 INFO: Resetting torch num_threads to 100
2:00:53.619205 PROGRESS: === Extracted 1975 precursors and 13426 fragments ===
2:00:53.619574 INFO: === FDR correction performed with classifier version -1 ===
2:00:53.620065 PROGRESS: ============================= Precursor FDR =============================
2:00:53.620149 PROGRESS: Total precursors accumulated: 317
2:00:53.620209 PROGRESS: Target precursors: 314 (99.05%)
2:00:53.620257 PROGRESS: Decoy precursors: 3 (0.95%)
2:00:53.620301 PROGRESS: 
2:00:53.620344 PROGRESS: Precursor Summary:
2:00:53.621411 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   314; 0.001 FDR:   286
2:00:53.621497 PROGRESS: 
2:00:53.621550 PROGRESS: Protein Summary:
2:00:53.622822 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   293; 0.001 FDR:   267
2:00:53.622913 PROGRESS: =========================================================================
2:00:53.623092 INFO: Target number of precursors not reached yet.
2:00:53.631025 INFO: Starting optimization step 1.
2:00:53.631147 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:00:53.631215 INFO: Using rust extraction backend
2:00:53.631272 PROGRESS: Extracting batch of 3959 precursors
2:00:53.639462 INFO: === Search parameters used ===
2:00:53.639569 INFO: rt_error       : 805.5992431640625
2:00:53.639619 INFO: mobility_error : 0.1
2:00:53.639663 INFO: num_candidates : 1
2:00:53.639705 INFO: ms1_error      : 30
2:00:53.639745 INFO: ms2_error      : 30
2:00:53.639784 INFO: fwhm_rt        : 5
2:00:53.639832 INFO: quant_window   : 3
2:00:53.639871 INFO: ==============================================
2:00:53.685293 INFO: performing precursor FDR with 40 features
2:00:53.685385 INFO: Decoy channel: -1
2:00:53.685409 INFO: competitive: True
2:00:53.691082 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:53.693640 INFO: Estimating optimal hyperparameters - samples: 4,741, batch_size: 128, learning_rate: 1.77e-04
2:00:53.693730 INFO: Using random state 720776 for train-test-split
2:00:54.105202 INFO: Test AUC: 0.804
2:00:54.105293 INFO: Train AUC: 0.809
2:00:54.105321 INFO: AUC difference: 0.72%
2:00:54.352901 INFO: Resetting torch num_threads to 100
2:00:54.356139 PROGRESS: === Extracted 5927 precursors and 40780 fragments ===
2:00:54.356521 INFO: === FDR correction performed with classifier version -1 ===
2:00:54.357135 PROGRESS: ============================= Precursor FDR =============================
2:00:54.357217 PROGRESS: Total precursors accumulated: 1,381
2:00:54.357272 PROGRESS: Target precursors: 1,368 (99.06%)
2:00:54.357320 PROGRESS: Decoy precursors: 13 (0.94%)
2:00:54.357363 PROGRESS: 
2:00:54.357405 PROGRESS: Precursor Summary:
2:00:54.358730 PROGRESS: Channel   0:	 0.050 FDR: 1,368; 0.010 FDR: 1,368; 0.001 FDR:   657
2:00:54.358824 PROGRESS: 
2:00:54.358877 PROGRESS: Protein Summary:
2:00:54.360585 PROGRESS: Channel   0:	 0.050 FDR: 1,112; 0.010 FDR: 1,112; 0.001 FDR:   566
2:00:54.360674 PROGRESS: =========================================================================
2:00:54.360909 INFO: Target number of precursors reached.
2:00:54.369634 INFO: fragments_df: keeping 5000 of 40780 [sum(precursor_idx_mask)=14294 sum(mass_error_mask)=40780 stop_rank=5000
2:00:54.380347 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:00:54.626808 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:00:55.347681 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:00:55.348163 INFO: Using score_cutoff 12.29761706829071 (fac=0.99, q=1)
2:00:55.348513 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:00:55.348587 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:00:55.348638 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.29761706829071
2:00:55.348701 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:00:55.352713 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:00:55.360511 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:00:55.360631 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:00:55.360723 INFO: Starting optimization step 2.
2:00:55.360802 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:00:55.360877 INFO: Using rust extraction backend
2:00:55.360954 PROGRESS: Extracting batch of 5936 precursors
2:00:55.372224 INFO: === Search parameters used ===
2:00:55.372347 INFO: rt_error       : 805.5992431640625
2:00:55.372397 INFO: mobility_error : 0.1
2:00:55.372443 INFO: num_candidates : 3
2:00:55.372489 INFO: ms1_error      : 30
2:00:55.372530 INFO: ms2_error      : 30
2:00:55.372570 INFO: fwhm_rt        : 3.0
2:00:55.372610 INFO: quant_window   : 3
2:00:55.372649 INFO: ==============================================
2:00:55.490477 INFO: performing precursor FDR with 40 features
2:00:55.490587 INFO: Decoy channel: -1
2:00:55.490611 INFO: competitive: True
2:00:55.496840 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:55.501655 INFO: Estimating optimal hyperparameters - samples: 14,208, batch_size: 128, learning_rate: 1.77e-04
2:00:55.501804 INFO: Using random state 315846 for train-test-split
2:00:56.939096 INFO: Test AUC: 0.684
2:00:56.939204 INFO: Train AUC: 0.690
2:00:56.939232 INFO: AUC difference: 0.78%
2:00:57.189213 INFO: Resetting torch num_threads to 100
2:00:57.191638 PROGRESS: === Extracted 17761 precursors and 106178 fragments ===
2:00:57.192033 INFO: === FDR correction performed with classifier version 1 ===
2:00:57.192692 PROGRESS: ============================= Precursor FDR =============================
2:00:57.192780 PROGRESS: Total precursors accumulated: 1,843
2:00:57.192838 PROGRESS: Target precursors: 1,825 (99.02%)
2:00:57.192886 PROGRESS: Decoy precursors: 18 (0.98%)
2:00:57.192929 PROGRESS: 
2:00:57.192970 PROGRESS: Precursor Summary:
2:00:57.194470 PROGRESS: Channel   0:	 0.050 FDR: 1,825; 0.010 FDR: 1,825; 0.001 FDR: 1,449
2:00:57.194570 PROGRESS: 
2:00:57.194628 PROGRESS: Protein Summary:
2:00:57.196608 PROGRESS: Channel   0:	 0.050 FDR: 1,450; 0.010 FDR: 1,450; 0.001 FDR: 1,181
2:00:57.196701 PROGRESS: =========================================================================
2:00:57.197067 INFO: Target number of precursors reached.
2:00:57.216327 INFO: fragments_df: keeping 5000 of 106178 [sum(precursor_idx_mask)=39328 sum(mass_error_mask)=106178 stop_rank=5000
2:00:57.227256 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:00:57.507622 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:00:58.224997 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:00:58.225462 INFO: Using score_cutoff 11.839465643692018 (fac=0.99, q=1)
2:00:58.225780 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:00:58.225871 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:00:58.225928 INFO: Updating optimization_manager: score_cutoff        : 12.29761706829071 -> 11.839465643692018
2:00:58.225979 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:00:58.229928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:00:58.237830 INFO: === checking if optimization conditions were reached ===
2:00:58.239564 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.4697575
2:00:58.239665 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:00:58.239734 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:00:58.239800 INFO: ==============================================
2:00:58.239868 INFO: Starting optimization step 3.
2:00:58.239926 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:00:58.239981 INFO: Using rust extraction backend
2:00:58.240033 PROGRESS: Extracting batch of 5936 precursors
2:00:58.251273 INFO: === Search parameters used ===
2:00:58.251405 INFO: rt_error       : 805.5992431640625
2:00:58.251457 INFO: mobility_error : 0.1
2:00:58.251501 INFO: num_candidates : 3
2:00:58.251544 INFO: ms1_error      : 30
2:00:58.251583 INFO: ms2_error      : 7.4697575
2:00:58.251624 INFO: fwhm_rt        : 3.0
2:00:58.251662 INFO: quant_window   : 3
2:00:58.251701 INFO: ==============================================
2:00:58.353087 INFO: performing precursor FDR with 40 features
2:00:58.353202 INFO: Decoy channel: -1
2:00:58.353226 INFO: competitive: True
2:00:58.358543 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:58.362894 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:00:58.363026 INFO: Using random state 308067 for train-test-split
2:00:59.793882 INFO: Test AUC: 0.744
2:00:59.793995 INFO: Train AUC: 0.733
2:00:59.794023 INFO: AUC difference: 1.57%
2:01:00.052473 INFO: Resetting torch num_threads to 100
2:01:00.054953 PROGRESS: === Extracted 17807 precursors and 122860 fragments ===
2:01:00.055332 INFO: === FDR correction performed with classifier version 2 ===
2:01:00.056017 PROGRESS: ============================= Precursor FDR =============================
2:01:00.056099 PROGRESS: Total precursors accumulated: 2,317
2:01:00.056155 PROGRESS: Target precursors: 2,295 (99.05%)
2:01:00.056203 PROGRESS: Decoy precursors: 22 (0.95%)
2:01:00.056246 PROGRESS: 
2:01:00.056288 PROGRESS: Precursor Summary:
2:01:00.057873 PROGRESS: Channel   0:	 0.050 FDR: 2,295; 0.010 FDR: 2,295; 0.001 FDR: 1,673
2:01:00.057968 PROGRESS: 
2:01:00.058022 PROGRESS: Protein Summary:
2:01:00.060173 PROGRESS: Channel   0:	 0.050 FDR: 1,794; 0.010 FDR: 1,794; 0.001 FDR: 1,340
2:01:00.060266 PROGRESS: =========================================================================
2:01:00.060652 INFO: Target number of precursors reached.
2:01:00.086941 INFO: fragments_df: keeping 5000 of 122860 [sum(precursor_idx_mask)=53854 sum(mass_error_mask)=122860 stop_rank=5000
2:01:00.098019 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:00.434496 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:01.151026 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:01.151481 INFO: Using score_cutoff 10.930738573265076 (fac=0.99, q=1)
2:01:01.151794 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:01.151868 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:01.151922 INFO: Updating optimization_manager: score_cutoff        : 11.839465643692018 -> 10.930738573265076
2:01:01.151973 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:01.155896 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:01.163484 INFO: === checking if optimization conditions were reached ===
2:01:01.165184 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:01:01.165290 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:01:01.165357 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:01:01.165413 INFO: ==============================================
2:01:01.165476 INFO: Starting optimization step 4.
2:01:01.165530 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:01.165584 INFO: Using rust extraction backend
2:01:01.165636 PROGRESS: Extracting batch of 5936 precursors
2:01:01.176811 INFO: === Search parameters used ===
2:01:01.176944 INFO: rt_error       : 805.5992431640625
2:01:01.176995 INFO: mobility_error : 0.1
2:01:01.177039 INFO: num_candidates : 3
2:01:01.177080 INFO: ms1_error      : 30
2:01:01.177120 INFO: ms2_error      : 7.4697575
2:01:01.177159 INFO: fwhm_rt        : 3.0
2:01:01.177198 INFO: quant_window   : 3
2:01:01.177236 INFO: ==============================================
2:01:01.277337 INFO: performing precursor FDR with 40 features
2:01:01.277448 INFO: Decoy channel: -1
2:01:01.277472 INFO: competitive: True
2:01:01.282699 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:01.287150 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:01:01.287291 INFO: Using random state 360835 for train-test-split
2:01:02.749707 INFO: Test AUC: 0.741
2:01:02.749826 INFO: Train AUC: 0.746
2:01:02.749871 INFO: AUC difference: 0.69%
2:01:03.008029 INFO: Resetting torch num_threads to 100
2:01:03.010456 PROGRESS: === Extracted 17807 precursors and 122858 fragments ===
2:01:03.011968 INFO: === FDR correction performed with classifier version 3 ===
2:01:03.012699 PROGRESS: ============================= Precursor FDR =============================
2:01:03.012786 PROGRESS: Total precursors accumulated: 2,378
2:01:03.012846 PROGRESS: Target precursors: 2,355 (99.03%)
2:01:03.012896 PROGRESS: Decoy precursors: 23 (0.97%)
2:01:03.012943 PROGRESS: 
2:01:03.012994 PROGRESS: Precursor Summary:
2:01:03.014595 PROGRESS: Channel   0:	 0.050 FDR: 2,355; 0.010 FDR: 2,355; 0.001 FDR: 1,854
2:01:03.014693 PROGRESS: 
2:01:03.014748 PROGRESS: Protein Summary:
2:01:03.016905 PROGRESS: Channel   0:	 0.050 FDR: 1,839; 0.010 FDR: 1,839; 0.001 FDR: 1,479
2:01:03.016996 PROGRESS: =========================================================================
2:01:03.017370 INFO: Target number of precursors reached.
2:01:03.043483 INFO: fragments_df: keeping 5000 of 122858 [sum(precursor_idx_mask)=54994 sum(mass_error_mask)=122858 stop_rank=5000
2:01:03.054395 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:03.399600 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:04.113029 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:04.113474 INFO: Using score_cutoff 10.486967232513429 (fac=0.99, q=1)
2:01:04.113795 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:04.113883 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:04.113951 INFO: Updating optimization_manager: score_cutoff        : 10.930738573265076 -> 10.486967232513429
2:01:04.114005 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:04.117975 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:04.125404 INFO: === checking if optimization conditions were reached ===
2:01:04.127076 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:01:04.127185 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:01:04.127249 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:01:04.127301 INFO: ==============================================
2:01:04.127363 INFO: Starting optimization step 5.
2:01:04.127415 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:04.127472 INFO: Using rust extraction backend
2:01:04.127523 PROGRESS: Extracting batch of 5936 precursors
2:01:04.138865 INFO: === Search parameters used ===
2:01:04.139011 INFO: rt_error       : 805.5992431640625
2:01:04.139065 INFO: mobility_error : 0.1
2:01:04.139111 INFO: num_candidates : 3
2:01:04.139154 INFO: ms1_error      : 30
2:01:04.139197 INFO: ms2_error      : 7.4697575
2:01:04.139239 INFO: fwhm_rt        : 3.0
2:01:04.139281 INFO: quant_window   : 3
2:01:04.139320 INFO: ==============================================
2:01:04.240023 INFO: performing precursor FDR with 40 features
2:01:04.240137 INFO: Decoy channel: -1
2:01:04.240161 INFO: competitive: True
2:01:04.245365 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:04.249939 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:01:04.250080 INFO: Using random state 191408 for train-test-split
2:01:05.686977 INFO: Test AUC: 0.739
2:01:05.687095 INFO: Train AUC: 0.755
2:01:05.687123 INFO: AUC difference: 2.12%
2:01:05.944474 INFO: Resetting torch num_threads to 100
2:01:05.946918 PROGRESS: === Extracted 17807 precursors and 122891 fragments ===
2:01:05.947286 INFO: === FDR correction performed with classifier version 4 ===
2:01:05.947991 PROGRESS: ============================= Precursor FDR =============================
2:01:05.948074 PROGRESS: Total precursors accumulated: 2,557
2:01:05.948130 PROGRESS: Target precursors: 2,532 (99.02%)
2:01:05.948185 PROGRESS: Decoy precursors: 25 (0.98%)
2:01:05.948231 PROGRESS: 
2:01:05.948273 PROGRESS: Precursor Summary:
2:01:05.949885 PROGRESS: Channel   0:	 0.050 FDR: 2,532; 0.010 FDR: 2,532; 0.001 FDR: 1,929
2:01:05.949980 PROGRESS: 
2:01:05.950032 PROGRESS: Protein Summary:
2:01:05.952240 PROGRESS: Channel   0:	 0.050 FDR: 1,963; 0.010 FDR: 1,963; 0.001 FDR: 1,537
2:01:05.952327 PROGRESS: =========================================================================
2:01:05.952691 INFO: Target number of precursors reached.
2:01:05.979848 INFO: fragments_df: keeping 5000 of 122891 [sum(precursor_idx_mask)=58498 sum(mass_error_mask)=122891 stop_rank=5000
2:01:05.990996 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:06.360394 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:07.075520 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:07.075980 INFO: Using score_cutoff 9.752424131298065 (fac=0.99, q=1)
2:01:07.076297 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:07.076387 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:07.076440 INFO: Updating optimization_manager: score_cutoff        : 10.486967232513429 -> 9.752424131298065
2:01:07.076491 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:07.080395 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:07.087854 INFO: === checking if optimization conditions were reached ===
2:01:07.089522 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:01:07.089616 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:01:07.089678 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:01:07.089742 INFO: ==============================================
2:01:07.089805 INFO: Starting optimization step 6.
2:01:07.089946 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:07.090018 INFO: Using rust extraction backend
2:01:07.090072 PROGRESS: Extracting batch of 5936 precursors
2:01:07.101238 INFO: === Search parameters used ===
2:01:07.101371 INFO: rt_error       : 805.5992431640625
2:01:07.101422 INFO: mobility_error : 0.1
2:01:07.101466 INFO: num_candidates : 3
2:01:07.101506 INFO: ms1_error      : 30
2:01:07.101545 INFO: ms2_error      : 7.4697575
2:01:07.101584 INFO: fwhm_rt        : 3.0
2:01:07.101621 INFO: quant_window   : 3
2:01:07.101659 INFO: ==============================================
2:01:07.206407 INFO: performing precursor FDR with 40 features
2:01:07.206527 INFO: Decoy channel: -1
2:01:07.206550 INFO: competitive: True
2:01:07.211791 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:07.216310 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:01:07.216449 INFO: Using random state 54788 for train-test-split
2:01:08.653033 INFO: Test AUC: 0.758
2:01:08.653150 INFO: Train AUC: 0.756
2:01:08.653179 INFO: AUC difference: 0.27%
2:01:08.907312 INFO: Resetting torch num_threads to 100
2:01:08.909737 PROGRESS: === Extracted 17807 precursors and 122860 fragments ===
2:01:08.910115 INFO: === FDR correction performed with classifier version 5 ===
2:01:08.910836 PROGRESS: ============================= Precursor FDR =============================
2:01:08.910927 PROGRESS: Total precursors accumulated: 2,627
2:01:08.910990 PROGRESS: Target precursors: 2,601 (99.01%)
2:01:08.911040 PROGRESS: Decoy precursors: 26 (0.99%)
2:01:08.911083 PROGRESS: 
2:01:08.911126 PROGRESS: Precursor Summary:
2:01:08.912785 PROGRESS: Channel   0:	 0.050 FDR: 2,601; 0.010 FDR: 2,601; 0.001 FDR: 2,085
2:01:08.912871 PROGRESS: 
2:01:08.912927 PROGRESS: Protein Summary:
2:01:08.915210 PROGRESS: Channel   0:	 0.050 FDR: 2,013; 0.010 FDR: 2,013; 0.001 FDR: 1,650
2:01:08.915303 PROGRESS: =========================================================================
2:01:08.915677 INFO: Target number of precursors reached.
2:01:08.943582 INFO: fragments_df: keeping 5000 of 122860 [sum(precursor_idx_mask)=59863 sum(mass_error_mask)=122860 stop_rank=5000
2:01:08.954583 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:09.330712 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:10.044435 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:10.044881 INFO: Using score_cutoff 9.606346778869629 (fac=0.99, q=1)
2:01:10.045189 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:10.045263 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:10.045315 INFO: Updating optimization_manager: score_cutoff        : 9.752424131298065 -> 9.606346778869629
2:01:10.045367 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:10.049291 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:10.056948 INFO: === checking if optimization conditions were reached ===
2:01:10.058615 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:01:10.058713 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:01:10.058776 PROGRESS: ✅ ms2_error      : 7.4698 <= 7.4698
2:01:10.058829 INFO: ==============================================
2:01:10.058900 PROGRESS: Optimization finished for ms2_error.
2:01:10.069212 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:10.073007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:10.081074 INFO: Starting optimization step 0.
2:01:10.081180 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:10.081251 INFO: Using rust extraction backend
2:01:10.081307 PROGRESS: Extracting batch of 5936 precursors
2:01:10.092459 INFO: === Search parameters used ===
2:01:10.092592 INFO: rt_error       : 805.5992431640625
2:01:10.092663 INFO: mobility_error : 0.1
2:01:10.092710 INFO: num_candidates : 3
2:01:10.092752 INFO: ms1_error      : 30
2:01:10.092793 INFO: ms2_error      : 7.4697575
2:01:10.092833 INFO: fwhm_rt        : 3.0
2:01:10.092872 INFO: quant_window   : 3
2:01:10.092912 INFO: ==============================================
2:01:10.198280 INFO: performing precursor FDR with 40 features
2:01:10.198394 INFO: Decoy channel: -1
2:01:10.198417 INFO: competitive: True
2:01:10.203530 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:10.208013 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:01:10.208147 INFO: Using random state 811275 for train-test-split
2:01:11.651612 INFO: Test AUC: 0.746
2:01:11.651750 INFO: Train AUC: 0.764
2:01:11.651778 INFO: AUC difference: 2.40%
2:01:11.905584 INFO: Resetting torch num_threads to 100
2:01:11.908062 PROGRESS: === Extracted 17807 precursors and 122881 fragments ===
2:01:11.908445 INFO: === FDR correction performed with classifier version 6 ===
2:01:11.909149 PROGRESS: ============================= Precursor FDR =============================
2:01:11.909232 PROGRESS: Total precursors accumulated: 2,641
2:01:11.909286 PROGRESS: Target precursors: 2,615 (99.02%)
2:01:11.909334 PROGRESS: Decoy precursors: 26 (0.98%)
2:01:11.909376 PROGRESS: 
2:01:11.909418 PROGRESS: Precursor Summary:
2:01:11.911059 PROGRESS: Channel   0:	 0.050 FDR: 2,615; 0.010 FDR: 2,615; 0.001 FDR: 2,068
2:01:11.911158 PROGRESS: 
2:01:11.911212 PROGRESS: Protein Summary:
2:01:11.913464 PROGRESS: Channel   0:	 0.050 FDR: 2,016; 0.010 FDR: 2,016; 0.001 FDR: 1,637
2:01:11.913556 PROGRESS: =========================================================================
2:01:11.913955 INFO: Target number of precursors reached.
2:01:11.941319 INFO: fragments_df: keeping 5000 of 122881 [sum(precursor_idx_mask)=60106 sum(mass_error_mask)=122881 stop_rank=5000
2:01:11.952205 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:12.328881 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:13.060441 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:13.062102 INFO: Using score_cutoff 9.5563784866333 (fac=0.99, q=1)
2:01:13.063226 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:13.063528 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:13.063747 INFO: Updating optimization_manager: score_cutoff        : 9.606346778869629 -> 9.5563784866333
2:01:13.063909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:13.075969 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:13.096694 INFO: === checking if optimization conditions were reached ===
2:01:13.097597 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:01:13.104998 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 292.7730076603755
2:01:13.105594 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 292.7730.
2:01:13.105734 INFO: ==============================================
2:01:13.105897 INFO: Starting optimization step 1.
2:01:13.106008 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:13.106167 INFO: Using rust extraction backend
2:01:13.106296 PROGRESS: Extracting batch of 5936 precursors
2:01:13.138992 INFO: === Search parameters used ===
2:01:13.139679 INFO: rt_error       : 292.7730076603755
2:01:13.139758 INFO: mobility_error : 0.1
2:01:13.139816 INFO: num_candidates : 3
2:01:13.139872 INFO: ms1_error      : 30
2:01:13.139926 INFO: ms2_error      : 7.4697575
2:01:13.139982 INFO: fwhm_rt        : 3.0
2:01:13.140071 INFO: quant_window   : 3
2:01:13.140150 INFO: ==============================================
2:01:13.453341 INFO: performing precursor FDR with 40 features
2:01:13.453640 INFO: Decoy channel: -1
2:01:13.453668 INFO: competitive: True
2:01:13.473388 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:13.491442 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:01:13.492026 INFO: Using random state 811275 for train-test-split
2:01:15.692217 INFO: Test AUC: 0.765
2:01:15.692333 INFO: Train AUC: 0.763
2:01:15.692363 INFO: AUC difference: 0.26%
2:01:15.946033 INFO: Resetting torch num_threads to 100
2:01:15.948463 PROGRESS: === Extracted 17807 precursors and 120838 fragments ===
2:01:15.948825 INFO: === FDR correction performed with classifier version 6 ===
2:01:15.949546 PROGRESS: ============================= Precursor FDR =============================
2:01:15.949631 PROGRESS: Total precursors accumulated: 2,685
2:01:15.949689 PROGRESS: Target precursors: 2,659 (99.03%)
2:01:15.949740 PROGRESS: Decoy precursors: 26 (0.97%)
2:01:15.949787 PROGRESS: 
2:01:15.949832 PROGRESS: Precursor Summary:
2:01:15.951539 PROGRESS: Channel   0:	 0.050 FDR: 2,659; 0.010 FDR: 2,659; 0.001 FDR: 2,106
2:01:15.951629 PROGRESS: 
2:01:15.951684 PROGRESS: Protein Summary:
2:01:15.953968 PROGRESS: Channel   0:	 0.050 FDR: 2,046; 0.010 FDR: 2,046; 0.001 FDR: 1,662
2:01:15.954063 PROGRESS: =========================================================================
2:01:15.954436 INFO: Target number of precursors reached.
2:01:15.981898 INFO: fragments_df: keeping 5000 of 120838 [sum(precursor_idx_mask)=60595 sum(mass_error_mask)=120838 stop_rank=5000
2:01:15.992900 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:16.382534 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:17.096590 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:17.097047 INFO: Using score_cutoff 9.647883318328857 (fac=0.99, q=1)
2:01:17.097349 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:17.097424 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:17.097477 INFO: Updating optimization_manager: score_cutoff        : 9.5563784866333 -> 9.647883318328857
2:01:17.097526 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:17.101417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:17.108915 INFO: === checking if optimization conditions were reached ===
2:01:17.109034 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:01:17.111909 INFO: Updating optimization_manager: rt_error            : 292.7730076603755 -> 219.10102014418948
2:01:17.112018 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 219.1010.
2:01:17.112082 INFO: ==============================================
2:01:17.112148 INFO: Starting optimization step 2.
2:01:17.112203 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:17.112259 INFO: Using rust extraction backend
2:01:17.112312 PROGRESS: Extracting batch of 5936 precursors
2:01:17.123955 INFO: === Search parameters used ===
2:01:17.124086 INFO: rt_error       : 219.10102014418948
2:01:17.124138 INFO: mobility_error : 0.1
2:01:17.124182 INFO: num_candidates : 3
2:01:17.124223 INFO: ms1_error      : 30
2:01:17.124274 INFO: ms2_error      : 7.4697575
2:01:17.124316 INFO: fwhm_rt        : 3.0
2:01:17.124356 INFO: quant_window   : 3
2:01:17.124395 INFO: ==============================================
2:01:17.228240 INFO: performing precursor FDR with 40 features
2:01:17.228352 INFO: Decoy channel: -1
2:01:17.228376 INFO: competitive: True
2:01:17.233568 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:17.237825 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:01:17.237970 INFO: Using random state 811275 for train-test-split
2:01:18.683633 INFO: Test AUC: 0.759
2:01:18.683749 INFO: Train AUC: 0.768
2:01:18.683778 INFO: AUC difference: 1.25%
2:01:18.937798 INFO: Resetting torch num_threads to 100
2:01:18.940276 PROGRESS: === Extracted 17806 precursors and 118727 fragments ===
2:01:18.940639 INFO: === FDR correction performed with classifier version 6 ===
2:01:18.941365 PROGRESS: ============================= Precursor FDR =============================
2:01:18.941454 PROGRESS: Total precursors accumulated: 2,699
2:01:18.941509 PROGRESS: Target precursors: 2,673 (99.04%)
2:01:18.941561 PROGRESS: Decoy precursors: 26 (0.96%)
2:01:18.941606 PROGRESS: 
2:01:18.941649 PROGRESS: Precursor Summary:
2:01:18.943294 PROGRESS: Channel   0:	 0.050 FDR: 2,673; 0.010 FDR: 2,673; 0.001 FDR: 2,109
2:01:18.943386 PROGRESS: 
2:01:18.943441 PROGRESS: Protein Summary:
2:01:18.945721 PROGRESS: Channel   0:	 0.050 FDR: 2,054; 0.010 FDR: 2,054; 0.001 FDR: 1,660
2:01:18.945816 PROGRESS: =========================================================================
2:01:18.946205 INFO: Target number of precursors reached.
2:01:18.973329 INFO: fragments_df: keeping 5000 of 118727 [sum(precursor_idx_mask)=60296 sum(mass_error_mask)=118727 stop_rank=5000
2:01:18.984337 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:19.370840 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:20.086743 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:20.087193 INFO: Using score_cutoff 9.596156475448607 (fac=0.99, q=1)
2:01:20.087502 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:20.087576 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:20.087627 INFO: Updating optimization_manager: score_cutoff        : 9.647883318328857 -> 9.596156475448607
2:01:20.087678 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:20.091564 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:20.098821 INFO: === checking if optimization conditions were reached ===
2:01:20.098929 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:01:20.101904 INFO: Updating optimization_manager: rt_error            : 219.10102014418948 -> 173.53828780988437
2:01:20.102010 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 173.5383.
2:01:20.102075 INFO: ==============================================
2:01:20.102144 INFO: Starting optimization step 3.
2:01:20.102200 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:20.102258 INFO: Using rust extraction backend
2:01:20.102310 PROGRESS: Extracting batch of 5936 precursors
2:01:20.113457 INFO: === Search parameters used ===
2:01:20.113574 INFO: rt_error       : 173.53828780988437
2:01:20.113624 INFO: mobility_error : 0.1
2:01:20.113689 INFO: num_candidates : 3
2:01:20.113731 INFO: ms1_error      : 30
2:01:20.113771 INFO: ms2_error      : 7.4697575
2:01:20.113811 INFO: fwhm_rt        : 3.0
2:01:20.113857 INFO: quant_window   : 3
2:01:20.113903 INFO: ==============================================
2:01:20.213215 INFO: performing precursor FDR with 40 features
2:01:20.213330 INFO: Decoy channel: -1
2:01:20.213354 INFO: competitive: True
2:01:20.218674 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:20.222940 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:01:20.223073 INFO: Using random state 811275 for train-test-split
2:01:21.648659 INFO: Test AUC: 0.758
2:01:21.648775 INFO: Train AUC: 0.773
2:01:21.648804 INFO: AUC difference: 1.88%
2:01:21.902709 INFO: Resetting torch num_threads to 100
2:01:21.905172 PROGRESS: === Extracted 17801 precursors and 116324 fragments ===
2:01:21.905542 INFO: === FDR correction performed with classifier version 6 ===
2:01:21.906292 PROGRESS: ============================= Precursor FDR =============================
2:01:21.906380 PROGRESS: Total precursors accumulated: 2,733
2:01:21.906437 PROGRESS: Target precursors: 2,706 (99.01%)
2:01:21.906484 PROGRESS: Decoy precursors: 27 (0.99%)
2:01:21.906527 PROGRESS: 
2:01:21.906569 PROGRESS: Precursor Summary:
2:01:21.908221 PROGRESS: Channel   0:	 0.050 FDR: 2,706; 0.010 FDR: 2,706; 0.001 FDR: 2,113
2:01:21.908306 PROGRESS: 
2:01:21.908357 PROGRESS: Protein Summary:
2:01:21.910691 PROGRESS: Channel   0:	 0.050 FDR: 2,083; 0.010 FDR: 2,083; 0.001 FDR: 1,660
2:01:21.910792 PROGRESS: =========================================================================
2:01:21.911222 INFO: Target number of precursors reached.
2:01:21.939750 INFO: fragments_df: keeping 5000 of 116324 [sum(precursor_idx_mask)=60014 sum(mass_error_mask)=116324 stop_rank=5000
2:01:21.953284 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:22.352161 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:23.066844 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:23.067331 INFO: Using score_cutoff 9.44605393409729 (fac=0.99, q=1)
2:01:23.067656 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:23.067736 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:23.067794 INFO: Updating optimization_manager: score_cutoff        : 9.596156475448607 -> 9.44605393409729
2:01:23.067847 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:23.071840 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:23.079420 INFO: === checking if optimization conditions were reached ===
2:01:23.079542 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:01:23.082594 INFO: Updating optimization_manager: rt_error            : 173.53828780988437 -> 166.2720039120781
2:01:23.082700 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 166.2720.
2:01:23.082765 INFO: ==============================================
2:01:23.082834 INFO: Starting optimization step 4.
2:01:23.082898 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:23.082961 INFO: Using rust extraction backend
2:01:23.083017 PROGRESS: Extracting batch of 5936 precursors
2:01:23.094436 INFO: === Search parameters used ===
2:01:23.094583 INFO: rt_error       : 166.2720039120781
2:01:23.094638 INFO: mobility_error : 0.1
2:01:23.094686 INFO: num_candidates : 3
2:01:23.094730 INFO: ms1_error      : 30
2:01:23.094773 INFO: ms2_error      : 7.4697575
2:01:23.094815 INFO: fwhm_rt        : 3.0
2:01:23.094856 INFO: quant_window   : 3
2:01:23.094898 INFO: ==============================================
2:01:23.192052 INFO: performing precursor FDR with 40 features
2:01:23.192170 INFO: Decoy channel: -1
2:01:23.192195 INFO: competitive: True
2:01:23.197269 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:23.201514 INFO: Estimating optimal hyperparameters - samples: 14,241, batch_size: 128, learning_rate: 1.77e-04
2:01:23.201655 INFO: Using random state 811275 for train-test-split
2:01:24.643795 INFO: Test AUC: 0.758
2:01:24.643912 INFO: Train AUC: 0.774
2:01:24.643941 INFO: AUC difference: 2.07%
2:01:24.897938 INFO: Resetting torch num_threads to 100
2:01:24.900384 PROGRESS: === Extracted 17802 precursors and 115846 fragments ===
2:01:24.900752 INFO: === FDR correction performed with classifier version 6 ===
2:01:24.901469 PROGRESS: ============================= Precursor FDR =============================
2:01:24.901558 PROGRESS: Total precursors accumulated: 2,717
2:01:24.901616 PROGRESS: Target precursors: 2,691 (99.04%)
2:01:24.901665 PROGRESS: Decoy precursors: 26 (0.96%)
2:01:24.901711 PROGRESS: 
2:01:24.901754 PROGRESS: Precursor Summary:
2:01:24.903422 PROGRESS: Channel   0:	 0.050 FDR: 2,691; 0.010 FDR: 2,691; 0.001 FDR: 2,078
2:01:24.903522 PROGRESS: 
2:01:24.903577 PROGRESS: Protein Summary:
2:01:24.905922 PROGRESS: Channel   0:	 0.050 FDR: 2,072; 0.010 FDR: 2,072; 0.001 FDR: 1,637
2:01:24.906017 PROGRESS: =========================================================================
2:01:24.906425 INFO: Target number of precursors reached.
2:01:24.932949 INFO: fragments_df: keeping 5000 of 115846 [sum(precursor_idx_mask)=59662 sum(mass_error_mask)=115846 stop_rank=5000
2:01:24.944895 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:25.332661 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:26.058508 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:26.058951 INFO: Using score_cutoff 9.516875581741333 (fac=0.99, q=1)
2:01:26.059266 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:26.059350 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:26.059402 INFO: Updating optimization_manager: score_cutoff        : 9.44605393409729 -> 9.516875581741333
2:01:26.059453 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:26.063510 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:26.071642 INFO: === checking if optimization conditions were reached ===
2:01:26.071765 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:01:26.072548 INFO: Updating optimization_manager: rt_error            : 166.2720039120781 -> 173.53828780988437
2:01:26.072670 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:01:26.072762 INFO: Updating optimization_manager: score_cutoff        : 9.516875581741333 -> 9.44605393409729
2:01:26.072853 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:26.072937 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:26.073019 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 173.5383 found after 5 searches.
2:01:26.073082 INFO: ==============================================
2:01:26.073148 PROGRESS: Optimization finished for rt_error.
2:01:26.084233 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:26.088257 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:26.095943 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:01:26.096064 PROGRESS: ==============================================
2:01:26.096137 PROGRESS: ms2_error      : 7.4698
2:01:26.096190 PROGRESS: rt_error       : 173.5383
2:01:26.096235 PROGRESS: ==============================================
2:01:26.097017 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:26.235050 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:26.589066 INFO: Using rust extraction backend
2:01:26.589419 PROGRESS: Extracting batch of 260426 precursors
2:01:26.999225 INFO: === Search parameters used ===
2:01:26.999534 INFO: rt_error       : 173.53828780988437
2:01:26.999591 INFO: mobility_error : 0.1
2:01:26.999640 INFO: num_candidates : 3
2:01:26.999686 INFO: ms1_error      : 30
2:01:26.999732 INFO: ms2_error      : 7.4697575
2:01:26.999775 INFO: fwhm_rt        : 3.0
2:01:26.999816 INFO: quant_window   : 3
2:01:26.999873 INFO: ==============================================
2:01:27.376529 INFO: Removed 159550 precursors with score below cutoff 9.44605393409729
2:01:27.853560 INFO: performing precursor FDR with 40 features
2:01:27.853680 INFO: Decoy channel: -1
2:01:27.853705 INFO: competitive: True
2:01:27.909754 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:27.940613 WARNING: FDR calculation for 341704 target and 279996 decoy PSMs
2:01:27.940750 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:01:28.108708 INFO: Estimating optimal hyperparameters - samples: 497,360, batch_size: 2,037, learning_rate: 7.05e-04
2:01:28.109662 INFO: Using random state 826821 for train-test-split
2:01:38.907681 INFO: Test AUC: 0.798
2:01:38.907867 INFO: Train AUC: 0.801
2:01:38.907902 INFO: AUC difference: 0.43%
2:01:39.369358 INFO: Resetting torch num_threads to 100
2:01:39.677426 PROGRESS: ============================= Precursor FDR =============================
2:01:39.677734 PROGRESS: Total precursors accumulated: 122,299
2:01:39.677809 PROGRESS: Target precursors: 121,089 (99.01%)
2:01:39.677877 PROGRESS: Decoy precursors: 1,210 (0.99%)
2:01:39.677930 PROGRESS: 
2:01:39.677977 PROGRESS: Precursor Summary:
2:01:39.714167 PROGRESS: Channel   0:	 0.050 FDR: 121,089; 0.010 FDR: 121,089; 0.001 FDR: 106,561
2:01:39.714427 PROGRESS: 
2:01:39.714494 PROGRESS: Protein Summary:
2:01:39.774620 PROGRESS: Channel   0:	 0.050 FDR: 10,098; 0.010 FDR: 10,098; 0.001 FDR: 9,972
2:01:39.774905 PROGRESS: =========================================================================
2:01:39.777432 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
2:01:39.969158 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
2:01:40.258992 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:01:40.624595 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
2:01:40.624746 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant
2:01:40.624850 INFO: Initializing TimingManager
2:01:40.625442 INFO: Initializing RawFileManager
2:01:50.860737 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.
2:01:50.868993 INFO: Determining DIA cycle
2:01:50.886385 INFO: Found cycle with start 0.00 min and length 300.
2:01:51.057178 INFO: RT (min)            : 0.0 - 26.9
2:01:51.057266 INFO: RT duration (sec)   : 1611.2
2:01:51.057296 INFO: RT duration (min)   : 26.9
2:01:51.057318 INFO: Cycle len (scans)   : 300
2:01:51.057338 INFO: Cycle len (sec)     : 1.65
2:01:51.057359 INFO: Number of cycles    : 978
2:01:51.057382 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:01:51.057417 INFO: Creating DIA data object took: 10.431872844696045
2:01:51.736722 INFO: Creating DIA data NG object took: 0.6791915893554688
2:01:51.767842 INFO: Initializing CalibrationManager
2:01:51.768136 INFO: Setting up calibration estimators ..
2:01:51.768195 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:01:51.768279 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'}' ..
2:01:51.768352 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:01:51.768402 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:01:51.768473 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}}' ..
2:01:51.768527 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:01:51.768573 INFO: Done setting up calibration estimators.
2:01:51.768789 INFO: Initializing OptimizationManager
2:01:51.768905 INFO: initial parameter: ms1_error = 30
2:01:51.768956 INFO: initial parameter: ms2_error = 30
2:01:51.769003 INFO: initial parameter: rt_error = 805.6019897460938
2:01:51.769046 INFO: initial parameter: mobility_error = 0.1
2:01:51.769088 INFO: initial parameter: num_candidates = 1
2:01:51.769128 INFO: initial parameter: fwhm_rt = 5
2:01:51.769167 INFO: initial parameter: fwhm_mobility = 0.01
2:01:51.769207 INFO: initial parameter: score_cutoff = 0
2:01:51.769246 INFO: initial parameter: classifier_version = -1
2:01:51.769315 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:01:51.769558 INFO: FDRManager: loading saved state not requested, will be initialized.
2:01:51.769593 INFO: Initializing FDRManager
2:01:51.769629 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:01:51.806556 PROGRESS: Initializing spectral library: 131,664 target precursors potentially observable (0 removed)
2:01:51.830681 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:01:51.831077 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
2:01:51.831182 PROGRESS: Starting initial search for precursors.
2:01:51.831285 INFO: Starting optimization step 0.
2:01:51.831350 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:01:51.831408 INFO: Using rust extraction backend
2:01:51.831463 PROGRESS: Extracting batch of 1977 precursors
2:01:51.836214 INFO: === Search parameters used ===
2:01:51.836312 INFO: rt_error       : 805.6019897460938
2:01:51.836366 INFO: mobility_error : 0.1
2:01:51.836411 INFO: num_candidates : 1
2:01:51.836453 INFO: ms1_error      : 30
2:01:51.836493 INFO: ms2_error      : 30
2:01:51.836533 INFO: fwhm_rt        : 5
2:01:51.836574 INFO: quant_window   : 3
2:01:51.836613 INFO: ==============================================
2:01:51.863585 INFO: performing precursor FDR with 40 features
2:01:51.863661 INFO: Decoy channel: -1
2:01:51.863684 INFO: competitive: True
2:01:51.864914 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:51.866753 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
2:01:51.867558 INFO: Using random state 635114 for train-test-split
2:01:52.017766 INFO: Test AUC: 0.784
2:01:52.017863 INFO: Train AUC: 0.780
2:01:52.017895 INFO: AUC difference: 0.60%
2:01:52.261265 INFO: Resetting torch num_threads to 100
2:01:52.262848 PROGRESS: === Extracted 1976 precursors and 13391 fragments ===
2:01:52.263217 INFO: === FDR correction performed with classifier version -1 ===
2:01:52.263705 PROGRESS: ============================= Precursor FDR =============================
2:01:52.263786 PROGRESS: Total precursors accumulated: 308
2:01:52.263842 PROGRESS: Target precursors: 305 (99.03%)
2:01:52.263890 PROGRESS: Decoy precursors: 3 (0.97%)
2:01:52.263935 PROGRESS: 
2:01:52.263979 PROGRESS: Precursor Summary:
2:01:52.265031 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:   249
2:01:52.265113 PROGRESS: 
2:01:52.265166 PROGRESS: Protein Summary:
2:01:52.266396 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   231
2:01:52.266485 PROGRESS: =========================================================================
2:01:52.266688 INFO: Target number of precursors not reached yet.
2:01:52.274289 INFO: Starting optimization step 1.
2:01:52.274396 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:01:52.274464 INFO: Using rust extraction backend
2:01:52.274520 PROGRESS: Extracting batch of 3959 precursors
2:01:52.282907 INFO: === Search parameters used ===
2:01:52.283011 INFO: rt_error       : 805.6019897460938
2:01:52.283060 INFO: mobility_error : 0.1
2:01:52.283104 INFO: num_candidates : 1
2:01:52.283145 INFO: ms1_error      : 30
2:01:52.283185 INFO: ms2_error      : 30
2:01:52.283224 INFO: fwhm_rt        : 5
2:01:52.283262 INFO: quant_window   : 3
2:01:52.283299 INFO: ==============================================
2:01:52.329670 INFO: performing precursor FDR with 40 features
2:01:52.329759 INFO: Decoy channel: -1
2:01:52.329782 INFO: competitive: True
2:01:52.333770 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:52.336103 INFO: Estimating optimal hyperparameters - samples: 4,744, batch_size: 128, learning_rate: 1.77e-04
2:01:52.336189 INFO: Using random state 688457 for train-test-split
2:01:52.810784 INFO: Test AUC: 0.811
2:01:52.810872 INFO: Train AUC: 0.829
2:01:52.810900 INFO: AUC difference: 2.15%
2:01:53.052524 INFO: Resetting torch num_threads to 100
2:01:53.055475 PROGRESS: === Extracted 5931 precursors and 40755 fragments ===
2:01:53.055851 INFO: === FDR correction performed with classifier version -1 ===
2:01:53.056438 PROGRESS: ============================= Precursor FDR =============================
2:01:53.056520 PROGRESS: Total precursors accumulated: 1,369
2:01:53.056576 PROGRESS: Target precursors: 1,356 (99.05%)
2:01:53.056626 PROGRESS: Decoy precursors: 13 (0.95%)
2:01:53.056672 PROGRESS: 
2:01:53.056715 PROGRESS: Precursor Summary:
2:01:53.058044 PROGRESS: Channel   0:	 0.050 FDR: 1,356; 0.010 FDR: 1,356; 0.001 FDR:   767
2:01:53.058136 PROGRESS: 
2:01:53.058191 PROGRESS: Protein Summary:
2:01:53.059880 PROGRESS: Channel   0:	 0.050 FDR: 1,114; 0.010 FDR: 1,114; 0.001 FDR:   662
2:01:53.059966 PROGRESS: =========================================================================
2:01:53.060218 INFO: Target number of precursors reached.
2:01:53.068903 INFO: fragments_df: keeping 5000 of 40755 [sum(precursor_idx_mask)=14159 sum(mass_error_mask)=40755 stop_rank=5000
2:01:53.079499 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:53.301941 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:54.016151 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:01:54.016593 INFO: Using score_cutoff 12.438250183582307 (fac=0.99, q=1)
2:01:54.016932 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:01:54.017013 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:01:54.017070 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.438250183582307
2:01:54.017132 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:54.020983 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:54.028912 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:01:54.029036 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:01:54.029117 INFO: Starting optimization step 2.
2:01:54.029198 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:54.029263 INFO: Using rust extraction backend
2:01:54.029318 PROGRESS: Extracting batch of 5936 precursors
2:01:54.040552 INFO: === Search parameters used ===
2:01:54.040674 INFO: rt_error       : 805.6019897460938
2:01:54.040726 INFO: mobility_error : 0.1
2:01:54.040771 INFO: num_candidates : 3
2:01:54.040814 INFO: ms1_error      : 30
2:01:54.040855 INFO: ms2_error      : 30
2:01:54.040897 INFO: fwhm_rt        : 3.0
2:01:54.040938 INFO: quant_window   : 3
2:01:54.040978 INFO: ==============================================
2:01:54.150248 INFO: performing precursor FDR with 40 features
2:01:54.150361 INFO: Decoy channel: -1
2:01:54.150386 INFO: competitive: True
2:01:54.156761 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:54.160863 INFO: Estimating optimal hyperparameters - samples: 14,212, batch_size: 128, learning_rate: 1.77e-04
2:01:54.161001 INFO: Using random state 496540 for train-test-split
2:01:55.599396 INFO: Test AUC: 0.690
2:01:55.599509 INFO: Train AUC: 0.698
2:01:55.599539 INFO: AUC difference: 1.13%
2:01:55.850709 INFO: Resetting torch num_threads to 100
2:01:55.852981 PROGRESS: === Extracted 17766 precursors and 106050 fragments ===
2:01:55.853342 INFO: === FDR correction performed with classifier version 1 ===
2:01:55.853969 PROGRESS: ============================= Precursor FDR =============================
2:01:55.854055 PROGRESS: Total precursors accumulated: 1,754
2:01:55.854112 PROGRESS: Target precursors: 1,737 (99.03%)
2:01:55.854160 PROGRESS: Decoy precursors: 17 (0.97%)
2:01:55.854205 PROGRESS: 
2:01:55.854248 PROGRESS: Precursor Summary:
2:01:55.855617 PROGRESS: Channel   0:	 0.050 FDR: 1,737; 0.010 FDR: 1,737; 0.001 FDR: 1,150
2:01:55.855715 PROGRESS: 
2:01:55.855772 PROGRESS: Protein Summary:
2:01:55.857592 PROGRESS: Channel   0:	 0.050 FDR: 1,401; 0.010 FDR: 1,401; 0.001 FDR:   960
2:01:55.857687 PROGRESS: =========================================================================
2:01:55.858079 INFO: Target number of precursors reached.
2:01:55.876924 INFO: fragments_df: keeping 5000 of 106050 [sum(precursor_idx_mask)=37677 sum(mass_error_mask)=106050 stop_rank=5000
2:01:55.887847 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:56.146177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:56.859307 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:56.859758 INFO: Using score_cutoff 12.23735403213501 (fac=0.99, q=1)
2:01:56.860060 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:56.860135 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:56.860189 INFO: Updating optimization_manager: score_cutoff        : 12.438250183582307 -> 12.23735403213501
2:01:56.860250 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:56.864142 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:56.872209 INFO: === checking if optimization conditions were reached ===
2:01:56.873908 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.4697575
2:01:56.874010 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:01:56.874076 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:01:56.874130 INFO: ==============================================
2:01:56.874205 INFO: Starting optimization step 3.
2:01:56.874269 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:01:56.874324 INFO: Using rust extraction backend
2:01:56.874375 PROGRESS: Extracting batch of 5936 precursors
2:01:56.885732 INFO: === Search parameters used ===
2:01:56.885857 INFO: rt_error       : 805.6019897460938
2:01:56.885913 INFO: mobility_error : 0.1
2:01:56.885958 INFO: num_candidates : 3
2:01:56.885998 INFO: ms1_error      : 30
2:01:56.886038 INFO: ms2_error      : 7.4697575
2:01:56.886077 INFO: fwhm_rt        : 3.0
2:01:56.886116 INFO: quant_window   : 3
2:01:56.886155 INFO: ==============================================
2:01:56.992514 INFO: performing precursor FDR with 40 features
2:01:56.992632 INFO: Decoy channel: -1
2:01:56.992656 INFO: competitive: True
2:01:56.999273 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:57.003325 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:01:57.003459 INFO: Using random state 157763 for train-test-split
2:01:58.421519 INFO: Test AUC: 0.736
2:01:58.421634 INFO: Train AUC: 0.748
2:01:58.421663 INFO: AUC difference: 1.55%
2:02:00.100671 INFO: Resetting torch num_threads to 100
2:02:00.103082 PROGRESS: === Extracted 17807 precursors and 122527 fragments ===
2:02:00.103454 INFO: === FDR correction performed with classifier version 2 ===
2:02:00.104147 PROGRESS: ============================= Precursor FDR =============================
2:02:00.104235 PROGRESS: Total precursors accumulated: 2,340
2:02:00.104294 PROGRESS: Target precursors: 2,317 (99.02%)
2:02:00.104346 PROGRESS: Decoy precursors: 23 (0.98%)
2:02:00.104393 PROGRESS: 
2:02:00.104440 PROGRESS: Precursor Summary:
2:02:00.105996 PROGRESS: Channel   0:	 0.050 FDR: 2,317; 0.010 FDR: 2,317; 0.001 FDR: 1,263
2:02:00.106090 PROGRESS: 
2:02:00.106146 PROGRESS: Protein Summary:
2:02:00.108230 PROGRESS: Channel   0:	 0.050 FDR: 1,814; 0.010 FDR: 1,814; 0.001 FDR: 1,041
2:02:00.108321 PROGRESS: =========================================================================
2:02:00.108674 INFO: Target number of precursors reached.
2:02:00.134983 INFO: fragments_df: keeping 5000 of 122527 [sum(precursor_idx_mask)=54415 sum(mass_error_mask)=122527 stop_rank=5000
2:02:00.145824 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:00.479918 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:01.197448 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:01.197912 INFO: Using score_cutoff 10.9129904296875 (fac=0.99, q=1)
2:02:01.198226 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:01.198304 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:01.198360 INFO: Updating optimization_manager: score_cutoff        : 12.23735403213501 -> 10.9129904296875
2:02:01.198414 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:01.202374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:01.209889 INFO: === checking if optimization conditions were reached ===
2:02:01.211539 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:02:01.211637 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:02:01.211719 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:02:01.211777 INFO: ==============================================
2:02:01.211847 INFO: Starting optimization step 4.
2:02:01.211902 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:01.211958 INFO: Using rust extraction backend
2:02:01.212010 PROGRESS: Extracting batch of 5936 precursors
2:02:01.223428 INFO: === Search parameters used ===
2:02:01.223549 INFO: rt_error       : 805.6019897460938
2:02:01.223601 INFO: mobility_error : 0.1
2:02:01.223645 INFO: num_candidates : 3
2:02:01.223685 INFO: ms1_error      : 30
2:02:01.223725 INFO: ms2_error      : 7.4697575
2:02:01.223764 INFO: fwhm_rt        : 3.0
2:02:01.223802 INFO: quant_window   : 3
2:02:01.223839 INFO: ==============================================
2:02:01.322254 INFO: performing precursor FDR with 40 features
2:02:01.322368 INFO: Decoy channel: -1
2:02:01.322392 INFO: competitive: True
2:02:01.327779 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:01.331937 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:01.332073 INFO: Using random state 812821 for train-test-split
2:02:02.757529 INFO: Test AUC: 0.746
2:02:02.757644 INFO: Train AUC: 0.758
2:02:02.757673 INFO: AUC difference: 1.54%
2:02:03.014117 INFO: Resetting torch num_threads to 100
2:02:03.016515 PROGRESS: === Extracted 17806 precursors and 122489 fragments ===
2:02:03.016883 INFO: === FDR correction performed with classifier version 3 ===
2:02:03.017584 PROGRESS: ============================= Precursor FDR =============================
2:02:03.017670 PROGRESS: Total precursors accumulated: 2,478
2:02:03.017729 PROGRESS: Target precursors: 2,454 (99.03%)
2:02:03.017777 PROGRESS: Decoy precursors: 24 (0.97%)
2:02:03.017821 PROGRESS: 
2:02:03.017888 PROGRESS: Precursor Summary:
2:02:03.019489 PROGRESS: Channel   0:	 0.050 FDR: 2,454; 0.010 FDR: 2,454; 0.001 FDR: 1,742
2:02:03.019582 PROGRESS: 
2:02:03.019635 PROGRESS: Protein Summary:
2:02:03.021802 PROGRESS: Channel   0:	 0.050 FDR: 1,903; 0.010 FDR: 1,903; 0.001 FDR: 1,414
2:02:03.021905 PROGRESS: =========================================================================
2:02:03.022289 INFO: Target number of precursors reached.
2:02:03.049089 INFO: fragments_df: keeping 5000 of 122489 [sum(precursor_idx_mask)=57206 sum(mass_error_mask)=122489 stop_rank=5000
2:02:03.060036 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:03.414058 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:04.132484 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:04.132945 INFO: Using score_cutoff 10.63169791431427 (fac=0.99, q=1)
2:02:04.133256 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:04.133329 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:04.133381 INFO: Updating optimization_manager: score_cutoff        : 10.9129904296875 -> 10.63169791431427
2:02:04.133430 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:04.137355 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:04.144857 INFO: === checking if optimization conditions were reached ===
2:02:04.146538 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:02:04.146642 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:02:04.146707 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:02:04.146762 INFO: ==============================================
2:02:04.146823 INFO: Starting optimization step 5.
2:02:04.146875 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:04.146930 INFO: Using rust extraction backend
2:02:04.146981 PROGRESS: Extracting batch of 5936 precursors
2:02:04.158306 INFO: === Search parameters used ===
2:02:04.158413 INFO: rt_error       : 805.6019897460938
2:02:04.158463 INFO: mobility_error : 0.1
2:02:04.158506 INFO: num_candidates : 3
2:02:04.158548 INFO: ms1_error      : 30
2:02:04.158587 INFO: ms2_error      : 7.4697575
2:02:04.158627 INFO: fwhm_rt        : 3.0
2:02:04.158667 INFO: quant_window   : 3
2:02:04.158705 INFO: ==============================================
2:02:04.262376 INFO: performing precursor FDR with 40 features
2:02:04.262497 INFO: Decoy channel: -1
2:02:04.262524 INFO: competitive: True
2:02:04.267773 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:04.271932 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:04.272072 INFO: Using random state 533813 for train-test-split
2:02:05.701185 INFO: Test AUC: 0.757
2:02:05.701301 INFO: Train AUC: 0.764
2:02:05.701331 INFO: AUC difference: 0.84%
2:02:05.957933 INFO: Resetting torch num_threads to 100
2:02:05.960391 PROGRESS: === Extracted 17806 precursors and 122479 fragments ===
2:02:05.960766 INFO: === FDR correction performed with classifier version 4 ===
2:02:05.961480 PROGRESS: ============================= Precursor FDR =============================
2:02:05.961568 PROGRESS: Total precursors accumulated: 2,604
2:02:05.961628 PROGRESS: Target precursors: 2,579 (99.04%)
2:02:05.961690 PROGRESS: Decoy precursors: 25 (0.96%)
2:02:05.961741 PROGRESS: 
2:02:05.961787 PROGRESS: Precursor Summary:
2:02:05.963434 PROGRESS: Channel   0:	 0.050 FDR: 2,579; 0.010 FDR: 2,579; 0.001 FDR: 1,984
2:02:05.963529 PROGRESS: 
2:02:05.963584 PROGRESS: Protein Summary:
2:02:05.965867 PROGRESS: Channel   0:	 0.050 FDR: 1,996; 0.010 FDR: 1,996; 0.001 FDR: 1,583
2:02:05.965972 PROGRESS: =========================================================================
2:02:05.966340 INFO: Target number of precursors reached.
2:02:05.993556 INFO: fragments_df: keeping 5000 of 122479 [sum(precursor_idx_mask)=59627 sum(mass_error_mask)=122479 stop_rank=5000
2:02:06.004499 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:06.377283 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:07.096207 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:07.096680 INFO: Using score_cutoff 10.245576841163636 (fac=0.99, q=1)
2:02:07.096998 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:07.097078 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:07.097133 INFO: Updating optimization_manager: score_cutoff        : 10.63169791431427 -> 10.245576841163636
2:02:07.097196 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:07.101135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:07.108711 INFO: === checking if optimization conditions were reached ===
2:02:07.110384 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:02:07.110493 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:02:07.110557 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:02:07.110613 INFO: ==============================================
2:02:07.110677 INFO: Starting optimization step 6.
2:02:07.110734 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:07.110793 INFO: Using rust extraction backend
2:02:07.110848 PROGRESS: Extracting batch of 5936 precursors
2:02:07.122103 INFO: === Search parameters used ===
2:02:07.122221 INFO: rt_error       : 805.6019897460938
2:02:07.122272 INFO: mobility_error : 0.1
2:02:07.122318 INFO: num_candidates : 3
2:02:07.122360 INFO: ms1_error      : 30
2:02:07.122401 INFO: ms2_error      : 7.4697575
2:02:07.122443 INFO: fwhm_rt        : 3.0
2:02:07.122484 INFO: quant_window   : 3
2:02:07.122525 INFO: ==============================================
2:02:07.229716 INFO: performing precursor FDR with 40 features
2:02:07.229833 INFO: Decoy channel: -1
2:02:07.229916 INFO: competitive: True
2:02:07.235119 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:07.239375 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:07.239508 INFO: Using random state 320540 for train-test-split
2:02:08.668952 INFO: Test AUC: 0.753
2:02:08.669064 INFO: Train AUC: 0.772
2:02:08.669093 INFO: AUC difference: 2.49%
2:02:08.923289 INFO: Resetting torch num_threads to 100
2:02:08.925712 PROGRESS: === Extracted 17806 precursors and 122475 fragments ===
2:02:08.926101 INFO: === FDR correction performed with classifier version 5 ===
2:02:08.926807 PROGRESS: ============================= Precursor FDR =============================
2:02:08.926888 PROGRESS: Total precursors accumulated: 2,628
2:02:08.926955 PROGRESS: Target precursors: 2,602 (99.01%)
2:02:08.927005 PROGRESS: Decoy precursors: 26 (0.99%)
2:02:08.927049 PROGRESS: 
2:02:08.927092 PROGRESS: Precursor Summary:
2:02:08.928714 PROGRESS: Channel   0:	 0.050 FDR: 2,602; 0.010 FDR: 2,602; 0.001 FDR: 2,031
2:02:08.928799 PROGRESS: 
2:02:08.928852 PROGRESS: Protein Summary:
2:02:08.931112 PROGRESS: Channel   0:	 0.050 FDR: 2,012; 0.010 FDR: 2,012; 0.001 FDR: 1,618
2:02:08.931208 PROGRESS: =========================================================================
2:02:08.931580 INFO: Target number of precursors reached.
2:02:08.958833 INFO: fragments_df: keeping 5000 of 122475 [sum(precursor_idx_mask)=60081 sum(mass_error_mask)=122475 stop_rank=5000
2:02:08.969630 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:09.346271 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:10.060409 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:10.060868 INFO: Using score_cutoff 9.831083905220032 (fac=0.99, q=1)
2:02:10.061197 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:10.061275 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:10.061331 INFO: Updating optimization_manager: score_cutoff        : 10.245576841163636 -> 9.831083905220032
2:02:10.061386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:10.065299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:10.072772 INFO: === checking if optimization conditions were reached ===
2:02:10.074444 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:02:10.074553 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:02:10.074621 PROGRESS: ✅ ms2_error      : 7.4698 <= 7.4698
2:02:10.074680 INFO: ==============================================
2:02:10.074744 PROGRESS: Optimization finished for ms2_error.
2:02:10.085041 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:10.088811 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:10.096226 INFO: Starting optimization step 0.
2:02:10.096332 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:10.096404 INFO: Using rust extraction backend
2:02:10.096464 PROGRESS: Extracting batch of 5936 precursors
2:02:10.107995 INFO: === Search parameters used ===
2:02:10.108120 INFO: rt_error       : 805.6019897460938
2:02:10.108173 INFO: mobility_error : 0.1
2:02:10.108221 INFO: num_candidates : 3
2:02:10.108264 INFO: ms1_error      : 30
2:02:10.108308 INFO: ms2_error      : 7.4697575
2:02:10.108350 INFO: fwhm_rt        : 3.0
2:02:10.108391 INFO: quant_window   : 3
2:02:10.108432 INFO: ==============================================
2:02:10.213366 INFO: performing precursor FDR with 40 features
2:02:10.213485 INFO: Decoy channel: -1
2:02:10.213511 INFO: competitive: True
2:02:10.218706 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:10.222855 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:10.222993 INFO: Using random state 834843 for train-test-split
2:02:11.658286 INFO: Test AUC: 0.766
2:02:11.658403 INFO: Train AUC: 0.776
2:02:11.658433 INFO: AUC difference: 1.36%
2:02:11.914449 INFO: Resetting torch num_threads to 100
2:02:11.916871 PROGRESS: === Extracted 17806 precursors and 122440 fragments ===
2:02:11.917246 INFO: === FDR correction performed with classifier version 6 ===
2:02:11.917982 PROGRESS: ============================= Precursor FDR =============================
2:02:11.918075 PROGRESS: Total precursors accumulated: 2,679
2:02:11.918134 PROGRESS: Target precursors: 2,653 (99.03%)
2:02:11.918183 PROGRESS: Decoy precursors: 26 (0.97%)
2:02:11.918238 PROGRESS: 
2:02:11.918281 PROGRESS: Precursor Summary:
2:02:11.919876 PROGRESS: Channel   0:	 0.050 FDR: 2,653; 0.010 FDR: 2,653; 0.001 FDR: 1,672
2:02:11.919968 PROGRESS: 
2:02:11.920021 PROGRESS: Protein Summary:
2:02:11.922236 PROGRESS: Channel   0:	 0.050 FDR: 2,047; 0.010 FDR: 2,047; 0.001 FDR: 1,364
2:02:11.922336 PROGRESS: =========================================================================
2:02:11.922703 INFO: Target number of precursors reached.
2:02:11.950265 INFO: fragments_df: keeping 5000 of 122440 [sum(precursor_idx_mask)=60994 sum(mass_error_mask)=122440 stop_rank=5000
2:02:11.961284 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:12.344352 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:13.060189 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:13.060642 INFO: Using score_cutoff 9.646309592056275 (fac=0.99, q=1)
2:02:13.060948 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:13.061027 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:13.061081 INFO: Updating optimization_manager: score_cutoff        : 9.831083905220032 -> 9.646309592056275
2:02:13.061132 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:13.065051 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:13.072757 INFO: === checking if optimization conditions were reached ===
2:02:13.072876 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:02:13.075628 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 428.5631238364446
2:02:13.075730 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 428.5631.
2:02:13.075791 INFO: ==============================================
2:02:13.075854 INFO: Starting optimization step 1.
2:02:13.075908 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:13.075964 INFO: Using rust extraction backend
2:02:13.076015 PROGRESS: Extracting batch of 5936 precursors
2:02:13.087469 INFO: === Search parameters used ===
2:02:13.087584 INFO: rt_error       : 428.5631238364446
2:02:13.087633 INFO: mobility_error : 0.1
2:02:13.087677 INFO: num_candidates : 3
2:02:13.087719 INFO: ms1_error      : 30
2:02:13.087760 INFO: ms2_error      : 7.4697575
2:02:13.087800 INFO: fwhm_rt        : 3.0
2:02:13.087850 INFO: quant_window   : 3
2:02:13.087890 INFO: ==============================================
2:02:13.186157 INFO: performing precursor FDR with 40 features
2:02:13.186271 INFO: Decoy channel: -1
2:02:13.186296 INFO: competitive: True
2:02:13.191459 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:13.195590 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:13.195718 INFO: Using random state 834843 for train-test-split
2:02:14.629153 INFO: Test AUC: 0.761
2:02:14.629279 INFO: Train AUC: 0.780
2:02:14.629308 INFO: AUC difference: 2.39%
2:02:14.881286 INFO: Resetting torch num_threads to 100
2:02:14.883682 PROGRESS: === Extracted 17806 precursors and 121979 fragments ===
2:02:14.884054 INFO: === FDR correction performed with classifier version 6 ===
2:02:14.884761 PROGRESS: ============================= Precursor FDR =============================
2:02:14.884848 PROGRESS: Total precursors accumulated: 2,689
2:02:14.884909 PROGRESS: Target precursors: 2,663 (99.03%)
2:02:14.884961 PROGRESS: Decoy precursors: 26 (0.97%)
2:02:14.885009 PROGRESS: 
2:02:14.885056 PROGRESS: Precursor Summary:
2:02:14.886697 PROGRESS: Channel   0:	 0.050 FDR: 2,663; 0.010 FDR: 2,663; 0.001 FDR: 2,037
2:02:14.886796 PROGRESS: 
2:02:14.886863 PROGRESS: Protein Summary:
2:02:14.889141 PROGRESS: Channel   0:	 0.050 FDR: 2,055; 0.010 FDR: 2,055; 0.001 FDR: 1,622
2:02:14.889234 PROGRESS: =========================================================================
2:02:14.889588 INFO: Target number of precursors reached.
2:02:14.917459 INFO: fragments_df: keeping 5000 of 121979 [sum(precursor_idx_mask)=61096 sum(mass_error_mask)=121979 stop_rank=5000
2:02:14.928274 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:15.314319 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:16.024428 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:16.024883 INFO: Using score_cutoff 9.788639199829102 (fac=0.99, q=1)
2:02:16.025187 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:16.025261 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:16.025312 INFO: Updating optimization_manager: score_cutoff        : 9.646309592056275 -> 9.788639199829102
2:02:16.025362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:16.029268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:16.036868 INFO: === checking if optimization conditions were reached ===
2:02:16.036988 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:02:16.039856 INFO: Updating optimization_manager: rt_error            : 428.5631238364446 -> 357.5864716666208
2:02:16.039956 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 357.5865.
2:02:16.040019 INFO: ==============================================
2:02:16.040084 INFO: Starting optimization step 2.
2:02:16.040138 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:16.040194 INFO: Using rust extraction backend
2:02:16.040245 PROGRESS: Extracting batch of 5936 precursors
2:02:16.051399 INFO: === Search parameters used ===
2:02:16.051504 INFO: rt_error       : 357.5864716666208
2:02:16.051555 INFO: mobility_error : 0.1
2:02:16.051600 INFO: num_candidates : 3
2:02:16.051641 INFO: ms1_error      : 30
2:02:16.051692 INFO: ms2_error      : 7.4697575
2:02:16.051734 INFO: fwhm_rt        : 3.0
2:02:16.051773 INFO: quant_window   : 3
2:02:16.051811 INFO: ==============================================
2:02:16.148389 INFO: performing precursor FDR with 40 features
2:02:16.148503 INFO: Decoy channel: -1
2:02:16.148526 INFO: competitive: True
2:02:16.153723 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:16.157783 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:16.157930 INFO: Using random state 834843 for train-test-split
2:02:17.613382 INFO: Test AUC: 0.770
2:02:17.613499 INFO: Train AUC: 0.777
2:02:17.613528 INFO: AUC difference: 0.91%
2:02:17.864355 INFO: Resetting torch num_threads to 100
2:02:17.866755 PROGRESS: === Extracted 17805 precursors and 121553 fragments ===
2:02:17.867127 INFO: === FDR correction performed with classifier version 6 ===
2:02:17.867836 PROGRESS: ============================= Precursor FDR =============================
2:02:17.867919 PROGRESS: Total precursors accumulated: 2,696
2:02:17.867976 PROGRESS: Target precursors: 2,670 (99.04%)
2:02:17.868036 PROGRESS: Decoy precursors: 26 (0.96%)
2:02:17.868081 PROGRESS: 
2:02:17.868123 PROGRESS: Precursor Summary:
2:02:17.869770 PROGRESS: Channel   0:	 0.050 FDR: 2,670; 0.010 FDR: 2,670; 0.001 FDR: 2,071
2:02:17.869869 PROGRESS: 
2:02:17.869929 PROGRESS: Protein Summary:
2:02:17.872213 PROGRESS: Channel   0:	 0.050 FDR: 2,057; 0.010 FDR: 2,057; 0.001 FDR: 1,649
2:02:17.872308 PROGRESS: =========================================================================
2:02:17.872673 INFO: Target number of precursors reached.
2:02:17.899996 INFO: fragments_df: keeping 5000 of 121553 [sum(precursor_idx_mask)=61111 sum(mass_error_mask)=121553 stop_rank=5000
2:02:17.910790 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:18.296359 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:19.004811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:19.005270 INFO: Using score_cutoff 9.72776896047592 (fac=0.99, q=1)
2:02:19.005579 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:19.005652 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:19.005712 INFO: Updating optimization_manager: score_cutoff        : 9.788639199829102 -> 9.72776896047592
2:02:19.005764 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:19.009684 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:19.017128 INFO: === checking if optimization conditions were reached ===
2:02:19.017248 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:02:19.020201 INFO: Updating optimization_manager: rt_error            : 357.5864716666208 -> 362.9054141515429
2:02:19.020305 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 362.9054.
2:02:19.020368 INFO: ==============================================
2:02:19.020433 INFO: Starting optimization step 3.
2:02:19.020488 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:19.020545 INFO: Using rust extraction backend
2:02:19.020600 PROGRESS: Extracting batch of 5936 precursors
2:02:19.031930 INFO: === Search parameters used ===
2:02:19.032046 INFO: rt_error       : 362.9054141515429
2:02:19.032095 INFO: mobility_error : 0.1
2:02:19.032151 INFO: num_candidates : 3
2:02:19.032195 INFO: ms1_error      : 30
2:02:19.032237 INFO: ms2_error      : 7.4697575
2:02:19.032278 INFO: fwhm_rt        : 3.0
2:02:19.032318 INFO: quant_window   : 3
2:02:19.032356 INFO: ==============================================
2:02:19.135188 INFO: performing precursor FDR with 40 features
2:02:19.135303 INFO: Decoy channel: -1
2:02:19.135326 INFO: competitive: True
2:02:19.140472 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:19.144597 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:19.144722 INFO: Using random state 834843 for train-test-split
2:02:20.562986 INFO: Test AUC: 0.771
2:02:20.563108 INFO: Train AUC: 0.777
2:02:20.563138 INFO: AUC difference: 0.76%
2:02:20.814080 INFO: Resetting torch num_threads to 100
2:02:20.816484 PROGRESS: === Extracted 17806 precursors and 121593 fragments ===
2:02:20.816862 INFO: === FDR correction performed with classifier version 6 ===
2:02:20.817573 PROGRESS: ============================= Precursor FDR =============================
2:02:20.817659 PROGRESS: Total precursors accumulated: 2,724
2:02:20.817717 PROGRESS: Target precursors: 2,698 (99.05%)
2:02:20.817767 PROGRESS: Decoy precursors: 26 (0.95%)
2:02:20.817813 PROGRESS: 
2:02:20.817883 PROGRESS: Precursor Summary:
2:02:20.819510 PROGRESS: Channel   0:	 0.050 FDR: 2,698; 0.010 FDR: 2,698; 0.001 FDR: 2,049
2:02:20.819599 PROGRESS: 
2:02:20.819654 PROGRESS: Protein Summary:
2:02:20.821939 PROGRESS: Channel   0:	 0.050 FDR: 2,078; 0.010 FDR: 2,078; 0.001 FDR: 1,632
2:02:20.822033 PROGRESS: =========================================================================
2:02:20.822406 INFO: Target number of precursors reached.
2:02:20.850214 INFO: fragments_df: keeping 5000 of 121593 [sum(precursor_idx_mask)=61667 sum(mass_error_mask)=121593 stop_rank=5000
2:02:20.860987 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:21.190522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:21.833753 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:21.834224 INFO: Using score_cutoff 9.521692533874512 (fac=0.99, q=1)
2:02:21.834541 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:21.834616 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:21.834671 INFO: Updating optimization_manager: score_cutoff        : 9.72776896047592 -> 9.521692533874512
2:02:21.834722 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:21.838670 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:21.846102 INFO: === checking if optimization conditions were reached ===
2:02:21.846220 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:02:21.849149 INFO: Updating optimization_manager: rt_error            : 362.9054141515429 -> 363.3549970892675
2:02:21.849262 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 363.3550.
2:02:21.849325 INFO: ==============================================
2:02:21.849391 INFO: Starting optimization step 4.
2:02:21.849446 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:21.849502 INFO: Using rust extraction backend
2:02:21.849553 PROGRESS: Extracting batch of 5936 precursors
2:02:21.860835 INFO: === Search parameters used ===
2:02:21.860966 INFO: rt_error       : 363.3549970892675
2:02:21.861019 INFO: mobility_error : 0.1
2:02:21.861064 INFO: num_candidates : 3
2:02:21.861105 INFO: ms1_error      : 30
2:02:21.861146 INFO: ms2_error      : 7.4697575
2:02:21.861186 INFO: fwhm_rt        : 3.0
2:02:21.861226 INFO: quant_window   : 3
2:02:21.861266 INFO: ==============================================
2:02:21.955529 INFO: performing precursor FDR with 40 features
2:02:21.955643 INFO: Decoy channel: -1
2:02:21.955667 INFO: competitive: True
2:02:21.960810 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:21.964828 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:21.964951 INFO: Using random state 834843 for train-test-split
2:02:23.399684 INFO: Test AUC: 0.767
2:02:23.399801 INFO: Train AUC: 0.777
2:02:23.399829 INFO: AUC difference: 1.27%
2:02:23.651073 INFO: Resetting torch num_threads to 100
2:02:23.653472 PROGRESS: === Extracted 17806 precursors and 121600 fragments ===
2:02:23.653835 INFO: === FDR correction performed with classifier version 6 ===
2:02:23.654559 PROGRESS: ============================= Precursor FDR =============================
2:02:23.654643 PROGRESS: Total precursors accumulated: 2,688
2:02:23.654698 PROGRESS: Target precursors: 2,662 (99.03%)
2:02:23.654746 PROGRESS: Decoy precursors: 26 (0.97%)
2:02:23.654788 PROGRESS: 
2:02:23.654830 PROGRESS: Precursor Summary:
2:02:23.656472 PROGRESS: Channel   0:	 0.050 FDR: 2,662; 0.010 FDR: 2,662; 0.001 FDR: 2,128
2:02:23.656559 PROGRESS: 
2:02:23.656611 PROGRESS: Protein Summary:
2:02:23.658887 PROGRESS: Channel   0:	 0.050 FDR: 2,049; 0.010 FDR: 2,049; 0.001 FDR: 1,688
2:02:23.658979 PROGRESS: =========================================================================
2:02:23.659339 INFO: Target number of precursors reached.
2:02:23.686839 INFO: fragments_df: keeping 5000 of 121600 [sum(precursor_idx_mask)=60887 sum(mass_error_mask)=121600 stop_rank=5000
2:02:23.697824 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:24.023094 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:24.667567 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:24.668027 INFO: Using score_cutoff 9.561704158973694 (fac=0.99, q=1)
2:02:24.668340 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:24.668415 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:24.668467 INFO: Updating optimization_manager: score_cutoff        : 9.521692533874512 -> 9.561704158973694
2:02:24.668518 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:24.672422 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:24.680155 INFO: === checking if optimization conditions were reached ===
2:02:24.680260 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:02:24.680960 INFO: Updating optimization_manager: rt_error            : 363.3549970892675 -> 362.9054141515429
2:02:24.681077 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:02:24.681170 INFO: Updating optimization_manager: score_cutoff        : 9.561704158973694 -> 9.521692533874512
2:02:24.681252 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:24.681333 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:24.681415 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 362.9054 found after 5 searches.
2:02:24.681479 INFO: ==============================================
2:02:24.681550 PROGRESS: Optimization finished for rt_error.
2:02:24.691936 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:24.695654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:24.703114 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:02:24.703218 PROGRESS: ==============================================
2:02:24.703283 PROGRESS: ms2_error      : 7.4698
2:02:24.703334 PROGRESS: rt_error       : 362.9054
2:02:24.703378 PROGRESS: ==============================================
2:02:24.704013 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:24.838302 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:25.193371 INFO: Using rust extraction backend
2:02:25.193696 PROGRESS: Extracting batch of 260426 precursors
2:02:25.602699 INFO: === Search parameters used ===
2:02:25.602988 INFO: rt_error       : 362.9054141515429
2:02:25.603045 INFO: mobility_error : 0.1
2:02:25.603095 INFO: num_candidates : 3
2:02:25.603141 INFO: ms1_error      : 30
2:02:25.603185 INFO: ms2_error      : 7.4697575
2:02:25.603228 INFO: fwhm_rt        : 3.0
2:02:25.603270 INFO: quant_window   : 3
2:02:25.603316 INFO: ==============================================
2:02:26.092715 INFO: Removed 104846 precursors with score below cutoff 9.521692533874512
2:02:26.550236 INFO: performing precursor FDR with 40 features
2:02:26.550356 INFO: Decoy channel: -1
2:02:26.550382 INFO: competitive: True
2:02:26.608700 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:26.641720 WARNING: FDR calculation for 359772 target and 316660 decoy PSMs
2:02:26.641863 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:02:26.809635 INFO: Estimating optimal hyperparameters - samples: 541,145, batch_size: 2,216, learning_rate: 7.36e-04
2:02:26.810411 INFO: Using random state 916040 for train-test-split
2:02:37.872424 INFO: Test AUC: 0.783
2:02:37.872560 INFO: Train AUC: 0.788
2:02:37.872591 INFO: AUC difference: 0.55%
2:02:38.355198 INFO: Resetting torch num_threads to 100
2:02:38.661565 PROGRESS: ============================= Precursor FDR =============================
2:02:38.661833 PROGRESS: Total precursors accumulated: 122,606
2:02:38.661920 PROGRESS: Target precursors: 121,393 (99.01%)
2:02:38.661976 PROGRESS: Decoy precursors: 1,213 (0.99%)
2:02:38.662028 PROGRESS: 
2:02:38.662075 PROGRESS: Precursor Summary:
2:02:38.698714 PROGRESS: Channel   0:	 0.050 FDR: 121,393; 0.010 FDR: 121,393; 0.001 FDR: 108,297
2:02:38.698976 PROGRESS: 
2:02:38.699040 PROGRESS: Protein Summary:
2:02:38.759690 PROGRESS: Channel   0:	 0.050 FDR: 10,101; 0.010 FDR: 10,101; 0.001 FDR: 9,987
2:02:38.759954 PROGRESS: =========================================================================
2:02:38.762427 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
2:02:38.949130 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
2:02:39.237748 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:02:39.341605 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
2:02:39.341746 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant
2:02:39.341830 INFO: Initializing TimingManager
2:02:39.342417 INFO: Initializing RawFileManager
2:02:49.414733 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:02:49.423248 INFO: Determining DIA cycle
2:02:49.439492 INFO: Found cycle with start 0.00 min and length 300.
2:02:49.603944 INFO: RT (min)            : 0.0 - 26.9
2:02:49.604035 INFO: RT duration (sec)   : 1611.2
2:02:49.604076 INFO: RT duration (min)   : 26.9
2:02:49.604100 INFO: Cycle len (scans)   : 300
2:02:49.604119 INFO: Cycle len (sec)     : 1.65
2:02:49.604138 INFO: Number of cycles    : 977
2:02:49.604156 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:02:49.604190 INFO: Creating DIA data object took: 10.261669874191284
2:02:50.265712 INFO: Creating DIA data NG object took: 0.6614022254943848
2:02:50.303155 INFO: Initializing CalibrationManager
2:02:50.303451 INFO: Setting up calibration estimators ..
2:02:50.303511 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:02:50.303600 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:02:50.303678 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:02:50.303729 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:02:50.303803 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:02:50.303856 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:02:50.303900 INFO: Done setting up calibration estimators.
2:02:50.304106 INFO: Initializing OptimizationManager
2:02:50.304225 INFO: initial parameter: ms1_error = 30
2:02:50.304274 INFO: initial parameter: ms2_error = 30
2:02:50.304319 INFO: initial parameter: rt_error = 805.6004638671875
2:02:50.304362 INFO: initial parameter: mobility_error = 0.1
2:02:50.304404 INFO: initial parameter: num_candidates = 1
2:02:50.304446 INFO: initial parameter: fwhm_rt = 5
2:02:50.304485 INFO: initial parameter: fwhm_mobility = 0.01
2:02:50.304524 INFO: initial parameter: score_cutoff = 0
2:02:50.304562 INFO: initial parameter: classifier_version = -1
2:02:50.304631 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:02:50.304866 INFO: FDRManager: loading saved state not requested, will be initialized.
2:02:50.304898 INFO: Initializing FDRManager
2:02:50.304929 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:02:50.341875 PROGRESS: Initializing spectral library: 131,664 target precursors potentially observable (0 removed)
2:02:50.366429 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:02:50.366822 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
2:02:50.366922 PROGRESS: Starting initial search for precursors.
2:02:50.367003 INFO: Starting optimization step 0.
2:02:50.367065 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:02:50.367124 INFO: Using rust extraction backend
2:02:50.367191 PROGRESS: Extracting batch of 1977 precursors
2:02:50.372008 INFO: === Search parameters used ===
2:02:50.372107 INFO: rt_error       : 805.6004638671875
2:02:50.372157 INFO: mobility_error : 0.1
2:02:50.372202 INFO: num_candidates : 1
2:02:50.372243 INFO: ms1_error      : 30
2:02:50.372286 INFO: ms2_error      : 30
2:02:50.372326 INFO: fwhm_rt        : 5
2:02:50.372365 INFO: quant_window   : 3
2:02:50.372403 INFO: ==============================================
2:02:50.398922 INFO: performing precursor FDR with 40 features
2:02:50.398993 INFO: Decoy channel: -1
2:02:50.399018 INFO: competitive: True
2:02:50.400273 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:50.402081 INFO: Estimating optimal hyperparameters - samples: 1,579, batch_size: 128, learning_rate: 1.77e-04
2:02:50.402897 INFO: Using random state 729851 for train-test-split
2:02:50.519919 INFO: Test AUC: 0.753
2:02:50.519997 INFO: Train AUC: 0.788
2:02:50.520025 INFO: AUC difference: 4.50%
2:02:50.759232 INFO: Resetting torch num_threads to 100
2:02:50.760825 PROGRESS: === Extracted 1974 precursors and 13445 fragments ===
2:02:50.761196 INFO: === FDR correction performed with classifier version -1 ===
2:02:50.761695 PROGRESS: ============================= Precursor FDR =============================
2:02:50.761777 PROGRESS: Total precursors accumulated: 314
2:02:50.761837 PROGRESS: Target precursors: 311 (99.04%)
2:02:50.761907 PROGRESS: Decoy precursors: 3 (0.96%)
2:02:50.761952 PROGRESS: 
2:02:50.761995 PROGRESS: Precursor Summary:
2:02:50.763037 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   311; 0.001 FDR:   228
2:02:50.763120 PROGRESS: 
2:02:50.763173 PROGRESS: Protein Summary:
2:02:50.764387 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   291; 0.001 FDR:   212
2:02:50.764479 PROGRESS: =========================================================================
2:02:50.764684 INFO: Target number of precursors not reached yet.
2:02:50.772207 INFO: Starting optimization step 1.
2:02:50.772310 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:02:50.772379 INFO: Using rust extraction backend
2:02:50.772436 PROGRESS: Extracting batch of 3959 precursors
2:02:50.780374 INFO: === Search parameters used ===
2:02:50.780473 INFO: rt_error       : 805.6004638671875
2:02:50.780523 INFO: mobility_error : 0.1
2:02:50.780567 INFO: num_candidates : 1
2:02:50.780609 INFO: ms1_error      : 30
2:02:50.780648 INFO: ms2_error      : 30
2:02:50.780687 INFO: fwhm_rt        : 5
2:02:50.780727 INFO: quant_window   : 3
2:02:50.780766 INFO: ==============================================
2:02:50.826775 INFO: performing precursor FDR with 40 features
2:02:50.826864 INFO: Decoy channel: -1
2:02:50.826887 INFO: competitive: True
2:02:50.830994 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:50.833250 INFO: Estimating optimal hyperparameters - samples: 4,738, batch_size: 128, learning_rate: 1.77e-04
2:02:50.833328 INFO: Using random state 878672 for train-test-split
2:02:51.234053 INFO: Test AUC: 0.834
2:02:51.234149 INFO: Train AUC: 0.826
2:02:51.234177 INFO: AUC difference: 1.05%
2:02:51.485718 INFO: Resetting torch num_threads to 100
2:02:51.488753 PROGRESS: === Extracted 5923 precursors and 40861 fragments ===
2:02:51.489138 INFO: === FDR correction performed with classifier version -1 ===
2:02:51.489743 PROGRESS: ============================= Precursor FDR =============================
2:02:51.489827 PROGRESS: Total precursors accumulated: 1,592
2:02:51.489896 PROGRESS: Target precursors: 1,577 (99.06%)
2:02:51.489946 PROGRESS: Decoy precursors: 15 (0.94%)
2:02:51.489990 PROGRESS: 
2:02:51.490033 PROGRESS: Precursor Summary:
2:02:51.491413 PROGRESS: Channel   0:	 0.050 FDR: 1,577; 0.010 FDR: 1,577; 0.001 FDR: 1,146
2:02:51.491499 PROGRESS: 
2:02:51.491553 PROGRESS: Protein Summary:
2:02:51.493377 PROGRESS: Channel   0:	 0.050 FDR: 1,286; 0.010 FDR: 1,286; 0.001 FDR:   958
2:02:51.493468 PROGRESS: =========================================================================
2:02:51.493721 INFO: Target number of precursors reached.
2:02:51.502797 INFO: fragments_df: keeping 5000 of 40861 [sum(precursor_idx_mask)=16193 sum(mass_error_mask)=40861 stop_rank=5000
2:02:51.513222 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:51.758995 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:52.473578 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:02:52.474032 INFO: Using score_cutoff 12.045955253219605 (fac=0.99, q=1)
2:02:52.474350 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:02:52.474428 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:02:52.474484 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.045955253219605
2:02:52.474544 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:52.478391 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:52.485966 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:02:52.486086 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:02:52.486167 INFO: Starting optimization step 2.
2:02:52.486237 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:52.486306 INFO: Using rust extraction backend
2:02:52.486362 PROGRESS: Extracting batch of 5936 precursors
2:02:52.497622 INFO: === Search parameters used ===
2:02:52.497746 INFO: rt_error       : 805.6004638671875
2:02:52.497798 INFO: mobility_error : 0.1
2:02:52.497844 INFO: num_candidates : 3
2:02:52.497899 INFO: ms1_error      : 30
2:02:52.497940 INFO: ms2_error      : 30
2:02:52.497978 INFO: fwhm_rt        : 3.0
2:02:52.498017 INFO: quant_window   : 3
2:02:52.498055 INFO: ==============================================
2:02:52.606437 INFO: performing precursor FDR with 40 features
2:02:52.606545 INFO: Decoy channel: -1
2:02:52.606569 INFO: competitive: True
2:02:52.612581 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:52.616647 INFO: Estimating optimal hyperparameters - samples: 14,208, batch_size: 128, learning_rate: 1.77e-04
2:02:52.616771 INFO: Using random state 938921 for train-test-split
2:02:54.049177 INFO: Test AUC: 0.681
2:02:54.049287 INFO: Train AUC: 0.701
2:02:54.049315 INFO: AUC difference: 2.87%
2:02:54.295415 INFO: Resetting torch num_threads to 100
2:02:54.297662 PROGRESS: === Extracted 17760 precursors and 106347 fragments ===
2:02:54.298034 INFO: === FDR correction performed with classifier version 1 ===
2:02:54.298691 PROGRESS: ============================= Precursor FDR =============================
2:02:54.298772 PROGRESS: Total precursors accumulated: 2,076
2:02:54.298827 PROGRESS: Target precursors: 2,056 (99.04%)
2:02:54.298876 PROGRESS: Decoy precursors: 20 (0.96%)
2:02:54.298919 PROGRESS: 
2:02:54.298960 PROGRESS: Precursor Summary:
2:02:54.300399 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,056; 0.001 FDR: 1,328
2:02:54.300489 PROGRESS: 
2:02:54.300542 PROGRESS: Protein Summary:
2:02:54.302477 PROGRESS: Channel   0:	 0.050 FDR: 1,621; 0.010 FDR: 1,621; 0.001 FDR: 1,096
2:02:54.302569 PROGRESS: =========================================================================
2:02:54.302915 INFO: Target number of precursors reached.
2:02:54.322527 INFO: fragments_df: keeping 5000 of 106347 [sum(precursor_idx_mask)=43800 sum(mass_error_mask)=106347 stop_rank=5000
2:02:54.333175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:54.636170 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:55.348876 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:55.349341 INFO: Using score_cutoff 11.608814703941345 (fac=0.99, q=1)
2:02:55.349645 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:55.349720 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:55.349772 INFO: Updating optimization_manager: score_cutoff        : 12.045955253219605 -> 11.608814703941345
2:02:55.349823 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:55.353735 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:55.361726 INFO: === checking if optimization conditions were reached ===
2:02:55.363384 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.4697575
2:02:55.363497 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:02:55.363560 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:02:55.363614 INFO: ==============================================
2:02:55.363695 INFO: Starting optimization step 3.
2:02:55.363754 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:55.363813 INFO: Using rust extraction backend
2:02:55.363865 PROGRESS: Extracting batch of 5936 precursors
2:02:55.375130 INFO: === Search parameters used ===
2:02:55.375263 INFO: rt_error       : 805.6004638671875
2:02:55.375314 INFO: mobility_error : 0.1
2:02:55.375357 INFO: num_candidates : 3
2:02:55.375397 INFO: ms1_error      : 30
2:02:55.375437 INFO: ms2_error      : 7.4697575
2:02:55.375478 INFO: fwhm_rt        : 3.0
2:02:55.375517 INFO: quant_window   : 3
2:02:55.375556 INFO: ==============================================
2:02:55.481022 INFO: performing precursor FDR with 40 features
2:02:55.481155 INFO: Decoy channel: -1
2:02:55.481182 INFO: competitive: True
2:02:55.485954 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:55.489875 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:02:55.489997 INFO: Using random state 494681 for train-test-split
2:02:56.921315 INFO: Test AUC: 0.738
2:02:56.921437 INFO: Train AUC: 0.746
2:02:56.921468 INFO: AUC difference: 1.05%
2:02:57.176145 INFO: Resetting torch num_threads to 100
2:02:57.178561 PROGRESS: === Extracted 17804 precursors and 122899 fragments ===
2:02:57.178936 INFO: === FDR correction performed with classifier version 2 ===
2:02:57.179640 PROGRESS: ============================= Precursor FDR =============================
2:02:57.179728 PROGRESS: Total precursors accumulated: 2,574
2:02:57.179791 PROGRESS: Target precursors: 2,549 (99.03%)
2:02:57.179844 PROGRESS: Decoy precursors: 25 (0.97%)
2:02:57.179891 PROGRESS: 
2:02:57.179938 PROGRESS: Precursor Summary:
2:02:57.181551 PROGRESS: Channel   0:	 0.050 FDR: 2,549; 0.010 FDR: 2,549; 0.001 FDR: 1,908
2:02:57.181641 PROGRESS: 
2:02:57.181697 PROGRESS: Protein Summary:
2:02:57.183931 PROGRESS: Channel   0:	 0.050 FDR: 1,982; 0.010 FDR: 1,982; 0.001 FDR: 1,523
2:02:57.184028 PROGRESS: =========================================================================
2:02:57.184389 INFO: Target number of precursors reached.
2:02:57.212062 INFO: fragments_df: keeping 5000 of 122899 [sum(precursor_idx_mask)=58988 sum(mass_error_mask)=122899 stop_rank=5000
2:02:57.223046 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:02:57.587794 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:02:58.298657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:02:58.299105 INFO: Using score_cutoff 10.095117057037353 (fac=0.99, q=1)
2:02:58.299433 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:02:58.299513 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:02:58.299566 INFO: Updating optimization_manager: score_cutoff        : 11.608814703941345 -> 10.095117057037353
2:02:58.299618 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:58.303560 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:58.311063 INFO: === checking if optimization conditions were reached ===
2:02:58.312738 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:02:58.312853 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:02:58.312925 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:02:58.312984 INFO: ==============================================
2:02:58.313054 INFO: Starting optimization step 4.
2:02:58.313116 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:02:58.313185 INFO: Using rust extraction backend
2:02:58.313246 PROGRESS: Extracting batch of 5936 precursors
2:02:58.324601 INFO: === Search parameters used ===
2:02:58.324709 INFO: rt_error       : 805.6004638671875
2:02:58.324760 INFO: mobility_error : 0.1
2:02:58.324805 INFO: num_candidates : 3
2:02:58.324848 INFO: ms1_error      : 30
2:02:58.324889 INFO: ms2_error      : 7.4697575
2:02:58.324931 INFO: fwhm_rt        : 3.0
2:02:58.324971 INFO: quant_window   : 3
2:02:58.325011 INFO: ==============================================
2:02:58.430168 INFO: performing precursor FDR with 40 features
2:02:58.430281 INFO: Decoy channel: -1
2:02:58.430306 INFO: competitive: True
2:02:58.435109 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:58.439277 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:02:58.439415 INFO: Using random state 12684 for train-test-split
2:02:59.920019 INFO: Test AUC: 0.744
2:02:59.920135 INFO: Train AUC: 0.757
2:02:59.920164 INFO: AUC difference: 1.76%
2:03:00.171807 INFO: Resetting torch num_threads to 100
2:03:00.174190 PROGRESS: === Extracted 17805 precursors and 122924 fragments ===
2:03:00.174555 INFO: === FDR correction performed with classifier version 3 ===
2:03:00.175267 PROGRESS: ============================= Precursor FDR =============================
2:03:00.175348 PROGRESS: Total precursors accumulated: 2,670
2:03:00.175404 PROGRESS: Target precursors: 2,644 (99.03%)
2:03:00.175451 PROGRESS: Decoy precursors: 26 (0.97%)
2:03:00.175493 PROGRESS: 
2:03:00.175541 PROGRESS: Precursor Summary:
2:03:00.177172 PROGRESS: Channel   0:	 0.050 FDR: 2,644; 0.010 FDR: 2,644; 0.001 FDR: 2,131
2:03:00.177257 PROGRESS: 
2:03:00.177310 PROGRESS: Protein Summary:
2:03:00.179579 PROGRESS: Channel   0:	 0.050 FDR: 2,048; 0.010 FDR: 2,048; 0.001 FDR: 1,681
2:03:00.179680 PROGRESS: =========================================================================
2:03:00.180046 INFO: Target number of precursors reached.
2:03:00.207807 INFO: fragments_df: keeping 5000 of 122924 [sum(precursor_idx_mask)=60950 sum(mass_error_mask)=122924 stop_rank=5000
2:03:00.218849 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:00.597865 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:01.300299 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:01.300758 INFO: Using score_cutoff 9.977017984771729 (fac=0.99, q=1)
2:03:01.301070 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:01.301145 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:01.301196 INFO: Updating optimization_manager: score_cutoff        : 10.095117057037353 -> 9.977017984771729
2:03:01.301245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:01.305182 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:01.312697 INFO: === checking if optimization conditions were reached ===
2:03:01.314334 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:03:01.314437 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:03:01.314501 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:03:01.314554 INFO: ==============================================
2:03:01.314616 INFO: Starting optimization step 5.
2:03:01.314670 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:01.314726 INFO: Using rust extraction backend
2:03:01.314777 PROGRESS: Extracting batch of 5936 precursors
2:03:01.326227 INFO: === Search parameters used ===
2:03:01.326350 INFO: rt_error       : 805.6004638671875
2:03:01.326399 INFO: mobility_error : 0.1
2:03:01.326441 INFO: num_candidates : 3
2:03:01.326482 INFO: ms1_error      : 30
2:03:01.326523 INFO: ms2_error      : 7.4697575
2:03:01.326562 INFO: fwhm_rt        : 3.0
2:03:01.326601 INFO: quant_window   : 3
2:03:01.326641 INFO: ==============================================
2:03:01.428585 INFO: performing precursor FDR with 40 features
2:03:01.428696 INFO: Decoy channel: -1
2:03:01.428720 INFO: competitive: True
2:03:01.433485 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:01.437794 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:03:01.437948 INFO: Using random state 402740 for train-test-split
2:03:02.876504 INFO: Test AUC: 0.750
2:03:02.876628 INFO: Train AUC: 0.767
2:03:02.876658 INFO: AUC difference: 2.30%
2:03:03.128484 INFO: Resetting torch num_threads to 100
2:03:03.130873 PROGRESS: === Extracted 17805 precursors and 122928 fragments ===
2:03:03.131243 INFO: === FDR correction performed with classifier version 4 ===
2:03:03.131944 PROGRESS: ============================= Precursor FDR =============================
2:03:03.132034 PROGRESS: Total precursors accumulated: 2,712
2:03:03.132094 PROGRESS: Target precursors: 2,686 (99.04%)
2:03:03.132152 PROGRESS: Decoy precursors: 26 (0.96%)
2:03:03.132201 PROGRESS: 
2:03:03.132248 PROGRESS: Precursor Summary:
2:03:03.133905 PROGRESS: Channel   0:	 0.050 FDR: 2,686; 0.010 FDR: 2,686; 0.001 FDR: 2,296
2:03:03.134004 PROGRESS: 
2:03:03.134059 PROGRESS: Protein Summary:
2:03:03.136379 PROGRESS: Channel   0:	 0.050 FDR: 2,073; 0.010 FDR: 2,073; 0.001 FDR: 1,798
2:03:03.136487 PROGRESS: =========================================================================
2:03:03.136850 INFO: Target number of precursors reached.
2:03:03.164043 INFO: fragments_df: keeping 5000 of 122928 [sum(precursor_idx_mask)=61745 sum(mass_error_mask)=122928 stop_rank=5000
2:03:03.174940 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:03.499294 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:04.141992 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:04.142449 INFO: Using score_cutoff 9.6563185172081 (fac=0.99, q=1)
2:03:04.142765 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:04.142841 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:04.142903 INFO: Updating optimization_manager: score_cutoff        : 9.977017984771729 -> 9.6563185172081
2:03:04.142954 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:04.146833 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:04.154269 INFO: === checking if optimization conditions were reached ===
2:03:04.155890 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:03:04.155987 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:03:04.156049 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:03:04.156101 INFO: ==============================================
2:03:04.156161 INFO: Starting optimization step 6.
2:03:04.156214 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:04.156271 INFO: Using rust extraction backend
2:03:04.156324 PROGRESS: Extracting batch of 5936 precursors
2:03:04.167513 INFO: === Search parameters used ===
2:03:04.167630 INFO: rt_error       : 805.6004638671875
2:03:04.167680 INFO: mobility_error : 0.1
2:03:04.167724 INFO: num_candidates : 3
2:03:04.167774 INFO: ms1_error      : 30
2:03:04.167814 INFO: ms2_error      : 7.4697575
2:03:04.167854 INFO: fwhm_rt        : 3.0
2:03:04.167892 INFO: quant_window   : 3
2:03:04.167932 INFO: ==============================================
2:03:04.273919 INFO: performing precursor FDR with 40 features
2:03:04.274028 INFO: Decoy channel: -1
2:03:04.274052 INFO: competitive: True
2:03:04.278713 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:04.282735 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:03:04.282859 INFO: Using random state 664050 for train-test-split
2:03:05.697434 INFO: Test AUC: 0.764
2:03:05.697550 INFO: Train AUC: 0.774
2:03:05.697578 INFO: AUC difference: 1.41%
2:03:05.949872 INFO: Resetting torch num_threads to 100
2:03:05.952248 PROGRESS: === Extracted 17805 precursors and 122928 fragments ===
2:03:05.952608 INFO: === FDR correction performed with classifier version 5 ===
2:03:05.953317 PROGRESS: ============================= Precursor FDR =============================
2:03:05.953398 PROGRESS: Total precursors accumulated: 2,759
2:03:05.953460 PROGRESS: Target precursors: 2,732 (99.02%)
2:03:05.953510 PROGRESS: Decoy precursors: 27 (0.98%)
2:03:05.953553 PROGRESS: 
2:03:05.953595 PROGRESS: Precursor Summary:
2:03:05.955256 PROGRESS: Channel   0:	 0.050 FDR: 2,732; 0.010 FDR: 2,732; 0.001 FDR: 2,298
2:03:05.955347 PROGRESS: 
2:03:05.955402 PROGRESS: Protein Summary:
2:03:05.957724 PROGRESS: Channel   0:	 0.050 FDR: 2,105; 0.010 FDR: 2,105; 0.001 FDR: 1,804
2:03:05.957812 PROGRESS: =========================================================================
2:03:05.958193 INFO: Target number of precursors reached.
2:03:05.985595 INFO: fragments_df: keeping 5000 of 122928 [sum(precursor_idx_mask)=62682 sum(mass_error_mask)=122928 stop_rank=5000
2:03:05.996472 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:06.331149 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:06.977005 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:06.977490 INFO: Using score_cutoff 9.607237610435487 (fac=0.99, q=1)
2:03:06.977812 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:06.977900 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:06.977959 INFO: Updating optimization_manager: score_cutoff        : 9.6563185172081 -> 9.607237610435487
2:03:06.978012 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:06.981909 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:06.989389 INFO: === checking if optimization conditions were reached ===
2:03:06.991005 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:03:06.991107 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:03:06.991170 PROGRESS: ✅ ms2_error      : 7.4698 <= 7.4698
2:03:06.991225 INFO: ==============================================
2:03:06.991297 PROGRESS: Optimization finished for ms2_error.
2:03:07.001743 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:07.005450 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:07.012971 INFO: Starting optimization step 0.
2:03:07.013085 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:07.013153 INFO: Using rust extraction backend
2:03:07.013208 PROGRESS: Extracting batch of 5936 precursors
2:03:07.024917 INFO: === Search parameters used ===
2:03:07.025035 INFO: rt_error       : 805.6004638671875
2:03:07.025085 INFO: mobility_error : 0.1
2:03:07.025129 INFO: num_candidates : 3
2:03:07.025171 INFO: ms1_error      : 30
2:03:07.025211 INFO: ms2_error      : 7.4697575
2:03:07.025251 INFO: fwhm_rt        : 3.0
2:03:07.025290 INFO: quant_window   : 3
2:03:07.025328 INFO: ==============================================
2:03:07.131501 INFO: performing precursor FDR with 40 features
2:03:07.131615 INFO: Decoy channel: -1
2:03:07.131638 INFO: competitive: True
2:03:07.136317 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:07.140247 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:03:07.140367 INFO: Using random state 729068 for train-test-split
2:03:08.573557 INFO: Test AUC: 0.764
2:03:08.573671 INFO: Train AUC: 0.780
2:03:08.573699 INFO: AUC difference: 2.05%
2:03:08.819119 INFO: Resetting torch num_threads to 100
2:03:08.821523 PROGRESS: === Extracted 17805 precursors and 122923 fragments ===
2:03:08.821908 INFO: === FDR correction performed with classifier version 6 ===
2:03:08.822628 PROGRESS: ============================= Precursor FDR =============================
2:03:08.822709 PROGRESS: Total precursors accumulated: 2,773
2:03:08.822764 PROGRESS: Target precursors: 2,746 (99.03%)
2:03:08.822812 PROGRESS: Decoy precursors: 27 (0.97%)
2:03:08.822855 PROGRESS: 
2:03:08.822897 PROGRESS: Precursor Summary:
2:03:08.824541 PROGRESS: Channel   0:	 0.050 FDR: 2,746; 0.010 FDR: 2,746; 0.001 FDR: 2,372
2:03:08.824625 PROGRESS: 
2:03:08.824676 PROGRESS: Protein Summary:
2:03:08.827025 PROGRESS: Channel   0:	 0.050 FDR: 2,117; 0.010 FDR: 2,117; 0.001 FDR: 1,858
2:03:08.827118 PROGRESS: =========================================================================
2:03:08.827496 INFO: Target number of precursors reached.
2:03:08.855184 INFO: fragments_df: keeping 5000 of 122923 [sum(precursor_idx_mask)=62984 sum(mass_error_mask)=122923 stop_rank=5000
2:03:08.865905 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:09.196648 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:09.839082 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:09.839521 INFO: Using score_cutoff 9.535394320964812 (fac=0.99, q=1)
2:03:09.839833 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:09.839913 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:09.839965 INFO: Updating optimization_manager: score_cutoff        : 9.607237610435487 -> 9.535394320964812
2:03:09.840015 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:09.843881 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:09.851304 INFO: === checking if optimization conditions were reached ===
2:03:09.851431 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:03:09.854234 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 363.61917120823756
2:03:09.854335 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 363.6192.
2:03:09.854396 INFO: ==============================================
2:03:09.854460 INFO: Starting optimization step 1.
2:03:09.854514 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:09.854571 INFO: Using rust extraction backend
2:03:09.854625 PROGRESS: Extracting batch of 5936 precursors
2:03:09.865902 INFO: === Search parameters used ===
2:03:09.866022 INFO: rt_error       : 363.61917120823756
2:03:09.866072 INFO: mobility_error : 0.1
2:03:09.866117 INFO: num_candidates : 3
2:03:09.866158 INFO: ms1_error      : 30
2:03:09.866199 INFO: ms2_error      : 7.4697575
2:03:09.866239 INFO: fwhm_rt        : 3.0
2:03:09.866288 INFO: quant_window   : 3
2:03:09.866329 INFO: ==============================================
2:03:09.968592 INFO: performing precursor FDR with 40 features
2:03:09.968704 INFO: Decoy channel: -1
2:03:09.968728 INFO: competitive: True
2:03:09.975101 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:09.979123 INFO: Estimating optimal hyperparameters - samples: 14,242, batch_size: 128, learning_rate: 1.77e-04
2:03:09.979245 INFO: Using random state 729068 for train-test-split
2:03:11.392700 INFO: Test AUC: 0.764
2:03:11.392813 INFO: Train AUC: 0.784
2:03:11.392841 INFO: AUC difference: 2.54%
2:03:11.637449 INFO: Resetting torch num_threads to 100
2:03:11.639836 PROGRESS: === Extracted 17803 precursors and 121931 fragments ===
2:03:11.640206 INFO: === FDR correction performed with classifier version 6 ===
2:03:11.640929 PROGRESS: ============================= Precursor FDR =============================
2:03:11.641011 PROGRESS: Total precursors accumulated: 2,816
2:03:11.641066 PROGRESS: Target precursors: 2,789 (99.04%)
2:03:11.641114 PROGRESS: Decoy precursors: 27 (0.96%)
2:03:11.641158 PROGRESS: 
2:03:11.641200 PROGRESS: Precursor Summary:
2:03:11.642877 PROGRESS: Channel   0:	 0.050 FDR: 2,789; 0.010 FDR: 2,789; 0.001 FDR: 2,365
2:03:11.642977 PROGRESS: 
2:03:11.643031 PROGRESS: Protein Summary:
2:03:11.645362 PROGRESS: Channel   0:	 0.050 FDR: 2,144; 0.010 FDR: 2,144; 0.001 FDR: 1,857
2:03:11.645457 PROGRESS: =========================================================================
2:03:11.645799 INFO: Target number of precursors reached.
2:03:11.673201 INFO: fragments_df: keeping 5000 of 121931 [sum(precursor_idx_mask)=63450 sum(mass_error_mask)=121931 stop_rank=5000
2:03:11.684071 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:12.018149 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:12.660512 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:12.660968 INFO: Using score_cutoff 9.05903740310669 (fac=0.99, q=1)
2:03:12.661275 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:12.661353 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:12.661407 INFO: Updating optimization_manager: score_cutoff        : 9.535394320964812 -> 9.05903740310669
2:03:12.661461 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:12.665351 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:12.672911 INFO: === checking if optimization conditions were reached ===
2:03:12.673020 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:03:12.675938 INFO: Updating optimization_manager: rt_error            : 363.61917120823756 -> 354.9315959421698
2:03:12.676039 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 354.9316.
2:03:12.676103 INFO: ==============================================
2:03:12.676171 INFO: Starting optimization step 2.
2:03:12.676237 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:12.676295 INFO: Using rust extraction backend
2:03:12.676347 PROGRESS: Extracting batch of 5936 precursors
2:03:12.687714 INFO: === Search parameters used ===
2:03:12.687829 INFO: rt_error       : 354.9315959421698
2:03:12.687880 INFO: mobility_error : 0.1
2:03:12.687925 INFO: num_candidates : 3
2:03:12.687968 INFO: ms1_error      : 30
2:03:12.688019 INFO: ms2_error      : 7.4697575
2:03:12.688062 INFO: fwhm_rt        : 3.0
2:03:12.688103 INFO: quant_window   : 3
2:03:12.688144 INFO: ==============================================
2:03:12.781530 INFO: performing precursor FDR with 40 features
2:03:12.781647 INFO: Decoy channel: -1
2:03:12.781672 INFO: competitive: True
2:03:12.786227 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:12.790471 INFO: Estimating optimal hyperparameters - samples: 14,242, batch_size: 128, learning_rate: 1.77e-04
2:03:12.790596 INFO: Using random state 729068 for train-test-split
2:03:14.267315 INFO: Test AUC: 0.777
2:03:14.267427 INFO: Train AUC: 0.779
2:03:14.267455 INFO: AUC difference: 0.32%
2:03:14.514024 INFO: Resetting torch num_threads to 100
2:03:14.516415 PROGRESS: === Extracted 17803 precursors and 121855 fragments ===
2:03:14.516779 INFO: === FDR correction performed with classifier version 6 ===
2:03:14.517488 PROGRESS: ============================= Precursor FDR =============================
2:03:14.517572 PROGRESS: Total precursors accumulated: 2,751
2:03:14.517637 PROGRESS: Target precursors: 2,724 (99.02%)
2:03:14.517686 PROGRESS: Decoy precursors: 27 (0.98%)
2:03:14.517730 PROGRESS: 
2:03:14.517773 PROGRESS: Precursor Summary:
2:03:14.519428 PROGRESS: Channel   0:	 0.050 FDR: 2,724; 0.010 FDR: 2,724; 0.001 FDR: 2,296
2:03:14.519518 PROGRESS: 
2:03:14.519571 PROGRESS: Protein Summary:
2:03:14.521879 PROGRESS: Channel   0:	 0.050 FDR: 2,101; 0.010 FDR: 2,101; 0.001 FDR: 1,795
2:03:14.521971 PROGRESS: =========================================================================
2:03:14.522333 INFO: Target number of precursors reached.
2:03:14.549693 INFO: fragments_df: keeping 5000 of 121855 [sum(precursor_idx_mask)=62265 sum(mass_error_mask)=121855 stop_rank=5000
2:03:14.560483 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:14.888162 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:15.535724 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:15.536170 INFO: Using score_cutoff 9.570966214656831 (fac=0.99, q=1)
2:03:15.536481 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:15.536555 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:15.536608 INFO: Updating optimization_manager: score_cutoff        : 9.05903740310669 -> 9.570966214656831
2:03:15.536658 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:15.540545 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:15.548090 INFO: === checking if optimization conditions were reached ===
2:03:15.548197 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:03:15.551211 INFO: Updating optimization_manager: rt_error            : 354.9315959421698 -> 278.29145377379075
2:03:15.551321 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 278.2915.
2:03:15.551382 INFO: ==============================================
2:03:15.551447 INFO: Starting optimization step 3.
2:03:15.551502 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:15.551559 INFO: Using rust extraction backend
2:03:15.551612 PROGRESS: Extracting batch of 5936 precursors
2:03:15.563176 INFO: === Search parameters used ===
2:03:15.563292 INFO: rt_error       : 278.29145377379075
2:03:15.563342 INFO: mobility_error : 0.1
2:03:15.563397 INFO: num_candidates : 3
2:03:15.563443 INFO: ms1_error      : 30
2:03:15.563483 INFO: ms2_error      : 7.4697575
2:03:15.563522 INFO: fwhm_rt        : 3.0
2:03:15.563560 INFO: quant_window   : 3
2:03:15.563605 INFO: ==============================================
2:03:15.654138 INFO: performing precursor FDR with 40 features
2:03:15.654246 INFO: Decoy channel: -1
2:03:15.654269 INFO: competitive: True
2:03:15.658855 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:15.662959 INFO: Estimating optimal hyperparameters - samples: 14,242, batch_size: 128, learning_rate: 1.77e-04
2:03:15.663081 INFO: Using random state 729068 for train-test-split
2:03:17.108293 INFO: Test AUC: 0.784
2:03:17.108401 INFO: Train AUC: 0.778
2:03:17.108428 INFO: AUC difference: 0.83%
2:03:17.353405 INFO: Resetting torch num_threads to 100
2:03:17.355849 PROGRESS: === Extracted 17803 precursors and 120496 fragments ===
2:03:17.356222 INFO: === FDR correction performed with classifier version 6 ===
2:03:17.356942 PROGRESS: ============================= Precursor FDR =============================
2:03:17.357027 PROGRESS: Total precursors accumulated: 2,814
2:03:17.357085 PROGRESS: Target precursors: 2,787 (99.04%)
2:03:17.357136 PROGRESS: Decoy precursors: 27 (0.96%)
2:03:17.357184 PROGRESS: 
2:03:17.357233 PROGRESS: Precursor Summary:
2:03:17.358924 PROGRESS: Channel   0:	 0.050 FDR: 2,787; 0.010 FDR: 2,787; 0.001 FDR: 2,342
2:03:17.359018 PROGRESS: 
2:03:17.359074 PROGRESS: Protein Summary:
2:03:17.361413 PROGRESS: Channel   0:	 0.050 FDR: 2,147; 0.010 FDR: 2,147; 0.001 FDR: 1,835
2:03:17.361504 PROGRESS: =========================================================================
2:03:17.361868 INFO: Target number of precursors reached.
2:03:17.389118 INFO: fragments_df: keeping 5000 of 120496 [sum(precursor_idx_mask)=63028 sum(mass_error_mask)=120496 stop_rank=5000
2:03:17.399879 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:17.731350 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:18.374783 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:18.375235 INFO: Using score_cutoff 9.14870137424469 (fac=0.99, q=1)
2:03:18.375546 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:18.375620 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:18.375674 INFO: Updating optimization_manager: score_cutoff        : 9.570966214656831 -> 9.14870137424469
2:03:18.375727 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:18.379638 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:18.387133 INFO: === checking if optimization conditions were reached ===
2:03:18.387249 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:03:18.390255 INFO: Updating optimization_manager: rt_error            : 278.29145377379075 -> 260.4935122856296
2:03:18.390358 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 260.4935.
2:03:18.390421 INFO: ==============================================
2:03:18.390490 INFO: Starting optimization step 4.
2:03:18.390547 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:18.390605 INFO: Using rust extraction backend
2:03:18.390660 PROGRESS: Extracting batch of 5936 precursors
2:03:18.401877 INFO: === Search parameters used ===
2:03:18.402000 INFO: rt_error       : 260.4935122856296
2:03:18.402056 INFO: mobility_error : 0.1
2:03:18.402103 INFO: num_candidates : 3
2:03:18.402148 INFO: ms1_error      : 30
2:03:18.402190 INFO: ms2_error      : 7.4697575
2:03:18.402235 INFO: fwhm_rt        : 3.0
2:03:18.402279 INFO: quant_window   : 3
2:03:18.402319 INFO: ==============================================
2:03:18.493495 INFO: performing precursor FDR with 40 features
2:03:18.493607 INFO: Decoy channel: -1
2:03:18.493632 INFO: competitive: True
2:03:18.498175 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:18.502319 INFO: Estimating optimal hyperparameters - samples: 14,241, batch_size: 128, learning_rate: 1.77e-04
2:03:18.502445 INFO: Using random state 729068 for train-test-split
2:03:19.929563 INFO: Test AUC: 0.769
2:03:19.929677 INFO: Train AUC: 0.783
2:03:19.929707 INFO: AUC difference: 1.74%
2:03:20.182139 INFO: Resetting torch num_threads to 100
2:03:20.184651 PROGRESS: === Extracted 17802 precursors and 120180 fragments ===
2:03:20.185016 INFO: === FDR correction performed with classifier version 6 ===
2:03:20.185731 PROGRESS: ============================= Precursor FDR =============================
2:03:20.185812 PROGRESS: Total precursors accumulated: 2,794
2:03:20.185878 PROGRESS: Target precursors: 2,767 (99.03%)
2:03:20.185932 PROGRESS: Decoy precursors: 27 (0.97%)
2:03:20.185977 PROGRESS: 
2:03:20.186019 PROGRESS: Precursor Summary:
2:03:20.187684 PROGRESS: Channel   0:	 0.050 FDR: 2,767; 0.010 FDR: 2,767; 0.001 FDR: 2,339
2:03:20.187769 PROGRESS: 
2:03:20.187821 PROGRESS: Protein Summary:
2:03:20.190170 PROGRESS: Channel   0:	 0.050 FDR: 2,129; 0.010 FDR: 2,129; 0.001 FDR: 1,837
2:03:20.190264 PROGRESS: =========================================================================
2:03:20.190617 INFO: Target number of precursors reached.
2:03:20.217485 INFO: fragments_df: keeping 5000 of 120180 [sum(precursor_idx_mask)=62644 sum(mass_error_mask)=120180 stop_rank=5000
2:03:20.228465 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:20.567277 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:21.211411 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:21.211858 INFO: Using score_cutoff 9.13122104473114 (fac=0.99, q=1)
2:03:21.212159 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:21.212233 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:21.212286 INFO: Updating optimization_manager: score_cutoff        : 9.14870137424469 -> 9.13122104473114
2:03:21.212337 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:21.216243 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:21.223822 INFO: === checking if optimization conditions were reached ===
2:03:21.223927 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:03:21.226898 INFO: Updating optimization_manager: rt_error            : 260.4935122856296 -> 185.5435654462828
2:03:21.226999 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 185.5436.
2:03:21.227061 INFO: ==============================================
2:03:21.227127 INFO: Starting optimization step 5.
2:03:21.227184 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:21.227241 INFO: Using rust extraction backend
2:03:21.227295 PROGRESS: Extracting batch of 5936 precursors
2:03:21.238834 INFO: === Search parameters used ===
2:03:21.238950 INFO: rt_error       : 185.5435654462828
2:03:21.239000 INFO: mobility_error : 0.1
2:03:21.239043 INFO: num_candidates : 3
2:03:21.239085 INFO: ms1_error      : 30
2:03:21.239127 INFO: ms2_error      : 7.4697575
2:03:21.239168 INFO: fwhm_rt        : 3.0
2:03:21.239210 INFO: quant_window   : 3
2:03:21.239249 INFO: ==============================================
2:03:21.325719 INFO: performing precursor FDR with 40 features
2:03:21.325832 INFO: Decoy channel: -1
2:03:21.325874 INFO: competitive: True
2:03:21.330424 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:21.334452 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:03:21.334572 INFO: Using random state 729068 for train-test-split
2:03:22.759501 INFO: Test AUC: 0.769
2:03:22.759626 INFO: Train AUC: 0.784
2:03:22.760782 INFO: AUC difference: 1.90%
2:03:23.006970 INFO: Resetting torch num_threads to 100
2:03:23.009343 PROGRESS: === Extracted 17801 precursors and 117303 fragments ===
2:03:23.009712 INFO: === FDR correction performed with classifier version 6 ===
2:03:23.010451 PROGRESS: ============================= Precursor FDR =============================
2:03:23.010541 PROGRESS: Total precursors accumulated: 2,821
2:03:23.010601 PROGRESS: Target precursors: 2,794 (99.04%)
2:03:23.010653 PROGRESS: Decoy precursors: 27 (0.96%)
2:03:23.010701 PROGRESS: 
2:03:23.010754 PROGRESS: Precursor Summary:
2:03:23.012420 PROGRESS: Channel   0:	 0.050 FDR: 2,794; 0.010 FDR: 2,794; 0.001 FDR: 2,353
2:03:23.012508 PROGRESS: 
2:03:23.012564 PROGRESS: Protein Summary:
2:03:23.014922 PROGRESS: Channel   0:	 0.050 FDR: 2,147; 0.010 FDR: 2,147; 0.001 FDR: 1,833
2:03:23.015031 PROGRESS: =========================================================================
2:03:23.015390 INFO: Target number of precursors reached.
2:03:23.042098 INFO: fragments_df: keeping 5000 of 117303 [sum(precursor_idx_mask)=62332 sum(mass_error_mask)=117303 stop_rank=5000
2:03:23.053022 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:23.389012 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:24.035110 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:24.035562 INFO: Using score_cutoff 9.366743611621857 (fac=0.99, q=1)
2:03:24.035876 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:24.035956 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:24.036010 INFO: Updating optimization_manager: score_cutoff        : 9.13122104473114 -> 9.366743611621857
2:03:24.036062 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:24.039950 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:24.047243 INFO: === checking if optimization conditions were reached ===
2:03:24.047350 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:03:24.050342 INFO: Updating optimization_manager: rt_error            : 185.5435654462828 -> 140.22037919741527
2:03:24.050446 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 140.2204.
2:03:24.050509 INFO: ==============================================
2:03:24.050576 INFO: Starting optimization step 6.
2:03:24.050633 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:24.050698 INFO: Using rust extraction backend
2:03:24.050753 PROGRESS: Extracting batch of 5936 precursors
2:03:24.062295 INFO: === Search parameters used ===
2:03:24.062420 INFO: rt_error       : 140.22037919741527
2:03:24.062472 INFO: mobility_error : 0.1
2:03:24.062518 INFO: num_candidates : 3
2:03:24.062565 INFO: ms1_error      : 30
2:03:24.062609 INFO: ms2_error      : 7.4697575
2:03:24.062652 INFO: fwhm_rt        : 3.0
2:03:24.062698 INFO: quant_window   : 3
2:03:24.062739 INFO: ==============================================
2:03:24.149633 INFO: performing precursor FDR with 40 features
2:03:24.149750 INFO: Decoy channel: -1
2:03:24.149775 INFO: competitive: True
2:03:24.154550 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:24.158749 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:03:24.158934 INFO: Using random state 729068 for train-test-split
2:03:25.609817 INFO: Test AUC: 0.783
2:03:25.609945 INFO: Train AUC: 0.785
2:03:25.609974 INFO: AUC difference: 0.27%
2:03:25.863899 INFO: Resetting torch num_threads to 100
2:03:25.866288 PROGRESS: === Extracted 17804 precursors and 114820 fragments ===
2:03:25.866656 INFO: === FDR correction performed with classifier version 6 ===
2:03:25.867375 PROGRESS: ============================= Precursor FDR =============================
2:03:25.867458 PROGRESS: Total precursors accumulated: 2,848
2:03:25.867514 PROGRESS: Target precursors: 2,820 (99.02%)
2:03:25.867562 PROGRESS: Decoy precursors: 28 (0.98%)
2:03:25.867605 PROGRESS: 
2:03:25.867648 PROGRESS: Precursor Summary:
2:03:25.869306 PROGRESS: Channel   0:	 0.050 FDR: 2,820; 0.010 FDR: 2,820; 0.001 FDR: 2,255
2:03:25.869396 PROGRESS: 
2:03:25.869449 PROGRESS: Protein Summary:
2:03:25.871817 PROGRESS: Channel   0:	 0.050 FDR: 2,170; 0.010 FDR: 2,170; 0.001 FDR: 1,765
2:03:25.871909 PROGRESS: =========================================================================
2:03:25.872261 INFO: Target number of precursors reached.
2:03:25.898643 INFO: fragments_df: keeping 5000 of 114820 [sum(precursor_idx_mask)=62058 sum(mass_error_mask)=114820 stop_rank=5000
2:03:25.909523 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:26.246271 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:26.893757 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:26.894221 INFO: Using score_cutoff 9.317026044559478 (fac=0.99, q=1)
2:03:26.894536 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:26.894612 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:26.894664 INFO: Updating optimization_manager: score_cutoff        : 9.366743611621857 -> 9.317026044559478
2:03:26.894715 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:26.898638 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:26.906214 INFO: === checking if optimization conditions were reached ===
2:03:26.906332 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:03:26.909328 INFO: Updating optimization_manager: rt_error            : 140.22037919741527 -> 151.51417730105504
2:03:26.909423 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 151.5142.
2:03:26.909484 INFO: ==============================================
2:03:26.909557 INFO: Starting optimization step 7.
2:03:26.909615 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:26.909670 INFO: Using rust extraction backend
2:03:26.909720 PROGRESS: Extracting batch of 5936 precursors
2:03:26.920925 INFO: === Search parameters used ===
2:03:26.921050 INFO: rt_error       : 151.51417730105504
2:03:26.921100 INFO: mobility_error : 0.1
2:03:26.921143 INFO: num_candidates : 3
2:03:26.921183 INFO: ms1_error      : 30
2:03:26.921222 INFO: ms2_error      : 7.4697575
2:03:26.921261 INFO: fwhm_rt        : 3.0
2:03:26.921299 INFO: quant_window   : 3
2:03:26.921349 INFO: ==============================================
2:03:27.007812 INFO: performing precursor FDR with 40 features
2:03:27.007920 INFO: Decoy channel: -1
2:03:27.007944 INFO: competitive: True
2:03:27.012732 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:27.016644 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:03:27.016757 INFO: Using random state 729068 for train-test-split
2:03:28.446404 INFO: Test AUC: 0.773
2:03:28.446524 INFO: Train AUC: 0.786
2:03:28.446554 INFO: AUC difference: 1.63%
2:03:28.700534 INFO: Resetting torch num_threads to 100
2:03:28.703356 PROGRESS: === Extracted 17804 precursors and 115519 fragments ===
2:03:28.703735 INFO: === FDR correction performed with classifier version 6 ===
2:03:28.704455 PROGRESS: ============================= Precursor FDR =============================
2:03:28.704541 PROGRESS: Total precursors accumulated: 2,835
2:03:28.704601 PROGRESS: Target precursors: 2,807 (99.01%)
2:03:28.704656 PROGRESS: Decoy precursors: 28 (0.99%)
2:03:28.704704 PROGRESS: 
2:03:28.704750 PROGRESS: Precursor Summary:
2:03:28.706450 PROGRESS: Channel   0:	 0.050 FDR: 2,807; 0.010 FDR: 2,807; 0.001 FDR: 2,202
2:03:28.706556 PROGRESS: 
2:03:28.706614 PROGRESS: Protein Summary:
2:03:28.708953 PROGRESS: Channel   0:	 0.050 FDR: 2,158; 0.010 FDR: 2,158; 0.001 FDR: 1,739
2:03:28.709046 PROGRESS: =========================================================================
2:03:28.709403 INFO: Target number of precursors reached.
2:03:28.735896 INFO: fragments_df: keeping 5000 of 115519 [sum(precursor_idx_mask)=61914 sum(mass_error_mask)=115519 stop_rank=5000
2:03:28.746629 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:29.078077 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:29.725303 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:29.725764 INFO: Using score_cutoff 9.06391379814148 (fac=0.99, q=1)
2:03:29.726099 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:29.726183 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:29.726238 INFO: Updating optimization_manager: score_cutoff        : 9.317026044559478 -> 9.06391379814148
2:03:29.726300 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:29.730175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:29.737643 INFO: === checking if optimization conditions were reached ===
2:03:29.737756 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:03:29.740764 INFO: Updating optimization_manager: rt_error            : 151.51417730105504 -> 172.44502671368463
2:03:29.740877 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 172.4450.
2:03:29.740949 INFO: ==============================================
2:03:29.741016 INFO: Starting optimization step 8.
2:03:29.741073 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:29.741131 INFO: Using rust extraction backend
2:03:29.741186 PROGRESS: Extracting batch of 5936 precursors
2:03:29.752409 INFO: === Search parameters used ===
2:03:29.752526 INFO: rt_error       : 172.44502671368463
2:03:29.752577 INFO: mobility_error : 0.1
2:03:29.752621 INFO: num_candidates : 3
2:03:29.752662 INFO: ms1_error      : 30
2:03:29.752702 INFO: ms2_error      : 7.4697575
2:03:29.752743 INFO: fwhm_rt        : 3.0
2:03:29.752782 INFO: quant_window   : 3
2:03:29.752822 INFO: ==============================================
2:03:29.838928 INFO: performing precursor FDR with 40 features
2:03:29.839039 INFO: Decoy channel: -1
2:03:29.839063 INFO: competitive: True
2:03:29.843810 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:29.847856 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:03:29.847981 INFO: Using random state 729068 for train-test-split
2:03:31.285715 INFO: Test AUC: 0.758
2:03:31.285826 INFO: Train AUC: 0.789
2:03:31.285863 INFO: AUC difference: 3.88%
2:03:31.531579 INFO: Resetting torch num_threads to 100
2:03:31.533951 PROGRESS: === Extracted 17804 precursors and 116680 fragments ===
2:03:31.534321 INFO: === FDR correction performed with classifier version 6 ===
2:03:31.535045 PROGRESS: ============================= Precursor FDR =============================
2:03:31.535127 PROGRESS: Total precursors accumulated: 2,834
2:03:31.535182 PROGRESS: Target precursors: 2,806 (99.01%)
2:03:31.535228 PROGRESS: Decoy precursors: 28 (0.99%)
2:03:31.535271 PROGRESS: 
2:03:31.535319 PROGRESS: Precursor Summary:
2:03:31.536988 PROGRESS: Channel   0:	 0.050 FDR: 2,806; 0.010 FDR: 2,806; 0.001 FDR: 2,296
2:03:31.537071 PROGRESS: 
2:03:31.537124 PROGRESS: Protein Summary:
2:03:31.539484 PROGRESS: Channel   0:	 0.050 FDR: 2,156; 0.010 FDR: 2,156; 0.001 FDR: 1,800
2:03:31.539575 PROGRESS: =========================================================================
2:03:31.539931 INFO: Target number of precursors reached.
2:03:31.566514 INFO: fragments_df: keeping 5000 of 116680 [sum(precursor_idx_mask)=62283 sum(mass_error_mask)=116680 stop_rank=5000
2:03:31.577469 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:31.915305 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:32.558549 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:32.558986 INFO: Using score_cutoff 9.16647147846222 (fac=0.99, q=1)
2:03:32.559300 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:32.559378 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:32.559436 INFO: Updating optimization_manager: score_cutoff        : 9.06391379814148 -> 9.16647147846222
2:03:32.559488 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:32.563401 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:32.570881 INFO: === checking if optimization conditions were reached ===
2:03:32.570988 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:03:32.574001 INFO: Updating optimization_manager: rt_error            : 172.44502671368463 -> 134.82604914013066
2:03:32.574101 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 134.8260.
2:03:32.574169 INFO: ==============================================
2:03:32.574240 INFO: Starting optimization step 9.
2:03:32.574296 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:32.574355 INFO: Using rust extraction backend
2:03:32.574409 PROGRESS: Extracting batch of 5936 precursors
2:03:32.585857 INFO: === Search parameters used ===
2:03:32.585970 INFO: rt_error       : 134.82604914013066
2:03:32.586021 INFO: mobility_error : 0.1
2:03:32.586065 INFO: num_candidates : 3
2:03:32.586109 INFO: ms1_error      : 30
2:03:32.586150 INFO: ms2_error      : 7.4697575
2:03:32.586190 INFO: fwhm_rt        : 3.0
2:03:32.586229 INFO: quant_window   : 3
2:03:32.586268 INFO: ==============================================
2:03:32.671925 INFO: performing precursor FDR with 40 features
2:03:32.672034 INFO: Decoy channel: -1
2:03:32.672058 INFO: competitive: True
2:03:32.677358 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:32.681264 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:03:32.681380 INFO: Using random state 729068 for train-test-split
2:03:34.122380 INFO: Test AUC: 0.781
2:03:34.122499 INFO: Train AUC: 0.786
2:03:34.122529 INFO: AUC difference: 0.69%
2:03:34.368665 INFO: Resetting torch num_threads to 100
2:03:34.371035 PROGRESS: === Extracted 17804 precursors and 114369 fragments ===
2:03:34.371412 INFO: === FDR correction performed with classifier version 6 ===
2:03:34.372141 PROGRESS: ============================= Precursor FDR =============================
2:03:34.372230 PROGRESS: Total precursors accumulated: 2,839
2:03:34.372293 PROGRESS: Target precursors: 2,811 (99.01%)
2:03:34.372355 PROGRESS: Decoy precursors: 28 (0.99%)
2:03:34.372404 PROGRESS: 
2:03:34.372450 PROGRESS: Precursor Summary:
2:03:34.374126 PROGRESS: Channel   0:	 0.050 FDR: 2,811; 0.010 FDR: 2,811; 0.001 FDR: 2,328
2:03:34.374218 PROGRESS: 
2:03:34.374273 PROGRESS: Protein Summary:
2:03:34.376609 PROGRESS: Channel   0:	 0.050 FDR: 2,162; 0.010 FDR: 2,162; 0.001 FDR: 1,821
2:03:34.376707 PROGRESS: =========================================================================
2:03:34.377060 INFO: Target number of precursors reached.
2:03:34.403543 INFO: fragments_df: keeping 5000 of 114369 [sum(precursor_idx_mask)=61676 sum(mass_error_mask)=114369 stop_rank=5000
2:03:34.414406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:34.748515 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:35.390424 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:35.390874 INFO: Using score_cutoff 9.064323251724243 (fac=0.99, q=1)
2:03:35.391182 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:35.391259 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:35.391315 INFO: Updating optimization_manager: score_cutoff        : 9.16647147846222 -> 9.064323251724243
2:03:35.391367 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:35.395263 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:35.402759 INFO: === checking if optimization conditions were reached ===
2:03:35.402871 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:03:35.405875 INFO: Updating optimization_manager: rt_error            : 134.82604914013066 -> 131.54312893092649
2:03:35.405978 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 131.5431.
2:03:35.406040 INFO: ==============================================
2:03:35.406106 INFO: Starting optimization step 10.
2:03:35.406162 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:03:35.406220 INFO: Using rust extraction backend
2:03:35.406273 PROGRESS: Extracting batch of 5936 precursors
2:03:35.417667 INFO: === Search parameters used ===
2:03:35.417776 INFO: rt_error       : 131.54312893092649
2:03:35.417828 INFO: mobility_error : 0.1
2:03:35.417894 INFO: num_candidates : 3
2:03:35.417941 INFO: ms1_error      : 30
2:03:35.417985 INFO: ms2_error      : 7.4697575
2:03:35.418026 INFO: fwhm_rt        : 3.0
2:03:35.418066 INFO: quant_window   : 3
2:03:35.418104 INFO: ==============================================
2:03:35.505629 INFO: performing precursor FDR with 40 features
2:03:35.505741 INFO: Decoy channel: -1
2:03:35.505765 INFO: competitive: True
2:03:35.510383 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:35.514225 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:03:35.514340 INFO: Using random state 729068 for train-test-split
2:03:36.931363 INFO: Test AUC: 0.764
2:03:36.931474 INFO: Train AUC: 0.789
2:03:36.931501 INFO: AUC difference: 3.09%
2:03:38.832652 INFO: Resetting torch num_threads to 100
2:03:38.835141 PROGRESS: === Extracted 17804 precursors and 114142 fragments ===
2:03:38.835515 INFO: === FDR correction performed with classifier version 6 ===
2:03:38.836249 PROGRESS: ============================= Precursor FDR =============================
2:03:38.836343 PROGRESS: Total precursors accumulated: 2,792
2:03:38.836403 PROGRESS: Target precursors: 2,765 (99.03%)
2:03:38.836454 PROGRESS: Decoy precursors: 27 (0.97%)
2:03:38.836499 PROGRESS: 
2:03:38.836543 PROGRESS: Precursor Summary:
2:03:38.838287 PROGRESS: Channel   0:	 0.050 FDR: 2,765; 0.010 FDR: 2,765; 0.001 FDR: 2,279
2:03:38.838382 PROGRESS: 
2:03:38.838437 PROGRESS: Protein Summary:
2:03:38.840851 PROGRESS: Channel   0:	 0.050 FDR: 2,121; 0.010 FDR: 2,121; 0.001 FDR: 1,784
2:03:38.840945 PROGRESS: =========================================================================
2:03:38.841301 INFO: Target number of precursors reached.
2:03:38.867222 INFO: fragments_df: keeping 5000 of 114142 [sum(precursor_idx_mask)=60674 sum(mass_error_mask)=114142 stop_rank=5000
2:03:38.878126 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:39.211561 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:39.861504 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:03:39.861971 INFO: Using score_cutoff 9.300292688369751 (fac=0.99, q=1)
2:03:39.862287 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:39.862365 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:39.862420 INFO: Updating optimization_manager: score_cutoff        : 9.064323251724243 -> 9.300292688369751
2:03:39.862481 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:39.866471 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:39.874322 INFO: === checking if optimization conditions were reached ===
2:03:39.874431 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:03:39.875129 INFO: Updating optimization_manager: rt_error            : 131.54312893092649 -> 140.22037919741527
2:03:39.875252 INFO: Updating optimization_manager: classifier_version  : 6 -> 13
2:03:39.875348 INFO: Updating optimization_manager: score_cutoff        : 9.300292688369751 -> 9.317026044559478
2:03:39.875437 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:03:39.875522 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:03:39.875608 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 140.2204 found after 11 searches.
2:03:39.875665 INFO: ==============================================
2:03:39.875730 PROGRESS: Optimization finished for rt_error.
2:03:39.886070 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:39.889903 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:39.897738 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:03:39.897862 PROGRESS: ==============================================
2:03:39.897933 PROGRESS: ms2_error      : 7.4698
2:03:39.897986 PROGRESS: rt_error       : 140.2204
2:03:39.898032 PROGRESS: ==============================================
2:03:39.898675 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:40.033146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:40.401134 INFO: Using rust extraction backend
2:03:40.401464 PROGRESS: Extracting batch of 260426 precursors
2:03:40.811224 INFO: === Search parameters used ===
2:03:40.811485 INFO: rt_error       : 140.22037919741527
2:03:40.811539 INFO: mobility_error : 0.1
2:03:40.811585 INFO: num_candidates : 3
2:03:40.811626 INFO: ms1_error      : 30
2:03:40.811666 INFO: ms2_error      : 7.4697575
2:03:40.811706 INFO: fwhm_rt        : 3.0
2:03:40.811748 INFO: quant_window   : 3
2:03:40.811794 INFO: ==============================================
2:03:41.123553 INFO: Removed 175172 precursors with score below cutoff 9.317026044559478
2:03:41.554717 INFO: performing precursor FDR with 40 features
2:03:41.554830 INFO: Decoy channel: -1
2:03:41.554853 INFO: competitive: True
2:03:41.605577 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:41.636351 WARNING: FDR calculation for 337053 target and 268977 decoy PSMs
2:03:41.636481 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:03:41.791055 INFO: Estimating optimal hyperparameters - samples: 484,824, batch_size: 1,985, learning_rate: 6.96e-04
2:03:41.792478 INFO: Using random state 232884 for train-test-split
2:03:53.259796 INFO: Test AUC: 0.806
2:03:53.259933 INFO: Train AUC: 0.809
2:03:53.259966 INFO: AUC difference: 0.36%
2:03:53.728456 INFO: Resetting torch num_threads to 100
2:03:54.032693 PROGRESS: ============================= Precursor FDR =============================
2:03:54.032996 PROGRESS: Total precursors accumulated: 123,282
2:03:54.033065 PROGRESS: Target precursors: 122,062 (99.01%)
2:03:54.033120 PROGRESS: Decoy precursors: 1,220 (0.99%)
2:03:54.033168 PROGRESS: 
2:03:54.033215 PROGRESS: Precursor Summary:
2:03:54.070201 PROGRESS: Channel   0:	 0.050 FDR: 122,062; 0.010 FDR: 122,062; 0.001 FDR: 109,860
2:03:54.070455 PROGRESS: 
2:03:54.070518 PROGRESS: Protein Summary:
2:03:54.129982 PROGRESS: Channel   0:	 0.050 FDR: 10,107; 0.010 FDR: 10,107; 0.001 FDR: 9,990
2:03:54.130249 PROGRESS: =========================================================================
2:03:54.132487 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
2:03:54.318606 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
2:03:54.613950 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:03:54.709014 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
2:03:54.709148 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant
2:03:54.709231 INFO: Initializing TimingManager
2:03:54.709905 INFO: Initializing RawFileManager
2:04:05.798037 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.
2:04:05.806293 INFO: Determining DIA cycle
2:04:05.823630 INFO: Found cycle with start 0.00 min and length 300.
2:04:05.994483 INFO: RT (min)            : 0.0 - 26.9
2:04:05.994571 INFO: RT duration (sec)   : 1611.2
2:04:05.994602 INFO: RT duration (min)   : 26.9
2:04:05.994625 INFO: Cycle len (scans)   : 300
2:04:05.994646 INFO: Cycle len (sec)     : 1.65
2:04:05.994665 INFO: Number of cycles    : 977
2:04:05.994686 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:04:05.994711 INFO: Creating DIA data object took: 11.284704446792603
2:04:06.661207 INFO: Creating DIA data NG object took: 0.6663806438446045
2:04:06.688106 INFO: Initializing CalibrationManager
2:04:06.688394 INFO: Setting up calibration estimators ..
2:04:06.688453 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:04:06.688536 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'}' ..
2:04:06.688597 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:04:06.688646 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:04:06.688696 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}}' ..
2:04:06.688745 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:04:06.688790 INFO: Done setting up calibration estimators.
2:04:06.688987 INFO: Initializing OptimizationManager
2:04:06.689098 INFO: initial parameter: ms1_error = 30
2:04:06.689147 INFO: initial parameter: ms2_error = 30
2:04:06.689192 INFO: initial parameter: rt_error = 805.5982666015625
2:04:06.689234 INFO: initial parameter: mobility_error = 0.1
2:04:06.689275 INFO: initial parameter: num_candidates = 1
2:04:06.689316 INFO: initial parameter: fwhm_rt = 5
2:04:06.689356 INFO: initial parameter: fwhm_mobility = 0.01
2:04:06.689396 INFO: initial parameter: score_cutoff = 0
2:04:06.689436 INFO: initial parameter: classifier_version = -1
2:04:06.689500 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:04:06.689688 INFO: FDRManager: loading saved state not requested, will be initialized.
2:04:06.689720 INFO: Initializing FDRManager
2:04:06.689748 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:04:06.725986 PROGRESS: Initializing spectral library: 131,664 target precursors potentially observable (0 removed)
2:04:06.750482 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:04:06.750854 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
2:04:06.750949 PROGRESS: Starting initial search for precursors.
2:04:06.751026 INFO: Starting optimization step 0.
2:04:06.751084 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:04:06.751137 INFO: Using rust extraction backend
2:04:06.751189 PROGRESS: Extracting batch of 1977 precursors
2:04:06.756162 INFO: === Search parameters used ===
2:04:06.756262 INFO: rt_error       : 805.5982666015625
2:04:06.756313 INFO: mobility_error : 0.1
2:04:06.756359 INFO: num_candidates : 1
2:04:06.756413 INFO: ms1_error      : 30
2:04:06.756456 INFO: ms2_error      : 30
2:04:06.756497 INFO: fwhm_rt        : 5
2:04:06.756537 INFO: quant_window   : 3
2:04:06.756577 INFO: ==============================================
2:04:06.782424 INFO: performing precursor FDR with 40 features
2:04:06.782493 INFO: Decoy channel: -1
2:04:06.782518 INFO: competitive: True
2:04:06.783735 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:06.785407 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
2:04:06.786213 INFO: Using random state 898227 for train-test-split
2:04:06.938875 INFO: Test AUC: 0.808
2:04:06.938956 INFO: Train AUC: 0.814
2:04:06.938983 INFO: AUC difference: 0.77%
2:04:07.180573 INFO: Resetting torch num_threads to 100
2:04:07.182201 PROGRESS: === Extracted 1976 precursors and 13536 fragments ===
2:04:07.182566 INFO: === FDR correction performed with classifier version -1 ===
2:04:07.183044 PROGRESS: ============================= Precursor FDR =============================
2:04:07.183137 PROGRESS: Total precursors accumulated: 225
2:04:07.183193 PROGRESS: Target precursors: 223 (99.11%)
2:04:07.183241 PROGRESS: Decoy precursors: 2 (0.89%)
2:04:07.183283 PROGRESS: 
2:04:07.183325 PROGRESS: Precursor Summary:
2:04:07.184327 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   223; 0.001 FDR:   169
2:04:07.184412 PROGRESS: 
2:04:07.184464 PROGRESS: Protein Summary:
2:04:07.185657 PROGRESS: Channel   0:	 0.050 FDR:   208; 0.010 FDR:   208; 0.001 FDR:   156
2:04:07.185739 PROGRESS: =========================================================================
2:04:07.185937 INFO: Target number of precursors not reached yet.
2:04:07.193522 INFO: Starting optimization step 1.
2:04:07.193625 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:04:07.193695 INFO: Using rust extraction backend
2:04:07.193750 PROGRESS: Extracting batch of 3959 precursors
2:04:07.201887 INFO: === Search parameters used ===
2:04:07.201991 INFO: rt_error       : 805.5982666015625
2:04:07.202042 INFO: mobility_error : 0.1
2:04:07.202086 INFO: num_candidates : 1
2:04:07.202128 INFO: ms1_error      : 30
2:04:07.202168 INFO: ms2_error      : 30
2:04:07.202206 INFO: fwhm_rt        : 5
2:04:07.202245 INFO: quant_window   : 3
2:04:07.202285 INFO: ==============================================
2:04:07.248273 INFO: performing precursor FDR with 40 features
2:04:07.248365 INFO: Decoy channel: -1
2:04:07.248389 INFO: competitive: True
2:04:07.252460 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:07.254781 INFO: Estimating optimal hyperparameters - samples: 4,742, batch_size: 128, learning_rate: 1.77e-04
2:04:07.254869 INFO: Using random state 510933 for train-test-split
2:04:07.735561 INFO: Test AUC: 0.814
2:04:07.735650 INFO: Train AUC: 0.830
2:04:07.735677 INFO: AUC difference: 1.96%
2:04:07.980558 INFO: Resetting torch num_threads to 100
2:04:07.983649 PROGRESS: === Extracted 5928 precursors and 41265 fragments ===
2:04:07.984030 INFO: === FDR correction performed with classifier version -1 ===
2:04:07.984663 PROGRESS: ============================= Precursor FDR =============================
2:04:07.984749 PROGRESS: Total precursors accumulated: 1,633
2:04:07.984807 PROGRESS: Target precursors: 1,617 (99.02%)
2:04:07.984856 PROGRESS: Decoy precursors: 16 (0.98%)
2:04:07.984910 PROGRESS: 
2:04:07.984957 PROGRESS: Precursor Summary:
2:04:07.986297 PROGRESS: Channel   0:	 0.050 FDR: 1,617; 0.010 FDR: 1,617; 0.001 FDR:   213
2:04:07.986395 PROGRESS: 
2:04:07.986449 PROGRESS: Protein Summary:
2:04:07.988125 PROGRESS: Channel   0:	 0.050 FDR: 1,313; 0.010 FDR: 1,313; 0.001 FDR:   203
2:04:07.988209 PROGRESS: =========================================================================
2:04:07.988447 INFO: Target number of precursors reached.
2:04:07.997570 INFO: fragments_df: keeping 5000 of 41265 [sum(precursor_idx_mask)=16692 sum(mass_error_mask)=41265 stop_rank=5000
2:04:08.008360 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:08.223539 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:08.880153 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:04:08.880605 INFO: Using score_cutoff 11.775589902877806 (fac=0.99, q=1)
2:04:08.880908 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:04:08.880983 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:04:08.881035 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.775589902877806
2:04:08.881086 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:08.885007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:08.892942 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:04:08.893053 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:04:08.893145 INFO: Starting optimization step 2.
2:04:08.893228 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:08.893304 INFO: Using rust extraction backend
2:04:08.893368 PROGRESS: Extracting batch of 5936 precursors
2:04:08.905066 INFO: === Search parameters used ===
2:04:08.905206 INFO: rt_error       : 805.5982666015625
2:04:08.905259 INFO: mobility_error : 0.1
2:04:08.905305 INFO: num_candidates : 3
2:04:08.905347 INFO: ms1_error      : 30
2:04:08.905388 INFO: ms2_error      : 30
2:04:08.905428 INFO: fwhm_rt        : 3.0
2:04:08.905468 INFO: quant_window   : 3
2:04:08.905508 INFO: ==============================================
2:04:09.013256 INFO: performing precursor FDR with 40 features
2:04:09.013367 INFO: Decoy channel: -1
2:04:09.013393 INFO: competitive: True
2:04:09.020093 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:09.024048 INFO: Estimating optimal hyperparameters - samples: 14,216, batch_size: 128, learning_rate: 1.77e-04
2:04:09.024177 INFO: Using random state 454502 for train-test-split
2:04:10.459836 INFO: Test AUC: 0.686
2:04:10.459960 INFO: Train AUC: 0.683
2:04:10.459991 INFO: AUC difference: 0.45%
2:04:10.705997 INFO: Resetting torch num_threads to 100
2:04:10.708369 PROGRESS: === Extracted 17770 precursors and 106984 fragments ===
2:04:10.708745 INFO: === FDR correction performed with classifier version 1 ===
2:04:10.709413 PROGRESS: ============================= Precursor FDR =============================
2:04:10.709500 PROGRESS: Total precursors accumulated: 2,021
2:04:10.709559 PROGRESS: Target precursors: 2,001 (99.01%)
2:04:10.709610 PROGRESS: Decoy precursors: 20 (0.99%)
2:04:10.709659 PROGRESS: 
2:04:10.709714 PROGRESS: Precursor Summary:
2:04:10.711240 PROGRESS: Channel   0:	 0.050 FDR: 2,001; 0.010 FDR: 2,001; 0.001 FDR: 1,356
2:04:10.711342 PROGRESS: 
2:04:10.711399 PROGRESS: Protein Summary:
2:04:10.713411 PROGRESS: Channel   0:	 0.050 FDR: 1,598; 0.010 FDR: 1,598; 0.001 FDR: 1,112
2:04:10.713503 PROGRESS: =========================================================================
2:04:10.713892 INFO: Target number of precursors reached.
2:04:10.733829 INFO: fragments_df: keeping 5000 of 106984 [sum(precursor_idx_mask)=43057 sum(mass_error_mask)=106984 stop_rank=5000
2:04:10.744659 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:10.995288 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:11.643777 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:11.644228 INFO: Using score_cutoff 11.771231575012207 (fac=0.99, q=1)
2:04:11.644533 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:11.644609 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:11.644663 INFO: Updating optimization_manager: score_cutoff        : 11.775589902877806 -> 11.771231575012207
2:04:11.644714 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:11.648615 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:11.656446 INFO: === checking if optimization conditions were reached ===
2:04:11.658153 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.4697575
2:04:11.658253 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:04:11.658319 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:04:11.658375 INFO: ==============================================
2:04:11.658449 INFO: Starting optimization step 3.
2:04:11.658508 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:11.658566 INFO: Using rust extraction backend
2:04:11.658621 PROGRESS: Extracting batch of 5936 precursors
2:04:11.670173 INFO: === Search parameters used ===
2:04:11.670292 INFO: rt_error       : 805.5982666015625
2:04:11.670344 INFO: mobility_error : 0.1
2:04:11.670394 INFO: num_candidates : 3
2:04:11.670438 INFO: ms1_error      : 30
2:04:11.670479 INFO: ms2_error      : 7.4697575
2:04:11.670521 INFO: fwhm_rt        : 3.0
2:04:11.670560 INFO: quant_window   : 3
2:04:11.670601 INFO: ==============================================
2:04:11.773243 INFO: performing precursor FDR with 40 features
2:04:11.773360 INFO: Decoy channel: -1
2:04:11.773386 INFO: competitive: True
2:04:11.780658 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:11.784694 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:04:11.784822 INFO: Using random state 743403 for train-test-split
2:04:13.221778 INFO: Test AUC: 0.734
2:04:13.221905 INFO: Train AUC: 0.741
2:04:13.221936 INFO: AUC difference: 0.88%
2:04:13.472800 INFO: Resetting torch num_threads to 100
2:04:13.475241 PROGRESS: === Extracted 17806 precursors and 123832 fragments ===
2:04:13.475625 INFO: === FDR correction performed with classifier version 2 ===
2:04:13.476356 PROGRESS: ============================= Precursor FDR =============================
2:04:13.476445 PROGRESS: Total precursors accumulated: 2,506
2:04:13.476502 PROGRESS: Target precursors: 2,482 (99.04%)
2:04:13.476550 PROGRESS: Decoy precursors: 24 (0.96%)
2:04:13.476593 PROGRESS: 
2:04:13.476635 PROGRESS: Precursor Summary:
2:04:13.478264 PROGRESS: Channel   0:	 0.050 FDR: 2,482; 0.010 FDR: 2,482; 0.001 FDR: 1,623
2:04:13.478361 PROGRESS: 
2:04:13.478416 PROGRESS: Protein Summary:
2:04:13.480599 PROGRESS: Channel   0:	 0.050 FDR: 1,923; 0.010 FDR: 1,923; 0.001 FDR: 1,322
2:04:13.480686 PROGRESS: =========================================================================
2:04:13.481053 INFO: Target number of precursors reached.
2:04:13.508043 INFO: fragments_df: keeping 5000 of 123832 [sum(precursor_idx_mask)=58146 sum(mass_error_mask)=123832 stop_rank=5000
2:04:13.519140 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:13.829249 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:14.477580 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:14.478043 INFO: Using score_cutoff 10.782961659908294 (fac=0.99, q=1)
2:04:14.478368 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:14.478445 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:14.478498 INFO: Updating optimization_manager: score_cutoff        : 11.771231575012207 -> 10.782961659908294
2:04:14.478551 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:14.482477 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:14.489987 INFO: === checking if optimization conditions were reached ===
2:04:14.491629 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:04:14.491723 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:04:14.491792 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:04:14.491846 INFO: ==============================================
2:04:14.491908 INFO: Starting optimization step 4.
2:04:14.491961 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:14.492015 INFO: Using rust extraction backend
2:04:14.492063 PROGRESS: Extracting batch of 5936 precursors
2:04:14.503505 INFO: === Search parameters used ===
2:04:14.503627 INFO: rt_error       : 805.5982666015625
2:04:14.503678 INFO: mobility_error : 0.1
2:04:14.503723 INFO: num_candidates : 3
2:04:14.503766 INFO: ms1_error      : 30
2:04:14.503806 INFO: ms2_error      : 7.4697575
2:04:14.503847 INFO: fwhm_rt        : 3.0
2:04:14.503887 INFO: quant_window   : 3
2:04:14.503927 INFO: ==============================================
2:04:14.608368 INFO: performing precursor FDR with 40 features
2:04:14.608493 INFO: Decoy channel: -1
2:04:14.608519 INFO: competitive: True
2:04:14.613711 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:14.617829 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:04:14.617975 INFO: Using random state 606214 for train-test-split
2:04:16.056673 INFO: Test AUC: 0.742
2:04:16.056788 INFO: Train AUC: 0.756
2:04:16.056818 INFO: AUC difference: 1.77%
2:04:16.307997 INFO: Resetting torch num_threads to 100
2:04:16.310445 PROGRESS: === Extracted 17806 precursors and 123806 fragments ===
2:04:16.310827 INFO: === FDR correction performed with classifier version 3 ===
2:04:16.311564 PROGRESS: ============================= Precursor FDR =============================
2:04:16.311652 PROGRESS: Total precursors accumulated: 2,606
2:04:16.311711 PROGRESS: Target precursors: 2,581 (99.04%)
2:04:16.311761 PROGRESS: Decoy precursors: 25 (0.96%)
2:04:16.311808 PROGRESS: 
2:04:16.311861 PROGRESS: Precursor Summary:
2:04:16.313512 PROGRESS: Channel   0:	 0.050 FDR: 2,581; 0.010 FDR: 2,581; 0.001 FDR: 1,857
2:04:16.313606 PROGRESS: 
2:04:16.313663 PROGRESS: Protein Summary:
2:04:16.315917 PROGRESS: Channel   0:	 0.050 FDR: 1,998; 0.010 FDR: 1,998; 0.001 FDR: 1,497
2:04:16.316020 PROGRESS: =========================================================================
2:04:16.316401 INFO: Target number of precursors reached.
2:04:16.344006 INFO: fragments_df: keeping 5000 of 123806 [sum(precursor_idx_mask)=60191 sum(mass_error_mask)=123806 stop_rank=5000
2:04:16.355058 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:16.674975 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:17.326922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:17.327374 INFO: Using score_cutoff 10.648048885345458 (fac=0.99, q=1)
2:04:17.327686 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:17.327761 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:17.327813 INFO: Updating optimization_manager: score_cutoff        : 10.782961659908294 -> 10.648048885345458
2:04:17.327863 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:17.331804 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:17.339349 INFO: === checking if optimization conditions were reached ===
2:04:17.340987 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:04:17.341089 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:04:17.341152 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:04:17.341206 INFO: ==============================================
2:04:17.341269 INFO: Starting optimization step 5.
2:04:17.341322 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:17.341376 INFO: Using rust extraction backend
2:04:17.341428 PROGRESS: Extracting batch of 5936 precursors
2:04:17.352850 INFO: === Search parameters used ===
2:04:17.352964 INFO: rt_error       : 805.5982666015625
2:04:17.353014 INFO: mobility_error : 0.1
2:04:17.353057 INFO: num_candidates : 3
2:04:17.353100 INFO: ms1_error      : 30
2:04:17.353142 INFO: ms2_error      : 7.4697575
2:04:17.353182 INFO: fwhm_rt        : 3.0
2:04:17.353221 INFO: quant_window   : 3
2:04:17.353260 INFO: ==============================================
2:04:17.455467 INFO: performing precursor FDR with 40 features
2:04:17.455580 INFO: Decoy channel: -1
2:04:17.455604 INFO: competitive: True
2:04:17.460801 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:17.464749 INFO: Estimating optimal hyperparameters - samples: 14,246, batch_size: 128, learning_rate: 1.77e-04
2:04:17.464880 INFO: Using random state 374025 for train-test-split
2:04:18.898697 INFO: Test AUC: 0.747
2:04:18.898813 INFO: Train AUC: 0.764
2:04:18.898842 INFO: AUC difference: 2.19%
2:04:19.149961 INFO: Resetting torch num_threads to 100
2:04:19.152380 PROGRESS: === Extracted 17808 precursors and 123832 fragments ===
2:04:19.152753 INFO: === FDR correction performed with classifier version 4 ===
2:04:19.153473 PROGRESS: ============================= Precursor FDR =============================
2:04:19.153556 PROGRESS: Total precursors accumulated: 2,678
2:04:19.153612 PROGRESS: Target precursors: 2,652 (99.03%)
2:04:19.153667 PROGRESS: Decoy precursors: 26 (0.97%)
2:04:19.153714 PROGRESS: 
2:04:19.153758 PROGRESS: Precursor Summary:
2:04:19.155451 PROGRESS: Channel   0:	 0.050 FDR: 2,652; 0.010 FDR: 2,652; 0.001 FDR: 2,118
2:04:19.155547 PROGRESS: 
2:04:19.155601 PROGRESS: Protein Summary:
2:04:19.157915 PROGRESS: Channel   0:	 0.050 FDR: 2,054; 0.010 FDR: 2,054; 0.001 FDR: 1,673
2:04:19.158009 PROGRESS: =========================================================================
2:04:19.158381 INFO: Target number of precursors reached.
2:04:19.185633 INFO: fragments_df: keeping 5000 of 123832 [sum(precursor_idx_mask)=61604 sum(mass_error_mask)=123832 stop_rank=5000
2:04:19.196449 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:19.523247 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:20.171564 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:20.172024 INFO: Using score_cutoff 10.2921511759758 (fac=0.99, q=1)
2:04:20.172348 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:20.172429 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:20.172486 INFO: Updating optimization_manager: score_cutoff        : 10.648048885345458 -> 10.2921511759758
2:04:20.172540 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:20.176457 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:20.183902 INFO: === checking if optimization conditions were reached ===
2:04:20.185600 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:04:20.185701 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:04:20.185766 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:04:20.185823 INFO: ==============================================
2:04:20.185919 INFO: Starting optimization step 6.
2:04:20.185979 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:20.186036 INFO: Using rust extraction backend
2:04:20.186088 PROGRESS: Extracting batch of 5936 precursors
2:04:20.197610 INFO: === Search parameters used ===
2:04:20.197721 INFO: rt_error       : 805.5982666015625
2:04:20.197773 INFO: mobility_error : 0.1
2:04:20.197818 INFO: num_candidates : 3
2:04:20.197870 INFO: ms1_error      : 30
2:04:20.197916 INFO: ms2_error      : 7.4697575
2:04:20.197958 INFO: fwhm_rt        : 3.0
2:04:20.197998 INFO: quant_window   : 3
2:04:20.198038 INFO: ==============================================
2:04:20.299488 INFO: performing precursor FDR with 40 features
2:04:20.299602 INFO: Decoy channel: -1
2:04:20.299627 INFO: competitive: True
2:04:20.304753 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:20.308744 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:04:20.308877 INFO: Using random state 862575 for train-test-split
2:04:21.753636 INFO: Test AUC: 0.757
2:04:21.753752 INFO: Train AUC: 0.769
2:04:21.753779 INFO: AUC difference: 1.59%
2:04:22.007911 INFO: Resetting torch num_threads to 100
2:04:22.010324 PROGRESS: === Extracted 17806 precursors and 123791 fragments ===
2:04:22.010694 INFO: === FDR correction performed with classifier version 5 ===
2:04:22.011409 PROGRESS: ============================= Precursor FDR =============================
2:04:22.011492 PROGRESS: Total precursors accumulated: 2,759
2:04:22.011555 PROGRESS: Target precursors: 2,732 (99.02%)
2:04:22.011606 PROGRESS: Decoy precursors: 27 (0.98%)
2:04:22.011650 PROGRESS: 
2:04:22.011692 PROGRESS: Precursor Summary:
2:04:22.013357 PROGRESS: Channel   0:	 0.050 FDR: 2,732; 0.010 FDR: 2,732; 0.001 FDR: 2,096
2:04:22.013443 PROGRESS: 
2:04:22.013496 PROGRESS: Protein Summary:
2:04:22.015837 PROGRESS: Channel   0:	 0.050 FDR: 2,115; 0.010 FDR: 2,115; 0.001 FDR: 1,656
2:04:22.015932 PROGRESS: =========================================================================
2:04:22.016298 INFO: Target number of precursors reached.
2:04:22.043609 INFO: fragments_df: keeping 5000 of 123791 [sum(precursor_idx_mask)=63138 sum(mass_error_mask)=123791 stop_rank=5000
2:04:22.054421 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:22.449616 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:23.159863 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:23.160320 INFO: Using score_cutoff 9.74805136756897 (fac=0.99, q=1)
2:04:23.160631 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:23.160705 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:23.160757 INFO: Updating optimization_manager: score_cutoff        : 10.2921511759758 -> 9.74805136756897
2:04:23.160806 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:23.164732 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:23.173130 INFO: === checking if optimization conditions were reached ===
2:04:23.174769 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:04:23.174884 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:04:23.174947 PROGRESS: ✅ ms2_error      : 7.4698 <= 7.4698
2:04:23.175000 INFO: ==============================================
2:04:23.175062 PROGRESS: Optimization finished for ms2_error.
2:04:23.185386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:23.189162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:23.196598 INFO: Starting optimization step 0.
2:04:23.196715 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:23.196783 INFO: Using rust extraction backend
2:04:23.196838 PROGRESS: Extracting batch of 5936 precursors
2:04:23.208384 INFO: === Search parameters used ===
2:04:23.208514 INFO: rt_error       : 805.5982666015625
2:04:23.208563 INFO: mobility_error : 0.1
2:04:23.208607 INFO: num_candidates : 3
2:04:23.208651 INFO: ms1_error      : 30
2:04:23.208692 INFO: ms2_error      : 7.4697575
2:04:23.208731 INFO: fwhm_rt        : 3.0
2:04:23.208771 INFO: quant_window   : 3
2:04:23.208809 INFO: ==============================================
2:04:23.310009 INFO: performing precursor FDR with 40 features
2:04:23.310121 INFO: Decoy channel: -1
2:04:23.310144 INFO: competitive: True
2:04:23.315309 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:23.319292 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:04:23.319420 INFO: Using random state 551889 for train-test-split
2:04:24.736397 INFO: Test AUC: 0.761
2:04:24.736511 INFO: Train AUC: 0.778
2:04:24.736538 INFO: AUC difference: 2.20%
2:04:24.989962 INFO: Resetting torch num_threads to 100
2:04:24.992368 PROGRESS: === Extracted 17806 precursors and 123771 fragments ===
2:04:24.992728 INFO: === FDR correction performed with classifier version 6 ===
2:04:24.993439 PROGRESS: ============================= Precursor FDR =============================
2:04:24.993520 PROGRESS: Total precursors accumulated: 2,776
2:04:24.993575 PROGRESS: Target precursors: 2,749 (99.03%)
2:04:24.993623 PROGRESS: Decoy precursors: 27 (0.97%)
2:04:24.993666 PROGRESS: 
2:04:24.993707 PROGRESS: Precursor Summary:
2:04:24.995395 PROGRESS: Channel   0:	 0.050 FDR: 2,749; 0.010 FDR: 2,749; 0.001 FDR: 2,293
2:04:24.995487 PROGRESS: 
2:04:24.995541 PROGRESS: Protein Summary:
2:04:24.997880 PROGRESS: Channel   0:	 0.050 FDR: 2,125; 0.010 FDR: 2,125; 0.001 FDR: 1,793
2:04:24.997974 PROGRESS: =========================================================================
2:04:24.998333 INFO: Target number of precursors reached.
2:04:25.026223 INFO: fragments_df: keeping 5000 of 123771 [sum(precursor_idx_mask)=63379 sum(mass_error_mask)=123771 stop_rank=5000
2:04:25.037288 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:25.433513 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:26.145635 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:26.146103 INFO: Using score_cutoff 9.679625827789307 (fac=0.99, q=1)
2:04:26.146418 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:26.146503 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:26.146559 INFO: Updating optimization_manager: score_cutoff        : 9.74805136756897 -> 9.679625827789307
2:04:26.146611 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:26.150510 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:26.157893 INFO: === checking if optimization conditions were reached ===
2:04:26.158000 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:04:26.160767 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 307.5526379379454
2:04:26.160865 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 307.5526.
2:04:26.160928 INFO: ==============================================
2:04:26.160995 INFO: Starting optimization step 1.
2:04:26.161052 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:26.161118 INFO: Using rust extraction backend
2:04:26.161173 PROGRESS: Extracting batch of 5936 precursors
2:04:26.172908 INFO: === Search parameters used ===
2:04:26.173021 INFO: rt_error       : 307.5526379379454
2:04:26.173072 INFO: mobility_error : 0.1
2:04:26.173117 INFO: num_candidates : 3
2:04:26.173162 INFO: ms1_error      : 30
2:04:26.173208 INFO: ms2_error      : 7.4697575
2:04:26.173250 INFO: fwhm_rt        : 3.0
2:04:26.173302 INFO: quant_window   : 3
2:04:26.173345 INFO: ==============================================
2:04:26.266689 INFO: performing precursor FDR with 40 features
2:04:26.266822 INFO: Decoy channel: -1
2:04:26.266845 INFO: competitive: True
2:04:26.272108 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:26.276079 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:04:26.276205 INFO: Using random state 551889 for train-test-split
2:04:27.712385 INFO: Test AUC: 0.787
2:04:27.712503 INFO: Train AUC: 0.781
2:04:27.712530 INFO: AUC difference: 0.72%
2:04:27.957903 INFO: Resetting torch num_threads to 100
2:04:27.960308 PROGRESS: === Extracted 17807 precursors and 122143 fragments ===
2:04:27.960682 INFO: === FDR correction performed with classifier version 6 ===
2:04:27.961408 PROGRESS: ============================= Precursor FDR =============================
2:04:27.961491 PROGRESS: Total precursors accumulated: 2,851
2:04:27.961547 PROGRESS: Target precursors: 2,823 (99.02%)
2:04:27.961596 PROGRESS: Decoy precursors: 28 (0.98%)
2:04:27.961640 PROGRESS: 
2:04:27.961684 PROGRESS: Precursor Summary:
2:04:27.963410 PROGRESS: Channel   0:	 0.050 FDR: 2,823; 0.010 FDR: 2,823; 0.001 FDR: 2,384
2:04:27.963502 PROGRESS: 
2:04:27.963557 PROGRESS: Protein Summary:
2:04:27.965954 PROGRESS: Channel   0:	 0.050 FDR: 2,163; 0.010 FDR: 2,163; 0.001 FDR: 1,850
2:04:27.966048 PROGRESS: =========================================================================
2:04:27.966399 INFO: Target number of precursors reached.
2:04:27.994266 INFO: fragments_df: keeping 5000 of 122143 [sum(precursor_idx_mask)=64462 sum(mass_error_mask)=122143 stop_rank=5000
2:04:28.005260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:28.423772 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:29.136971 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:29.137437 INFO: Using score_cutoff 9.453865105247496 (fac=0.99, q=1)
2:04:29.137748 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:29.137822 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:29.137885 INFO: Updating optimization_manager: score_cutoff        : 9.679625827789307 -> 9.453865105247496
2:04:29.137941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:29.141835 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:29.149176 INFO: === checking if optimization conditions were reached ===
2:04:29.149294 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:04:29.152231 INFO: Updating optimization_manager: rt_error            : 307.5526379379454 -> 256.53676707680586
2:04:29.152333 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 256.5368.
2:04:29.152395 INFO: ==============================================
2:04:29.152460 INFO: Starting optimization step 2.
2:04:29.152514 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:29.152570 INFO: Using rust extraction backend
2:04:29.152621 PROGRESS: Extracting batch of 5936 precursors
2:04:29.164398 INFO: === Search parameters used ===
2:04:29.164522 INFO: rt_error       : 256.53676707680586
2:04:29.164575 INFO: mobility_error : 0.1
2:04:29.164634 INFO: num_candidates : 3
2:04:29.164676 INFO: ms1_error      : 30
2:04:29.164720 INFO: ms2_error      : 7.4697575
2:04:29.164761 INFO: fwhm_rt        : 3.0
2:04:29.164799 INFO: quant_window   : 3
2:04:29.164837 INFO: ==============================================
2:04:29.256904 INFO: performing precursor FDR with 40 features
2:04:29.257015 INFO: Decoy channel: -1
2:04:29.257039 INFO: competitive: True
2:04:29.261815 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:29.265657 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:04:29.265772 INFO: Using random state 551889 for train-test-split
2:04:30.693970 INFO: Test AUC: 0.767
2:04:30.694089 INFO: Train AUC: 0.784
2:04:30.694119 INFO: AUC difference: 2.21%
2:04:30.940243 INFO: Resetting torch num_threads to 100
2:04:30.942700 PROGRESS: === Extracted 17807 precursors and 120967 fragments ===
2:04:30.943074 INFO: === FDR correction performed with classifier version 6 ===
2:04:30.943795 PROGRESS: ============================= Precursor FDR =============================
2:04:30.943882 PROGRESS: Total precursors accumulated: 2,850
2:04:30.943943 PROGRESS: Target precursors: 2,822 (99.02%)
2:04:30.943997 PROGRESS: Decoy precursors: 28 (0.98%)
2:04:30.944046 PROGRESS: 
2:04:30.944093 PROGRESS: Precursor Summary:
2:04:30.945776 PROGRESS: Channel   0:	 0.050 FDR: 2,822; 0.010 FDR: 2,822; 0.001 FDR: 2,384
2:04:30.945889 PROGRESS: 
2:04:30.945950 PROGRESS: Protein Summary:
2:04:30.948323 PROGRESS: Channel   0:	 0.050 FDR: 2,166; 0.010 FDR: 2,166; 0.001 FDR: 1,858
2:04:30.948415 PROGRESS: =========================================================================
2:04:30.948776 INFO: Target number of precursors reached.
2:04:30.976532 INFO: fragments_df: keeping 5000 of 120967 [sum(precursor_idx_mask)=64094 sum(mass_error_mask)=120967 stop_rank=5000
2:04:30.987517 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:31.398281 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:32.110151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:32.110595 INFO: Using score_cutoff 9.185623752880096 (fac=0.99, q=1)
2:04:32.110911 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:32.110988 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:32.111043 INFO: Updating optimization_manager: score_cutoff        : 9.453865105247496 -> 9.185623752880096
2:04:32.111096 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:32.115038 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:32.122468 INFO: === checking if optimization conditions were reached ===
2:04:32.122586 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:04:32.125618 INFO: Updating optimization_manager: rt_error            : 256.53676707680586 -> 191.99201695139644
2:04:32.125718 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 191.9920.
2:04:32.125784 INFO: ==============================================
2:04:32.125859 INFO: Starting optimization step 3.
2:04:32.125924 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:32.125995 INFO: Using rust extraction backend
2:04:32.126049 PROGRESS: Extracting batch of 5936 precursors
2:04:32.137740 INFO: === Search parameters used ===
2:04:32.137861 INFO: rt_error       : 191.99201695139644
2:04:32.137917 INFO: mobility_error : 0.1
2:04:32.137969 INFO: num_candidates : 3
2:04:32.138015 INFO: ms1_error      : 30
2:04:32.138057 INFO: ms2_error      : 7.4697575
2:04:32.138098 INFO: fwhm_rt        : 3.0
2:04:32.138138 INFO: quant_window   : 3
2:04:32.138178 INFO: ==============================================
2:04:32.226682 INFO: performing precursor FDR with 40 features
2:04:32.226796 INFO: Decoy channel: -1
2:04:32.226821 INFO: competitive: True
2:04:32.231520 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:32.235433 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:04:32.235561 INFO: Using random state 551889 for train-test-split
2:04:33.675135 INFO: Test AUC: 0.761
2:04:33.675251 INFO: Train AUC: 0.784
2:04:33.675281 INFO: AUC difference: 2.98%
2:04:33.922625 INFO: Resetting torch num_threads to 100
2:04:33.925012 PROGRESS: === Extracted 17804 precursors and 118444 fragments ===
2:04:33.925378 INFO: === FDR correction performed with classifier version 6 ===
2:04:33.926129 PROGRESS: ============================= Precursor FDR =============================
2:04:33.926217 PROGRESS: Total precursors accumulated: 2,839
2:04:33.926273 PROGRESS: Target precursors: 2,811 (99.01%)
2:04:33.926322 PROGRESS: Decoy precursors: 28 (0.99%)
2:04:33.926367 PROGRESS: 
2:04:33.926409 PROGRESS: Precursor Summary:
2:04:33.928066 PROGRESS: Channel   0:	 0.050 FDR: 2,811; 0.010 FDR: 2,811; 0.001 FDR: 2,376
2:04:33.928152 PROGRESS: 
2:04:33.928205 PROGRESS: Protein Summary:
2:04:33.930563 PROGRESS: Channel   0:	 0.050 FDR: 2,166; 0.010 FDR: 2,166; 0.001 FDR: 1,850
2:04:33.930664 PROGRESS: =========================================================================
2:04:33.931016 INFO: Target number of precursors reached.
2:04:33.957430 INFO: fragments_df: keeping 5000 of 118444 [sum(precursor_idx_mask)=63197 sum(mass_error_mask)=118444 stop_rank=5000
2:04:33.968105 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:34.374059 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:35.086823 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:35.087286 INFO: Using score_cutoff 9.192454899787903 (fac=0.99, q=1)
2:04:35.087593 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:35.087666 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:35.087719 INFO: Updating optimization_manager: score_cutoff        : 9.185623752880096 -> 9.192454899787903
2:04:35.087769 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:35.091668 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:35.099214 INFO: === checking if optimization conditions were reached ===
2:04:35.099325 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:04:35.102324 INFO: Updating optimization_manager: rt_error            : 191.99201695139644 -> 164.40997814771106
2:04:35.102434 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 164.4100.
2:04:35.102495 INFO: ==============================================
2:04:35.102560 INFO: Starting optimization step 4.
2:04:35.102615 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:35.102671 INFO: Using rust extraction backend
2:04:35.102724 PROGRESS: Extracting batch of 5936 precursors
2:04:35.114136 INFO: === Search parameters used ===
2:04:35.114278 INFO: rt_error       : 164.40997814771106
2:04:35.114332 INFO: mobility_error : 0.1
2:04:35.114376 INFO: num_candidates : 3
2:04:35.114417 INFO: ms1_error      : 30
2:04:35.114456 INFO: ms2_error      : 7.4697575
2:04:35.114496 INFO: fwhm_rt        : 3.0
2:04:35.114535 INFO: quant_window   : 3
2:04:35.114573 INFO: ==============================================
2:04:35.202308 INFO: performing precursor FDR with 40 features
2:04:35.202420 INFO: Decoy channel: -1
2:04:35.202444 INFO: competitive: True
2:04:35.207484 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:35.211438 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:04:35.211572 INFO: Using random state 551889 for train-test-split
2:04:36.660475 INFO: Test AUC: 0.782
2:04:36.660595 INFO: Train AUC: 0.781
2:04:36.660625 INFO: AUC difference: 0.08%
2:04:36.906798 INFO: Resetting torch num_threads to 100
2:04:36.909186 PROGRESS: === Extracted 17800 precursors and 116992 fragments ===
2:04:36.909555 INFO: === FDR correction performed with classifier version 6 ===
2:04:36.910284 PROGRESS: ============================= Precursor FDR =============================
2:04:36.910372 PROGRESS: Total precursors accumulated: 2,840
2:04:36.910432 PROGRESS: Target precursors: 2,812 (99.01%)
2:04:36.910484 PROGRESS: Decoy precursors: 28 (0.99%)
2:04:36.910533 PROGRESS: 
2:04:36.910581 PROGRESS: Precursor Summary:
2:04:36.912261 PROGRESS: Channel   0:	 0.050 FDR: 2,812; 0.010 FDR: 2,812; 0.001 FDR: 2,415
2:04:36.912351 PROGRESS: 
2:04:36.912406 PROGRESS: Protein Summary:
2:04:36.914778 PROGRESS: Channel   0:	 0.050 FDR: 2,160; 0.010 FDR: 2,160; 0.001 FDR: 1,877
2:04:36.914871 PROGRESS: =========================================================================
2:04:36.915223 INFO: Target number of precursors reached.
2:04:36.942105 INFO: fragments_df: keeping 5000 of 116992 [sum(precursor_idx_mask)=62793 sum(mass_error_mask)=116992 stop_rank=5000
2:04:36.952819 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:37.357721 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:38.068183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:38.068635 INFO: Using score_cutoff 9.453216322231292 (fac=0.99, q=1)
2:04:38.068950 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:38.069027 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:38.069081 INFO: Updating optimization_manager: score_cutoff        : 9.192454899787903 -> 9.453216322231292
2:04:38.069134 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:38.073001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:38.080352 INFO: === checking if optimization conditions were reached ===
2:04:38.080466 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:04:38.083481 INFO: Updating optimization_manager: rt_error            : 164.40997814771106 -> 141.85472323667796
2:04:38.083583 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 141.8547.
2:04:38.083645 INFO: ==============================================
2:04:38.083711 INFO: Starting optimization step 5.
2:04:38.083767 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:38.083822 INFO: Using rust extraction backend
2:04:38.083884 PROGRESS: Extracting batch of 5936 precursors
2:04:38.095312 INFO: === Search parameters used ===
2:04:38.095429 INFO: rt_error       : 141.85472323667796
2:04:38.095484 INFO: mobility_error : 0.1
2:04:38.095528 INFO: num_candidates : 3
2:04:38.095571 INFO: ms1_error      : 30
2:04:38.095614 INFO: ms2_error      : 7.4697575
2:04:38.095658 INFO: fwhm_rt        : 3.0
2:04:38.095697 INFO: quant_window   : 3
2:04:38.095736 INFO: ==============================================
2:04:38.183913 INFO: performing precursor FDR with 40 features
2:04:38.184027 INFO: Decoy channel: -1
2:04:38.184051 INFO: competitive: True
2:04:38.188667 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:38.192561 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:04:38.192688 INFO: Using random state 551889 for train-test-split
2:04:39.610416 INFO: Test AUC: 0.774
2:04:39.610527 INFO: Train AUC: 0.787
2:04:39.610555 INFO: AUC difference: 1.65%
2:04:39.855903 INFO: Resetting torch num_threads to 100
2:04:39.858294 PROGRESS: === Extracted 17801 precursors and 115689 fragments ===
2:04:39.858658 INFO: === FDR correction performed with classifier version 6 ===
2:04:39.859371 PROGRESS: ============================= Precursor FDR =============================
2:04:39.859454 PROGRESS: Total precursors accumulated: 2,815
2:04:39.859509 PROGRESS: Target precursors: 2,788 (99.04%)
2:04:39.859557 PROGRESS: Decoy precursors: 27 (0.96%)
2:04:39.859600 PROGRESS: 
2:04:39.859642 PROGRESS: Precursor Summary:
2:04:39.861304 PROGRESS: Channel   0:	 0.050 FDR: 2,788; 0.010 FDR: 2,788; 0.001 FDR: 2,407
2:04:39.861389 PROGRESS: 
2:04:39.861442 PROGRESS: Protein Summary:
2:04:39.863808 PROGRESS: Channel   0:	 0.050 FDR: 2,139; 0.010 FDR: 2,139; 0.001 FDR: 1,873
2:04:39.863913 PROGRESS: =========================================================================
2:04:39.864300 INFO: Target number of precursors reached.
2:04:39.890867 INFO: fragments_df: keeping 5000 of 115689 [sum(precursor_idx_mask)=61980 sum(mass_error_mask)=115689 stop_rank=5000
2:04:39.901671 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:40.301784 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:41.015126 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:41.015564 INFO: Using score_cutoff 9.232781536388396 (fac=0.99, q=1)
2:04:41.015880 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:41.015967 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:41.016023 INFO: Updating optimization_manager: score_cutoff        : 9.453216322231292 -> 9.232781536388396
2:04:41.016076 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:41.019965 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:41.027643 INFO: === checking if optimization conditions were reached ===
2:04:41.027749 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:04:41.030750 INFO: Updating optimization_manager: rt_error            : 141.85472323667796 -> 129.61976958956808
2:04:41.030865 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 129.6198.
2:04:41.030930 INFO: ==============================================
2:04:41.030998 INFO: Starting optimization step 6.
2:04:41.031058 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:41.031126 INFO: Using rust extraction backend
2:04:41.031183 PROGRESS: Extracting batch of 5936 precursors
2:04:41.042641 INFO: === Search parameters used ===
2:04:41.042759 INFO: rt_error       : 129.61976958956808
2:04:41.042811 INFO: mobility_error : 0.1
2:04:41.042856 INFO: num_candidates : 3
2:04:41.042899 INFO: ms1_error      : 30
2:04:41.042941 INFO: ms2_error      : 7.4697575
2:04:41.042983 INFO: fwhm_rt        : 3.0
2:04:41.043024 INFO: quant_window   : 3
2:04:41.043063 INFO: ==============================================
2:04:41.129256 INFO: performing precursor FDR with 40 features
2:04:41.129370 INFO: Decoy channel: -1
2:04:41.129395 INFO: competitive: True
2:04:41.134047 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:41.137954 INFO: Estimating optimal hyperparameters - samples: 14,239, batch_size: 128, learning_rate: 1.77e-04
2:04:41.138080 INFO: Using random state 551889 for train-test-split
2:04:42.555529 INFO: Test AUC: 0.783
2:04:42.555640 INFO: Train AUC: 0.788
2:04:42.555668 INFO: AUC difference: 0.64%
2:04:42.800782 INFO: Resetting torch num_threads to 100
2:04:42.803197 PROGRESS: === Extracted 17799 precursors and 114915 fragments ===
2:04:42.803568 INFO: === FDR correction performed with classifier version 6 ===
2:04:42.804277 PROGRESS: ============================= Precursor FDR =============================
2:04:42.804365 PROGRESS: Total precursors accumulated: 2,820
2:04:42.804422 PROGRESS: Target precursors: 2,793 (99.04%)
2:04:42.804472 PROGRESS: Decoy precursors: 27 (0.96%)
2:04:42.804518 PROGRESS: 
2:04:42.804563 PROGRESS: Precursor Summary:
2:04:42.806256 PROGRESS: Channel   0:	 0.050 FDR: 2,793; 0.010 FDR: 2,793; 0.001 FDR: 2,578
2:04:42.806351 PROGRESS: 
2:04:42.806414 PROGRESS: Protein Summary:
2:04:42.808795 PROGRESS: Channel   0:	 0.050 FDR: 2,145; 0.010 FDR: 2,145; 0.001 FDR: 1,995
2:04:42.808887 PROGRESS: =========================================================================
2:04:42.809245 INFO: Target number of precursors reached.
2:04:42.835631 INFO: fragments_df: keeping 5000 of 114915 [sum(precursor_idx_mask)=61811 sum(mass_error_mask)=114915 stop_rank=5000
2:04:42.846329 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:43.247537 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:43.959876 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:43.960341 INFO: Using score_cutoff 9.457993724441529 (fac=0.99, q=1)
2:04:43.960646 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:43.960721 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:43.960777 INFO: Updating optimization_manager: score_cutoff        : 9.232781536388396 -> 9.457993724441529
2:04:43.960838 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:43.964750 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:43.972281 INFO: === checking if optimization conditions were reached ===
2:04:43.972399 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:04:43.975427 INFO: Updating optimization_manager: rt_error            : 129.61976958956808 -> 99.21778147987631
2:04:43.975530 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 99.2178.
2:04:43.975593 INFO: ==============================================
2:04:43.975667 INFO: Starting optimization step 7.
2:04:43.975725 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:43.975784 INFO: Using rust extraction backend
2:04:43.975837 PROGRESS: Extracting batch of 5936 precursors
2:04:43.987459 INFO: === Search parameters used ===
2:04:43.987577 INFO: rt_error       : 99.21778147987631
2:04:43.987628 INFO: mobility_error : 0.1
2:04:43.987672 INFO: num_candidates : 3
2:04:43.987714 INFO: ms1_error      : 30
2:04:43.987754 INFO: ms2_error      : 7.4697575
2:04:43.987793 INFO: fwhm_rt        : 3.0
2:04:43.987832 INFO: quant_window   : 3
2:04:43.987870 INFO: ==============================================
2:04:44.073647 INFO: performing precursor FDR with 40 features
2:04:44.073761 INFO: Decoy channel: -1
2:04:44.073786 INFO: competitive: True
2:04:44.078448 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:44.082323 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
2:04:44.082444 INFO: Using random state 551889 for train-test-split
2:04:45.503584 INFO: Test AUC: 0.775
2:04:45.503682 INFO: Train AUC: 0.788
2:04:45.503713 INFO: AUC difference: 1.53%
2:04:45.750536 INFO: Resetting torch num_threads to 100
2:04:45.752909 PROGRESS: === Extracted 17796 precursors and 112307 fragments ===
2:04:45.753280 INFO: === FDR correction performed with classifier version 6 ===
2:04:45.754012 PROGRESS: ============================= Precursor FDR =============================
2:04:45.754102 PROGRESS: Total precursors accumulated: 2,796
2:04:45.754163 PROGRESS: Target precursors: 2,769 (99.03%)
2:04:45.754215 PROGRESS: Decoy precursors: 27 (0.97%)
2:04:45.754262 PROGRESS: 
2:04:45.754308 PROGRESS: Precursor Summary:
2:04:45.755977 PROGRESS: Channel   0:	 0.050 FDR: 2,769; 0.010 FDR: 2,769; 0.001 FDR: 2,457
2:04:45.756075 PROGRESS: 
2:04:45.756132 PROGRESS: Protein Summary:
2:04:45.758501 PROGRESS: Channel   0:	 0.050 FDR: 2,127; 0.010 FDR: 2,127; 0.001 FDR: 1,909
2:04:45.758604 PROGRESS: =========================================================================
2:04:45.758969 INFO: Target number of precursors reached.
2:04:45.784847 INFO: fragments_df: keeping 5000 of 112307 [sum(precursor_idx_mask)=60575 sum(mass_error_mask)=112307 stop_rank=5000
2:04:45.795783 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:46.200420 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:46.913778 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:46.914238 INFO: Using score_cutoff 9.632285523605347 (fac=0.99, q=1)
2:04:46.914552 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:46.914629 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:46.914681 INFO: Updating optimization_manager: score_cutoff        : 9.457993724441529 -> 9.632285523605347
2:04:46.914734 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:46.918651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:46.925964 INFO: === checking if optimization conditions were reached ===
2:04:46.926072 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:04:46.929037 INFO: Updating optimization_manager: rt_error            : 99.21778147987631 -> 86.26311359893135
2:04:46.929135 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 86.2631.
2:04:46.929213 INFO: ==============================================
2:04:46.929281 INFO: Starting optimization step 8.
2:04:46.929336 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:46.929394 INFO: Using rust extraction backend
2:04:46.929449 PROGRESS: Extracting batch of 5936 precursors
2:04:46.941113 INFO: === Search parameters used ===
2:04:46.941234 INFO: rt_error       : 86.26311359893135
2:04:46.941285 INFO: mobility_error : 0.1
2:04:46.941329 INFO: num_candidates : 3
2:04:46.941372 INFO: ms1_error      : 30
2:04:46.941412 INFO: ms2_error      : 7.4697575
2:04:46.941452 INFO: fwhm_rt        : 3.0
2:04:46.941491 INFO: quant_window   : 3
2:04:46.941530 INFO: ==============================================
2:04:47.026783 INFO: performing precursor FDR with 40 features
2:04:47.026895 INFO: Decoy channel: -1
2:04:47.026918 INFO: competitive: True
2:04:47.031537 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:47.035452 INFO: Estimating optimal hyperparameters - samples: 14,233, batch_size: 128, learning_rate: 1.77e-04
2:04:47.035572 INFO: Using random state 551889 for train-test-split
2:04:48.458146 INFO: Test AUC: 0.776
2:04:48.458256 INFO: Train AUC: 0.791
2:04:48.458283 INFO: AUC difference: 1.84%
2:04:48.702786 INFO: Resetting torch num_threads to 100
2:04:48.705148 PROGRESS: === Extracted 17792 precursors and 110946 fragments ===
2:04:48.705515 INFO: === FDR correction performed with classifier version 6 ===
2:04:48.706244 PROGRESS: ============================= Precursor FDR =============================
2:04:48.706336 PROGRESS: Total precursors accumulated: 2,805
2:04:48.706393 PROGRESS: Target precursors: 2,778 (99.04%)
2:04:48.706441 PROGRESS: Decoy precursors: 27 (0.96%)
2:04:48.706487 PROGRESS: 
2:04:48.706538 PROGRESS: Precursor Summary:
2:04:48.708205 PROGRESS: Channel   0:	 0.050 FDR: 2,778; 0.010 FDR: 2,778; 0.001 FDR: 2,350
2:04:48.708290 PROGRESS: 
2:04:48.708344 PROGRESS: Protein Summary:
2:04:48.710708 PROGRESS: Channel   0:	 0.050 FDR: 2,136; 0.010 FDR: 2,136; 0.001 FDR: 1,830
2:04:48.710802 PROGRESS: =========================================================================
2:04:48.711151 INFO: Target number of precursors reached.
2:04:48.736627 INFO: fragments_df: keeping 5000 of 110946 [sum(precursor_idx_mask)=60183 sum(mass_error_mask)=110946 stop_rank=5000
2:04:48.747295 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:49.148881 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:49.861271 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:49.861727 INFO: Using score_cutoff 9.103616510868072 (fac=0.99, q=1)
2:04:49.862052 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:49.862132 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:49.862185 INFO: Updating optimization_manager: score_cutoff        : 9.632285523605347 -> 9.103616510868072
2:04:49.862234 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:49.866132 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:49.873701 INFO: === checking if optimization conditions were reached ===
2:04:49.873818 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:04:49.876821 INFO: Updating optimization_manager: rt_error            : 86.26311359893135 -> 68.28982956324151
2:04:49.876935 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 68.2898.
2:04:49.876997 INFO: ==============================================
2:04:49.877060 INFO: Starting optimization step 9.
2:04:49.877115 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:49.877170 INFO: Using rust extraction backend
2:04:49.877223 PROGRESS: Extracting batch of 5936 precursors
2:04:49.888819 INFO: === Search parameters used ===
2:04:49.888935 INFO: rt_error       : 68.28982956324151
2:04:49.888985 INFO: mobility_error : 0.1
2:04:49.889041 INFO: num_candidates : 3
2:04:49.889083 INFO: ms1_error      : 30
2:04:49.889125 INFO: ms2_error      : 7.4697575
2:04:49.889165 INFO: fwhm_rt        : 3.0
2:04:49.889204 INFO: quant_window   : 3
2:04:49.889243 INFO: ==============================================
2:04:49.973435 INFO: performing precursor FDR with 40 features
2:04:49.973551 INFO: Decoy channel: -1
2:04:49.973574 INFO: competitive: True
2:04:49.978158 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:49.981995 INFO: Estimating optimal hyperparameters - samples: 14,191, batch_size: 128, learning_rate: 1.77e-04
2:04:49.982121 INFO: Using random state 551889 for train-test-split
2:04:51.384725 INFO: Test AUC: 0.797
2:04:51.384846 INFO: Train AUC: 0.792
2:04:51.384876 INFO: AUC difference: 0.63%
2:04:51.629869 INFO: Resetting torch num_threads to 100
2:04:51.632212 PROGRESS: === Extracted 17739 precursors and 107831 fragments ===
2:04:51.632582 INFO: === FDR correction performed with classifier version 6 ===
2:04:51.633299 PROGRESS: ============================= Precursor FDR =============================
2:04:51.633394 PROGRESS: Total precursors accumulated: 2,757
2:04:51.633452 PROGRESS: Target precursors: 2,730 (99.02%)
2:04:51.633508 PROGRESS: Decoy precursors: 27 (0.98%)
2:04:51.633555 PROGRESS: 
2:04:51.633598 PROGRESS: Precursor Summary:
2:04:51.635234 PROGRESS: Channel   0:	 0.050 FDR: 2,730; 0.010 FDR: 2,730; 0.001 FDR: 2,279
2:04:51.635325 PROGRESS: 
2:04:51.635380 PROGRESS: Protein Summary:
2:04:51.637674 PROGRESS: Channel   0:	 0.050 FDR: 2,100; 0.010 FDR: 2,100; 0.001 FDR: 1,779
2:04:51.637774 PROGRESS: =========================================================================
2:04:51.638127 INFO: Target number of precursors reached.
2:04:51.662490 INFO: fragments_df: keeping 5000 of 107831 [sum(precursor_idx_mask)=58065 sum(mass_error_mask)=107831 stop_rank=5000
2:04:51.673302 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:52.063489 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:52.773548 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:52.774008 INFO: Using score_cutoff 9.098193856716156 (fac=0.99, q=1)
2:04:52.774324 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:52.774401 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:52.774455 INFO: Updating optimization_manager: score_cutoff        : 9.103616510868072 -> 9.098193856716156
2:04:52.774508 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:52.778423 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:52.786052 INFO: === checking if optimization conditions were reached ===
2:04:52.786172 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:04:52.789116 INFO: Updating optimization_manager: rt_error            : 68.28982956324151 -> 68.34232254131898
2:04:52.789221 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 68.3423.
2:04:52.789284 INFO: ==============================================
2:04:52.789350 INFO: Starting optimization step 10.
2:04:52.789406 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:04:52.789464 INFO: Using rust extraction backend
2:04:52.789517 PROGRESS: Extracting batch of 5936 precursors
2:04:52.801050 INFO: === Search parameters used ===
2:04:52.801156 INFO: rt_error       : 68.34232254131898
2:04:52.801207 INFO: mobility_error : 0.1
2:04:52.801253 INFO: num_candidates : 3
2:04:52.801295 INFO: ms1_error      : 30
2:04:52.801337 INFO: ms2_error      : 7.4697575
2:04:52.801380 INFO: fwhm_rt        : 3.0
2:04:52.801422 INFO: quant_window   : 3
2:04:52.801464 INFO: ==============================================
2:04:52.885365 INFO: performing precursor FDR with 40 features
2:04:52.885479 INFO: Decoy channel: -1
2:04:52.885503 INFO: competitive: True
2:04:52.890044 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:52.893965 INFO: Estimating optimal hyperparameters - samples: 14,190, batch_size: 128, learning_rate: 1.77e-04
2:04:52.894102 INFO: Using random state 551889 for train-test-split
2:04:54.319157 INFO: Test AUC: 0.778
2:04:54.319267 INFO: Train AUC: 0.796
2:04:54.319296 INFO: AUC difference: 2.20%
2:04:54.564236 INFO: Resetting torch num_threads to 100
2:04:54.566591 PROGRESS: === Extracted 17738 precursors and 107776 fragments ===
2:04:54.566958 INFO: === FDR correction performed with classifier version 6 ===
2:04:54.567652 PROGRESS: ============================= Precursor FDR =============================
2:04:54.567742 PROGRESS: Total precursors accumulated: 2,765
2:04:54.567800 PROGRESS: Target precursors: 2,738 (99.02%)
2:04:54.567848 PROGRESS: Decoy precursors: 27 (0.98%)
2:04:54.567893 PROGRESS: 
2:04:54.567935 PROGRESS: Precursor Summary:
2:04:54.569568 PROGRESS: Channel   0:	 0.050 FDR: 2,738; 0.010 FDR: 2,738; 0.001 FDR: 2,432
2:04:54.569651 PROGRESS: 
2:04:54.569704 PROGRESS: Protein Summary:
2:04:54.572022 PROGRESS: Channel   0:	 0.050 FDR: 2,107; 0.010 FDR: 2,107; 0.001 FDR: 1,889
2:04:54.572118 PROGRESS: =========================================================================
2:04:54.572461 INFO: Target number of precursors reached.
2:04:54.596670 INFO: fragments_df: keeping 5000 of 107776 [sum(precursor_idx_mask)=58274 sum(mass_error_mask)=107776 stop_rank=5000
2:04:54.607427 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:54.998999 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:55.709518 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:55.709988 INFO: Using score_cutoff 9.18594657239914 (fac=0.99, q=1)
2:04:55.710307 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:55.710379 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:55.710431 INFO: Updating optimization_manager: score_cutoff        : 9.098193856716156 -> 9.18594657239914
2:04:55.710481 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:55.714384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:55.721926 INFO: === checking if optimization conditions were reached ===
2:04:55.722036 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:04:55.722736 INFO: Updating optimization_manager: rt_error            : 68.34232254131898 -> 307.5526379379454
2:04:55.722860 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
2:04:55.722952 INFO: Updating optimization_manager: score_cutoff        : 9.18594657239914 -> 9.453865105247496
2:04:55.723037 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:55.723117 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:55.723197 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 307.5526 found after 11 searches.
2:04:55.723253 INFO: ==============================================
2:04:55.723315 PROGRESS: Optimization finished for rt_error.
2:04:55.733909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:55.737659 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:55.745347 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:04:55.745465 PROGRESS: ==============================================
2:04:55.745530 PROGRESS: ms2_error      : 7.4698
2:04:55.745585 PROGRESS: rt_error       : 307.5526
2:04:55.745633 PROGRESS: ==============================================
2:04:55.746252 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:55.880458 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:56.245359 INFO: Using rust extraction backend
2:04:56.245665 PROGRESS: Extracting batch of 260426 precursors
2:04:56.653938 INFO: === Search parameters used ===
2:04:56.654201 INFO: rt_error       : 307.5526379379454
2:04:56.654260 INFO: mobility_error : 0.1
2:04:56.654310 INFO: num_candidates : 3
2:04:56.654355 INFO: ms1_error      : 30
2:04:56.654399 INFO: ms2_error      : 7.4697575
2:04:56.654466 INFO: fwhm_rt        : 3.0
2:04:56.654506 INFO: quant_window   : 3
2:04:56.654545 INFO: ==============================================
2:04:57.106508 INFO: Removed 105635 precursors with score below cutoff 9.453865105247496
2:04:57.573727 INFO: performing precursor FDR with 40 features
2:04:57.573881 INFO: Decoy channel: -1
2:04:57.573909 INFO: competitive: True
2:04:57.629536 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:57.661701 WARNING: FDR calculation for 360183 target and 315459 decoy PSMs
2:04:57.661827 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:04:57.828479 INFO: Estimating optimal hyperparameters - samples: 540,513, batch_size: 2,213, learning_rate: 7.35e-04
2:04:57.829242 INFO: Using random state 932123 for train-test-split
2:05:09.208139 INFO: Test AUC: 0.785
2:05:09.208279 INFO: Train AUC: 0.790
2:05:09.208311 INFO: AUC difference: 0.62%
2:05:09.692427 INFO: Resetting torch num_threads to 100
2:05:09.994904 PROGRESS: ============================= Precursor FDR =============================
2:05:09.995173 PROGRESS: Total precursors accumulated: 124,571
2:05:09.995245 PROGRESS: Target precursors: 123,338 (99.01%)
2:05:09.995301 PROGRESS: Decoy precursors: 1,233 (0.99%)
2:05:09.995352 PROGRESS: 
2:05:09.995399 PROGRESS: Precursor Summary:
2:05:10.032776 PROGRESS: Channel   0:	 0.050 FDR: 123,338; 0.010 FDR: 123,338; 0.001 FDR: 110,261
2:05:10.033031 PROGRESS: 
2:05:10.033097 PROGRESS: Protein Summary:
2:05:10.094465 PROGRESS: Channel   0:	 0.050 FDR: 10,114; 0.010 FDR: 10,114; 0.001 FDR: 10,026
2:05:10.094714 PROGRESS: =========================================================================
2:05:10.098107 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
2:05:10.290367 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
2:05:10.587064 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:05:10.666911 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
2:05:10.667047 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant
2:05:10.667130 INFO: Initializing TimingManager
2:05:10.667711 INFO: Initializing RawFileManager
2:05:21.742566 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.
2:05:21.751007 INFO: Determining DIA cycle
2:05:21.768403 INFO: Found cycle with start 0.00 min and length 300.
2:05:21.959602 INFO: RT (min)            : 0.0 - 26.9
2:05:21.959693 INFO: RT duration (sec)   : 1611.2
2:05:21.959722 INFO: RT duration (min)   : 26.9
2:05:21.959746 INFO: Cycle len (scans)   : 300
2:05:21.959766 INFO: Cycle len (sec)     : 1.65
2:05:21.959785 INFO: Number of cycles    : 977
2:05:21.959805 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:05:21.959829 INFO: Creating DIA data object took: 11.292016983032227
2:05:22.654158 INFO: Creating DIA data NG object took: 0.6942164897918701
2:05:22.682007 INFO: Initializing CalibrationManager
2:05:22.682309 INFO: Setting up calibration estimators ..
2:05:22.682369 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:05:22.682434 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'}' ..
2:05:22.682496 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:05:22.682545 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:05:22.682596 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}}' ..
2:05:22.682667 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:05:22.682719 INFO: Done setting up calibration estimators.
2:05:22.682937 INFO: Initializing OptimizationManager
2:05:22.683048 INFO: initial parameter: ms1_error = 30
2:05:22.683097 INFO: initial parameter: ms2_error = 30
2:05:22.683142 INFO: initial parameter: rt_error = 805.6002197265625
2:05:22.683183 INFO: initial parameter: mobility_error = 0.1
2:05:22.683223 INFO: initial parameter: num_candidates = 1
2:05:22.683262 INFO: initial parameter: fwhm_rt = 5
2:05:22.683301 INFO: initial parameter: fwhm_mobility = 0.01
2:05:22.683340 INFO: initial parameter: score_cutoff = 0
2:05:22.683379 INFO: initial parameter: classifier_version = -1
2:05:22.683441 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:05:22.683663 INFO: FDRManager: loading saved state not requested, will be initialized.
2:05:22.683693 INFO: Initializing FDRManager
2:05:22.683719 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:05:22.720176 PROGRESS: Initializing spectral library: 131,664 target precursors potentially observable (0 removed)
2:05:22.744414 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:05:22.744784 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
2:05:22.744869 PROGRESS: Starting initial search for precursors.
2:05:22.744942 INFO: Starting optimization step 0.
2:05:22.744995 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:05:22.745045 INFO: Using rust extraction backend
2:05:22.745100 PROGRESS: Extracting batch of 1977 precursors
2:05:22.749819 INFO: === Search parameters used ===
2:05:22.749923 INFO: rt_error       : 805.6002197265625
2:05:22.749974 INFO: mobility_error : 0.1
2:05:22.750018 INFO: num_candidates : 1
2:05:22.750060 INFO: ms1_error      : 30
2:05:22.750100 INFO: ms2_error      : 30
2:05:22.750143 INFO: fwhm_rt        : 5
2:05:22.750184 INFO: quant_window   : 3
2:05:22.750223 INFO: ==============================================
2:05:22.776475 INFO: performing precursor FDR with 40 features
2:05:22.776546 INFO: Decoy channel: -1
2:05:22.776570 INFO: competitive: True
2:05:22.777725 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:22.779380 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
2:05:22.780188 INFO: Using random state 76855 for train-test-split
2:05:22.928961 INFO: Test AUC: 0.806
2:05:22.929049 INFO: Train AUC: 0.790
2:05:22.929076 INFO: AUC difference: 2.03%
2:05:23.163647 INFO: Resetting torch num_threads to 100
2:05:23.165195 PROGRESS: === Extracted 1975 precursors and 13445 fragments ===
2:05:23.165558 INFO: === FDR correction performed with classifier version -1 ===
2:05:23.166049 PROGRESS: ============================= Precursor FDR =============================
2:05:23.166136 PROGRESS: Total precursors accumulated: 265
2:05:23.166192 PROGRESS: Target precursors: 263 (99.25%)
2:05:23.166240 PROGRESS: Decoy precursors: 2 (0.75%)
2:05:23.166283 PROGRESS: 
2:05:23.166326 PROGRESS: Precursor Summary:
2:05:23.167373 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   207
2:05:23.167454 PROGRESS: 
2:05:23.167507 PROGRESS: Protein Summary:
2:05:23.168685 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   245; 0.001 FDR:   197
2:05:23.168766 PROGRESS: =========================================================================
2:05:23.168967 INFO: Target number of precursors not reached yet.
2:05:23.177372 INFO: Starting optimization step 1.
2:05:23.177491 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:05:23.177559 INFO: Using rust extraction backend
2:05:23.177625 PROGRESS: Extracting batch of 3959 precursors
2:05:23.185584 INFO: === Search parameters used ===
2:05:23.185706 INFO: rt_error       : 805.6002197265625
2:05:23.185766 INFO: mobility_error : 0.1
2:05:23.185809 INFO: num_candidates : 1
2:05:23.185857 INFO: ms1_error      : 30
2:05:23.185904 INFO: ms2_error      : 30
2:05:23.185945 INFO: fwhm_rt        : 5
2:05:23.185984 INFO: quant_window   : 3
2:05:23.186023 INFO: ==============================================
2:05:23.231923 INFO: performing precursor FDR with 40 features
2:05:23.232019 INFO: Decoy channel: -1
2:05:23.232044 INFO: competitive: True
2:05:23.235958 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:23.238212 INFO: Estimating optimal hyperparameters - samples: 4,744, batch_size: 128, learning_rate: 1.77e-04
2:05:23.238297 INFO: Using random state 777846 for train-test-split
2:05:23.704836 INFO: Test AUC: 0.821
2:05:23.704922 INFO: Train AUC: 0.835
2:05:23.704950 INFO: AUC difference: 1.68%
2:05:23.947073 INFO: Resetting torch num_threads to 100
2:05:23.949983 PROGRESS: === Extracted 5931 precursors and 40982 fragments ===
2:05:23.950361 INFO: === FDR correction performed with classifier version -1 ===
2:05:23.950968 PROGRESS: ============================= Precursor FDR =============================
2:05:23.951049 PROGRESS: Total precursors accumulated: 1,550
2:05:23.951105 PROGRESS: Target precursors: 1,535 (99.03%)
2:05:23.951152 PROGRESS: Decoy precursors: 15 (0.97%)
2:05:23.951197 PROGRESS: 
2:05:23.951241 PROGRESS: Precursor Summary:
2:05:23.952545 PROGRESS: Channel   0:	 0.050 FDR: 1,535; 0.010 FDR: 1,535; 0.001 FDR:   253
2:05:23.952630 PROGRESS: 
2:05:23.952684 PROGRESS: Protein Summary:
2:05:23.954354 PROGRESS: Channel   0:	 0.050 FDR: 1,249; 0.010 FDR: 1,249; 0.001 FDR:   233
2:05:23.954445 PROGRESS: =========================================================================
2:05:23.954694 INFO: Target number of precursors reached.
2:05:23.963567 INFO: fragments_df: keeping 5000 of 40982 [sum(precursor_idx_mask)=15931 sum(mass_error_mask)=40982 stop_rank=5000
2:05:23.975480 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:24.206069 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:24.915099 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:05:24.915547 INFO: Using score_cutoff 12.09097854938507 (fac=0.99, q=1)
2:05:24.915860 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:05:24.915933 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:05:24.915984 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.09097854938507
2:05:24.916033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:24.919884 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:24.927615 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:05:24.927718 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:05:24.927794 INFO: Starting optimization step 2.
2:05:24.927859 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:24.927918 INFO: Using rust extraction backend
2:05:24.927970 PROGRESS: Extracting batch of 5936 precursors
2:05:24.939396 INFO: === Search parameters used ===
2:05:24.939517 INFO: rt_error       : 805.6002197265625
2:05:24.939567 INFO: mobility_error : 0.1
2:05:24.939612 INFO: num_candidates : 3
2:05:24.939656 INFO: ms1_error      : 30
2:05:24.939701 INFO: ms2_error      : 30
2:05:24.939742 INFO: fwhm_rt        : 3.0
2:05:24.939782 INFO: quant_window   : 3
2:05:24.939833 INFO: ==============================================
2:05:25.044456 INFO: performing precursor FDR with 40 features
2:05:25.044568 INFO: Decoy channel: -1
2:05:25.044592 INFO: competitive: True
2:05:25.049221 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:25.053093 INFO: Estimating optimal hyperparameters - samples: 14,220, batch_size: 128, learning_rate: 1.77e-04
2:05:25.053215 INFO: Using random state 646202 for train-test-split
2:05:26.452421 INFO: Test AUC: 0.679
2:05:26.452537 INFO: Train AUC: 0.695
2:05:26.452565 INFO: AUC difference: 2.31%
2:05:26.701435 INFO: Resetting torch num_threads to 100
2:05:26.703673 PROGRESS: === Extracted 17775 precursors and 106927 fragments ===
2:05:26.704048 INFO: === FDR correction performed with classifier version 1 ===
2:05:26.704662 PROGRESS: ============================= Precursor FDR =============================
2:05:26.704744 PROGRESS: Total precursors accumulated: 1,851
2:05:26.704800 PROGRESS: Target precursors: 1,833 (99.03%)
2:05:26.704846 PROGRESS: Decoy precursors: 18 (0.97%)
2:05:26.704890 PROGRESS: 
2:05:26.704932 PROGRESS: Precursor Summary:
2:05:26.706363 PROGRESS: Channel   0:	 0.050 FDR: 1,833; 0.010 FDR: 1,833; 0.001 FDR: 1,122
2:05:26.706460 PROGRESS: 
2:05:26.706520 PROGRESS: Protein Summary:
2:05:26.708390 PROGRESS: Channel   0:	 0.050 FDR: 1,465; 0.010 FDR: 1,465; 0.001 FDR:   930
2:05:26.708477 PROGRESS: =========================================================================
2:05:26.708824 INFO: Target number of precursors reached.
2:05:26.727817 INFO: fragments_df: keeping 5000 of 106927 [sum(precursor_idx_mask)=39918 sum(mass_error_mask)=106927 stop_rank=5000
2:05:26.739759 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:27.007407 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:27.717950 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:27.718390 INFO: Using score_cutoff 12.554370201873779 (fac=0.99, q=1)
2:05:27.718690 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:27.718768 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:27.718823 INFO: Updating optimization_manager: score_cutoff        : 12.09097854938507 -> 12.554370201873779
2:05:27.718878 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:27.722744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:27.730285 INFO: === checking if optimization conditions were reached ===
2:05:27.731923 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.4697575
2:05:27.732021 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:05:27.732086 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:05:27.732144 INFO: ==============================================
2:05:27.732217 INFO: Starting optimization step 3.
2:05:27.732277 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:27.732336 INFO: Using rust extraction backend
2:05:27.732389 PROGRESS: Extracting batch of 5936 precursors
2:05:27.743773 INFO: === Search parameters used ===
2:05:27.743890 INFO: rt_error       : 805.6002197265625
2:05:27.743943 INFO: mobility_error : 0.1
2:05:27.744002 INFO: num_candidates : 3
2:05:27.744047 INFO: ms1_error      : 30
2:05:27.744094 INFO: ms2_error      : 7.4697575
2:05:27.744137 INFO: fwhm_rt        : 3.0
2:05:27.744179 INFO: quant_window   : 3
2:05:27.744220 INFO: ==============================================
2:05:27.847331 INFO: performing precursor FDR with 40 features
2:05:27.847445 INFO: Decoy channel: -1
2:05:27.847470 INFO: competitive: True
2:05:27.852206 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:27.855999 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:05:27.856118 INFO: Using random state 297927 for train-test-split
2:05:29.294598 INFO: Test AUC: 0.728
2:05:29.294715 INFO: Train AUC: 0.744
2:05:29.294743 INFO: AUC difference: 2.15%
2:05:29.547556 INFO: Resetting torch num_threads to 100
2:05:29.549881 PROGRESS: === Extracted 17807 precursors and 123601 fragments ===
2:05:29.550249 INFO: === FDR correction performed with classifier version 2 ===
2:05:29.550937 PROGRESS: ============================= Precursor FDR =============================
2:05:29.551022 PROGRESS: Total precursors accumulated: 2,493
2:05:29.551079 PROGRESS: Target precursors: 2,469 (99.04%)
2:05:29.551127 PROGRESS: Decoy precursors: 24 (0.96%)
2:05:29.551172 PROGRESS: 
2:05:29.551215 PROGRESS: Precursor Summary:
2:05:29.552728 PROGRESS: Channel   0:	 0.050 FDR: 2,469; 0.010 FDR: 2,469; 0.001 FDR: 1,428
2:05:29.552814 PROGRESS: 
2:05:29.552881 PROGRESS: Protein Summary:
2:05:29.554988 PROGRESS: Channel   0:	 0.050 FDR: 1,926; 0.010 FDR: 1,926; 0.001 FDR: 1,175
2:05:29.555090 PROGRESS: =========================================================================
2:05:29.555427 INFO: Target number of precursors reached.
2:05:29.581501 INFO: fragments_df: keeping 5000 of 123601 [sum(precursor_idx_mask)=57646 sum(mass_error_mask)=123601 stop_rank=5000
2:05:29.593766 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:29.891696 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:30.540572 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:30.541039 INFO: Using score_cutoff 10.47985666809082 (fac=0.99, q=1)
2:05:30.541354 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:30.541434 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:30.541487 INFO: Updating optimization_manager: score_cutoff        : 12.554370201873779 -> 10.47985666809082
2:05:30.541538 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:30.545515 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:30.552992 INFO: === checking if optimization conditions were reached ===
2:05:30.554669 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:05:30.554779 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:05:30.554857 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:05:30.554914 INFO: ==============================================
2:05:30.554977 INFO: Starting optimization step 4.
2:05:30.555033 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:30.555090 INFO: Using rust extraction backend
2:05:30.555158 PROGRESS: Extracting batch of 5936 precursors
2:05:30.566815 INFO: === Search parameters used ===
2:05:30.566946 INFO: rt_error       : 805.6002197265625
2:05:30.566997 INFO: mobility_error : 0.1
2:05:30.567039 INFO: num_candidates : 3
2:05:30.567084 INFO: ms1_error      : 30
2:05:30.567125 INFO: ms2_error      : 7.4697575
2:05:30.567165 INFO: fwhm_rt        : 3.0
2:05:30.567204 INFO: quant_window   : 3
2:05:30.567242 INFO: ==============================================
2:05:30.673358 INFO: performing precursor FDR with 40 features
2:05:30.673479 INFO: Decoy channel: -1
2:05:30.673503 INFO: competitive: True
2:05:30.678282 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:30.682485 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:05:30.682611 INFO: Using random state 350755 for train-test-split
2:05:32.145803 INFO: Test AUC: 0.746
2:05:32.145927 INFO: Train AUC: 0.753
2:05:32.145957 INFO: AUC difference: 0.86%
2:05:32.403704 INFO: Resetting torch num_threads to 100
2:05:32.406062 PROGRESS: === Extracted 17807 precursors and 123618 fragments ===
2:05:32.406437 INFO: === FDR correction performed with classifier version 3 ===
2:05:32.407138 PROGRESS: ============================= Precursor FDR =============================
2:05:32.407227 PROGRESS: Total precursors accumulated: 2,578
2:05:32.407286 PROGRESS: Target precursors: 2,553 (99.03%)
2:05:32.407338 PROGRESS: Decoy precursors: 25 (0.97%)
2:05:32.407387 PROGRESS: 
2:05:32.407445 PROGRESS: Precursor Summary:
2:05:32.409014 PROGRESS: Channel   0:	 0.050 FDR: 2,553; 0.010 FDR: 2,553; 0.001 FDR: 1,604
2:05:32.409103 PROGRESS: 
2:05:32.409160 PROGRESS: Protein Summary:
2:05:32.411348 PROGRESS: Channel   0:	 0.050 FDR: 1,981; 0.010 FDR: 1,981; 0.001 FDR: 1,306
2:05:32.411448 PROGRESS: =========================================================================
2:05:32.411797 INFO: Target number of precursors reached.
2:05:32.438503 INFO: fragments_df: keeping 5000 of 123618 [sum(precursor_idx_mask)=59246 sum(mass_error_mask)=123618 stop_rank=5000
2:05:32.450470 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:32.822070 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:33.534676 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:33.535149 INFO: Using score_cutoff 10.335709331130982 (fac=0.99, q=1)
2:05:33.535461 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:33.535538 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:33.535592 INFO: Updating optimization_manager: score_cutoff        : 10.47985666809082 -> 10.335709331130982
2:05:33.535645 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:33.539557 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:33.547043 INFO: === checking if optimization conditions were reached ===
2:05:33.548655 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:05:33.548758 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:05:33.548824 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:05:33.548887 INFO: ==============================================
2:05:33.548950 INFO: Starting optimization step 5.
2:05:33.549003 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:33.549057 INFO: Using rust extraction backend
2:05:33.549108 PROGRESS: Extracting batch of 5936 precursors
2:05:33.560533 INFO: === Search parameters used ===
2:05:33.560655 INFO: rt_error       : 805.6002197265625
2:05:33.560707 INFO: mobility_error : 0.1
2:05:33.560752 INFO: num_candidates : 3
2:05:33.560794 INFO: ms1_error      : 30
2:05:33.560834 INFO: ms2_error      : 7.4697575
2:05:33.560873 INFO: fwhm_rt        : 3.0
2:05:33.560912 INFO: quant_window   : 3
2:05:33.560951 INFO: ==============================================
2:05:33.664935 INFO: performing precursor FDR with 40 features
2:05:33.665044 INFO: Decoy channel: -1
2:05:33.665068 INFO: competitive: True
2:05:33.669631 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:33.673548 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:05:33.673670 INFO: Using random state 827066 for train-test-split
2:05:35.121603 INFO: Test AUC: 0.753
2:05:35.121710 INFO: Train AUC: 0.760
2:05:35.121738 INFO: AUC difference: 1.00%
2:05:35.372422 INFO: Resetting torch num_threads to 100
2:05:35.374780 PROGRESS: === Extracted 17807 precursors and 123593 fragments ===
2:05:35.375145 INFO: === FDR correction performed with classifier version 4 ===
2:05:35.375853 PROGRESS: ============================= Precursor FDR =============================
2:05:35.375935 PROGRESS: Total precursors accumulated: 2,661
2:05:35.375990 PROGRESS: Target precursors: 2,635 (99.02%)
2:05:35.376045 PROGRESS: Decoy precursors: 26 (0.98%)
2:05:35.376090 PROGRESS: 
2:05:35.376131 PROGRESS: Precursor Summary:
2:05:35.377748 PROGRESS: Channel   0:	 0.050 FDR: 2,635; 0.010 FDR: 2,635; 0.001 FDR: 2,154
2:05:35.377832 PROGRESS: 
2:05:35.377899 PROGRESS: Protein Summary:
2:05:35.380128 PROGRESS: Channel   0:	 0.050 FDR: 2,044; 0.010 FDR: 2,044; 0.001 FDR: 1,700
2:05:35.380215 PROGRESS: =========================================================================
2:05:35.380553 INFO: Target number of precursors reached.
2:05:35.407693 INFO: fragments_df: keeping 5000 of 123593 [sum(precursor_idx_mask)=60868 sum(mass_error_mask)=123593 stop_rank=5000
2:05:35.419794 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:35.798966 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:36.506564 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:36.507018 INFO: Using score_cutoff 10.13247004737854 (fac=0.99, q=1)
2:05:36.507318 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:36.507391 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:36.507442 INFO: Updating optimization_manager: score_cutoff        : 10.335709331130982 -> 10.13247004737854
2:05:36.507492 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:36.511397 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:36.518910 INFO: === checking if optimization conditions were reached ===
2:05:36.520546 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:05:36.520654 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:05:36.520717 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:05:36.520771 INFO: ==============================================
2:05:36.520832 INFO: Starting optimization step 6.
2:05:36.520888 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:36.520945 INFO: Using rust extraction backend
2:05:36.520998 PROGRESS: Extracting batch of 5936 precursors
2:05:36.532425 INFO: === Search parameters used ===
2:05:36.532532 INFO: rt_error       : 805.6002197265625
2:05:36.532584 INFO: mobility_error : 0.1
2:05:36.532628 INFO: num_candidates : 3
2:05:36.532670 INFO: ms1_error      : 30
2:05:36.532710 INFO: ms2_error      : 7.4697575
2:05:36.532750 INFO: fwhm_rt        : 3.0
2:05:36.532790 INFO: quant_window   : 3
2:05:36.532829 INFO: ==============================================
2:05:36.636827 INFO: performing precursor FDR with 40 features
2:05:36.636939 INFO: Decoy channel: -1
2:05:36.636963 INFO: competitive: True
2:05:36.641657 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:36.645513 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:05:36.645624 INFO: Using random state 934661 for train-test-split
2:05:38.075497 INFO: Test AUC: 0.762
2:05:38.075609 INFO: Train AUC: 0.766
2:05:38.075639 INFO: AUC difference: 0.41%
2:05:38.328833 INFO: Resetting torch num_threads to 100
2:05:38.331204 PROGRESS: === Extracted 17807 precursors and 123564 fragments ===
2:05:38.331579 INFO: === FDR correction performed with classifier version 5 ===
2:05:38.332298 PROGRESS: ============================= Precursor FDR =============================
2:05:38.332387 PROGRESS: Total precursors accumulated: 2,733
2:05:38.332452 PROGRESS: Target precursors: 2,706 (99.01%)
2:05:38.332505 PROGRESS: Decoy precursors: 27 (0.99%)
2:05:38.332554 PROGRESS: 
2:05:38.332601 PROGRESS: Precursor Summary:
2:05:38.334309 PROGRESS: Channel   0:	 0.050 FDR: 2,706; 0.010 FDR: 2,706; 0.001 FDR: 2,048
2:05:38.334401 PROGRESS: 
2:05:38.334458 PROGRESS: Protein Summary:
2:05:38.336743 PROGRESS: Channel   0:	 0.050 FDR: 2,093; 0.010 FDR: 2,093; 0.001 FDR: 1,625
2:05:38.336841 PROGRESS: =========================================================================
2:05:38.337185 INFO: Target number of precursors reached.
2:05:38.364449 INFO: fragments_df: keeping 5000 of 123564 [sum(precursor_idx_mask)=62155 sum(mass_error_mask)=123564 stop_rank=5000
2:05:38.376852 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:38.765096 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:39.477326 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:39.477785 INFO: Using score_cutoff 9.658048649311064 (fac=0.99, q=1)
2:05:39.478120 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:39.478200 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:39.478256 INFO: Updating optimization_manager: score_cutoff        : 10.13247004737854 -> 9.658048649311064
2:05:39.478307 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:39.482237 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:39.489908 INFO: === checking if optimization conditions were reached ===
2:05:39.491518 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:05:39.491613 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:05:39.491676 PROGRESS: ✅ ms2_error      : 7.4698 <= 7.4698
2:05:39.491731 INFO: ==============================================
2:05:39.491795 PROGRESS: Optimization finished for ms2_error.
2:05:39.503717 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:39.507491 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:39.514998 INFO: Starting optimization step 0.
2:05:39.515113 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:39.515197 INFO: Using rust extraction backend
2:05:39.515255 PROGRESS: Extracting batch of 5936 precursors
2:05:39.526945 INFO: === Search parameters used ===
2:05:39.527059 INFO: rt_error       : 805.6002197265625
2:05:39.527109 INFO: mobility_error : 0.1
2:05:39.527154 INFO: num_candidates : 3
2:05:39.527195 INFO: ms1_error      : 30
2:05:39.527235 INFO: ms2_error      : 7.4697575
2:05:39.527275 INFO: fwhm_rt        : 3.0
2:05:39.527314 INFO: quant_window   : 3
2:05:39.527354 INFO: ==============================================
2:05:39.631652 INFO: performing precursor FDR with 40 features
2:05:39.631768 INFO: Decoy channel: -1
2:05:39.631791 INFO: competitive: True
2:05:39.636491 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:39.640324 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:05:39.640435 INFO: Using random state 752927 for train-test-split
2:05:41.101499 INFO: Test AUC: 0.763
2:05:41.101611 INFO: Train AUC: 0.772
2:05:41.101639 INFO: AUC difference: 1.19%
2:05:41.347338 INFO: Resetting torch num_threads to 100
2:05:41.349705 PROGRESS: === Extracted 17807 precursors and 123574 fragments ===
2:05:41.350083 INFO: === FDR correction performed with classifier version 6 ===
2:05:41.350802 PROGRESS: ============================= Precursor FDR =============================
2:05:41.350886 PROGRESS: Total precursors accumulated: 2,740
2:05:41.350941 PROGRESS: Target precursors: 2,713 (99.01%)
2:05:41.350989 PROGRESS: Decoy precursors: 27 (0.99%)
2:05:41.351033 PROGRESS: 
2:05:41.351076 PROGRESS: Precursor Summary:
2:05:41.352706 PROGRESS: Channel   0:	 0.050 FDR: 2,713; 0.010 FDR: 2,713; 0.001 FDR: 2,070
2:05:41.352791 PROGRESS: 
2:05:41.352843 PROGRESS: Protein Summary:
2:05:41.355138 PROGRESS: Channel   0:	 0.050 FDR: 2,100; 0.010 FDR: 2,100; 0.001 FDR: 1,646
2:05:41.355231 PROGRESS: =========================================================================
2:05:41.355576 INFO: Target number of precursors reached.
2:05:41.382883 INFO: fragments_df: keeping 5000 of 123574 [sum(precursor_idx_mask)=62369 sum(mass_error_mask)=123574 stop_rank=5000
2:05:41.395069 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:41.785001 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:42.494283 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:42.494754 INFO: Using score_cutoff 9.56471163368225 (fac=0.99, q=1)
2:05:42.495061 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:42.495143 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:42.495198 INFO: Updating optimization_manager: score_cutoff        : 9.658048649311064 -> 9.56471163368225
2:05:42.495250 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:42.499135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:42.506539 INFO: === checking if optimization conditions were reached ===
2:05:42.506654 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:05:42.509403 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 295.34330728141475
2:05:42.509501 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 295.3433.
2:05:42.509565 INFO: ==============================================
2:05:42.509630 INFO: Starting optimization step 1.
2:05:42.509687 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:42.509747 INFO: Using rust extraction backend
2:05:42.509801 PROGRESS: Extracting batch of 5936 precursors
2:05:42.521181 INFO: === Search parameters used ===
2:05:42.521298 INFO: rt_error       : 295.34330728141475
2:05:42.521351 INFO: mobility_error : 0.1
2:05:42.521396 INFO: num_candidates : 3
2:05:42.521440 INFO: ms1_error      : 30
2:05:42.521482 INFO: ms2_error      : 7.4697575
2:05:42.521524 INFO: fwhm_rt        : 3.0
2:05:42.521578 INFO: quant_window   : 3
2:05:42.521620 INFO: ==============================================
2:05:42.612800 INFO: performing precursor FDR with 40 features
2:05:42.612912 INFO: Decoy channel: -1
2:05:42.612936 INFO: competitive: True
2:05:42.617501 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:42.621603 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:05:42.621719 INFO: Using random state 752927 for train-test-split
2:05:44.057154 INFO: Test AUC: 0.770
2:05:44.057263 INFO: Train AUC: 0.778
2:05:44.057291 INFO: AUC difference: 0.98%
2:05:46.226386 INFO: Resetting torch num_threads to 100
2:05:46.228880 PROGRESS: === Extracted 17806 precursors and 121421 fragments ===
2:05:46.229245 INFO: === FDR correction performed with classifier version 6 ===
2:05:46.229986 PROGRESS: ============================= Precursor FDR =============================
2:05:46.230075 PROGRESS: Total precursors accumulated: 2,777
2:05:46.230131 PROGRESS: Target precursors: 2,750 (99.03%)
2:05:46.230178 PROGRESS: Decoy precursors: 27 (0.97%)
2:05:46.230222 PROGRESS: 
2:05:46.230264 PROGRESS: Precursor Summary:
2:05:46.231917 PROGRESS: Channel   0:	 0.050 FDR: 2,750; 0.010 FDR: 2,750; 0.001 FDR: 1,819
2:05:46.232009 PROGRESS: 
2:05:46.232062 PROGRESS: Protein Summary:
2:05:46.234424 PROGRESS: Channel   0:	 0.050 FDR: 2,122; 0.010 FDR: 2,122; 0.001 FDR: 1,456
2:05:46.234523 PROGRESS: =========================================================================
2:05:46.234867 INFO: Target number of precursors reached.
2:05:46.262528 INFO: fragments_df: keeping 5000 of 121421 [sum(precursor_idx_mask)=62674 sum(mass_error_mask)=121421 stop_rank=5000
2:05:46.274836 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:46.671988 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:47.389333 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:47.389837 INFO: Using score_cutoff 9.545461253929137 (fac=0.99, q=1)
2:05:47.390175 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:47.390251 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:47.390304 INFO: Updating optimization_manager: score_cutoff        : 9.56471163368225 -> 9.545461253929137
2:05:47.390355 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:47.394304 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:47.401896 INFO: === checking if optimization conditions were reached ===
2:05:47.402017 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:05:47.405002 INFO: Updating optimization_manager: rt_error            : 295.34330728141475 -> 206.95901916077867
2:05:47.405101 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 206.9590.
2:05:47.405162 INFO: ==============================================
2:05:47.405227 INFO: Starting optimization step 2.
2:05:47.405282 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:47.405339 INFO: Using rust extraction backend
2:05:47.405390 PROGRESS: Extracting batch of 5936 precursors
2:05:47.416976 INFO: === Search parameters used ===
2:05:47.417105 INFO: rt_error       : 206.95901916077867
2:05:47.417156 INFO: mobility_error : 0.1
2:05:47.417199 INFO: num_candidates : 3
2:05:47.417240 INFO: ms1_error      : 30
2:05:47.417295 INFO: ms2_error      : 7.4697575
2:05:47.417337 INFO: fwhm_rt        : 3.0
2:05:47.417376 INFO: quant_window   : 3
2:05:47.417415 INFO: ==============================================
2:05:47.506008 INFO: performing precursor FDR with 40 features
2:05:47.506129 INFO: Decoy channel: -1
2:05:47.506156 INFO: competitive: True
2:05:47.511292 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:47.515329 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:05:47.515466 INFO: Using random state 752927 for train-test-split
2:05:48.937180 INFO: Test AUC: 0.778
2:05:48.937307 INFO: Train AUC: 0.779
2:05:48.937338 INFO: AUC difference: 0.23%
2:05:49.185319 INFO: Resetting torch num_threads to 100
2:05:49.187835 PROGRESS: === Extracted 17804 precursors and 118755 fragments ===
2:05:49.188215 INFO: === FDR correction performed with classifier version 6 ===
2:05:49.188989 PROGRESS: ============================= Precursor FDR =============================
2:05:49.189080 PROGRESS: Total precursors accumulated: 2,812
2:05:49.189139 PROGRESS: Target precursors: 2,785 (99.04%)
2:05:49.189190 PROGRESS: Decoy precursors: 27 (0.96%)
2:05:49.189238 PROGRESS: 
2:05:49.189283 PROGRESS: Precursor Summary:
2:05:49.191047 PROGRESS: Channel   0:	 0.050 FDR: 2,785; 0.010 FDR: 2,785; 0.001 FDR: 2,402
2:05:49.191142 PROGRESS: 
2:05:49.191207 PROGRESS: Protein Summary:
2:05:49.193642 PROGRESS: Channel   0:	 0.050 FDR: 2,145; 0.010 FDR: 2,145; 0.001 FDR: 1,878
2:05:49.193734 PROGRESS: =========================================================================
2:05:49.194127 INFO: Target number of precursors reached.
2:05:49.220725 INFO: fragments_df: keeping 5000 of 118755 [sum(precursor_idx_mask)=62440 sum(mass_error_mask)=118755 stop_rank=5000
2:05:49.232878 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:49.647381 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:50.362924 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:50.363372 INFO: Using score_cutoff 9.098213372039794 (fac=0.99, q=1)
2:05:50.363685 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:50.363760 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:50.363812 INFO: Updating optimization_manager: score_cutoff        : 9.545461253929137 -> 9.098213372039794
2:05:50.363862 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:50.367786 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:50.375468 INFO: === checking if optimization conditions were reached ===
2:05:50.375572 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:05:50.378643 INFO: Updating optimization_manager: rt_error            : 206.95901916077867 -> 177.80309951528332
2:05:50.378747 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 177.8031.
2:05:50.378809 INFO: ==============================================
2:05:50.378875 INFO: Starting optimization step 3.
2:05:50.378931 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:50.378987 INFO: Using rust extraction backend
2:05:50.379039 PROGRESS: Extracting batch of 5936 precursors
2:05:50.390355 INFO: === Search parameters used ===
2:05:50.390486 INFO: rt_error       : 177.80309951528332
2:05:50.390536 INFO: mobility_error : 0.1
2:05:50.390591 INFO: num_candidates : 3
2:05:50.390635 INFO: ms1_error      : 30
2:05:50.390676 INFO: ms2_error      : 7.4697575
2:05:50.390717 INFO: fwhm_rt        : 3.0
2:05:50.390757 INFO: quant_window   : 3
2:05:50.390796 INFO: ==============================================
2:05:50.479965 INFO: performing precursor FDR with 40 features
2:05:50.480078 INFO: Decoy channel: -1
2:05:50.480102 INFO: competitive: True
2:05:50.485220 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:50.489350 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
2:05:50.489487 INFO: Using random state 752927 for train-test-split
2:05:51.917294 INFO: Test AUC: 0.764
2:05:51.917419 INFO: Train AUC: 0.783
2:05:51.917449 INFO: AUC difference: 2.33%
2:05:52.165106 INFO: Resetting torch num_threads to 100
2:05:52.167599 PROGRESS: === Extracted 17806 precursors and 117476 fragments ===
2:05:52.167991 INFO: === FDR correction performed with classifier version 6 ===
2:05:52.168722 PROGRESS: ============================= Precursor FDR =============================
2:05:52.168804 PROGRESS: Total precursors accumulated: 2,850
2:05:52.168859 PROGRESS: Target precursors: 2,822 (99.02%)
2:05:52.168918 PROGRESS: Decoy precursors: 28 (0.98%)
2:05:52.168962 PROGRESS: 
2:05:52.169004 PROGRESS: Precursor Summary:
2:05:52.170741 PROGRESS: Channel   0:	 0.050 FDR: 2,822; 0.010 FDR: 2,822; 0.001 FDR: 2,403
2:05:52.170834 PROGRESS: 
2:05:52.170887 PROGRESS: Protein Summary:
2:05:52.173328 PROGRESS: Channel   0:	 0.050 FDR: 2,175; 0.010 FDR: 2,175; 0.001 FDR: 1,880
2:05:52.173418 PROGRESS: =========================================================================
2:05:52.173779 INFO: Target number of precursors reached.
2:05:52.204414 INFO: fragments_df: keeping 5000 of 117476 [sum(precursor_idx_mask)=62833 sum(mass_error_mask)=117476 stop_rank=5000
2:05:52.216618 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:52.623743 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:53.337047 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:53.337518 INFO: Using score_cutoff 9.188549276447297 (fac=0.99, q=1)
2:05:53.337844 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:53.337934 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:53.337990 INFO: Updating optimization_manager: score_cutoff        : 9.098213372039794 -> 9.188549276447297
2:05:53.338045 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:53.342031 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:53.349578 INFO: === checking if optimization conditions were reached ===
2:05:53.349691 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:05:53.352783 INFO: Updating optimization_manager: rt_error            : 177.80309951528332 -> 129.5975361620016
2:05:53.352897 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 129.5975.
2:05:53.352964 INFO: ==============================================
2:05:53.353033 INFO: Starting optimization step 4.
2:05:53.353096 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:53.353158 INFO: Using rust extraction backend
2:05:53.353213 PROGRESS: Extracting batch of 5936 precursors
2:05:53.364477 INFO: === Search parameters used ===
2:05:53.364623 INFO: rt_error       : 129.5975361620016
2:05:53.364679 INFO: mobility_error : 0.1
2:05:53.364726 INFO: num_candidates : 3
2:05:53.364771 INFO: ms1_error      : 30
2:05:53.364813 INFO: ms2_error      : 7.4697575
2:05:53.364854 INFO: fwhm_rt        : 3.0
2:05:53.364895 INFO: quant_window   : 3
2:05:53.364935 INFO: ==============================================
2:05:53.453462 INFO: performing precursor FDR with 40 features
2:05:53.453580 INFO: Decoy channel: -1
2:05:53.453606 INFO: competitive: True
2:05:53.458613 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:53.462660 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:05:53.462793 INFO: Using random state 752927 for train-test-split
2:05:54.896870 INFO: Test AUC: 0.773
2:05:54.896984 INFO: Train AUC: 0.788
2:05:54.897013 INFO: AUC difference: 1.92%
2:05:55.144381 INFO: Resetting torch num_threads to 100
2:05:55.146853 PROGRESS: === Extracted 17801 precursors and 114417 fragments ===
2:05:55.147248 INFO: === FDR correction performed with classifier version 6 ===
2:05:55.147989 PROGRESS: ============================= Precursor FDR =============================
2:05:55.148072 PROGRESS: Total precursors accumulated: 2,851
2:05:55.148130 PROGRESS: Target precursors: 2,823 (99.02%)
2:05:55.148181 PROGRESS: Decoy precursors: 28 (0.98%)
2:05:55.148226 PROGRESS: 
2:05:55.148270 PROGRESS: Precursor Summary:
2:05:55.149990 PROGRESS: Channel   0:	 0.050 FDR: 2,823; 0.010 FDR: 2,823; 0.001 FDR: 2,410
2:05:55.150081 PROGRESS: 
2:05:55.150136 PROGRESS: Protein Summary:
2:05:55.152543 PROGRESS: Channel   0:	 0.050 FDR: 2,181; 0.010 FDR: 2,181; 0.001 FDR: 1,878
2:05:55.152630 PROGRESS: =========================================================================
2:05:55.152989 INFO: Target number of precursors reached.
2:05:55.179489 INFO: fragments_df: keeping 5000 of 114417 [sum(precursor_idx_mask)=61923 sum(mass_error_mask)=114417 stop_rank=5000
2:05:55.191595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:55.603866 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:56.316649 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:56.317101 INFO: Using score_cutoff 8.959022832870483 (fac=0.99, q=1)
2:05:56.317409 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:56.317487 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:56.317538 INFO: Updating optimization_manager: score_cutoff        : 9.188549276447297 -> 8.959022832870483
2:05:56.317588 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:56.321511 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:56.329270 INFO: === checking if optimization conditions were reached ===
2:05:56.329372 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:05:56.332419 INFO: Updating optimization_manager: rt_error            : 129.5975361620016 -> 90.41780518835094
2:05:56.332523 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 90.4178.
2:05:56.332585 INFO: ==============================================
2:05:56.332648 INFO: Starting optimization step 5.
2:05:56.332704 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:56.332760 INFO: Using rust extraction backend
2:05:56.332811 PROGRESS: Extracting batch of 5936 precursors
2:05:56.344061 INFO: === Search parameters used ===
2:05:56.344192 INFO: rt_error       : 90.41780518835094
2:05:56.344244 INFO: mobility_error : 0.1
2:05:56.344287 INFO: num_candidates : 3
2:05:56.344329 INFO: ms1_error      : 30
2:05:56.344368 INFO: ms2_error      : 7.4697575
2:05:56.344409 INFO: fwhm_rt        : 3.0
2:05:56.344447 INFO: quant_window   : 3
2:05:56.344486 INFO: ==============================================
2:05:56.429872 INFO: performing precursor FDR with 40 features
2:05:56.429984 INFO: Decoy channel: -1
2:05:56.430007 INFO: competitive: True
2:05:56.435142 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:56.439318 INFO: Estimating optimal hyperparameters - samples: 14,238, batch_size: 128, learning_rate: 1.77e-04
2:05:56.439453 INFO: Using random state 752927 for train-test-split
2:05:57.872067 INFO: Test AUC: 0.781
2:05:57.872185 INFO: Train AUC: 0.792
2:05:57.872214 INFO: AUC difference: 1.30%
2:05:58.118792 INFO: Resetting torch num_threads to 100
2:05:58.121237 PROGRESS: === Extracted 17798 precursors and 110925 fragments ===
2:05:58.121610 INFO: === FDR correction performed with classifier version 6 ===
2:05:58.122368 PROGRESS: ============================= Precursor FDR =============================
2:05:58.122458 PROGRESS: Total precursors accumulated: 2,836
2:05:58.122518 PROGRESS: Target precursors: 2,808 (99.01%)
2:05:58.122571 PROGRESS: Decoy precursors: 28 (0.99%)
2:05:58.122619 PROGRESS: 
2:05:58.122664 PROGRESS: Precursor Summary:
2:05:58.124361 PROGRESS: Channel   0:	 0.050 FDR: 2,808; 0.010 FDR: 2,808; 0.001 FDR: 2,224
2:05:58.124460 PROGRESS: 
2:05:58.124517 PROGRESS: Protein Summary:
2:05:58.126889 PROGRESS: Channel   0:	 0.050 FDR: 2,165; 0.010 FDR: 2,165; 0.001 FDR: 1,749
2:05:58.126997 PROGRESS: =========================================================================
2:05:58.127360 INFO: Target number of precursors reached.
2:05:58.153067 INFO: fragments_df: keeping 5000 of 110925 [sum(precursor_idx_mask)=60594 sum(mass_error_mask)=110925 stop_rank=5000
2:05:58.165136 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:58.575995 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:59.292474 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:59.292937 INFO: Using score_cutoff 8.87748319387436 (fac=0.99, q=1)
2:05:59.293257 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:59.293333 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:59.293387 INFO: Updating optimization_manager: score_cutoff        : 8.959022832870483 -> 8.87748319387436
2:05:59.293447 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:59.297425 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:59.305110 INFO: === checking if optimization conditions were reached ===
2:05:59.305221 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:05:59.308311 INFO: Updating optimization_manager: rt_error            : 90.41780518835094 -> 68.63572817934852
2:05:59.308417 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 68.6357.
2:05:59.308480 INFO: ==============================================
2:05:59.308545 INFO: Starting optimization step 6.
2:05:59.308601 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:05:59.308669 INFO: Using rust extraction backend
2:05:59.308726 PROGRESS: Extracting batch of 5936 precursors
2:05:59.320113 INFO: === Search parameters used ===
2:05:59.320246 INFO: rt_error       : 68.63572817934852
2:05:59.320297 INFO: mobility_error : 0.1
2:05:59.320342 INFO: num_candidates : 3
2:05:59.320383 INFO: ms1_error      : 30
2:05:59.320423 INFO: ms2_error      : 7.4697575
2:05:59.320463 INFO: fwhm_rt        : 3.0
2:05:59.320503 INFO: quant_window   : 3
2:05:59.320541 INFO: ==============================================
2:05:59.404467 INFO: performing precursor FDR with 40 features
2:05:59.404580 INFO: Decoy channel: -1
2:05:59.404606 INFO: competitive: True
2:05:59.409702 INFO: Setting torch num_threads to 2 for FDR classification task
2:05:59.413675 INFO: Estimating optimal hyperparameters - samples: 14,196, batch_size: 128, learning_rate: 1.77e-04
2:05:59.413814 INFO: Using random state 752927 for train-test-split
2:06:00.831414 INFO: Test AUC: 0.800
2:06:00.831534 INFO: Train AUC: 0.797
2:06:00.831563 INFO: AUC difference: 0.43%
2:06:01.081158 INFO: Resetting torch num_threads to 100
2:06:01.083644 PROGRESS: === Extracted 17745 precursors and 107211 fragments ===
2:06:01.084010 INFO: === FDR correction performed with classifier version 6 ===
2:06:01.084749 PROGRESS: ============================= Precursor FDR =============================
2:06:01.084831 PROGRESS: Total precursors accumulated: 2,858
2:06:01.084887 PROGRESS: Target precursors: 2,830 (99.02%)
2:06:01.084935 PROGRESS: Decoy precursors: 28 (0.98%)
2:06:01.084978 PROGRESS: 
2:06:01.085020 PROGRESS: Precursor Summary:
2:06:01.086758 PROGRESS: Channel   0:	 0.050 FDR: 2,830; 0.010 FDR: 2,830; 0.001 FDR: 2,520
2:06:01.086855 PROGRESS: 
2:06:01.086911 PROGRESS: Protein Summary:
2:06:01.089351 PROGRESS: Channel   0:	 0.050 FDR: 2,176; 0.010 FDR: 2,176; 0.001 FDR: 1,958
2:06:01.089450 PROGRESS: =========================================================================
2:06:01.089814 INFO: Target number of precursors reached.
2:06:01.114809 INFO: fragments_df: keeping 5000 of 107211 [sum(precursor_idx_mask)=59564 sum(mass_error_mask)=107211 stop_rank=5000
2:06:01.126882 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:01.536030 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:02.251474 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:02.251932 INFO: Using score_cutoff 8.769434050655365 (fac=0.99, q=1)
2:06:02.252255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:02.252331 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:02.252383 INFO: Updating optimization_manager: score_cutoff        : 8.87748319387436 -> 8.769434050655365
2:06:02.252433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:02.256392 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:02.264120 INFO: === checking if optimization conditions were reached ===
2:06:02.264237 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:06:02.267297 INFO: Updating optimization_manager: rt_error            : 68.63572817934852 -> 57.531220763327255
2:06:02.267403 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 57.5312.
2:06:02.267476 INFO: ==============================================
2:06:02.267546 INFO: Starting optimization step 7.
2:06:02.267602 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:02.267659 INFO: Using rust extraction backend
2:06:02.267711 PROGRESS: Extracting batch of 5936 precursors
2:06:02.278989 INFO: === Search parameters used ===
2:06:02.279127 INFO: rt_error       : 57.531220763327255
2:06:02.279177 INFO: mobility_error : 0.1
2:06:02.279220 INFO: num_candidates : 3
2:06:02.279261 INFO: ms1_error      : 30
2:06:02.279301 INFO: ms2_error      : 7.4697575
2:06:02.279340 INFO: fwhm_rt        : 3.0
2:06:02.279378 INFO: quant_window   : 3
2:06:02.279416 INFO: ==============================================
2:06:02.362578 INFO: performing precursor FDR with 40 features
2:06:02.362689 INFO: Decoy channel: -1
2:06:02.362714 INFO: competitive: True
2:06:02.367315 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:02.371254 INFO: Estimating optimal hyperparameters - samples: 13,902, batch_size: 128, learning_rate: 1.77e-04
2:06:02.371405 INFO: Using random state 752927 for train-test-split
2:06:03.769945 INFO: Test AUC: 0.789
2:06:03.770063 INFO: Train AUC: 0.821
2:06:03.770093 INFO: AUC difference: 3.89%
2:06:04.018812 INFO: Resetting torch num_threads to 100
2:06:04.021232 PROGRESS: === Extracted 17378 precursors and 102784 fragments ===
2:06:04.021605 INFO: === FDR correction performed with classifier version 6 ===
2:06:04.022346 PROGRESS: ============================= Precursor FDR =============================
2:06:04.022436 PROGRESS: Total precursors accumulated: 2,786
2:06:04.022498 PROGRESS: Target precursors: 2,759 (99.03%)
2:06:04.022550 PROGRESS: Decoy precursors: 27 (0.97%)
2:06:04.022598 PROGRESS: 
2:06:04.022644 PROGRESS: Precursor Summary:
2:06:04.024337 PROGRESS: Channel   0:	 0.050 FDR: 2,759; 0.010 FDR: 2,759; 0.001 FDR: 2,448
2:06:04.024438 PROGRESS: 
2:06:04.024496 PROGRESS: Protein Summary:
2:06:04.026893 PROGRESS: Channel   0:	 0.050 FDR: 2,128; 0.010 FDR: 2,128; 0.001 FDR: 1,906
2:06:04.026999 PROGRESS: =========================================================================
2:06:04.027366 INFO: Target number of precursors reached.
2:06:04.050921 INFO: fragments_df: keeping 5000 of 102784 [sum(precursor_idx_mask)=56033 sum(mass_error_mask)=102784 stop_rank=5000
2:06:04.062966 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:04.464212 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:05.179393 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:05.179868 INFO: Using score_cutoff 8.986220792770386 (fac=0.99, q=1)
2:06:05.180184 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:05.180267 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:05.180322 INFO: Updating optimization_manager: score_cutoff        : 8.769434050655365 -> 8.986220792770386
2:06:05.180376 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:05.184334 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:05.192420 INFO: === checking if optimization conditions were reached ===
2:06:05.192530 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:06:05.195612 INFO: Updating optimization_manager: rt_error            : 57.531220763327255 -> 53.300964556744766
2:06:05.195716 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 53.3010.
2:06:05.195790 INFO: ==============================================
2:06:05.195859 INFO: Starting optimization step 8.
2:06:05.195918 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:05.195976 INFO: Using rust extraction backend
2:06:05.196031 PROGRESS: Extracting batch of 5936 precursors
2:06:05.207389 INFO: === Search parameters used ===
2:06:05.207527 INFO: rt_error       : 53.300964556744766
2:06:05.207581 INFO: mobility_error : 0.1
2:06:05.207628 INFO: num_candidates : 3
2:06:05.207686 INFO: ms1_error      : 30
2:06:05.207734 INFO: ms2_error      : 7.4697575
2:06:05.207776 INFO: fwhm_rt        : 3.0
2:06:05.207817 INFO: quant_window   : 3
2:06:05.207857 INFO: ==============================================
2:06:05.291447 INFO: performing precursor FDR with 40 features
2:06:05.291559 INFO: Decoy channel: -1
2:06:05.291583 INFO: competitive: True
2:06:05.296544 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:05.300537 INFO: Estimating optimal hyperparameters - samples: 13,540, batch_size: 128, learning_rate: 1.77e-04
2:06:05.300672 INFO: Using random state 752927 for train-test-split
2:06:06.645960 INFO: Test AUC: 0.807
2:06:06.646072 INFO: Train AUC: 0.830
2:06:06.646101 INFO: AUC difference: 2.73%
2:06:06.892907 INFO: Resetting torch num_threads to 100
2:06:06.895339 PROGRESS: === Extracted 16925 precursors and 99412 fragments ===
2:06:06.895704 INFO: === FDR correction performed with classifier version 6 ===
2:06:06.896431 PROGRESS: ============================= Precursor FDR =============================
2:06:06.896513 PROGRESS: Total precursors accumulated: 2,882
2:06:06.896569 PROGRESS: Target precursors: 2,854 (99.03%)
2:06:06.896616 PROGRESS: Decoy precursors: 28 (0.97%)
2:06:06.896660 PROGRESS: 
2:06:06.896708 PROGRESS: Precursor Summary:
2:06:06.898453 PROGRESS: Channel   0:	 0.050 FDR: 2,854; 0.010 FDR: 2,854; 0.001 FDR: 2,507
2:06:06.898546 PROGRESS: 
2:06:06.898600 PROGRESS: Protein Summary:
2:06:06.901023 PROGRESS: Channel   0:	 0.050 FDR: 2,203; 0.010 FDR: 2,203; 0.001 FDR: 1,950
2:06:06.901112 PROGRESS: =========================================================================
2:06:06.901473 INFO: Target number of precursors reached.
2:06:06.924757 INFO: fragments_df: keeping 5000 of 99412 [sum(precursor_idx_mask)=55571 sum(mass_error_mask)=99412 stop_rank=5000
2:06:06.937024 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:07.349822 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:08.064368 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:08.064811 INFO: Using score_cutoff 8.166770313835144 (fac=0.99, q=1)
2:06:08.065125 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:08.065198 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:08.065250 INFO: Updating optimization_manager: score_cutoff        : 8.986220792770386 -> 8.166770313835144
2:06:08.065299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:08.069236 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:08.077079 INFO: === checking if optimization conditions were reached ===
2:06:08.077184 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:06:08.080265 INFO: Updating optimization_manager: rt_error            : 53.300964556744766 -> 52.29677461399938
2:06:08.080369 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 52.2968.
2:06:08.080430 INFO: ==============================================
2:06:08.080494 INFO: Starting optimization step 9.
2:06:08.080549 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:08.080606 INFO: Using rust extraction backend
2:06:08.080658 PROGRESS: Extracting batch of 5936 precursors
2:06:08.091950 INFO: === Search parameters used ===
2:06:08.092071 INFO: rt_error       : 52.29677461399938
2:06:08.092136 INFO: mobility_error : 0.1
2:06:08.092181 INFO: num_candidates : 3
2:06:08.092222 INFO: ms1_error      : 30
2:06:08.092261 INFO: ms2_error      : 7.4697575
2:06:08.092300 INFO: fwhm_rt        : 3.0
2:06:08.092339 INFO: quant_window   : 3
2:06:08.092378 INFO: ==============================================
2:06:08.174165 INFO: performing precursor FDR with 40 features
2:06:08.174275 INFO: Decoy channel: -1
2:06:08.174301 INFO: competitive: True
2:06:08.179392 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:08.183169 INFO: Estimating optimal hyperparameters - samples: 13,419, batch_size: 128, learning_rate: 1.77e-04
2:06:08.183311 INFO: Using random state 752927 for train-test-split
2:06:09.503296 INFO: Test AUC: 0.813
2:06:09.503420 INFO: Train AUC: 0.832
2:06:09.503449 INFO: AUC difference: 2.29%
2:06:09.752520 INFO: Resetting torch num_threads to 100
2:06:09.754927 PROGRESS: === Extracted 16774 precursors and 98454 fragments ===
2:06:09.755299 INFO: === FDR correction performed with classifier version 6 ===
2:06:09.756034 PROGRESS: ============================= Precursor FDR =============================
2:06:09.756121 PROGRESS: Total precursors accumulated: 2,880
2:06:09.756182 PROGRESS: Target precursors: 2,852 (99.03%)
2:06:09.756242 PROGRESS: Decoy precursors: 28 (0.97%)
2:06:09.756293 PROGRESS: 
2:06:09.756338 PROGRESS: Precursor Summary:
2:06:09.758090 PROGRESS: Channel   0:	 0.050 FDR: 2,852; 0.010 FDR: 2,852; 0.001 FDR: 2,444
2:06:09.758184 PROGRESS: 
2:06:09.758240 PROGRESS: Protein Summary:
2:06:09.760651 PROGRESS: Channel   0:	 0.050 FDR: 2,200; 0.010 FDR: 2,200; 0.001 FDR: 1,905
2:06:09.760743 PROGRESS: =========================================================================
2:06:09.761100 INFO: Target number of precursors reached.
2:06:09.784524 INFO: fragments_df: keeping 5000 of 98454 [sum(precursor_idx_mask)=55041 sum(mass_error_mask)=98454 stop_rank=5000
2:06:09.796625 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:10.209065 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:10.920780 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:10.921225 INFO: Using score_cutoff 8.16655999774933 (fac=0.99, q=1)
2:06:10.921540 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:10.921617 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:10.921671 INFO: Updating optimization_manager: score_cutoff        : 8.166770313835144 -> 8.16655999774933
2:06:10.921725 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:10.925613 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:10.933652 INFO: === checking if optimization conditions were reached ===
2:06:10.933764 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:06:10.934481 INFO: Updating optimization_manager: rt_error            : 52.29677461399938 -> 53.300964556744766
2:06:10.934609 INFO: Updating optimization_manager: classifier_version  : 6 -> 15
2:06:10.934705 INFO: Updating optimization_manager: score_cutoff        : 8.16655999774933 -> 8.166770313835144
2:06:10.934792 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:10.934885 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:10.934970 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 53.3010 found after 10 searches.
2:06:10.935028 INFO: ==============================================
2:06:10.935091 PROGRESS: Optimization finished for rt_error.
2:06:10.946654 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:10.950468 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:10.958305 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:06:10.958418 PROGRESS: ==============================================
2:06:10.958483 PROGRESS: ms2_error      : 7.4698
2:06:10.958536 PROGRESS: rt_error       : 53.3010
2:06:10.958583 PROGRESS: ==============================================
2:06:10.959256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:11.091506 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:11.469958 INFO: Using rust extraction backend
2:06:11.470281 PROGRESS: Extracting batch of 260426 precursors
2:06:11.878437 INFO: === Search parameters used ===
2:06:11.878694 INFO: rt_error       : 53.300964556744766
2:06:11.878752 INFO: mobility_error : 0.1
2:06:11.878802 INFO: num_candidates : 3
2:06:11.878848 INFO: ms1_error      : 30
2:06:11.878894 INFO: ms2_error      : 7.4697575
2:06:11.878937 INFO: fwhm_rt        : 3.0
2:06:11.878998 INFO: quant_window   : 3
2:06:11.879039 INFO: ==============================================
2:06:12.138673 INFO: Removed 248666 precursors with score below cutoff 8.166770313835144
2:06:12.491200 INFO: performing precursor FDR with 40 features
2:06:12.491312 INFO: Decoy channel: -1
2:06:12.491336 INFO: competitive: True
2:06:12.534809 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:12.560131 WARNING: FDR calculation for 289369 target and 206204 decoy PSMs
2:06:12.560253 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:06:12.677287 INFO: Estimating optimal hyperparameters - samples: 396,458, batch_size: 1,623, learning_rate: 6.29e-04
2:06:12.678036 INFO: Using random state 61057 for train-test-split
2:06:21.933388 INFO: Test AUC: 0.858
2:06:21.933525 INFO: Train AUC: 0.859
2:06:21.933557 INFO: AUC difference: 0.04%
2:06:22.324939 INFO: Resetting torch num_threads to 100
2:06:22.619921 PROGRESS: ============================= Precursor FDR =============================
2:06:22.620186 PROGRESS: Total precursors accumulated: 125,571
2:06:22.620254 PROGRESS: Target precursors: 124,328 (99.01%)
2:06:22.620308 PROGRESS: Decoy precursors: 1,243 (0.99%)
2:06:22.620357 PROGRESS: 
2:06:22.620403 PROGRESS: Precursor Summary:
2:06:22.658343 PROGRESS: Channel   0:	 0.050 FDR: 124,328; 0.010 FDR: 124,328; 0.001 FDR: 114,910
2:06:22.658597 PROGRESS: 
2:06:22.658660 PROGRESS: Protein Summary:
2:06:22.724977 PROGRESS: Channel   0:	 0.050 FDR: 10,115; 0.010 FDR: 10,115; 0.001 FDR: 10,080
2:06:22.725235 PROGRESS: =========================================================================
2:06:22.727922 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
2:06:22.925437 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
2:06:23.224852 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:06:23.300816 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:06:23.300953 INFO: Quantification results path: /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant
2:06:23.301040 INFO: Initializing TimingManager
2:06:23.301645 INFO: Initializing RawFileManager
2:06:34.523428 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.
2:06:34.532234 INFO: Determining DIA cycle
2:06:34.548488 INFO: Found cycle with start 0.00 min and length 300.
2:06:34.719131 INFO: RT (min)            : 0.0 - 26.9
2:06:34.719217 INFO: RT duration (sec)   : 1611.2
2:06:34.719245 INFO: RT duration (min)   : 26.9
2:06:34.719267 INFO: Cycle len (scans)   : 300
2:06:34.719286 INFO: Cycle len (sec)     : 1.65
2:06:34.719305 INFO: Number of cycles    : 978
2:06:34.719323 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:06:34.719352 INFO: Creating DIA data object took: 11.417603254318237
2:06:35.412514 INFO: Creating DIA data NG object took: 0.6930475234985352
2:06:35.442207 INFO: Initializing CalibrationManager
2:06:35.442493 INFO: Setting up calibration estimators ..
2:06:35.442562 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:06:35.442629 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'}' ..
2:06:35.442689 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:06:35.442736 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:06:35.442788 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}}' ..
2:06:35.442856 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:06:35.442900 INFO: Done setting up calibration estimators.
2:06:35.443077 INFO: Initializing OptimizationManager
2:06:35.443192 INFO: initial parameter: ms1_error = 30
2:06:35.443242 INFO: initial parameter: ms2_error = 30
2:06:35.443287 INFO: initial parameter: rt_error = 805.611083984375
2:06:35.443328 INFO: initial parameter: mobility_error = 0.1
2:06:35.443368 INFO: initial parameter: num_candidates = 1
2:06:35.443408 INFO: initial parameter: fwhm_rt = 5
2:06:35.443446 INFO: initial parameter: fwhm_mobility = 0.01
2:06:35.443485 INFO: initial parameter: score_cutoff = 0
2:06:35.443524 INFO: initial parameter: classifier_version = -1
2:06:35.443592 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:06:35.443794 INFO: FDRManager: loading saved state not requested, will be initialized.
2:06:35.443823 INFO: Initializing FDRManager
2:06:35.443850 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:06:35.480314 PROGRESS: Initializing spectral library: 131,664 target precursors potentially observable (0 removed)
2:06:35.505590 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:06:35.505975 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:06:35.506067 PROGRESS: Starting initial search for precursors.
2:06:35.506142 INFO: Starting optimization step 0.
2:06:35.506197 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:06:35.506248 INFO: Using rust extraction backend
2:06:35.506299 PROGRESS: Extracting batch of 1977 precursors
2:06:35.510883 INFO: === Search parameters used ===
2:06:35.510981 INFO: rt_error       : 805.611083984375
2:06:35.511032 INFO: mobility_error : 0.1
2:06:35.511077 INFO: num_candidates : 1
2:06:35.511118 INFO: ms1_error      : 30
2:06:35.511158 INFO: ms2_error      : 30
2:06:35.511197 INFO: fwhm_rt        : 5
2:06:35.511236 INFO: quant_window   : 3
2:06:35.511273 INFO: ==============================================
2:06:35.537571 INFO: performing precursor FDR with 40 features
2:06:35.537646 INFO: Decoy channel: -1
2:06:35.537669 INFO: competitive: True
2:06:35.538884 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:35.540559 INFO: Estimating optimal hyperparameters - samples: 1,579, batch_size: 128, learning_rate: 1.77e-04
2:06:35.541356 INFO: Using random state 208515 for train-test-split
2:06:35.689903 INFO: Test AUC: 0.807
2:06:35.689985 INFO: Train AUC: 0.804
2:06:35.690014 INFO: AUC difference: 0.44%
2:06:35.930230 INFO: Resetting torch num_threads to 100
2:06:35.931799 PROGRESS: === Extracted 1974 precursors and 13474 fragments ===
2:06:35.932160 INFO: === FDR correction performed with classifier version -1 ===
2:06:35.932636 PROGRESS: ============================= Precursor FDR =============================
2:06:35.932716 PROGRESS: Total precursors accumulated: 236
2:06:35.932771 PROGRESS: Target precursors: 234 (99.15%)
2:06:35.932819 PROGRESS: Decoy precursors: 2 (0.85%)
2:06:35.932863 PROGRESS: 
2:06:35.932906 PROGRESS: Precursor Summary:
2:06:35.933917 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   209
2:06:35.934004 PROGRESS: 
2:06:35.934058 PROGRESS: Protein Summary:
2:06:35.935217 PROGRESS: Channel   0:	 0.050 FDR:   218; 0.010 FDR:   218; 0.001 FDR:   194
2:06:35.935298 PROGRESS: =========================================================================
2:06:35.935494 INFO: Target number of precursors not reached yet.
2:06:35.943097 INFO: Starting optimization step 1.
2:06:35.943210 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:06:35.943280 INFO: Using rust extraction backend
2:06:35.943334 PROGRESS: Extracting batch of 3959 precursors
2:06:35.951735 INFO: === Search parameters used ===
2:06:35.951837 INFO: rt_error       : 805.611083984375
2:06:35.951887 INFO: mobility_error : 0.1
2:06:35.951943 INFO: num_candidates : 1
2:06:35.951986 INFO: ms1_error      : 30
2:06:35.952025 INFO: ms2_error      : 30
2:06:35.952064 INFO: fwhm_rt        : 5
2:06:35.952103 INFO: quant_window   : 3
2:06:35.952143 INFO: ==============================================
2:06:35.998523 INFO: performing precursor FDR with 40 features
2:06:35.998622 INFO: Decoy channel: -1
2:06:35.998646 INFO: competitive: True
2:06:36.002666 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:36.004875 INFO: Estimating optimal hyperparameters - samples: 4,741, batch_size: 128, learning_rate: 1.77e-04
2:06:36.004950 INFO: Using random state 555984 for train-test-split
2:06:36.469492 INFO: Test AUC: 0.834
2:06:36.469583 INFO: Train AUC: 0.835
2:06:36.469612 INFO: AUC difference: 0.14%
2:06:36.713250 INFO: Resetting torch num_threads to 100
2:06:36.716204 PROGRESS: === Extracted 5927 precursors and 41114 fragments ===
2:06:36.716582 INFO: === FDR correction performed with classifier version -1 ===
2:06:36.717199 PROGRESS: ============================= Precursor FDR =============================
2:06:36.717282 PROGRESS: Total precursors accumulated: 1,572
2:06:36.717340 PROGRESS: Target precursors: 1,557 (99.05%)
2:06:36.717388 PROGRESS: Decoy precursors: 15 (0.95%)
2:06:36.717434 PROGRESS: 
2:06:36.717477 PROGRESS: Precursor Summary:
2:06:36.718874 PROGRESS: Channel   0:	 0.050 FDR: 1,557; 0.010 FDR: 1,557; 0.001 FDR: 1,307
2:06:36.718967 PROGRESS: 
2:06:36.719023 PROGRESS: Protein Summary:
2:06:36.720842 PROGRESS: Channel   0:	 0.050 FDR: 1,261; 0.010 FDR: 1,261; 0.001 FDR: 1,081
2:06:36.720932 PROGRESS: =========================================================================
2:06:36.721184 INFO: Target number of precursors reached.
2:06:36.730243 INFO: fragments_df: keeping 5000 of 41114 [sum(precursor_idx_mask)=16192 sum(mass_error_mask)=41114 stop_rank=5000
2:06:36.740867 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:36.983293 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:37.642296 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:06:37.642736 INFO: Using score_cutoff 11.788542375183104 (fac=0.99, q=1)
2:06:37.643034 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:06:37.643107 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:06:37.643159 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.788542375183104
2:06:37.643213 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:37.647058 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:37.654626 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:06:37.654733 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:06:37.654810 INFO: Starting optimization step 2.
2:06:37.654874 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:37.654932 INFO: Using rust extraction backend
2:06:37.654985 PROGRESS: Extracting batch of 5936 precursors
2:06:37.666374 INFO: === Search parameters used ===
2:06:37.666493 INFO: rt_error       : 805.611083984375
2:06:37.666543 INFO: mobility_error : 0.1
2:06:37.666586 INFO: num_candidates : 3
2:06:37.666627 INFO: ms1_error      : 30
2:06:37.666667 INFO: ms2_error      : 30
2:06:37.666706 INFO: fwhm_rt        : 3.0
2:06:37.666744 INFO: quant_window   : 3
2:06:37.666783 INFO: ==============================================
2:06:37.773760 INFO: performing precursor FDR with 40 features
2:06:37.773887 INFO: Decoy channel: -1
2:06:37.773913 INFO: competitive: True
2:06:37.778597 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:37.782549 INFO: Estimating optimal hyperparameters - samples: 14,220, batch_size: 128, learning_rate: 1.77e-04
2:06:37.782679 INFO: Using random state 451729 for train-test-split
2:06:39.219248 INFO: Test AUC: 0.680
2:06:39.219362 INFO: Train AUC: 0.691
2:06:39.219389 INFO: AUC difference: 1.53%
2:06:39.466262 INFO: Resetting torch num_threads to 100
2:06:39.468536 PROGRESS: === Extracted 17775 precursors and 106519 fragments ===
2:06:39.468913 INFO: === FDR correction performed with classifier version 1 ===
2:06:39.469569 PROGRESS: ============================= Precursor FDR =============================
2:06:39.469654 PROGRESS: Total precursors accumulated: 2,003
2:06:39.469712 PROGRESS: Target precursors: 1,984 (99.05%)
2:06:39.469762 PROGRESS: Decoy precursors: 19 (0.95%)
2:06:39.469809 PROGRESS: 
2:06:39.469864 PROGRESS: Precursor Summary:
2:06:39.471291 PROGRESS: Channel   0:	 0.050 FDR: 1,984; 0.010 FDR: 1,984; 0.001 FDR: 1,198
2:06:39.471387 PROGRESS: 
2:06:39.471450 PROGRESS: Protein Summary:
2:06:39.473399 PROGRESS: Channel   0:	 0.050 FDR: 1,562; 0.010 FDR: 1,562; 0.001 FDR:   983
2:06:39.473486 PROGRESS: =========================================================================
2:06:39.473834 INFO: Target number of precursors reached.
2:06:39.493585 INFO: fragments_df: keeping 5000 of 106519 [sum(precursor_idx_mask)=42783 sum(mass_error_mask)=106519 stop_rank=5000
2:06:39.504318 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:39.791384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:40.501366 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:40.501824 INFO: Using score_cutoff 11.861383665275573 (fac=0.99, q=1)
2:06:40.502159 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:40.502235 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:40.502287 INFO: Updating optimization_manager: score_cutoff        : 11.788542375183104 -> 11.861383665275573
2:06:40.502338 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:40.506231 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:40.513822 INFO: === checking if optimization conditions were reached ===
2:06:40.515510 INFO: Updating optimization_manager: ms2_error           : 30 -> 7.4697575
2:06:40.515607 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:06:40.515668 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:06:40.515722 INFO: ==============================================
2:06:40.515797 INFO: Starting optimization step 3.
2:06:40.515854 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:40.515912 INFO: Using rust extraction backend
2:06:40.515965 PROGRESS: Extracting batch of 5936 precursors
2:06:40.527407 INFO: === Search parameters used ===
2:06:40.527534 INFO: rt_error       : 805.611083984375
2:06:40.527586 INFO: mobility_error : 0.1
2:06:40.527631 INFO: num_candidates : 3
2:06:40.527673 INFO: ms1_error      : 30
2:06:40.527713 INFO: ms2_error      : 7.4697575
2:06:40.527753 INFO: fwhm_rt        : 3.0
2:06:40.527792 INFO: quant_window   : 3
2:06:40.527833 INFO: ==============================================
2:06:40.634294 INFO: performing precursor FDR with 40 features
2:06:40.634405 INFO: Decoy channel: -1
2:06:40.634429 INFO: competitive: True
2:06:40.639065 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:40.643139 INFO: Estimating optimal hyperparameters - samples: 14,246, batch_size: 128, learning_rate: 1.77e-04
2:06:40.643273 INFO: Using random state 294510 for train-test-split
2:06:42.022992 INFO: Test AUC: 0.737
2:06:42.023103 INFO: Train AUC: 0.738
2:06:42.023131 INFO: AUC difference: 0.16%
2:06:42.276386 INFO: Resetting torch num_threads to 100
2:06:42.278751 PROGRESS: === Extracted 17808 precursors and 123458 fragments ===
2:06:42.279122 INFO: === FDR correction performed with classifier version 2 ===
2:06:42.279825 PROGRESS: ============================= Precursor FDR =============================
2:06:42.279907 PROGRESS: Total precursors accumulated: 2,598
2:06:42.279962 PROGRESS: Target precursors: 2,573 (99.04%)
2:06:42.280010 PROGRESS: Decoy precursors: 25 (0.96%)
2:06:42.280054 PROGRESS: 
2:06:42.280096 PROGRESS: Precursor Summary:
2:06:42.281665 PROGRESS: Channel   0:	 0.050 FDR: 2,573; 0.010 FDR: 2,573; 0.001 FDR: 1,628
2:06:42.281750 PROGRESS: 
2:06:42.281803 PROGRESS: Protein Summary:
2:06:42.283982 PROGRESS: Channel   0:	 0.050 FDR: 1,986; 0.010 FDR: 1,986; 0.001 FDR: 1,309
2:06:42.284081 PROGRESS: =========================================================================
2:06:42.284430 INFO: Target number of precursors reached.
2:06:42.311203 INFO: fragments_df: keeping 5000 of 123458 [sum(precursor_idx_mask)=59767 sum(mass_error_mask)=123458 stop_rank=5000
2:06:42.322148 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:42.693889 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:43.402002 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:43.402454 INFO: Using score_cutoff 10.627879349899292 (fac=0.99, q=1)
2:06:43.402764 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:43.402839 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:43.402890 INFO: Updating optimization_manager: score_cutoff        : 11.861383665275573 -> 10.627879349899292
2:06:43.402938 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:43.406857 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:43.414342 INFO: === checking if optimization conditions were reached ===
2:06:43.415957 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:06:43.416049 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:06:43.416118 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:06:43.416175 INFO: ==============================================
2:06:43.416238 INFO: Starting optimization step 4.
2:06:43.416290 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:43.416345 INFO: Using rust extraction backend
2:06:43.416403 PROGRESS: Extracting batch of 5936 precursors
2:06:43.427878 INFO: === Search parameters used ===
2:06:43.428001 INFO: rt_error       : 805.611083984375
2:06:43.428051 INFO: mobility_error : 0.1
2:06:43.428096 INFO: num_candidates : 3
2:06:43.428137 INFO: ms1_error      : 30
2:06:43.428177 INFO: ms2_error      : 7.4697575
2:06:43.428216 INFO: fwhm_rt        : 3.0
2:06:43.428256 INFO: quant_window   : 3
2:06:43.428297 INFO: ==============================================
2:06:43.534164 INFO: performing precursor FDR with 40 features
2:06:43.534276 INFO: Decoy channel: -1
2:06:43.534300 INFO: competitive: True
2:06:43.538979 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:43.542985 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:06:43.543115 INFO: Using random state 119145 for train-test-split
2:06:44.985394 INFO: Test AUC: 0.735
2:06:44.985511 INFO: Train AUC: 0.754
2:06:44.985543 INFO: AUC difference: 2.46%
2:06:45.236378 INFO: Resetting torch num_threads to 100
2:06:45.238754 PROGRESS: === Extracted 17807 precursors and 123506 fragments ===
2:06:45.239128 INFO: === FDR correction performed with classifier version 3 ===
2:06:45.239836 PROGRESS: ============================= Precursor FDR =============================
2:06:45.239923 PROGRESS: Total precursors accumulated: 2,643
2:06:45.239983 PROGRESS: Target precursors: 2,617 (99.02%)
2:06:45.240034 PROGRESS: Decoy precursors: 26 (0.98%)
2:06:45.240082 PROGRESS: 
2:06:45.240134 PROGRESS: Precursor Summary:
2:06:45.241748 PROGRESS: Channel   0:	 0.050 FDR: 2,617; 0.010 FDR: 2,617; 0.001 FDR: 2,005
2:06:45.241838 PROGRESS: 
2:06:45.241907 PROGRESS: Protein Summary:
2:06:45.244122 PROGRESS: Channel   0:	 0.050 FDR: 2,017; 0.010 FDR: 2,017; 0.001 FDR: 1,579
2:06:45.244211 PROGRESS: =========================================================================
2:06:45.244558 INFO: Target number of precursors reached.
2:06:45.271485 INFO: fragments_df: keeping 5000 of 123506 [sum(precursor_idx_mask)=60595 sum(mass_error_mask)=123506 stop_rank=5000
2:06:45.282237 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:45.659173 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:46.367388 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:46.367857 INFO: Using score_cutoff 10.51564748840332 (fac=0.99, q=1)
2:06:46.368159 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:46.368234 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:46.368284 INFO: Updating optimization_manager: score_cutoff        : 10.627879349899292 -> 10.51564748840332
2:06:46.368335 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:46.372214 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:46.379651 INFO: === checking if optimization conditions were reached ===
2:06:46.381251 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:06:46.381352 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:06:46.381414 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:06:46.381468 INFO: ==============================================
2:06:46.381529 INFO: Starting optimization step 5.
2:06:46.381585 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:46.381642 INFO: Using rust extraction backend
2:06:46.381694 PROGRESS: Extracting batch of 5936 precursors
2:06:46.392950 INFO: === Search parameters used ===
2:06:46.393071 INFO: rt_error       : 805.611083984375
2:06:46.393120 INFO: mobility_error : 0.1
2:06:46.393163 INFO: num_candidates : 3
2:06:46.393204 INFO: ms1_error      : 30
2:06:46.393243 INFO: ms2_error      : 7.4697575
2:06:46.393282 INFO: fwhm_rt        : 3.0
2:06:46.393320 INFO: quant_window   : 3
2:06:46.393358 INFO: ==============================================
2:06:46.496730 INFO: performing precursor FDR with 40 features
2:06:46.496846 INFO: Decoy channel: -1
2:06:46.496870 INFO: competitive: True
2:06:46.501468 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:46.505535 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:06:46.505666 INFO: Using random state 590007 for train-test-split
2:06:47.933040 INFO: Test AUC: 0.755
2:06:47.933149 INFO: Train AUC: 0.759
2:06:47.933177 INFO: AUC difference: 0.65%
2:06:48.185063 INFO: Resetting torch num_threads to 100
2:06:48.187408 PROGRESS: === Extracted 17807 precursors and 123544 fragments ===
2:06:48.187776 INFO: === FDR correction performed with classifier version 4 ===
2:06:48.188464 PROGRESS: ============================= Precursor FDR =============================
2:06:48.188546 PROGRESS: Total precursors accumulated: 2,613
2:06:48.188602 PROGRESS: Target precursors: 2,588 (99.04%)
2:06:48.188657 PROGRESS: Decoy precursors: 25 (0.96%)
2:06:48.188705 PROGRESS: 
2:06:48.188754 PROGRESS: Precursor Summary:
2:06:48.190218 PROGRESS: Channel   0:	 0.050 FDR: 2,588; 0.010 FDR: 2,588; 0.001 FDR:     1
2:06:48.190309 PROGRESS: 
2:06:48.190362 PROGRESS: Protein Summary:
2:06:48.192283 PROGRESS: Channel   0:	 0.050 FDR: 1,997; 0.010 FDR: 1,997; 0.001 FDR:     1
2:06:48.192368 PROGRESS: =========================================================================
2:06:48.192712 INFO: Target number of precursors reached.
2:06:48.219818 INFO: fragments_df: keeping 5000 of 123544 [sum(precursor_idx_mask)=60082 sum(mass_error_mask)=123544 stop_rank=5000
2:06:48.230724 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:48.602774 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:49.315441 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:49.315890 INFO: Using score_cutoff 10.628371339988709 (fac=0.99, q=1)
2:06:49.316198 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:49.316271 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:49.316322 INFO: Updating optimization_manager: score_cutoff        : 10.51564748840332 -> 10.628371339988709
2:06:49.316372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:49.320264 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:49.327614 INFO: === checking if optimization conditions were reached ===
2:06:49.329219 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:06:49.329319 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:06:49.329381 PROGRESS: ❌ ms2_error      : 7.4698 > 7.4698 or insufficient steps taken.
2:06:49.329433 INFO: ==============================================
2:06:49.329494 INFO: Starting optimization step 6.
2:06:49.329549 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:49.329604 INFO: Using rust extraction backend
2:06:49.329654 PROGRESS: Extracting batch of 5936 precursors
2:06:49.340875 INFO: === Search parameters used ===
2:06:49.341003 INFO: rt_error       : 805.611083984375
2:06:49.341051 INFO: mobility_error : 0.1
2:06:49.341095 INFO: num_candidates : 3
2:06:49.341138 INFO: ms1_error      : 30
2:06:49.341179 INFO: ms2_error      : 7.4697575
2:06:49.341219 INFO: fwhm_rt        : 3.0
2:06:49.341258 INFO: quant_window   : 3
2:06:49.341296 INFO: ==============================================
2:06:49.442586 INFO: performing precursor FDR with 40 features
2:06:49.442699 INFO: Decoy channel: -1
2:06:49.442724 INFO: competitive: True
2:06:49.447546 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:49.451754 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:06:49.451888 INFO: Using random state 935286 for train-test-split
2:06:50.890507 INFO: Test AUC: 0.760
2:06:50.890628 INFO: Train AUC: 0.766
2:06:50.890658 INFO: AUC difference: 0.67%
2:06:51.146578 INFO: Resetting torch num_threads to 100
2:06:51.148950 PROGRESS: === Extracted 17807 precursors and 123539 fragments ===
2:06:51.149323 INFO: === FDR correction performed with classifier version 5 ===
2:06:51.150061 PROGRESS: ============================= Precursor FDR =============================
2:06:51.150156 PROGRESS: Total precursors accumulated: 2,703
2:06:51.150230 PROGRESS: Target precursors: 2,677 (99.04%)
2:06:51.150283 PROGRESS: Decoy precursors: 26 (0.96%)
2:06:51.150329 PROGRESS: 
2:06:51.150374 PROGRESS: Precursor Summary:
2:06:51.151974 PROGRESS: Channel   0:	 0.050 FDR: 2,677; 0.010 FDR: 2,677; 0.001 FDR: 1,638
2:06:51.152067 PROGRESS: 
2:06:51.152121 PROGRESS: Protein Summary:
2:06:51.154388 PROGRESS: Channel   0:	 0.050 FDR: 2,061; 0.010 FDR: 2,061; 0.001 FDR: 1,315
2:06:51.154489 PROGRESS: =========================================================================
2:06:51.154840 INFO: Target number of precursors reached.
2:06:51.182230 INFO: fragments_df: keeping 5000 of 123539 [sum(precursor_idx_mask)=61706 sum(mass_error_mask)=123539 stop_rank=5000
2:06:51.193178 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:51.576959 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:52.289446 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:52.289912 INFO: Using score_cutoff 9.932439736175537 (fac=0.99, q=1)
2:06:52.290225 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:52.290300 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:52.290354 INFO: Updating optimization_manager: score_cutoff        : 10.628371339988709 -> 9.932439736175537
2:06:52.290407 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:52.294324 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:52.301692 INFO: === checking if optimization conditions were reached ===
2:06:52.303333 INFO: Updating optimization_manager: ms2_error           : 7.4697575 -> 7.4697575
2:06:52.303436 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:06:52.303501 PROGRESS: ✅ ms2_error      : 7.4698 <= 7.4698
2:06:52.303557 INFO: ==============================================
2:06:52.303622 PROGRESS: Optimization finished for ms2_error.
2:06:52.313827 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:52.317584 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:52.324793 INFO: Starting optimization step 0.
2:06:52.324902 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:52.324989 INFO: Using rust extraction backend
2:06:52.325046 PROGRESS: Extracting batch of 5936 precursors
2:06:52.336295 INFO: === Search parameters used ===
2:06:52.336423 INFO: rt_error       : 805.611083984375
2:06:52.336474 INFO: mobility_error : 0.1
2:06:52.336519 INFO: num_candidates : 3
2:06:52.336560 INFO: ms1_error      : 30
2:06:52.336601 INFO: ms2_error      : 7.4697575
2:06:52.336641 INFO: fwhm_rt        : 3.0
2:06:52.336681 INFO: quant_window   : 3
2:06:52.336720 INFO: ==============================================
2:06:52.439605 INFO: performing precursor FDR with 40 features
2:06:52.439715 INFO: Decoy channel: -1
2:06:52.439740 INFO: competitive: True
2:06:52.444425 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:52.448470 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:06:52.448596 INFO: Using random state 824410 for train-test-split
2:06:53.899847 INFO: Test AUC: 0.763
2:06:53.899990 INFO: Train AUC: 0.770
2:06:53.900018 INFO: AUC difference: 0.87%
2:06:54.144553 INFO: Resetting torch num_threads to 100
2:06:54.146928 PROGRESS: === Extracted 17807 precursors and 123533 fragments ===
2:06:54.147297 INFO: === FDR correction performed with classifier version 6 ===
2:06:54.148009 PROGRESS: ============================= Precursor FDR =============================
2:06:54.148091 PROGRESS: Total precursors accumulated: 2,776
2:06:54.148147 PROGRESS: Target precursors: 2,749 (99.03%)
2:06:54.148195 PROGRESS: Decoy precursors: 27 (0.97%)
2:06:54.148238 PROGRESS: 
2:06:54.148280 PROGRESS: Precursor Summary:
2:06:54.149917 PROGRESS: Channel   0:	 0.050 FDR: 2,749; 0.010 FDR: 2,749; 0.001 FDR: 2,028
2:06:54.150007 PROGRESS: 
2:06:54.150061 PROGRESS: Protein Summary:
2:06:54.152339 PROGRESS: Channel   0:	 0.050 FDR: 2,116; 0.010 FDR: 2,116; 0.001 FDR: 1,586
2:06:54.152428 PROGRESS: =========================================================================
2:06:54.152773 INFO: Target number of precursors reached.
2:06:54.180003 INFO: fragments_df: keeping 5000 of 123533 [sum(precursor_idx_mask)=63043 sum(mass_error_mask)=123533 stop_rank=5000
2:06:54.190660 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:54.582952 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:55.292473 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:55.292934 INFO: Using score_cutoff 9.44465581741333 (fac=0.99, q=1)
2:06:55.293241 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:55.293326 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:55.293383 INFO: Updating optimization_manager: score_cutoff        : 9.932439736175537 -> 9.44465581741333
2:06:55.293437 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:55.297341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:55.304716 INFO: === checking if optimization conditions were reached ===
2:06:55.304819 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:06:55.307593 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 242.6584360186792
2:06:55.307694 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 242.6584.
2:06:55.307758 INFO: ==============================================
2:06:55.307826 INFO: Starting optimization step 1.
2:06:55.307884 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:55.307943 INFO: Using rust extraction backend
2:06:55.307997 PROGRESS: Extracting batch of 5936 precursors
2:06:55.319258 INFO: === Search parameters used ===
2:06:55.319381 INFO: rt_error       : 242.6584360186792
2:06:55.319433 INFO: mobility_error : 0.1
2:06:55.319479 INFO: num_candidates : 3
2:06:55.319522 INFO: ms1_error      : 30
2:06:55.319565 INFO: ms2_error      : 7.4697575
2:06:55.319606 INFO: fwhm_rt        : 3.0
2:06:55.319661 INFO: quant_window   : 3
2:06:55.319705 INFO: ==============================================
2:06:55.409136 INFO: performing precursor FDR with 40 features
2:06:55.409270 INFO: Decoy channel: -1
2:06:55.409301 INFO: competitive: True
2:06:55.414026 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:55.417983 INFO: Estimating optimal hyperparameters - samples: 14,245, batch_size: 128, learning_rate: 1.77e-04
2:06:55.418115 INFO: Using random state 824410 for train-test-split
2:06:56.852724 INFO: Test AUC: 0.771
2:06:56.852836 INFO: Train AUC: 0.774
2:06:56.852864 INFO: AUC difference: 0.35%
2:06:57.095970 INFO: Resetting torch num_threads to 100
2:06:57.098344 PROGRESS: === Extracted 17807 precursors and 120288 fragments ===
2:06:57.098707 INFO: === FDR correction performed with classifier version 6 ===
2:06:57.099410 PROGRESS: ============================= Precursor FDR =============================
2:06:57.099491 PROGRESS: Total precursors accumulated: 2,807
2:06:57.099546 PROGRESS: Target precursors: 2,780 (99.04%)
2:06:57.099594 PROGRESS: Decoy precursors: 27 (0.96%)
2:06:57.099637 PROGRESS: 
2:06:57.099679 PROGRESS: Precursor Summary:
2:06:57.101295 PROGRESS: Channel   0:	 0.050 FDR: 2,780; 0.010 FDR: 2,780; 0.001 FDR: 2,128
2:06:57.101380 PROGRESS: 
2:06:57.101433 PROGRESS: Protein Summary:
2:06:57.103730 PROGRESS: Channel   0:	 0.050 FDR: 2,132; 0.010 FDR: 2,132; 0.001 FDR: 1,667
2:06:57.103824 PROGRESS: =========================================================================
2:06:57.104167 INFO: Target number of precursors reached.
2:06:57.131027 INFO: fragments_df: keeping 5000 of 120288 [sum(precursor_idx_mask)=62896 sum(mass_error_mask)=120288 stop_rank=5000
2:06:57.141901 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:57.540066 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:58.249265 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:58.249720 INFO: Using score_cutoff 9.515807847118378 (fac=0.99, q=1)
2:06:58.250047 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:58.250129 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:58.250182 INFO: Updating optimization_manager: score_cutoff        : 9.44465581741333 -> 9.515807847118378
2:06:58.250232 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:58.254137 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:06:58.261614 INFO: === checking if optimization conditions were reached ===
2:06:58.261719 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:06:58.264603 INFO: Updating optimization_manager: rt_error            : 242.6584360186792 -> 146.87873774017487
2:06:58.264702 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 146.8787.
2:06:58.264763 INFO: ==============================================
2:06:58.264826 INFO: Starting optimization step 2.
2:06:58.264880 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:06:58.264936 INFO: Using rust extraction backend
2:06:58.264988 PROGRESS: Extracting batch of 5936 precursors
2:06:58.276383 INFO: === Search parameters used ===
2:06:58.276502 INFO: rt_error       : 146.87873774017487
2:06:58.276553 INFO: mobility_error : 0.1
2:06:58.276596 INFO: num_candidates : 3
2:06:58.276638 INFO: ms1_error      : 30
2:06:58.276690 INFO: ms2_error      : 7.4697575
2:06:58.276730 INFO: fwhm_rt        : 3.0
2:06:58.276768 INFO: quant_window   : 3
2:06:58.276806 INFO: ==============================================
2:06:58.364187 INFO: performing precursor FDR with 40 features
2:06:58.364298 INFO: Decoy channel: -1
2:06:58.364323 INFO: competitive: True
2:06:58.368926 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:58.372881 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:06:58.373006 INFO: Using random state 824410 for train-test-split
2:06:59.804060 INFO: Test AUC: 0.779
2:06:59.804178 INFO: Train AUC: 0.779
2:06:59.804206 INFO: AUC difference: 0.09%
2:07:00.048934 INFO: Resetting torch num_threads to 100
2:07:00.051325 PROGRESS: === Extracted 17804 precursors and 115859 fragments ===
2:07:00.051689 INFO: === FDR correction performed with classifier version 6 ===
2:07:00.052399 PROGRESS: ============================= Precursor FDR =============================
2:07:00.052481 PROGRESS: Total precursors accumulated: 2,907
2:07:00.052536 PROGRESS: Target precursors: 2,879 (99.04%)
2:07:00.052583 PROGRESS: Decoy precursors: 28 (0.96%)
2:07:00.052627 PROGRESS: 
2:07:00.052670 PROGRESS: Precursor Summary:
2:07:00.054137 PROGRESS: Channel   0:	 0.050 FDR: 2,879; 0.010 FDR: 2,879; 0.001 FDR:     1
2:07:00.054227 PROGRESS: 
2:07:00.054280 PROGRESS: Protein Summary:
2:07:00.056284 PROGRESS: Channel   0:	 0.050 FDR: 2,204; 0.010 FDR: 2,204; 0.001 FDR:     1
2:07:00.056368 PROGRESS: =========================================================================
2:07:00.056706 INFO: Target number of precursors reached.
2:07:00.082615 INFO: fragments_df: keeping 5000 of 115859 [sum(precursor_idx_mask)=63456 sum(mass_error_mask)=115859 stop_rank=5000
2:07:00.093259 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:07:00.511606 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:07:01.220773 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:07:01.221223 INFO: Using score_cutoff 9.448151581192016 (fac=0.99, q=1)
2:07:01.221539 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:07:01.221617 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:07:01.221672 INFO: Updating optimization_manager: score_cutoff        : 9.515807847118378 -> 9.448151581192016
2:07:01.221725 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:01.225667 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:01.233133 INFO: === checking if optimization conditions were reached ===
2:07:01.233240 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:07:01.236317 INFO: Updating optimization_manager: rt_error            : 146.87873774017487 -> 125.79210281241198
2:07:01.236432 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 125.7921.
2:07:01.236497 INFO: ==============================================
2:07:01.236564 INFO: Starting optimization step 3.
2:07:01.236623 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:07:01.236683 INFO: Using rust extraction backend
2:07:01.236737 PROGRESS: Extracting batch of 5936 precursors
2:07:01.248260 INFO: === Search parameters used ===
2:07:01.248389 INFO: rt_error       : 125.79210281241198
2:07:01.248443 INFO: mobility_error : 0.1
2:07:01.248504 INFO: num_candidates : 3
2:07:01.248550 INFO: ms1_error      : 30
2:07:01.248595 INFO: ms2_error      : 7.4697575
2:07:01.248637 INFO: fwhm_rt        : 3.0
2:07:01.248678 INFO: quant_window   : 3
2:07:01.248720 INFO: ==============================================
2:07:01.333525 INFO: performing precursor FDR with 40 features
2:07:01.333644 INFO: Decoy channel: -1
2:07:01.333670 INFO: competitive: True
2:07:01.338422 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:01.342323 INFO: Estimating optimal hyperparameters - samples: 14,243, batch_size: 128, learning_rate: 1.77e-04
2:07:01.342450 INFO: Using random state 824410 for train-test-split
2:07:02.763528 INFO: Test AUC: 0.763
2:07:02.763640 INFO: Train AUC: 0.784
2:07:02.763669 INFO: AUC difference: 2.72%
2:07:03.009312 INFO: Resetting torch num_threads to 100
2:07:03.011763 PROGRESS: === Extracted 17804 precursors and 114379 fragments ===
2:07:03.012138 INFO: === FDR correction performed with classifier version 6 ===
2:07:03.012870 PROGRESS: ============================= Precursor FDR =============================
2:07:03.012954 PROGRESS: Total precursors accumulated: 2,929
2:07:03.013011 PROGRESS: Target precursors: 2,900 (99.01%)
2:07:03.013061 PROGRESS: Decoy precursors: 29 (0.99%)
2:07:03.013106 PROGRESS: 
2:07:03.013149 PROGRESS: Precursor Summary:
2:07:03.014637 PROGRESS: Channel   0:	 0.050 FDR: 2,900; 0.010 FDR: 2,899; 0.001 FDR:     1
2:07:03.014738 PROGRESS: 
2:07:03.014792 PROGRESS: Protein Summary:
2:07:03.016823 PROGRESS: Channel   0:	 0.050 FDR: 2,223; 0.010 FDR: 2,222; 0.001 FDR:     1
2:07:03.016906 PROGRESS: =========================================================================
2:07:03.017259 INFO: Target number of precursors reached.
2:07:03.043346 INFO: fragments_df: keeping 5000 of 114379 [sum(precursor_idx_mask)=63231 sum(mass_error_mask)=114379 stop_rank=5000
2:07:03.054606 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:07:03.474291 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:07:04.188468 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:07:04.188931 INFO: Using score_cutoff 9.164817915916442 (fac=0.99, q=1)
2:07:04.189230 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:07:04.189303 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:07:04.189354 INFO: Updating optimization_manager: score_cutoff        : 9.448151581192016 -> 9.164817915916442
2:07:04.189404 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:04.193341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:04.200940 INFO: === checking if optimization conditions were reached ===
2:07:04.201045 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:07:04.204106 INFO: Updating optimization_manager: rt_error            : 125.79210281241198 -> 123.93626696493544
2:07:04.204206 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 123.9363.
2:07:04.204269 INFO: ==============================================
2:07:04.204333 INFO: Starting optimization step 4.
2:07:04.204388 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:07:04.204443 INFO: Using rust extraction backend
2:07:04.204495 PROGRESS: Extracting batch of 5936 precursors
2:07:04.215743 INFO: === Search parameters used ===
2:07:04.215875 INFO: rt_error       : 123.93626696493544
2:07:04.215930 INFO: mobility_error : 0.1
2:07:04.215975 INFO: num_candidates : 3
2:07:04.216017 INFO: ms1_error      : 30
2:07:04.216063 INFO: ms2_error      : 7.4697575
2:07:04.216103 INFO: fwhm_rt        : 3.0
2:07:04.216143 INFO: quant_window   : 3
2:07:04.216184 INFO: ==============================================
2:07:04.302049 INFO: performing precursor FDR with 40 features
2:07:04.302160 INFO: Decoy channel: -1
2:07:04.302184 INFO: competitive: True
2:07:04.306894 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:04.310791 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:07:04.310915 INFO: Using random state 824410 for train-test-split
2:07:05.766176 INFO: Test AUC: 0.788
2:07:05.766295 INFO: Train AUC: 0.779
2:07:05.766327 INFO: AUC difference: 1.17%
2:07:06.012057 INFO: Resetting torch num_threads to 100
2:07:06.014415 PROGRESS: === Extracted 17800 precursors and 114200 fragments ===
2:07:06.014784 INFO: === FDR correction performed with classifier version 6 ===
2:07:06.015505 PROGRESS: ============================= Precursor FDR =============================
2:07:06.015593 PROGRESS: Total precursors accumulated: 2,848
2:07:06.015652 PROGRESS: Target precursors: 2,820 (99.02%)
2:07:06.015703 PROGRESS: Decoy precursors: 28 (0.98%)
2:07:06.015751 PROGRESS: 
2:07:06.015798 PROGRESS: Precursor Summary:
2:07:06.017257 PROGRESS: Channel   0:	 0.050 FDR: 2,820; 0.010 FDR: 2,820; 0.001 FDR:     1
2:07:06.017350 PROGRESS: 
2:07:06.017409 PROGRESS: Protein Summary:
2:07:06.019424 PROGRESS: Channel   0:	 0.050 FDR: 2,166; 0.010 FDR: 2,166; 0.001 FDR:     1
2:07:06.019520 PROGRESS: =========================================================================
2:07:06.019871 INFO: Target number of precursors reached.
2:07:06.045584 INFO: fragments_df: keeping 5000 of 114200 [sum(precursor_idx_mask)=61800 sum(mass_error_mask)=114200 stop_rank=5000
2:07:06.056456 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:07:06.468387 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:07:07.181148 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:07:07.181608 INFO: Using score_cutoff 9.479537839221955 (fac=0.99, q=1)
2:07:07.181931 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:07:07.182011 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:07:07.182066 INFO: Updating optimization_manager: score_cutoff        : 9.164817915916442 -> 9.479537839221955
2:07:07.182120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:07.185992 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:07.193308 INFO: === checking if optimization conditions were reached ===
2:07:07.193424 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:07:07.194130 INFO: Updating optimization_manager: rt_error            : 123.93626696493544 -> 125.79210281241198
2:07:07.194257 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:07:07.194355 INFO: Updating optimization_manager: score_cutoff        : 9.479537839221955 -> 9.164817915916442
2:07:07.194443 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:07:07.194527 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:07:07.194625 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 125.7921 found after 5 searches.
2:07:07.194687 INFO: ==============================================
2:07:07.194751 PROGRESS: Optimization finished for rt_error.
2:07:07.205033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:07.208756 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:07.215992 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:07:07.216091 PROGRESS: ==============================================
2:07:07.216155 PROGRESS: ms2_error      : 7.4698
2:07:07.216207 PROGRESS: rt_error       : 125.7921
2:07:07.216252 PROGRESS: ==============================================
2:07:07.216887 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:07.350046 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:07.708643 INFO: Using rust extraction backend
2:07:07.708944 PROGRESS: Extracting batch of 260426 precursors
2:07:08.117244 INFO: === Search parameters used ===
2:07:08.117510 INFO: rt_error       : 125.79210281241198
2:07:08.117565 INFO: mobility_error : 0.1
2:07:08.117610 INFO: num_candidates : 3
2:07:08.117654 INFO: ms1_error      : 30
2:07:08.117695 INFO: ms2_error      : 7.4697575
2:07:08.117734 INFO: fwhm_rt        : 3.0
2:07:08.117773 INFO: quant_window   : 3
2:07:08.117828 INFO: ==============================================
2:07:08.421109 INFO: Removed 176844 precursors with score below cutoff 9.164817915916442
2:07:08.838993 INFO: performing precursor FDR with 40 features
2:07:08.839109 INFO: Decoy channel: -1
2:07:08.839133 INFO: competitive: True
2:07:08.889491 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:08.918896 WARNING: FDR calculation for 337542 target and 266784 decoy PSMs
2:07:08.919023 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:07:09.061118 INFO: Estimating optimal hyperparameters - samples: 483,460, batch_size: 1,980, learning_rate: 6.95e-04
2:07:09.061934 INFO: Using random state 306761 for train-test-split
2:07:19.210309 INFO: Test AUC: 0.812
2:07:19.210471 INFO: Train AUC: 0.815
2:07:19.210503 INFO: AUC difference: 0.30%
2:07:19.652890 INFO: Resetting torch num_threads to 100
2:07:19.956094 PROGRESS: ============================= Precursor FDR =============================
2:07:19.956376 PROGRESS: Total precursors accumulated: 125,585
2:07:19.956448 PROGRESS: Target precursors: 124,342 (99.01%)
2:07:19.956506 PROGRESS: Decoy precursors: 1,243 (0.99%)
2:07:19.956556 PROGRESS: 
2:07:19.956604 PROGRESS: Precursor Summary:
2:07:19.994919 PROGRESS: Channel   0:	 0.050 FDR: 124,342; 0.010 FDR: 124,342; 0.001 FDR: 114,095
2:07:19.995174 PROGRESS: 
2:07:19.995235 PROGRESS: Protein Summary:
2:07:20.057119 PROGRESS: Channel   0:	 0.050 FDR: 10,114; 0.010 FDR: 10,114; 0.001 FDR: 10,059
2:07:20.057368 PROGRESS: =========================================================================
2:07:20.059958 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
2:07:20.257648 INFO: Saving results to /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
2:07:20.557727 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:07:21.196885 PROGRESS: Processing search outputs
2:07:21.197010 PROGRESS: === Performing protein grouping and FDR ===
2:07:21.197044 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:07:21.281900 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:07:21.363801 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:07:21.451108 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:07:21.535681 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:07:21.620624 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:07:21.737741 INFO: Performing protein inference
2:07:22.794800 INFO: Inference strategy: library. Using library grouping for protein inference
2:07:22.799077 INFO: Performing protein FDR
2:07:28.761770 INFO: Normalizing q-values using 10,119 targets and 3,695 decoys
2:07:28.764495 INFO: Test AUC: 1.000
2:07:28.764543 INFO: Train AUC: 1.000
2:07:28.764571 INFO: AUC difference: 0.00%
2:07:29.592972 INFO: ================ Protein FDR =================
2:07:29.593116 INFO: Unique protein groups in output
2:07:29.593144 INFO:   1% protein FDR: 10,118
2:07:29.593163 INFO: 
2:07:29.593180 INFO: Unique precursor in output
2:07:29.593198 INFO:   1% protein FDR: 131,525
2:07:29.593214 INFO: ================================================
2:07:29.681680 PROGRESS: Building search statistics
2:07:29.817333 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:07:29.817519 INFO: Initializing OptimizationManager
2:07:29.817756 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:07:29.817825 INFO: Initializing CalibrationManager
2:07:29.818057 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:07:29.818132 INFO: Initializing RawFileManager
2:07:29.862238 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:07:29.862416 INFO: Initializing OptimizationManager
2:07:29.862641 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:07:29.862713 INFO: Initializing CalibrationManager
2:07:29.862929 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:07:29.863000 INFO: Initializing RawFileManager
2:07:29.907768 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:07:29.907948 INFO: Initializing OptimizationManager
2:07:29.908158 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:07:29.908246 INFO: Initializing CalibrationManager
2:07:29.908463 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:07:29.908539 INFO: Initializing RawFileManager
2:07:29.953720 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:07:29.953930 INFO: Initializing OptimizationManager
2:07:29.954145 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:07:29.954216 INFO: Initializing CalibrationManager
2:07:29.954433 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:07:29.954507 INFO: Initializing RawFileManager
2:07:29.999190 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:07:29.999364 INFO: Initializing OptimizationManager
2:07:29.999565 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:07:29.999634 INFO: Initializing CalibrationManager
2:07:29.999846 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:07:29.999916 INFO: Initializing RawFileManager
2:07:30.044456 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:07:30.044630 INFO: Initializing OptimizationManager
2:07:30.044849 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:07:30.044918 INFO: Initializing CalibrationManager
2:07:30.045132 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:07:30.045202 INFO: Initializing RawFileManager
2:07:30.049091 INFO: Writing stat output to disk
2:07:30.049154 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
2:07:30.060846 PROGRESS: Building internal statistics
2:07:30.061170 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:07:30.061212 INFO: Initializing TimingManager
2:07:30.061602 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:07:30.061639 INFO: Initializing TimingManager
2:07:30.061840 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:07:30.061887 INFO: Initializing TimingManager
2:07:30.062082 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:07:30.062114 INFO: Initializing TimingManager
2:07:30.062304 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:07:30.062336 INFO: Initializing TimingManager
2:07:30.062519 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:07:30.062568 INFO: Initializing TimingManager
2:07:30.063031 INFO: Writing internal output to disk
2:07:30.063077 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
2:07:30.158209 INFO: Performing label free quantification
2:07:30.158350 INFO: Accumulating fragment data
2:07:30.158409 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:07:30.246347 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:07:31.852279 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:07:33.443349 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:07:35.126374 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:07:36.815447 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:07:38.757611 INFO: Performing label free quantification on the precursor level
2:07:38.757767 INFO: Filtering fragments by quality
2:07:39.155320 INFO: Performing label-free quantification with directlfq normalization
2:07:39.763041 INFO: 131525 lfq-groups total
2:08:37.102018 INFO: using 100 processes
2:08:37.339808 INFO: lfq-object 0
2:08:38.193397 INFO: lfq-object 100
2:08:38.247800 INFO: lfq-object 400
2:08:38.297091 INFO: lfq-object 700
2:08:38.326785 INFO: lfq-object 200
2:08:38.354234 INFO: lfq-object 1000
2:08:38.380888 INFO: lfq-object 500
2:08:38.426049 INFO: lfq-object 800
2:08:38.458526 INFO: lfq-object 300
2:08:38.485168 INFO: lfq-object 1100
2:08:38.511903 INFO: lfq-object 600
2:08:38.542339 INFO: lfq-object 1400
2:08:38.560163 INFO: lfq-object 900
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2:12:30.551565 INFO: lfq-object 115400
2:12:30.676523 INFO: lfq-object 115300
2:12:30.680415 INFO: lfq-object 115500
2:12:30.684536 INFO: lfq-object 115700
2:12:30.768845 INFO: lfq-object 116000
2:12:30.813359 INFO: lfq-object 115600
2:12:30.815238 INFO: lfq-object 115800
2:12:30.900742 INFO: lfq-object 116100
2:12:30.944461 INFO: lfq-object 115900
2:12:30.957839 INFO: lfq-object 116300
2:12:31.029643 INFO: lfq-object 116200
2:12:31.072424 INFO: lfq-object 116600
2:12:31.089492 INFO: lfq-object 116400
2:12:31.203716 INFO: lfq-object 116700
2:12:31.221644 INFO: lfq-object 116500
2:12:31.226008 INFO: lfq-object 116900
2:12:31.334790 INFO: lfq-object 116800
2:12:31.353629 INFO: lfq-object 117000
2:12:31.359208 INFO: lfq-object 117200
2:12:31.484951 INFO: lfq-object 117100
2:12:31.487175 INFO: lfq-object 117300
2:12:31.490684 INFO: lfq-object 117500
2:12:31.583810 INFO: lfq-object 117800
2:12:31.617294 INFO: lfq-object 117400
2:12:31.627980 INFO: lfq-object 117600
2:12:31.706783 INFO: lfq-object 118100
2:12:31.712010 INFO: lfq-object 117900
2:12:31.761198 INFO: lfq-object 117700
2:12:31.836944 INFO: lfq-object 118200
2:12:31.841775 INFO: lfq-object 118000
2:12:31.848946 INFO: lfq-object 118400
2:12:31.964778 INFO: lfq-object 118300
2:12:31.980271 INFO: lfq-object 118500
2:12:32.108505 INFO: lfq-object 118600
2:12:32.110704 INFO: lfq-object 118700
2:12:32.243318 INFO: lfq-object 118800
2:12:32.372689 INFO: lfq-object 118900
2:12:32.385311 INFO: lfq-object 119000
2:12:32.515211 INFO: lfq-object 119100
2:12:32.574811 INFO: lfq-object 119300
2:12:32.645655 INFO: lfq-object 119200
2:12:32.661021 INFO: lfq-object 119600
2:12:32.702316 INFO: lfq-object 119400
2:12:32.788467 INFO: lfq-object 119700
2:12:32.833947 INFO: lfq-object 119500
2:12:32.918951 INFO: lfq-object 119800
2:12:38.901788 INFO: lfq-object 119900
2:12:39.032308 INFO: lfq-object 120000
2:12:39.096429 INFO: lfq-object 120200
2:12:39.117838 INFO: lfq-object 120500
2:12:39.161611 INFO: lfq-object 120100
2:12:39.225997 INFO: lfq-object 120300
2:12:39.358598 INFO: lfq-object 120400
2:12:45.425015 INFO: Performing label free quantification on the pg level
2:12:45.425439 INFO: Filtering fragments by quality
2:12:45.872249 INFO: Performing label-free quantification with directlfq normalization
2:12:46.086920 INFO: 10118 lfq-groups total
2:13:17.400584 INFO: using 100 processes
2:13:17.436489 INFO: lfq-object 0
2:13:18.143593 INFO: lfq-object 1300
2:13:18.457248 INFO: lfq-object 100
2:13:18.481124 INFO: lfq-object 400
2:13:18.540453 INFO: lfq-object 200
2:13:18.686886 INFO: lfq-object 600
2:13:18.698103 INFO: lfq-object 1000
2:13:18.747417 INFO: lfq-object 300
2:13:18.775757 INFO: lfq-object 500
2:13:18.847016 INFO: lfq-object 1100
2:13:18.875290 INFO: lfq-object 2400
2:13:18.895167 INFO: lfq-object 700
2:13:18.916973 INFO: lfq-object 2600
2:13:19.129035 INFO: lfq-object 800
2:13:19.157706 INFO: lfq-object 1200
2:13:19.169687 INFO: lfq-object 900
2:13:19.171849 INFO: lfq-object 2700
2:13:19.219378 INFO: lfq-object 2900
2:13:19.366825 INFO: lfq-object 1400
2:13:19.385385 INFO: lfq-object 1900
2:13:19.386573 INFO: lfq-object 3100
2:13:19.409979 INFO: lfq-object 2800
2:13:19.426593 INFO: lfq-object 3000
2:13:19.439140 INFO: lfq-object 3200
2:13:19.522260 INFO: lfq-object 1600
2:13:19.537739 INFO: lfq-object 1800
2:13:19.541625 INFO: lfq-object 1700
2:13:19.554462 INFO: lfq-object 3300
2:13:19.561876 INFO: lfq-object 3400
2:13:19.573951 INFO: lfq-object 3500
2:13:19.636966 INFO: lfq-object 2000
2:13:19.683940 INFO: lfq-object 2200
2:13:19.694897 INFO: lfq-object 1500
2:13:19.768274 INFO: lfq-object 3700
2:13:19.771120 INFO: lfq-object 3600
2:13:19.793531 INFO: lfq-object 2100
2:13:19.863723 INFO: lfq-object 3800
2:13:19.895277 INFO: lfq-object 3900
2:13:19.968479 INFO: lfq-object 2300
2:13:20.006586 INFO: lfq-object 4000
2:13:20.046348 INFO: lfq-object 2500
2:13:20.051962 INFO: lfq-object 4100
2:13:20.169064 INFO: lfq-object 4300
2:13:20.171006 INFO: lfq-object 4200
2:13:20.236877 INFO: lfq-object 4500
2:13:20.281285 INFO: lfq-object 4400
2:13:20.383743 INFO: lfq-object 4600
2:13:20.460348 INFO: lfq-object 5000
2:13:20.496435 INFO: lfq-object 4900
2:13:20.498781 INFO: lfq-object 5100
2:13:20.500974 INFO: lfq-object 4700
2:13:20.509119 INFO: lfq-object 4800
2:13:20.568885 INFO: lfq-object 5200
2:13:20.747334 INFO: lfq-object 5500
2:13:20.840841 INFO: lfq-object 5400
2:13:20.841904 INFO: lfq-object 5300
2:13:20.932476 INFO: lfq-object 5600
2:13:20.959351 INFO: lfq-object 5700
2:13:21.019018 INFO: lfq-object 5800
2:13:21.150248 INFO: lfq-object 5900
2:13:21.151937 INFO: lfq-object 6000
2:13:21.212790 INFO: lfq-object 6200
2:13:21.248561 INFO: lfq-object 6300
2:13:21.280980 INFO: lfq-object 6400
2:13:21.282825 INFO: lfq-object 6100
2:13:21.361888 INFO: lfq-object 6500
2:13:21.630169 INFO: lfq-object 7000
2:13:21.634144 INFO: lfq-object 6700
2:13:21.635200 INFO: lfq-object 6800
2:13:21.650645 INFO: lfq-object 6900
2:13:21.656980 INFO: lfq-object 7100
2:13:21.721519 INFO: lfq-object 6600
2:13:21.749713 INFO: lfq-object 7200
2:13:21.797622 INFO: lfq-object 7300
2:13:21.845145 INFO: lfq-object 7400
2:13:21.978765 INFO: lfq-object 7500
2:13:22.000444 INFO: lfq-object 7600
2:13:22.025677 INFO: lfq-object 7700
2:13:22.057669 INFO: lfq-object 7800
2:13:22.132909 INFO: lfq-object 7900
2:13:22.205785 INFO: lfq-object 8000
2:13:22.251723 INFO: lfq-object 8200
2:13:22.303356 INFO: lfq-object 8100
2:13:22.312496 INFO: lfq-object 8300
2:13:22.321194 INFO: lfq-object 8400
2:13:22.427070 INFO: lfq-object 8500
2:13:22.585364 INFO: lfq-object 8600
2:13:22.599437 INFO: lfq-object 8800
2:13:22.606637 INFO: lfq-object 8700
2:13:22.613945 INFO: lfq-object 8900
2:13:22.667582 INFO: lfq-object 9000
2:13:22.678326 INFO: lfq-object 9100
2:13:22.755467 INFO: lfq-object 9200
2:13:22.818422 INFO: lfq-object 9300
2:13:22.841337 INFO: lfq-object 9400
2:13:22.859802 INFO: lfq-object 9500
2:13:22.911396 INFO: lfq-object 9700
2:13:22.956103 INFO: lfq-object 9600
2:13:23.048142 INFO: lfq-object 9900
2:13:23.145975 INFO: lfq-object 9800
2:13:23.187422 INFO: lfq-object 10100
2:13:23.218052 INFO: lfq-object 10000
2:13:26.782115 INFO: Writing psm output to disk
2:13:26.960592 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
2:13:28.076967 INFO: Writing precursor output to disk
2:13:28.083741 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
2:13:28.227861 INFO: Writing peptide output to disk
2:13:28.234181 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
2:13:28.354696 INFO: Writing pg output to disk
2:13:28.358347 INFO: Saving /home/robbe/PB_output/results/AstralAlphaDIA/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
2:13:28.468997 PROGRESS: Building MBR spectral library
2:13:28.469247 INFO: Running MbrLibraryBuilder
2:13:29.049128 INFO: MBR spectral library contains 131,525 precursors, 10,118 proteins
2:13:29.049288 INFO: Writing MBR spectral library to disk
2:13:29.980225 PROGRESS: =================== Search step 'mbr' finished ===================
2:13:30.084466 INFO: =================== Search Finished ===================
