0:00:00.000033 INFO: Moved old log file /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/log.txt to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/log.0.bkp.txt
0:00:00.000154 INFO: Output directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output/work/77/c4a4a755d2004d7a8cf9fd2ca55547.
0:00:00.000186 INFO: User provided config file: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.014233 PROGRESS:           _      _         ___ ___   _   
0:00:00.014294 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014320 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014341 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014366 PROGRESS:            |_|                           
0:00:00.014389 PROGRESS: 
0:00:00.014409 PROGRESS: version: 2.1.1
0:00:00.014427 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.014450 INFO: hostname: thestral
0:00:00.014478 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.014504 PROGRESS: python: 3.11.11 (CPython)
0:00:00.014553 INFO: date: 2026-07-09 09:51:52
0:00:00.014572 INFO: ================ AlphaX Environment ===============
0:00:00.014591 INFO: alphabase       : 1.8.1
0:00:00.014608 INFO: alpharaw        : 0.5.0
0:00:00.014625 INFO: alphatims       : 1.0.9
0:00:00.014642 INFO: alphapeptdeep   : 1.4.2
0:00:00.014658 INFO: directlfq       : 0.3.3
0:00:00.014674 INFO: ===================================================
0:00:00.014689 INFO: ================= Pip Environment =================
0:00:00.083950 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
0:00:00.084055 INFO: ===================================================
0:00:00.084083 INFO: =================== Running step 'library' ===================
0:00:00.084158 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
0:00:00.096333 INFO: loading additional config provided via CLI
0:00:00.096387 INFO: loading additional config provided via CLI parameters
0:00:00.096740 INFO: Updating config with 'user defined'
0:00:00.096812 INFO: Updating config with 'user defined (cli)'
0:00:00.096879 INFO: updating config with user defined values: [{'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta'], 'output_directory': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 24, 'mbr_step_enabled': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [380.0, 980.0], 'fragment_mz': [150.0, 2000.0]}, 'search': {'target_ms1_tolerance': 3, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': False}, 'search_initial': {'ms1_tolerance': 3, 'ms2_tolerance': 10}}, {'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'output_directory': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library'}]
0:00:00.097084 INFO: Updating config with 'user defined'
0:00:00.097129 INFO: Updating config with 'user defined (cli)'
0:00:00.097147 INFO: Updating config with 'multistep search'
0:00:00.097183 INFO: ├──version: None
0:00:00.097206 INFO: ├──workflow_name: None
0:00:00.097226 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library [multistep search, default: None][0m
0:00:00.097246 INFO: ├──library_path: None
0:00:00.097263 INFO: ├──raw_paths:
0:00:00.097282 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.097300 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.097317 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.097337 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.097360 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.097381 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.097399 INFO: ├──fasta_paths:
0:00:00.097417 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.097435 INFO: ├──quant_directory: None
0:00:00.097452 INFO: ├──general
0:00:00.097471 INFO: │   [32;20m├──thread_count: 24 [user defined, default: 10][0m
0:00:00.097489 INFO: │   ├──transfer_step_enabled: False
0:00:00.097507 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.097525 INFO: │   ├──reuse_calibration: False
0:00:00.097542 INFO: │   ├──reuse_quant: False
0:00:00.097559 INFO: │   ├──log_level: INFO
0:00:00.097577 INFO: │   ├──use_gpu: True
0:00:00.097596 INFO: │   ├──save_figures: True
0:00:00.097615 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.097633 INFO: │   ├──save_flat_library: False
0:00:00.097650 INFO: │   ├──input_library_type: base
0:00:00.097667 INFO: │   ├──save_mbr_library: True
0:00:00.097684 INFO: │   ├──random_state: None
0:00:00.097702 INFO: │   └──fail_fast: False
0:00:00.097720 INFO: ├──library_loading
0:00:00.097739 INFO: │   └──drop_decoys: False
0:00:00.097756 INFO: ├──library_prediction
0:00:00.097774 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.097791 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.097809 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.097826 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.097845 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.097863 INFO: │   ├──missed_cleavages: 1
0:00:00.097881 INFO: │   ├──precursor_len:
0:00:00.097899 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.097916 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.097933 INFO: │   ├──precursor_charge:
0:00:00.097950 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.097966 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.097982 INFO: │   ├──precursor_mz:
0:00:00.098000 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
0:00:00.098017 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
0:00:00.098033 INFO: │   ├──fragment_mz:
0:00:00.098050 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
0:00:00.098066 INFO: │   │   - 2000.0
0:00:00.098084 INFO: │   ├──nce: 25.0
0:00:00.098100 INFO: │   ├──fragment_types:
0:00:00.098117 INFO: │   │   - b
0:00:00.098134 INFO: │   │   - y
0:00:00.098151 INFO: │   ├──max_fragment_charge: 2
0:00:00.098168 INFO: │   ├──instrument: Lumos
0:00:00.098185 INFO: │   ├──peptdeep_model_path: None
0:00:00.098203 INFO: │   ├──peptdeep_model_type: generic
0:00:00.098220 INFO: │   ├──predict_charge: False
0:00:00.098238 INFO: │   └──min_charge_probability: 0.1
0:00:00.098254 INFO: ├──custom_modifications:
0:00:00.098271 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.098288 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098306 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.098323 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098340 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.098356 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098373 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.098390 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.098411 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.098427 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.098447 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.098464 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.098481 INFO: │   ├──name: Label:13C(12)@K
0:00:00.098498 INFO: │   └──composition: C(12)
0:00:00.098515 INFO: ├──search
0:00:00.098532 INFO: │   ├──extraction_backend: rust
0:00:00.098549 INFO: │   [32;20m├──target_ms1_tolerance: 3 [user defined, default: 5][0m
0:00:00.098566 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.098583 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.098600 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.098618 INFO: │   ├──quant_window: 3
0:00:00.098635 INFO: │   ├──target_num_candidates: 3
0:00:00.098651 INFO: │   ├──channel_filter: 
0:00:00.098668 INFO: │   ├──compete_for_fragments: True
0:00:00.098685 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.098702 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.098719 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.098736 INFO: │   ├──optimized_peak_group_score: False
0:00:00.098753 INFO: │   ├──exclude_shared_ions: True
0:00:00.098770 INFO: │   ├──quant_all: True
0:00:00.098788 INFO: │   └──experimental_xic: True
0:00:00.098806 INFO: ├──calibration
0:00:00.098824 INFO: │   ├──batch_size: 1000
0:00:00.098842 INFO: │   ├──optimization_lock_target: 1000
0:00:00.098859 INFO: │   ├──max_steps: 20
0:00:00.098877 INFO: │   ├──min_steps: 5
0:00:00.098895 INFO: │   ├──max_skips: 1
0:00:00.098912 INFO: │   ├──max_fragments: 5000
0:00:00.098930 INFO: │   └──min_correlation: 0.7
0:00:00.098947 INFO: ├──search_initial
0:00:00.098965 INFO: │   ├──num_candidates: 1
0:00:00.099003 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
0:00:00.099020 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
0:00:00.099038 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.099057 INFO: │   └──rt_tolerance: 0.5
0:00:00.099074 INFO: ├──library_multiplexing
0:00:00.099092 INFO: │   ├──enabled: False
0:00:00.099110 INFO: │   ├──input_channel: 0
0:00:00.099127 INFO: │   └──multiplex_mapping:
0:00:00.099143 INFO: ├──multiplexing
0:00:00.099160 INFO: │   ├──enabled: False
0:00:00.099177 INFO: │   ├──target_channels: 4,8
0:00:00.099194 INFO: │   ├──decoy_channel: 12
0:00:00.099211 INFO: │   ├──reference_channel: 0
0:00:00.099228 INFO: │   └──competitive_scoring: True
0:00:00.099244 INFO: ├──fdr
0:00:00.099262 INFO: │   ├──fdr: 0.01
0:00:00.099278 INFO: │   ├──group_level: proteins
0:00:00.099295 INFO: │   ├──inference_strategy: heuristic
0:00:00.099314 INFO: │   ├──competitive_scoring: True
0:00:00.099331 INFO: │   ├──keep_decoys: False
0:00:00.099349 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.099366 INFO: │   ├──channel_wise_fdr: False
0:00:00.099383 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.099399 INFO: ├──search_output
0:00:00.099416 INFO: │   ├──file_format: parquet
0:00:00.099433 INFO: │   ├──precursor_level_lfq: True
0:00:00.099450 INFO: │   ├──peptide_level_lfq: True
0:00:00.099466 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.099483 INFO: │   ├──min_k_fragments: 12
0:00:00.099500 INFO: │   ├──min_correlation: 0.9
0:00:00.099518 INFO: │   ├──num_samples_quadratic: 50
0:00:00.099535 INFO: │   ├──min_nonnan: 3
0:00:00.099552 INFO: │   ├──normalization_method: directlfq
0:00:00.099569 INFO: │   [32;20m└──normalize_directlfq: False [user defined, default: True][0m
0:00:00.099586 INFO: ├──optimization
0:00:00.099608 INFO: │   ├──order_of_optimization: None
0:00:00.099625 INFO: │   ├──ms2_error
0:00:00.099645 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.099664 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.099682 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.099699 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.099717 INFO: │   │   ├──try_narrower_values: True
0:00:00.099734 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.099751 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.099768 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.099785 INFO: │   ├──ms1_error
0:00:00.099802 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.099821 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.099838 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.099855 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.099872 INFO: │   │   ├──try_narrower_values: False
0:00:00.099889 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.099905 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.099923 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.099939 INFO: │   ├──mobility_error
0:00:00.099956 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.099973 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.099992 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.100009 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.100026 INFO: │   │   ├──try_narrower_values: False
0:00:00.100044 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.100061 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.100079 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.100096 INFO: │   └──rt_error
0:00:00.100113 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.100130 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.100148 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.100165 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.100182 INFO: │       ├──try_narrower_values: True
0:00:00.100199 INFO: │       ├──maximal_decrease: 0.1
0:00:00.100216 INFO: │       ├──favour_narrower_optimum: False
0:00:00.100234 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.100251 INFO: ├──optimization_manager
0:00:00.100270 INFO: │   ├──fwhm_rt: 5
0:00:00.100287 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.100305 INFO: │   └──score_cutoff: 0
0:00:00.100321 INFO: ├──transfer_library
0:00:00.100338 INFO: │   ├──enabled: False
0:00:00.100355 INFO: │   ├──fragment_types:
0:00:00.100371 INFO: │   │   - b
0:00:00.100388 INFO: │   │   - y
0:00:00.100405 INFO: │   ├──max_charge: 2
0:00:00.100421 INFO: │   ├──top_k_samples: 3
0:00:00.100438 INFO: │   ├──norm_delta_max: True
0:00:00.100455 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.100472 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.100488 INFO: └──transfer_learning
0:00:00.100505 INFO:     ├──enabled: False
0:00:00.100522 INFO:     ├──batch_size: 2000
0:00:00.100539 INFO:     ├──max_lr: 0.0001
0:00:00.100556 INFO:     ├──train_fraction: 0.7
0:00:00.100573 INFO:     ├──validation_fraction: 0.2
0:00:00.100590 INFO:     ├──test_fraction: 0.1
0:00:00.100607 INFO:     ├──test_interval: 1
0:00:00.100623 INFO:     ├──lr_patience: 3
0:00:00.100640 INFO:     ├──epochs: 51
0:00:00.100656 INFO:     ├──warmup_epochs: 5
0:00:00.100674 INFO:     ├──nce: 25
0:00:00.100691 INFO:     └──instrument: Lumos
0:00:00.105784 INFO: Moved existing config file /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/frozen_config.yaml to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/frozen_config.0.bkp.yaml
0:00:00.105994 INFO: Registering 7 custom modifications
0:00:00.147165 INFO: Searching 6 files:
0:00:00.147315 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.147340 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.147359 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.147376 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.147393 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.147409 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.147425 INFO: Using 1 fasta files:
0:00:00.147441 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.147460 INFO: Using library: None
0:00:00.147476 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library
0:00:00.147514 PROGRESS: Loading spectral library
0:00:00.147542 PROGRESS: No library provided. Building library from fasta files.
0:00:00.147589 INFO: Running FastaDigest
0:00:00.149992 INFO: Digesting fasta file
0:00:07.032130 INFO: Adding modifications
0:01:55.475571 INFO: Removing non-canonical amino acids
0:02:02.021161 INFO: Fasta library contains 6,091,314 precursors
0:02:02.021375 PROGRESS: Predicting library properties.
0:02:02.021457 INFO: Running PeptDeepPrediction
0:02:02.022884 INFO: Device set to cpu
0:02:03.184127 INFO: Loading PeptDeep models of type generic
0:02:04.161230 INFO: Predicting RT, MS2 and mobility
0:02:04.161388 INFO: Using multiprocessing with 24 processes ...
0:02:04.540751 INFO: Predicting rt,ms2,mobility ...
0:10:00.168855 INFO: Adding fragment mz information
0:10:00.474561 INFO: Adding fragment intensity information
0:10:00.779882 INFO: Adding precursor information
0:10:01.234855 INFO: Running PrecursorInitializer
0:10:01.259476 INFO: Running AnnotateFasta
0:10:28.363999 INFO: Running IsotopeGenerator
0:10:28.365098 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:14:54.820245 INFO: Running RTNormalization
0:14:54.820618 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:14:54.820735 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.hdf
0:15:29.549440 INFO: Running DecoyGenerator
0:17:23.182171 INFO: Running FlattenLibrary
0:17:55.649278 INFO: Running InitFlatColumns
0:17:55.889170 INFO: Running LogFlatLibraryStats
0:17:55.889313 INFO: ============ Library Stats ============
0:17:55.889351 INFO: Number of precursors: 12,150,378
0:17:57.490044 INFO: 	thereof targets:6,091,314
0:17:57.490189 INFO: 	thereof decoys: 6,059,064
0:17:57.569800 INFO: Number of elution groups: 6,091,314
0:17:57.569931 INFO: 	average size: 1.99
0:17:57.848095 INFO: Number of proteins: 117,993
0:17:57.880637 INFO: Number of channels: 1 ([0])
0:17:57.880794 INFO: Isotopes Distribution for 4 isotopes
0:17:57.880823 INFO: =======================================
0:17:57.899686 PROGRESS: =================== Starting Search Workflows for step library ===================
0:17:57.899938 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:17:57.900004 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
0:17:57.900120 INFO: Initializing TimingManager
0:17:57.900764 INFO: Initializing RawFileManager
0:18:10.885933 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.
0:18:10.894497 INFO: Determining DIA cycle
0:18:11.211569 INFO: Found cycle with start 0.00 min and length 300.
0:18:11.372459 INFO: RT (min)            : 0.0 - 26.9
0:18:11.372542 INFO: RT duration (sec)   : 1611.2
0:18:11.372570 INFO: RT duration (min)   : 26.9
0:18:11.372593 INFO: Cycle len (scans)   : 300
0:18:11.372614 INFO: Cycle len (sec)     : 1.65
0:18:11.372633 INFO: Number of cycles    : 977
0:18:11.372664 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:18:11.372690 INFO: Creating DIA data object took: 13.471831560134888
0:18:13.185141 INFO: Creating DIA data NG object took: 1.8123254776000977
0:18:14.468292 INFO: Initializing CalibrationManager
0:18:14.468600 INFO: Setting up calibration estimators ..
0:18:14.468670 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:18:14.468754 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'}' ..
0:18:14.468840 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:18:14.468899 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:18:14.468960 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}}' ..
0:18:14.469012 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:18:14.469058 INFO: Done setting up calibration estimators.
0:18:14.469292 INFO: Initializing OptimizationManager
0:18:14.469459 INFO: initial parameter: ms1_error = 3
0:18:14.469513 INFO: initial parameter: ms2_error = 10
0:18:14.469561 INFO: initial parameter: rt_error = 805.5992431640625
0:18:14.469607 INFO: initial parameter: mobility_error = 0.1
0:18:14.469650 INFO: initial parameter: num_candidates = 1
0:18:14.469690 INFO: initial parameter: fwhm_rt = 5
0:18:14.469731 INFO: initial parameter: fwhm_mobility = 0.01
0:18:14.469772 INFO: initial parameter: score_cutoff = 0
0:18:14.469812 INFO: initial parameter: classifier_version = -1
0:18:14.469882 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:18:14.470154 INFO: FDRManager: loading saved state not requested, will be initialized.
0:18:14.470189 INFO: Initializing FDRManager
0:18:14.470227 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:18:15.924161 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:18:17.474370 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:18:17.474849 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:18:17.474989 PROGRESS: Starting initial search for precursors.
0:18:17.475091 INFO: Starting optimization step 0.
0:18:17.475161 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:18:17.475228 INFO: Using rust extraction backend
0:18:17.475306 PROGRESS: Extracting batch of 1976 precursors
0:18:17.480341 INFO: === Search parameters used ===
0:18:17.480445 INFO: rt_error       : 805.5992431640625
0:18:17.480501 INFO: mobility_error : 0.1
0:18:17.480549 INFO: num_candidates : 1
0:18:17.480592 INFO: ms1_error      : 3
0:18:17.480647 INFO: ms2_error      : 10
0:18:17.480690 INFO: fwhm_rt        : 5
0:18:17.480735 INFO: quant_window   : 3
0:18:17.480778 INFO: ==============================================
0:18:17.509121 INFO: performing precursor FDR with 40 features
0:18:17.509186 INFO: Decoy channel: -1
0:18:17.509210 INFO: competitive: True
0:18:17.510468 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:17.512555 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
0:18:17.513376 INFO: Using random state 651412 for train-test-split
0:18:17.671134 INFO: Test AUC: 0.482
0:18:17.671214 INFO: Train AUC: 0.611
0:18:17.671242 INFO: AUC difference: 21.21%
0:18:17.671264 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:17.960900 INFO: Resetting torch num_threads to 24
0:18:17.962435 PROGRESS: === Extracted 1975 precursors and 10952 fragments ===
0:18:17.962801 INFO: === FDR correction performed with classifier version -1 ===
0:18:17.963302 PROGRESS: ============================= Precursor FDR =============================
0:18:17.963399 PROGRESS: Total precursors accumulated: 9
0:18:17.963459 PROGRESS: Target precursors: 9 (100.00%)
0:18:17.963508 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:17.963552 PROGRESS: 
0:18:17.963594 PROGRESS: Precursor Summary:
0:18:17.964677 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
0:18:17.964760 PROGRESS: 
0:18:17.964813 PROGRESS: Protein Summary:
0:18:17.965961 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
0:18:17.966046 PROGRESS: =========================================================================
0:18:17.966234 INFO: Target number of precursors not reached yet.
0:18:18.052658 INFO: Starting optimization step 1.
0:18:18.052894 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:18:18.052978 INFO: Using rust extraction backend
0:18:18.053041 PROGRESS: Extracting batch of 3939 precursors
0:18:18.061481 INFO: === Search parameters used ===
0:18:18.061641 INFO: rt_error       : 805.5992431640625
0:18:18.061695 INFO: mobility_error : 0.1
0:18:18.061739 INFO: num_candidates : 1
0:18:18.061781 INFO: ms1_error      : 3
0:18:18.061821 INFO: ms2_error      : 10
0:18:18.061860 INFO: fwhm_rt        : 5
0:18:18.061899 INFO: quant_window   : 3
0:18:18.061939 INFO: ==============================================
0:18:18.106924 INFO: performing precursor FDR with 40 features
0:18:18.107005 INFO: Decoy channel: -1
0:18:18.107030 INFO: competitive: True
0:18:18.111155 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:18.113511 INFO: Estimating optimal hyperparameters - samples: 4,725, batch_size: 128, learning_rate: 1.77e-04
0:18:18.113589 INFO: Using random state 169314 for train-test-split
0:18:18.569697 INFO: Test AUC: 0.528
0:18:18.569792 INFO: Train AUC: 0.607
0:18:18.569819 INFO: AUC difference: 13.00%
0:18:18.569840 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:18.809732 INFO: Resetting torch num_threads to 24
0:18:18.812531 PROGRESS: === Extracted 5907 precursors and 33225 fragments ===
0:18:18.812903 INFO: === FDR correction performed with classifier version -1 ===
0:18:18.813378 PROGRESS: ============================= Precursor FDR =============================
0:18:18.813458 PROGRESS: Total precursors accumulated: 6
0:18:18.813514 PROGRESS: Target precursors: 6 (100.00%)
0:18:18.813569 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:18.813614 PROGRESS: 
0:18:18.813659 PROGRESS: Precursor Summary:
0:18:18.814698 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
0:18:18.814783 PROGRESS: 
0:18:18.814837 PROGRESS: Protein Summary:
0:18:18.815995 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
0:18:18.816082 PROGRESS: =========================================================================
0:18:18.816310 INFO: Target number of precursors not reached yet.
0:18:18.910334 INFO: Starting optimization step 2.
0:18:18.910579 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:18:18.910659 INFO: Using rust extraction backend
0:18:18.910722 PROGRESS: Extracting batch of 7882 precursors
0:18:18.925673 INFO: === Search parameters used ===
0:18:18.925807 INFO: rt_error       : 805.5992431640625
0:18:18.925858 INFO: mobility_error : 0.1
0:18:18.925904 INFO: num_candidates : 1
0:18:18.925947 INFO: ms1_error      : 3
0:18:18.925990 INFO: ms2_error      : 10
0:18:18.926031 INFO: fwhm_rt        : 5
0:18:18.926070 INFO: quant_window   : 3
0:18:18.926109 INFO: ==============================================
0:18:19.027328 INFO: performing precursor FDR with 40 features
0:18:19.027428 INFO: Decoy channel: -1
0:18:19.027451 INFO: competitive: True
0:18:19.033463 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:19.037120 INFO: Estimating optimal hyperparameters - samples: 11,014, batch_size: 128, learning_rate: 1.77e-04
0:18:19.037225 INFO: Using random state 493865 for train-test-split
0:18:20.149758 INFO: Test AUC: 0.553
0:18:20.149861 INFO: Train AUC: 0.598
0:18:20.149889 INFO: AUC difference: 7.59%
0:18:20.149911 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:20.392839 INFO: Resetting torch num_threads to 24
0:18:20.396676 PROGRESS: === Extracted 13768 precursors and 77700 fragments ===
0:18:20.397077 INFO: === FDR correction performed with classifier version -1 ===
0:18:20.397584 PROGRESS: ============================= Precursor FDR =============================
0:18:20.397666 PROGRESS: Total precursors accumulated: 59
0:18:20.397723 PROGRESS: Target precursors: 59 (100.00%)
0:18:20.397772 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:20.397816 PROGRESS: 
0:18:20.397858 PROGRESS: Precursor Summary:
0:18:20.398918 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
0:18:20.399026 PROGRESS: 
0:18:20.399085 PROGRESS: Protein Summary:
0:18:20.400275 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
0:18:20.400357 PROGRESS: =========================================================================
0:18:20.400651 INFO: Target number of precursors not reached yet.
0:18:20.506511 INFO: Starting optimization step 3.
0:18:20.506750 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:18:20.506829 INFO: Using rust extraction backend
0:18:20.506890 PROGRESS: Extracting batch of 15793 precursors
0:18:20.534776 INFO: === Search parameters used ===
0:18:20.534952 INFO: rt_error       : 805.5992431640625
0:18:20.535015 INFO: mobility_error : 0.1
0:18:20.535061 INFO: num_candidates : 1
0:18:20.535102 INFO: ms1_error      : 3
0:18:20.535142 INFO: ms2_error      : 10
0:18:20.535187 INFO: fwhm_rt        : 5
0:18:20.535230 INFO: quant_window   : 3
0:18:20.535270 INFO: ==============================================
0:18:20.693046 INFO: performing precursor FDR with 40 features
0:18:20.693160 INFO: Decoy channel: -1
0:18:20.693184 INFO: competitive: True
0:18:20.704001 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:20.710364 INFO: Estimating optimal hyperparameters - samples: 23,616, batch_size: 128, learning_rate: 1.77e-04
0:18:20.710531 INFO: Using random state 14211 for train-test-split
0:18:23.152527 INFO: Test AUC: 0.588
0:18:23.152649 INFO: Train AUC: 0.610
0:18:23.152679 INFO: AUC difference: 3.59%
0:18:23.410787 INFO: Resetting torch num_threads to 24
0:18:23.416740 PROGRESS: === Extracted 29520 precursors and 166319 fragments ===
0:18:23.417180 INFO: === FDR correction performed with classifier version -1 ===
0:18:23.417663 PROGRESS: ============================= Precursor FDR =============================
0:18:23.417750 PROGRESS: Total precursors accumulated: 118
0:18:23.417810 PROGRESS: Target precursors: 117 (99.15%)
0:18:23.417863 PROGRESS: Decoy precursors: 1 (0.85%)
0:18:23.417913 PROGRESS: 
0:18:23.417960 PROGRESS: Precursor Summary:
0:18:23.418913 PROGRESS: Channel   0:	 0.050 FDR:   117; 0.010 FDR:   117; 0.001 FDR:   109
0:18:23.419018 PROGRESS: 
0:18:23.419077 PROGRESS: Protein Summary:
0:18:23.420161 PROGRESS: Channel   0:	 0.050 FDR:   115; 0.010 FDR:   115; 0.001 FDR:   107
0:18:23.420247 PROGRESS: =========================================================================
0:18:23.420675 INFO: Target number of precursors not reached yet.
0:18:23.549916 INFO: Starting optimization step 4.
0:18:23.550178 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:18:23.550264 INFO: Using rust extraction backend
0:18:23.550332 PROGRESS: Extracting batch of 31556 precursors
0:18:23.604753 INFO: === Search parameters used ===
0:18:23.604977 INFO: rt_error       : 805.5992431640625
0:18:23.605031 INFO: mobility_error : 0.1
0:18:23.605078 INFO: num_candidates : 1
0:18:23.605122 INFO: ms1_error      : 3
0:18:23.605165 INFO: ms2_error      : 10
0:18:23.605209 INFO: fwhm_rt        : 5
0:18:23.605251 INFO: quant_window   : 3
0:18:23.605292 INFO: ==============================================
0:18:23.860051 INFO: performing precursor FDR with 40 features
0:18:23.860161 INFO: Decoy channel: -1
0:18:23.860187 INFO: competitive: True
0:18:23.901533 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:23.933504 INFO: Estimating optimal hyperparameters - samples: 48,796, batch_size: 199, learning_rate: 2.20e-04
0:18:23.933720 INFO: Using random state 868779 for train-test-split
0:18:27.717416 INFO: Test AUC: 0.581
0:18:27.717536 INFO: Train AUC: 0.616
0:18:27.717566 INFO: AUC difference: 5.69%
0:18:27.717591 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:28.323885 INFO: Resetting torch num_threads to 24
0:18:28.338227 PROGRESS: === Extracted 60995 precursors and 343343 fragments ===
0:18:28.338711 INFO: === FDR correction performed with classifier version -1 ===
0:18:28.339274 PROGRESS: ============================= Precursor FDR =============================
0:18:28.339365 PROGRESS: Total precursors accumulated: 266
0:18:28.339426 PROGRESS: Target precursors: 264 (99.25%)
0:18:28.339480 PROGRESS: Decoy precursors: 2 (0.75%)
0:18:28.339528 PROGRESS: 
0:18:28.339574 PROGRESS: Precursor Summary:
0:18:28.340585 PROGRESS: Channel   0:	 0.050 FDR:   264; 0.010 FDR:   264; 0.001 FDR:   232
0:18:28.340671 PROGRESS: 
0:18:28.340727 PROGRESS: Protein Summary:
0:18:28.341892 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   225
0:18:28.341985 PROGRESS: =========================================================================
0:18:28.342732 INFO: Target number of precursors not reached yet.
0:18:28.512913 INFO: Starting optimization step 5.
0:18:28.513166 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:18:28.513247 INFO: Using rust extraction backend
0:18:28.513311 PROGRESS: Extracting batch of 63064 precursors
0:18:28.623503 INFO: === Search parameters used ===
0:18:28.623751 INFO: rt_error       : 805.5992431640625
0:18:28.623804 INFO: mobility_error : 0.1
0:18:28.623852 INFO: num_candidates : 1
0:18:28.623896 INFO: ms1_error      : 3
0:18:28.623939 INFO: ms2_error      : 10
0:18:28.623981 INFO: fwhm_rt        : 5
0:18:28.624023 INFO: quant_window   : 3
0:18:28.624063 INFO: ==============================================
0:18:29.152363 INFO: performing precursor FDR with 40 features
0:18:29.152474 INFO: Decoy channel: -1
0:18:29.152500 INFO: competitive: True
0:18:29.258846 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:29.334282 INFO: Estimating optimal hyperparameters - samples: 99,139, batch_size: 406, learning_rate: 3.15e-04
0:18:29.334605 INFO: Using random state 51597 for train-test-split
0:18:33.959493 INFO: Test AUC: 0.587
0:18:33.959616 INFO: Train AUC: 0.612
0:18:33.959646 INFO: AUC difference: 3.99%
0:18:34.241460 INFO: Resetting torch num_threads to 24
0:18:34.261633 PROGRESS: === Extracted 123924 precursors and 696527 fragments ===
0:18:34.262239 INFO: === FDR correction performed with classifier version -1 ===
0:18:34.262844 PROGRESS: ============================= Precursor FDR =============================
0:18:34.262933 PROGRESS: Total precursors accumulated: 585
0:18:34.263011 PROGRESS: Target precursors: 580 (99.15%)
0:18:34.263068 PROGRESS: Decoy precursors: 5 (0.85%)
0:18:34.263133 PROGRESS: 
0:18:34.263185 PROGRESS: Precursor Summary:
0:18:34.264284 PROGRESS: Channel   0:	 0.050 FDR:   580; 0.010 FDR:   580; 0.001 FDR:   302
0:18:34.264369 PROGRESS: 
0:18:34.264425 PROGRESS: Protein Summary:
0:18:34.265733 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   542; 0.001 FDR:   284
0:18:34.265818 PROGRESS: =========================================================================
0:18:34.267667 INFO: Target number of precursors not reached yet.
0:18:34.520794 INFO: Starting optimization step 6.
0:18:34.521053 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:18:34.521151 INFO: Using rust extraction backend
0:18:34.521219 PROGRESS: Extracting batch of 126165 precursors
0:18:34.738736 INFO: === Search parameters used ===
0:18:34.738984 INFO: rt_error       : 805.5992431640625
0:18:34.739041 INFO: mobility_error : 0.1
0:18:34.739088 INFO: num_candidates : 1
0:18:34.739132 INFO: ms1_error      : 3
0:18:34.739174 INFO: ms2_error      : 10
0:18:34.739217 INFO: fwhm_rt        : 5
0:18:34.739259 INFO: quant_window   : 3
0:18:34.739299 INFO: ==============================================
0:18:35.712802 INFO: performing precursor FDR with 40 features
0:18:35.712919 INFO: Decoy channel: -1
0:18:35.712942 INFO: competitive: True
0:18:35.910088 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:36.084965 INFO: Estimating optimal hyperparameters - samples: 199,825, batch_size: 818, learning_rate: 4.47e-04
0:18:36.085335 INFO: Using random state 637268 for train-test-split
0:18:42.865821 INFO: Test AUC: 0.594
0:18:42.865952 INFO: Train AUC: 0.611
0:18:42.865983 INFO: AUC difference: 2.72%
0:18:43.187081 INFO: Resetting torch num_threads to 24
0:18:43.237453 PROGRESS: === Extracted 249782 precursors and 1403599 fragments ===
0:18:43.238091 INFO: === FDR correction performed with classifier version -1 ===
0:18:43.238860 PROGRESS: ============================= Precursor FDR =============================
0:18:43.238948 PROGRESS: Total precursors accumulated: 1,226
0:18:43.239026 PROGRESS: Target precursors: 1,214 (99.02%)
0:18:43.239080 PROGRESS: Decoy precursors: 12 (0.98%)
0:18:43.239128 PROGRESS: 
0:18:43.239173 PROGRESS: Precursor Summary:
0:18:43.240441 PROGRESS: Channel   0:	 0.050 FDR: 1,214; 0.010 FDR: 1,214; 0.001 FDR:   831
0:18:43.240528 PROGRESS: 
0:18:43.240582 PROGRESS: Protein Summary:
0:18:43.242183 PROGRESS: Channel   0:	 0.050 FDR: 1,046; 0.010 FDR: 1,046; 0.001 FDR:   732
0:18:43.242272 PROGRESS: =========================================================================
0:18:43.245799 INFO: Target number of precursors reached.
0:18:43.410655 INFO: fragments_df: keeping 5000 of 1403599 [sum(precursor_idx_mask)=12932 sum(mass_error_mask)=1403599 stop_rank=5000
0:18:43.809835 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:44.030135 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:44.742483 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:18:44.742929 INFO: Using score_cutoff 13.245122861766815 (fac=0.99, q=1)
0:18:44.743308 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:18:44.743396 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:18:44.743451 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.245122861766815
0:18:44.743520 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:44.895792 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:45.247322 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:18:45.247613 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:18:45.247728 INFO: Starting optimization step 7.
0:18:45.247813 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:45.247905 INFO: Using rust extraction backend
0:18:45.247991 PROGRESS: Extracting batch of 250375 precursors
0:18:45.679124 INFO: === Search parameters used ===
0:18:45.679386 INFO: rt_error       : 805.5992431640625
0:18:45.679441 INFO: mobility_error : 0.1
0:18:45.679487 INFO: num_candidates : 3
0:18:45.679530 INFO: ms1_error      : 3
0:18:45.679571 INFO: ms2_error      : 10
0:18:45.679613 INFO: fwhm_rt        : 3.0
0:18:45.679653 INFO: quant_window   : 3
0:18:45.679693 INFO: ==============================================
0:18:50.163108 INFO: performing precursor FDR with 40 features
0:18:50.163232 INFO: Decoy channel: -1
0:18:50.163259 INFO: competitive: True
0:18:50.818521 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:51.800159 INFO: Estimating optimal hyperparameters - samples: 599,443, batch_size: 2,455, learning_rate: 7.74e-04
0:18:51.801157 INFO: Using random state 750192 for train-test-split
0:19:06.325543 INFO: Test AUC: 0.597
0:19:06.325695 INFO: Train AUC: 0.606
0:19:06.325727 INFO: AUC difference: 1.53%
0:19:06.807237 INFO: Resetting torch num_threads to 24
0:19:06.837520 PROGRESS: === Extracted 749304 precursors and 4034775 fragments ===
0:19:06.838016 INFO: === FDR correction performed with classifier version 6 ===
0:19:06.838717 PROGRESS: ============================= Precursor FDR =============================
0:19:06.838826 PROGRESS: Total precursors accumulated: 1,369
0:19:06.838885 PROGRESS: Target precursors: 1,356 (99.05%)
0:19:06.838936 PROGRESS: Decoy precursors: 13 (0.95%)
0:19:06.838994 PROGRESS: 
0:19:06.839042 PROGRESS: Precursor Summary:
0:19:06.840359 PROGRESS: Channel   0:	 0.050 FDR: 1,356; 0.010 FDR: 1,356; 0.001 FDR:   653
0:19:06.840446 PROGRESS: 
0:19:06.840501 PROGRESS: Protein Summary:
0:19:06.842151 PROGRESS: Channel   0:	 0.050 FDR: 1,156; 0.010 FDR: 1,156; 0.001 FDR:   583
0:19:06.842239 PROGRESS: =========================================================================
0:19:06.856519 INFO: Target number of precursors reached.
0:19:07.300983 INFO: fragments_df: keeping 5000 of 4034775 [sum(precursor_idx_mask)=32915 sum(mass_error_mask)=4034775 stop_rank=5000
0:19:07.813818 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:08.040823 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:08.752891 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:08.753333 INFO: Using score_cutoff 12.880254655838012 (fac=0.99, q=1)
0:19:08.753651 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:08.753741 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:08.753795 INFO: Updating optimization_manager: score_cutoff        : 13.245122861766815 -> 12.880254655838012
0:19:08.753852 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:08.906416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:09.258318 INFO: === checking if optimization conditions were reached ===
0:19:09.260941 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:19:09.261108 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:19:09.261190 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:19:09.261264 INFO: ==============================================
0:19:09.261347 INFO: Starting optimization step 8.
0:19:09.261418 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:09.261497 INFO: Using rust extraction backend
0:19:09.261573 PROGRESS: Extracting batch of 250375 precursors
0:19:09.690934 INFO: === Search parameters used ===
0:19:09.691198 INFO: rt_error       : 805.5992431640625
0:19:09.691270 INFO: mobility_error : 0.1
0:19:09.691321 INFO: num_candidates : 3
0:19:09.691367 INFO: ms1_error      : 3
0:19:09.691411 INFO: ms2_error      : 10.0
0:19:09.691453 INFO: fwhm_rt        : 3.0
0:19:09.691497 INFO: quant_window   : 3
0:19:09.691540 INFO: ==============================================
0:19:13.789398 INFO: performing precursor FDR with 40 features
0:19:13.789521 INFO: Decoy channel: -1
0:19:13.789549 INFO: competitive: True
0:19:14.344564 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:15.343346 INFO: Estimating optimal hyperparameters - samples: 599,440, batch_size: 2,455, learning_rate: 7.74e-04
0:19:15.344457 INFO: Using random state 503742 for train-test-split
0:19:31.767865 INFO: Test AUC: 0.602
0:19:31.768023 INFO: Train AUC: 0.614
0:19:31.768055 INFO: AUC difference: 2.09%
0:19:32.243776 INFO: Resetting torch num_threads to 24
0:19:32.275888 PROGRESS: === Extracted 749301 precursors and 4034593 fragments ===
0:19:32.276359 INFO: === FDR correction performed with classifier version 7 ===
0:19:32.277066 PROGRESS: ============================= Precursor FDR =============================
0:19:32.277157 PROGRESS: Total precursors accumulated: 1,460
0:19:32.277217 PROGRESS: Target precursors: 1,446 (99.04%)
0:19:32.277268 PROGRESS: Decoy precursors: 14 (0.96%)
0:19:32.277314 PROGRESS: 
0:19:32.277358 PROGRESS: Precursor Summary:
0:19:32.278656 PROGRESS: Channel   0:	 0.050 FDR: 1,446; 0.010 FDR: 1,446; 0.001 FDR:   731
0:19:32.278744 PROGRESS: 
0:19:32.278800 PROGRESS: Protein Summary:
0:19:32.280495 PROGRESS: Channel   0:	 0.050 FDR: 1,231; 0.010 FDR: 1,231; 0.001 FDR:   650
0:19:32.280588 PROGRESS: =========================================================================
0:19:32.297434 INFO: Target number of precursors reached.
0:19:32.747131 INFO: fragments_df: keeping 5000 of 4034593 [sum(precursor_idx_mask)=34662 sum(mass_error_mask)=4034593 stop_rank=5000
0:19:33.169930 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:33.411768 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:34.124159 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:34.124597 INFO: Using score_cutoff 11.664852478981016 (fac=0.99, q=1)
0:19:34.124911 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:34.124985 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:34.125038 INFO: Updating optimization_manager: score_cutoff        : 12.880254655838012 -> 11.664852478981016
0:19:34.125100 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:34.275986 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:34.620617 INFO: === checking if optimization conditions were reached ===
0:19:34.623510 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:19:34.623676 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:19:34.623758 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:19:34.623827 INFO: ==============================================
0:19:34.623906 INFO: Starting optimization step 9.
0:19:34.623976 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:34.624056 INFO: Using rust extraction backend
0:19:34.624137 PROGRESS: Extracting batch of 250375 precursors
0:19:35.053558 INFO: === Search parameters used ===
0:19:35.053816 INFO: rt_error       : 805.5992431640625
0:19:35.053873 INFO: mobility_error : 0.1
0:19:35.053922 INFO: num_candidates : 3
0:19:35.053968 INFO: ms1_error      : 3
0:19:35.054012 INFO: ms2_error      : 10.0
0:19:35.054053 INFO: fwhm_rt        : 3.0
0:19:35.054094 INFO: quant_window   : 3
0:19:35.054132 INFO: ==============================================
0:19:38.910834 INFO: performing precursor FDR with 40 features
0:19:38.910965 INFO: Decoy channel: -1
0:19:38.911020 INFO: competitive: True
0:19:39.367186 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:40.111267 INFO: Estimating optimal hyperparameters - samples: 599,453, batch_size: 2,455, learning_rate: 7.74e-04
0:19:40.112282 INFO: Using random state 819782 for train-test-split
0:19:53.086634 INFO: Test AUC: 0.607
0:19:53.086816 INFO: Train AUC: 0.618
0:19:53.086849 INFO: AUC difference: 1.76%
0:19:53.570201 INFO: Resetting torch num_threads to 24
0:19:53.600172 PROGRESS: === Extracted 749317 precursors and 4035277 fragments ===
0:19:53.600690 INFO: === FDR correction performed with classifier version 8 ===
0:19:53.601406 PROGRESS: ============================= Precursor FDR =============================
0:19:53.601500 PROGRESS: Total precursors accumulated: 1,431
0:19:53.601563 PROGRESS: Target precursors: 1,417 (99.02%)
0:19:53.601616 PROGRESS: Decoy precursors: 14 (0.98%)
0:19:53.601663 PROGRESS: 
0:19:53.601706 PROGRESS: Precursor Summary:
0:19:53.603091 PROGRESS: Channel   0:	 0.050 FDR: 1,417; 0.010 FDR: 1,417; 0.001 FDR: 1,047
0:19:53.603189 PROGRESS: 
0:19:53.603248 PROGRESS: Protein Summary:
0:19:53.604989 PROGRESS: Channel   0:	 0.050 FDR: 1,215; 0.010 FDR: 1,215; 0.001 FDR:   912
0:19:53.605083 PROGRESS: =========================================================================
0:19:53.622454 INFO: Target number of precursors reached.
0:19:54.080659 INFO: fragments_df: keeping 5000 of 4035277 [sum(precursor_idx_mask)=33423 sum(mass_error_mask)=4035277 stop_rank=5000
0:19:54.517375 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:54.761163 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:55.475107 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:55.475547 INFO: Using score_cutoff 8.754071223449706 (fac=0.99, q=1)
0:19:55.475871 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:55.475947 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:55.476013 INFO: Updating optimization_manager: score_cutoff        : 11.664852478981016 -> 8.754071223449706
0:19:55.476073 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:55.626179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:55.985835 INFO: === checking if optimization conditions were reached ===
0:19:55.988437 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:19:55.988607 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:19:55.988687 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:19:55.988757 INFO: ==============================================
0:19:55.988838 INFO: Starting optimization step 10.
0:19:55.988908 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:55.988995 INFO: Using rust extraction backend
0:19:55.989078 PROGRESS: Extracting batch of 250375 precursors
0:19:56.412742 INFO: === Search parameters used ===
0:19:56.413004 INFO: rt_error       : 805.5992431640625
0:19:56.413059 INFO: mobility_error : 0.1
0:19:56.413107 INFO: num_candidates : 3
0:19:56.413151 INFO: ms1_error      : 3
0:19:56.413192 INFO: ms2_error      : 10.0
0:19:56.413235 INFO: fwhm_rt        : 3.0
0:19:56.413279 INFO: quant_window   : 3
0:19:56.413319 INFO: ==============================================
0:19:59.811804 INFO: performing precursor FDR with 40 features
0:19:59.811923 INFO: Decoy channel: -1
0:19:59.811949 INFO: competitive: True
0:19:59.991316 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:00.275965 INFO: Estimating optimal hyperparameters - samples: 599,469, batch_size: 2,455, learning_rate: 7.74e-04
0:20:00.276897 INFO: Using random state 491 for train-test-split
0:20:13.210045 INFO: Test AUC: 0.611
0:20:13.210226 INFO: Train AUC: 0.620
0:20:13.210258 INFO: AUC difference: 1.57%
0:20:13.685403 INFO: Resetting torch num_threads to 24
0:20:13.716141 PROGRESS: === Extracted 749337 precursors and 4034944 fragments ===
0:20:13.716638 INFO: === FDR correction performed with classifier version 9 ===
0:20:13.717348 PROGRESS: ============================= Precursor FDR =============================
0:20:13.717443 PROGRESS: Total precursors accumulated: 1,464
0:20:13.717506 PROGRESS: Target precursors: 1,450 (99.04%)
0:20:13.717558 PROGRESS: Decoy precursors: 14 (0.96%)
0:20:13.717606 PROGRESS: 
0:20:13.717653 PROGRESS: Precursor Summary:
0:20:13.718997 PROGRESS: Channel   0:	 0.050 FDR: 1,450; 0.010 FDR: 1,450; 0.001 FDR:   629
0:20:13.719094 PROGRESS: 
0:20:13.719151 PROGRESS: Protein Summary:
0:20:13.720845 PROGRESS: Channel   0:	 0.050 FDR: 1,230; 0.010 FDR: 1,230; 0.001 FDR:   564
0:20:13.720952 PROGRESS: =========================================================================
0:20:13.734162 INFO: Target number of precursors reached.
0:20:14.192773 INFO: fragments_df: keeping 5000 of 4034944 [sum(precursor_idx_mask)=34809 sum(mass_error_mask)=4034944 stop_rank=5000
0:20:14.630448 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:14.865258 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:15.575601 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:15.576041 INFO: Using score_cutoff 12.10184256105423 (fac=0.99, q=1)
0:20:15.576355 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:15.576438 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:15.576494 INFO: Updating optimization_manager: score_cutoff        : 8.754071223449706 -> 12.10184256105423
0:20:15.576552 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:15.729680 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:16.076243 INFO: === checking if optimization conditions were reached ===
0:20:16.078779 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:20:16.078916 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:20:16.079010 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:20:16.079089 INFO: ==============================================
0:20:16.079195 INFO: Starting optimization step 11.
0:20:16.079264 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:16.079349 INFO: Using rust extraction backend
0:20:16.079432 PROGRESS: Extracting batch of 250375 precursors
0:20:16.501432 INFO: === Search parameters used ===
0:20:16.501694 INFO: rt_error       : 805.5992431640625
0:20:16.501750 INFO: mobility_error : 0.1
0:20:16.501799 INFO: num_candidates : 3
0:20:16.501847 INFO: ms1_error      : 3
0:20:16.501889 INFO: ms2_error      : 10.0
0:20:16.501928 INFO: fwhm_rt        : 3.0
0:20:16.501986 INFO: quant_window   : 3
0:20:16.502027 INFO: ==============================================
0:20:19.852304 INFO: performing precursor FDR with 40 features
0:20:19.852425 INFO: Decoy channel: -1
0:20:19.852451 INFO: competitive: True
0:20:20.038911 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:20.329900 INFO: Estimating optimal hyperparameters - samples: 599,449, batch_size: 2,455, learning_rate: 7.74e-04
0:20:20.330987 INFO: Using random state 681295 for train-test-split
0:20:33.740697 INFO: Test AUC: 0.610
0:20:33.740858 INFO: Train AUC: 0.623
0:20:33.740890 INFO: AUC difference: 2.23%
0:20:34.214605 INFO: Resetting torch num_threads to 24
0:20:34.245808 PROGRESS: === Extracted 749312 precursors and 4035060 fragments ===
0:20:34.246275 INFO: === FDR correction performed with classifier version 10 ===
0:20:34.246982 PROGRESS: ============================= Precursor FDR =============================
0:20:34.247079 PROGRESS: Total precursors accumulated: 1,452
0:20:34.247142 PROGRESS: Target precursors: 1,438 (99.04%)
0:20:34.247196 PROGRESS: Decoy precursors: 14 (0.96%)
0:20:34.247244 PROGRESS: 
0:20:34.247292 PROGRESS: Precursor Summary:
0:20:34.248650 PROGRESS: Channel   0:	 0.050 FDR: 1,438; 0.010 FDR: 1,438; 0.001 FDR: 1,018
0:20:34.248748 PROGRESS: 
0:20:34.248804 PROGRESS: Protein Summary:
0:20:34.250552 PROGRESS: Channel   0:	 0.050 FDR: 1,215; 0.010 FDR: 1,215; 0.001 FDR:   882
0:20:34.250644 PROGRESS: =========================================================================
0:20:34.264349 INFO: Target number of precursors reached.
0:20:34.708440 INFO: fragments_df: keeping 5000 of 4035060 [sum(precursor_idx_mask)=34588 sum(mass_error_mask)=4035060 stop_rank=5000
0:20:35.121968 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:35.345283 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:36.055444 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:36.055876 INFO: Using score_cutoff 12.087260960483551 (fac=0.99, q=1)
0:20:36.056191 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:36.056269 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:36.056324 INFO: Updating optimization_manager: score_cutoff        : 12.10184256105423 -> 12.087260960483551
0:20:36.056384 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:36.208839 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:36.544898 INFO: === checking if optimization conditions were reached ===
0:20:36.547411 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:20:36.547549 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:20:36.547634 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:20:36.547706 INFO: ==============================================
0:20:36.547797 PROGRESS: Optimization finished for ms2_error.
0:20:36.942713 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:37.094740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:37.431037 INFO: Starting optimization step 0.
0:20:37.431298 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:37.431385 INFO: Using rust extraction backend
0:20:37.431459 PROGRESS: Extracting batch of 250375 precursors
0:20:37.850453 INFO: === Search parameters used ===
0:20:37.850715 INFO: rt_error       : 805.5992431640625
0:20:37.850788 INFO: mobility_error : 0.1
0:20:37.850845 INFO: num_candidates : 3
0:20:37.850890 INFO: ms1_error      : 3
0:20:37.850934 INFO: ms2_error      : 10.0
0:20:37.850999 INFO: fwhm_rt        : 3.0
0:20:37.851047 INFO: quant_window   : 3
0:20:37.851089 INFO: ==============================================
0:20:41.160285 INFO: performing precursor FDR with 40 features
0:20:41.160416 INFO: Decoy channel: -1
0:20:41.160442 INFO: competitive: True
0:20:41.336411 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:41.616898 INFO: Estimating optimal hyperparameters - samples: 599,440, batch_size: 2,455, learning_rate: 7.74e-04
0:20:41.618036 INFO: Using random state 911578 for train-test-split
0:20:54.467824 INFO: Test AUC: 0.611
0:20:54.467978 INFO: Train AUC: 0.624
0:20:54.468012 INFO: AUC difference: 2.18%
0:20:55.369372 INFO: Resetting torch num_threads to 24
0:20:55.400939 PROGRESS: === Extracted 749300 precursors and 4034473 fragments ===
0:20:55.401380 INFO: === FDR correction performed with classifier version 11 ===
0:20:55.402090 PROGRESS: ============================= Precursor FDR =============================
0:20:55.402188 PROGRESS: Total precursors accumulated: 1,526
0:20:55.402254 PROGRESS: Target precursors: 1,511 (99.02%)
0:20:55.402306 PROGRESS: Decoy precursors: 15 (0.98%)
0:20:55.402353 PROGRESS: 
0:20:55.402399 PROGRESS: Precursor Summary:
0:20:55.403774 PROGRESS: Channel   0:	 0.050 FDR: 1,511; 0.010 FDR: 1,511; 0.001 FDR:   777
0:20:55.403869 PROGRESS: 
0:20:55.403925 PROGRESS: Protein Summary:
0:20:55.405659 PROGRESS: Channel   0:	 0.050 FDR: 1,286; 0.010 FDR: 1,286; 0.001 FDR:   684
0:20:55.405753 PROGRESS: =========================================================================
0:20:55.419239 INFO: Target number of precursors reached.
0:20:55.860525 INFO: fragments_df: keeping 5000 of 4034473 [sum(precursor_idx_mask)=36212 sum(mass_error_mask)=4034473 stop_rank=5000
0:20:56.270360 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:56.508193 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:57.221340 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:57.221771 INFO: Using score_cutoff 11.612154307365417 (fac=0.99, q=1)
0:20:57.222064 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:57.222140 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:57.222195 INFO: Updating optimization_manager: score_cutoff        : 12.087260960483551 -> 11.612154307365417
0:20:57.222251 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:57.375943 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:57.720895 INFO: === checking if optimization conditions were reached ===
0:20:57.721207 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:20:57.724260 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 648.1199638882574
0:20:57.724379 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 648.1200.
0:20:57.724455 INFO: ==============================================
0:20:57.724534 INFO: Starting optimization step 1.
0:20:57.724602 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:57.724680 INFO: Using rust extraction backend
0:20:57.724752 PROGRESS: Extracting batch of 250375 precursors
0:20:58.153393 INFO: === Search parameters used ===
0:20:58.153684 INFO: rt_error       : 648.1199638882574
0:20:58.153744 INFO: mobility_error : 0.1
0:20:58.153791 INFO: num_candidates : 3
0:20:58.153836 INFO: ms1_error      : 3
0:20:58.153880 INFO: ms2_error      : 10.0
0:20:58.153923 INFO: fwhm_rt        : 3.0
0:20:58.153964 INFO: quant_window   : 3
0:20:58.154004 INFO: ==============================================
0:21:01.323591 INFO: performing precursor FDR with 40 features
0:21:01.323717 INFO: Decoy channel: -1
0:21:01.323743 INFO: competitive: True
0:21:01.506680 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:01.806819 INFO: Estimating optimal hyperparameters - samples: 599,382, batch_size: 2,455, learning_rate: 7.74e-04
0:21:01.807968 INFO: Using random state 911578 for train-test-split
0:21:15.102209 INFO: Test AUC: 0.610
0:21:15.102439 INFO: Train AUC: 0.626
0:21:15.102472 INFO: AUC difference: 2.53%
0:21:15.578370 INFO: Resetting torch num_threads to 24
0:21:15.612002 PROGRESS: === Extracted 749228 precursors and 4026405 fragments ===
0:21:15.612499 INFO: === FDR correction performed with classifier version 11 ===
0:21:15.613208 PROGRESS: ============================= Precursor FDR =============================
0:21:15.613306 PROGRESS: Total precursors accumulated: 1,441
0:21:15.613372 PROGRESS: Target precursors: 1,427 (99.03%)
0:21:15.613427 PROGRESS: Decoy precursors: 14 (0.97%)
0:21:15.613475 PROGRESS: 
0:21:15.613522 PROGRESS: Precursor Summary:
0:21:15.614874 PROGRESS: Channel   0:	 0.050 FDR: 1,427; 0.010 FDR: 1,427; 0.001 FDR:   799
0:21:15.614965 PROGRESS: 
0:21:15.615035 PROGRESS: Protein Summary:
0:21:15.616759 PROGRESS: Channel   0:	 0.050 FDR: 1,224; 0.010 FDR: 1,224; 0.001 FDR:   706
0:21:15.616853 PROGRESS: =========================================================================
0:21:15.630524 INFO: Target number of precursors reached.
0:21:16.069321 INFO: fragments_df: keeping 5000 of 4026405 [sum(precursor_idx_mask)=34093 sum(mass_error_mask)=4026405 stop_rank=5000
0:21:16.494487 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:16.721779 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:17.433534 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:17.433978 INFO: Using score_cutoff 10.603280487442017 (fac=0.99, q=1)
0:21:17.434295 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:17.434373 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:17.434430 INFO: Updating optimization_manager: score_cutoff        : 11.612154307365417 -> 10.603280487442017
0:21:17.434487 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:17.584454 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:17.915997 INFO: === checking if optimization conditions were reached ===
0:21:17.916313 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:21:17.919462 INFO: Updating optimization_manager: rt_error            : 648.1199638882574 -> 688.0715335360403
0:21:17.919592 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 688.0715.
0:21:17.919670 INFO: ==============================================
0:21:17.919760 INFO: Starting optimization step 2.
0:21:17.919834 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:17.919922 INFO: Using rust extraction backend
0:21:17.920038 PROGRESS: Extracting batch of 250375 precursors
0:21:18.342866 INFO: === Search parameters used ===
0:21:18.343149 INFO: rt_error       : 688.0715335360403
0:21:18.343208 INFO: mobility_error : 0.1
0:21:18.343256 INFO: num_candidates : 3
0:21:18.343300 INFO: ms1_error      : 3
0:21:18.343343 INFO: ms2_error      : 10.0
0:21:18.343384 INFO: fwhm_rt        : 3.0
0:21:18.343426 INFO: quant_window   : 3
0:21:18.343467 INFO: ==============================================
0:21:21.596396 INFO: performing precursor FDR with 40 features
0:21:21.596518 INFO: Decoy channel: -1
0:21:21.596543 INFO: competitive: True
0:21:21.777831 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:22.059758 INFO: Estimating optimal hyperparameters - samples: 599,433, batch_size: 2,455, learning_rate: 7.74e-04
0:21:22.061039 INFO: Using random state 911578 for train-test-split
0:21:35.211543 INFO: Test AUC: 0.613
0:21:35.211769 INFO: Train AUC: 0.624
0:21:35.211803 INFO: AUC difference: 1.75%
0:21:35.697367 INFO: Resetting torch num_threads to 24
0:21:35.726902 PROGRESS: === Extracted 749292 precursors and 4030613 fragments ===
0:21:35.727427 INFO: === FDR correction performed with classifier version 11 ===
0:21:35.728135 PROGRESS: ============================= Precursor FDR =============================
0:21:35.728241 PROGRESS: Total precursors accumulated: 1,548
0:21:35.728305 PROGRESS: Target precursors: 1,533 (99.03%)
0:21:35.728356 PROGRESS: Decoy precursors: 15 (0.97%)
0:21:35.728403 PROGRESS: 
0:21:35.728450 PROGRESS: Precursor Summary:
0:21:35.729855 PROGRESS: Channel   0:	 0.050 FDR: 1,533; 0.010 FDR: 1,533; 0.001 FDR: 1,130
0:21:35.729945 PROGRESS: 
0:21:35.730002 PROGRESS: Protein Summary:
0:21:35.731805 PROGRESS: Channel   0:	 0.050 FDR: 1,310; 0.010 FDR: 1,310; 0.001 FDR:   977
0:21:35.731908 PROGRESS: =========================================================================
0:21:35.748214 INFO: Target number of precursors reached.
0:21:36.201703 INFO: fragments_df: keeping 5000 of 4030613 [sum(precursor_idx_mask)=35965 sum(mass_error_mask)=4030613 stop_rank=5000
0:21:36.631774 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:36.865054 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:37.580426 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:37.580870 INFO: Using score_cutoff 9.17557253036499 (fac=0.99, q=1)
0:21:37.581188 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:37.581267 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:37.581322 INFO: Updating optimization_manager: score_cutoff        : 10.603280487442017 -> 9.17557253036499
0:21:37.581378 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:37.732787 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:38.071366 INFO: === checking if optimization conditions were reached ===
0:21:38.071693 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:21:38.075069 INFO: Updating optimization_manager: rt_error            : 688.0715335360403 -> 688.9787422674246
0:21:38.075187 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 688.9787.
0:21:38.075263 INFO: ==============================================
0:21:38.075348 INFO: Starting optimization step 3.
0:21:38.075452 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:38.075541 INFO: Using rust extraction backend
0:21:38.075623 PROGRESS: Extracting batch of 250375 precursors
0:21:38.498092 INFO: === Search parameters used ===
0:21:38.498365 INFO: rt_error       : 688.9787422674246
0:21:38.498424 INFO: mobility_error : 0.1
0:21:38.498475 INFO: num_candidates : 3
0:21:38.498523 INFO: ms1_error      : 3
0:21:38.498568 INFO: ms2_error      : 10.0
0:21:38.498611 INFO: fwhm_rt        : 3.0
0:21:38.498653 INFO: quant_window   : 3
0:21:38.498696 INFO: ==============================================
0:21:41.757266 INFO: performing precursor FDR with 40 features
0:21:41.757384 INFO: Decoy channel: -1
0:21:41.757411 INFO: competitive: True
0:21:41.939889 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:42.234083 INFO: Estimating optimal hyperparameters - samples: 599,490, batch_size: 2,455, learning_rate: 7.74e-04
0:21:42.235050 INFO: Using random state 911578 for train-test-split
0:21:55.657387 INFO: Test AUC: 0.611
0:21:55.657548 INFO: Train AUC: 0.624
0:21:55.657580 INFO: AUC difference: 2.02%
0:21:56.136640 INFO: Resetting torch num_threads to 24
0:21:56.165359 PROGRESS: === Extracted 749363 precursors and 4034628 fragments ===
0:21:56.165851 INFO: === FDR correction performed with classifier version 11 ===
0:21:56.166548 PROGRESS: ============================= Precursor FDR =============================
0:21:56.166644 PROGRESS: Total precursors accumulated: 1,454
0:21:56.166708 PROGRESS: Target precursors: 1,440 (99.04%)
0:21:56.166761 PROGRESS: Decoy precursors: 14 (0.96%)
0:21:56.166809 PROGRESS: 
0:21:56.166856 PROGRESS: Precursor Summary:
0:21:56.168247 PROGRESS: Channel   0:	 0.050 FDR: 1,440; 0.010 FDR: 1,440; 0.001 FDR: 1,099
0:21:56.168355 PROGRESS: 
0:21:56.168411 PROGRESS: Protein Summary:
0:21:56.170152 PROGRESS: Channel   0:	 0.050 FDR: 1,223; 0.010 FDR: 1,223; 0.001 FDR:   949
0:21:56.170254 PROGRESS: =========================================================================
0:21:56.183865 INFO: Target number of precursors reached.
0:21:56.634763 INFO: fragments_df: keeping 5000 of 4034628 [sum(precursor_idx_mask)=34439 sum(mass_error_mask)=4034628 stop_rank=5000
0:21:57.062696 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:57.292533 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:58.006807 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:58.007257 INFO: Using score_cutoff 11.255145621871948 (fac=0.99, q=1)
0:21:58.007566 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:58.007642 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:58.007696 INFO: Updating optimization_manager: score_cutoff        : 9.17557253036499 -> 11.255145621871948
0:21:58.007751 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:58.159861 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:58.496297 INFO: === checking if optimization conditions were reached ===
0:21:58.496614 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:21:58.499877 INFO: Updating optimization_manager: rt_error            : 688.9787422674246 -> 774.0205275399189
0:21:58.499997 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 774.0205.
0:21:58.500092 INFO: ==============================================
0:21:58.500185 INFO: Starting optimization step 4.
0:21:58.500258 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:58.500342 INFO: Using rust extraction backend
0:21:58.500425 PROGRESS: Extracting batch of 250375 precursors
0:21:58.922536 INFO: === Search parameters used ===
0:21:58.922813 INFO: rt_error       : 774.0205275399189
0:21:58.922870 INFO: mobility_error : 0.1
0:21:58.922919 INFO: num_candidates : 3
0:21:58.922979 INFO: ms1_error      : 3
0:21:58.923028 INFO: ms2_error      : 10.0
0:21:58.923071 INFO: fwhm_rt        : 3.0
0:21:58.923112 INFO: quant_window   : 3
0:21:58.923152 INFO: ==============================================
0:22:02.184767 INFO: performing precursor FDR with 40 features
0:22:02.184893 INFO: Decoy channel: -1
0:22:02.184935 INFO: competitive: True
0:22:02.360097 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:02.650816 INFO: Estimating optimal hyperparameters - samples: 599,463, batch_size: 2,455, learning_rate: 7.74e-04
0:22:02.651953 INFO: Using random state 911578 for train-test-split
0:22:15.238388 INFO: Test AUC: 0.611
0:22:15.238525 INFO: Train AUC: 0.624
0:22:15.238556 INFO: AUC difference: 2.16%
0:22:15.716805 INFO: Resetting torch num_threads to 24
0:22:15.747759 PROGRESS: === Extracted 749329 precursors and 4034830 fragments ===
0:22:15.748203 INFO: === FDR correction performed with classifier version 11 ===
0:22:15.748900 PROGRESS: ============================= Precursor FDR =============================
0:22:15.748991 PROGRESS: Total precursors accumulated: 1,530
0:22:15.749052 PROGRESS: Target precursors: 1,515 (99.02%)
0:22:15.749105 PROGRESS: Decoy precursors: 15 (0.98%)
0:22:15.749153 PROGRESS: 
0:22:15.749201 PROGRESS: Precursor Summary:
0:22:15.750590 PROGRESS: Channel   0:	 0.050 FDR: 1,515; 0.010 FDR: 1,515; 0.001 FDR: 1,143
0:22:15.750682 PROGRESS: 
0:22:15.750738 PROGRESS: Protein Summary:
0:22:15.752517 PROGRESS: Channel   0:	 0.050 FDR: 1,304; 0.010 FDR: 1,304; 0.001 FDR:   989
0:22:15.752608 PROGRESS: =========================================================================
0:22:15.765991 INFO: Target number of precursors reached.
0:22:16.205962 INFO: fragments_df: keeping 5000 of 4034830 [sum(precursor_idx_mask)=35197 sum(mass_error_mask)=4034830 stop_rank=5000
0:22:16.615735 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:16.852825 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:17.563416 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:17.563854 INFO: Using score_cutoff 8.30964195098877 (fac=0.99, q=1)
0:22:17.564162 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:17.564237 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:17.564293 INFO: Updating optimization_manager: score_cutoff        : 11.255145621871948 -> 8.30964195098877
0:22:17.564349 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:17.714641 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:18.057167 INFO: === checking if optimization conditions were reached ===
0:22:18.057482 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:22:18.060773 INFO: Updating optimization_manager: rt_error            : 774.0205275399189 -> 721.5692994024864
0:22:18.060924 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 721.5693.
0:22:18.061001 INFO: ==============================================
0:22:18.061083 INFO: Starting optimization step 5.
0:22:18.061150 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:22:18.061221 INFO: Using rust extraction backend
0:22:18.061288 PROGRESS: Extracting batch of 250375 precursors
0:22:18.482429 INFO: === Search parameters used ===
0:22:18.482690 INFO: rt_error       : 721.5692994024864
0:22:18.482747 INFO: mobility_error : 0.1
0:22:18.482798 INFO: num_candidates : 3
0:22:18.482862 INFO: ms1_error      : 3
0:22:18.482905 INFO: ms2_error      : 10.0
0:22:18.482945 INFO: fwhm_rt        : 3.0
0:22:18.482997 INFO: quant_window   : 3
0:22:18.483042 INFO: ==============================================
0:22:21.748447 INFO: performing precursor FDR with 40 features
0:22:21.748565 INFO: Decoy channel: -1
0:22:21.748589 INFO: competitive: True
0:22:21.925327 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:22.206887 INFO: Estimating optimal hyperparameters - samples: 599,489, batch_size: 2,455, learning_rate: 7.74e-04
0:22:22.208016 INFO: Using random state 911578 for train-test-split
0:22:35.237134 INFO: Test AUC: 0.613
0:22:35.237271 INFO: Train AUC: 0.625
0:22:35.237303 INFO: AUC difference: 1.95%
0:22:35.713715 INFO: Resetting torch num_threads to 24
0:22:35.742529 PROGRESS: === Extracted 749362 precursors and 4035099 fragments ===
0:22:35.743005 INFO: === FDR correction performed with classifier version 11 ===
0:22:35.743710 PROGRESS: ============================= Precursor FDR =============================
0:22:35.743807 PROGRESS: Total precursors accumulated: 1,555
0:22:35.743868 PROGRESS: Target precursors: 1,540 (99.04%)
0:22:35.743922 PROGRESS: Decoy precursors: 15 (0.96%)
0:22:35.743981 PROGRESS: 
0:22:35.744030 PROGRESS: Precursor Summary:
0:22:35.745425 PROGRESS: Channel   0:	 0.050 FDR: 1,540; 0.010 FDR: 1,540; 0.001 FDR: 1,141
0:22:35.745517 PROGRESS: 
0:22:35.745574 PROGRESS: Protein Summary:
0:22:35.747380 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR:   987
0:22:35.747479 PROGRESS: =========================================================================
0:22:35.760924 INFO: Target number of precursors reached.
0:22:36.211841 INFO: fragments_df: keeping 5000 of 4035099 [sum(precursor_idx_mask)=36665 sum(mass_error_mask)=4035099 stop_rank=5000
0:22:36.619726 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:36.859349 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:37.571612 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:37.572049 INFO: Using score_cutoff 10.81192730026245 (fac=0.99, q=1)
0:22:37.572351 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:37.572429 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:37.572484 INFO: Updating optimization_manager: score_cutoff        : 8.30964195098877 -> 10.81192730026245
0:22:37.572538 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:37.723274 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:38.062281 INFO: === checking if optimization conditions were reached ===
0:22:38.062614 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:22:38.065906 INFO: Updating optimization_manager: rt_error            : 721.5692994024864 -> 794.184474201415
0:22:38.066024 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 794.1845.
0:22:38.066100 INFO: ==============================================
0:22:38.066180 INFO: Starting optimization step 6.
0:22:38.066247 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:22:38.066326 INFO: Using rust extraction backend
0:22:38.066394 PROGRESS: Extracting batch of 250375 precursors
0:22:38.487454 INFO: === Search parameters used ===
0:22:38.487723 INFO: rt_error       : 794.184474201415
0:22:38.487782 INFO: mobility_error : 0.1
0:22:38.487832 INFO: num_candidates : 3
0:22:38.487878 INFO: ms1_error      : 3
0:22:38.487922 INFO: ms2_error      : 10.0
0:22:38.487965 INFO: fwhm_rt        : 3.0
0:22:38.488007 INFO: quant_window   : 3
0:22:38.488048 INFO: ==============================================
0:22:41.806747 INFO: performing precursor FDR with 40 features
0:22:41.806871 INFO: Decoy channel: -1
0:22:41.806897 INFO: competitive: True
0:22:41.984883 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:42.273297 INFO: Estimating optimal hyperparameters - samples: 599,458, batch_size: 2,455, learning_rate: 7.74e-04
0:22:42.274429 INFO: Using random state 911578 for train-test-split
0:22:55.244142 INFO: Test AUC: 0.609
0:22:55.244290 INFO: Train AUC: 0.624
0:22:55.244323 INFO: AUC difference: 2.39%
0:22:55.717639 INFO: Resetting torch num_threads to 24
0:22:55.745661 PROGRESS: === Extracted 749323 precursors and 4035088 fragments ===
0:22:55.746110 INFO: === FDR correction performed with classifier version 11 ===
0:22:55.746792 PROGRESS: ============================= Precursor FDR =============================
0:22:55.746884 PROGRESS: Total precursors accumulated: 1,419
0:22:55.746954 PROGRESS: Target precursors: 1,405 (99.01%)
0:22:55.747026 PROGRESS: Decoy precursors: 14 (0.99%)
0:22:55.747075 PROGRESS: 
0:22:55.747120 PROGRESS: Precursor Summary:
0:22:55.748441 PROGRESS: Channel   0:	 0.050 FDR: 1,405; 0.010 FDR: 1,405; 0.001 FDR:   250
0:22:55.748531 PROGRESS: 
0:22:55.748587 PROGRESS: Protein Summary:
0:22:55.750207 PROGRESS: Channel   0:	 0.050 FDR: 1,193; 0.010 FDR: 1,193; 0.001 FDR:   244
0:22:55.750295 PROGRESS: =========================================================================
0:22:55.763632 INFO: Target number of precursors reached.
0:22:56.206554 INFO: fragments_df: keeping 5000 of 4035088 [sum(precursor_idx_mask)=33650 sum(mass_error_mask)=4035088 stop_rank=5000
0:22:56.612350 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:56.856737 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:57.567586 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:57.568022 INFO: Using score_cutoff 11.622060519790649 (fac=0.99, q=1)
0:22:57.568314 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:57.568391 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:57.568446 INFO: Updating optimization_manager: score_cutoff        : 10.81192730026245 -> 11.622060519790649
0:22:57.568500 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:57.720688 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:58.070359 INFO: === checking if optimization conditions were reached ===
0:22:58.070691 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:22:58.073987 INFO: Updating optimization_manager: rt_error            : 794.184474201415 -> 752.5790809123262
0:22:58.074148 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 752.5791.
0:22:58.074226 INFO: ==============================================
0:22:58.074308 INFO: Starting optimization step 7.
0:22:58.074376 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:22:58.074458 INFO: Using rust extraction backend
0:22:58.074528 PROGRESS: Extracting batch of 250375 precursors
0:22:58.496019 INFO: === Search parameters used ===
0:22:58.496279 INFO: rt_error       : 752.5790809123262
0:22:58.496334 INFO: mobility_error : 0.1
0:22:58.496380 INFO: num_candidates : 3
0:22:58.496422 INFO: ms1_error      : 3
0:22:58.496463 INFO: ms2_error      : 10.0
0:22:58.496503 INFO: fwhm_rt        : 3.0
0:22:58.496542 INFO: quant_window   : 3
0:22:58.496583 INFO: ==============================================
0:23:01.817915 INFO: performing precursor FDR with 40 features
0:23:01.818043 INFO: Decoy channel: -1
0:23:01.818070 INFO: competitive: True
0:23:02.005787 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:02.297876 INFO: Estimating optimal hyperparameters - samples: 599,466, batch_size: 2,455, learning_rate: 7.74e-04
0:23:02.298814 INFO: Using random state 911578 for train-test-split
0:23:15.893332 INFO: Test AUC: 0.612
0:23:15.893473 INFO: Train AUC: 0.625
0:23:15.893506 INFO: AUC difference: 2.14%
0:23:16.370688 INFO: Resetting torch num_threads to 24
0:23:16.399616 PROGRESS: === Extracted 749333 precursors and 4033932 fragments ===
0:23:16.400046 INFO: === FDR correction performed with classifier version 11 ===
0:23:16.400730 PROGRESS: ============================= Precursor FDR =============================
0:23:16.400821 PROGRESS: Total precursors accumulated: 1,531
0:23:16.400879 PROGRESS: Target precursors: 1,516 (99.02%)
0:23:16.400930 PROGRESS: Decoy precursors: 15 (0.98%)
0:23:16.400977 PROGRESS: 
0:23:16.401022 PROGRESS: Precursor Summary:
0:23:16.402317 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR:   373
0:23:16.402405 PROGRESS: 
0:23:16.402461 PROGRESS: Protein Summary:
0:23:16.404167 PROGRESS: Channel   0:	 0.050 FDR: 1,289; 0.010 FDR: 1,289; 0.001 FDR:   346
0:23:16.404258 PROGRESS: =========================================================================
0:23:16.418476 INFO: Target number of precursors reached.
0:23:16.854405 INFO: fragments_df: keeping 5000 of 4033932 [sum(precursor_idx_mask)=35809 sum(mass_error_mask)=4033932 stop_rank=5000
0:23:17.259310 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:17.493873 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:18.206627 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:18.207124 INFO: Using score_cutoff 9.341545363426208 (fac=0.99, q=1)
0:23:18.207428 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:18.207504 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:18.207559 INFO: Updating optimization_manager: score_cutoff        : 11.622060519790649 -> 9.341545363426208
0:23:18.207618 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:18.358328 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:18.697523 INFO: === checking if optimization conditions were reached ===
0:23:18.697837 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:23:18.701224 INFO: Updating optimization_manager: rt_error            : 752.5790809123262 -> 784.915784388061
0:23:18.701387 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 784.9158.
0:23:18.701465 INFO: ==============================================
0:23:18.701547 INFO: Starting optimization step 8.
0:23:18.701616 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:23:18.701688 INFO: Using rust extraction backend
0:23:18.701754 PROGRESS: Extracting batch of 250375 precursors
0:23:19.122710 INFO: === Search parameters used ===
0:23:19.122995 INFO: rt_error       : 784.915784388061
0:23:19.123058 INFO: mobility_error : 0.1
0:23:19.123107 INFO: num_candidates : 3
0:23:19.123153 INFO: ms1_error      : 3
0:23:19.123196 INFO: ms2_error      : 10.0
0:23:19.123238 INFO: fwhm_rt        : 3.0
0:23:19.123278 INFO: quant_window   : 3
0:23:19.123319 INFO: ==============================================
0:23:22.464887 INFO: performing precursor FDR with 40 features
0:23:22.465080 INFO: Decoy channel: -1
0:23:22.465423 INFO: competitive: True
0:23:22.652652 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:22.941270 INFO: Estimating optimal hyperparameters - samples: 599,479, batch_size: 2,455, learning_rate: 7.74e-04
0:23:22.942173 INFO: Using random state 911578 for train-test-split
0:23:35.781626 INFO: Test AUC: 0.610
0:23:35.781788 INFO: Train AUC: 0.625
0:23:35.781824 INFO: AUC difference: 2.42%
0:23:36.774363 INFO: Resetting torch num_threads to 24
0:23:36.806860 PROGRESS: === Extracted 749349 precursors and 4034784 fragments ===
0:23:36.807333 INFO: === FDR correction performed with classifier version 11 ===
0:23:36.808054 PROGRESS: ============================= Precursor FDR =============================
0:23:36.808148 PROGRESS: Total precursors accumulated: 1,470
0:23:36.808207 PROGRESS: Target precursors: 1,456 (99.05%)
0:23:36.808268 PROGRESS: Decoy precursors: 14 (0.95%)
0:23:36.808314 PROGRESS: 
0:23:36.808358 PROGRESS: Precursor Summary:
0:23:36.809728 PROGRESS: Channel   0:	 0.050 FDR: 1,456; 0.010 FDR: 1,456; 0.001 FDR: 1,040
0:23:36.809819 PROGRESS: 
0:23:36.809875 PROGRESS: Protein Summary:
0:23:36.811648 PROGRESS: Channel   0:	 0.050 FDR: 1,243; 0.010 FDR: 1,243; 0.001 FDR:   901
0:23:36.811743 PROGRESS: =========================================================================
0:23:36.825352 INFO: Target number of precursors reached.
0:23:37.266672 INFO: fragments_df: keeping 5000 of 4034784 [sum(precursor_idx_mask)=34779 sum(mass_error_mask)=4034784 stop_rank=5000
0:23:37.688946 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:37.918387 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:38.633522 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:38.633952 INFO: Using score_cutoff 10.259873472690582 (fac=0.99, q=1)
0:23:38.634252 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:38.634330 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:38.634393 INFO: Updating optimization_manager: score_cutoff        : 9.341545363426208 -> 10.259873472690582
0:23:38.634449 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:38.786098 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:39.145138 INFO: === checking if optimization conditions were reached ===
0:23:39.145444 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:23:39.146504 INFO: Updating optimization_manager: rt_error            : 784.915784388061 -> 721.5692994024864
0:23:39.146650 INFO: Updating optimization_manager: classifier_version  : 11 -> 17
0:23:39.146765 INFO: Updating optimization_manager: score_cutoff        : 10.259873472690582 -> 10.81192730026245
0:23:39.146873 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:39.146993 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:39.147111 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 721.5693 found after 9 searches.
0:23:39.147186 INFO: ==============================================
0:23:39.147268 PROGRESS: Optimization finished for rt_error.
0:23:39.541539 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:39.693004 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:40.036452 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:23:40.036751 PROGRESS: ==============================================
0:23:40.036834 PROGRESS: ms2_error      : 10.0000
0:23:40.036925 PROGRESS: rt_error       : 721.5693
0:23:40.036989 PROGRESS: ==============================================
0:23:40.045850 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:47.685715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:04.492700 INFO: Using rust extraction backend
0:24:04.493185 PROGRESS: Extracting batch of 11997144 precursors
0:24:20.469674 INFO: === Search parameters used ===
0:24:20.470020 INFO: rt_error       : 721.5692994024864
0:24:20.470088 INFO: mobility_error : 0.1
0:24:20.470140 INFO: num_candidates : 3
0:24:20.470188 INFO: ms1_error      : 3
0:24:20.470240 INFO: ms2_error      : 10.0
0:24:20.470296 INFO: fwhm_rt        : 3.0
0:24:20.470346 INFO: quant_window   : 3
0:24:20.470396 INFO: ==============================================
0:25:22.350309 INFO: Removed 8760157 precursors with score below cutoff 10.81192730026245
0:25:52.287345 INFO: performing precursor FDR with 40 features
0:25:52.287649 INFO: Decoy channel: -1
0:25:52.287681 INFO: competitive: True
0:25:55.153705 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:06.139661 INFO: Estimating optimal hyperparameters - samples: 21,784,626, batch_size: 4,096, learning_rate: 1.00e-03
0:26:06.205519 INFO: Using random state 301778 for train-test-split
0:33:43.369772 INFO: Test AUC: 0.622
0:33:43.370360 INFO: Train AUC: 0.622
0:33:43.370458 INFO: AUC difference: 0.08%
0:33:52.246101 INFO: Resetting torch num_threads to 24
0:33:57.712027 PROGRESS: ============================= Precursor FDR =============================
0:33:57.712895 PROGRESS: Total precursors accumulated: 93,632
0:33:57.713029 PROGRESS: Target precursors: 92,705 (99.01%)
0:33:57.713089 PROGRESS: Decoy precursors: 927 (0.99%)
0:33:57.713147 PROGRESS: 
0:33:57.713208 PROGRESS: Precursor Summary:
0:33:57.808129 PROGRESS: Channel   0:	 0.050 FDR: 92,705; 0.010 FDR: 92,705; 0.001 FDR: 62,059
0:33:57.808815 PROGRESS: 
0:33:57.808881 PROGRESS: Protein Summary:
0:33:57.958396 PROGRESS: Channel   0:	 0.050 FDR: 14,676; 0.010 FDR: 14,676; 0.001 FDR: 9,818
0:33:57.959101 PROGRESS: =========================================================================
0:33:58.258902 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:33:58.804548 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:33:59.474569 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:34:01.097032 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
0:34:01.097420 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
0:34:01.097638 INFO: Initializing TimingManager
0:34:01.099820 INFO: Initializing RawFileManager
0:34:31.518491 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.
0:34:31.531453 INFO: Determining DIA cycle
0:34:31.550367 INFO: Found cycle with start 0.00 min and length 300.
0:34:32.160703 INFO: RT (min)            : 0.0 - 26.9
0:34:32.161035 INFO: RT duration (sec)   : 1611.2
0:34:32.161073 INFO: RT duration (min)   : 26.9
0:34:32.161110 INFO: Cycle len (scans)   : 300
0:34:32.161135 INFO: Cycle len (sec)     : 1.65
0:34:32.161158 INFO: Number of cycles    : 978
0:34:32.161186 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:34:32.161263 INFO: Creating DIA data object took: 31.061201095581055
0:34:35.913606 INFO: Creating DIA data NG object took: 3.7518982887268066
0:34:40.386304 INFO: Initializing CalibrationManager
0:34:40.387292 INFO: Setting up calibration estimators ..
0:34:40.387446 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:34:40.387615 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'}' ..
0:34:40.387853 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:34:40.387944 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:34:40.388076 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}}' ..
0:34:40.388151 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:34:40.388216 INFO: Done setting up calibration estimators.
0:34:40.389958 INFO: Initializing OptimizationManager
0:34:40.390435 INFO: initial parameter: ms1_error = 3
0:34:40.390542 INFO: initial parameter: ms2_error = 10
0:34:40.390629 INFO: initial parameter: rt_error = 805.6019897460938
0:34:40.390698 INFO: initial parameter: mobility_error = 0.1
0:34:40.390761 INFO: initial parameter: num_candidates = 1
0:34:40.390829 INFO: initial parameter: fwhm_rt = 5
0:34:40.390890 INFO: initial parameter: fwhm_mobility = 0.01
0:34:40.390946 INFO: initial parameter: score_cutoff = 0
0:34:40.391025 INFO: initial parameter: classifier_version = -1
0:34:40.391157 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:34:40.391982 INFO: FDRManager: loading saved state not requested, will be initialized.
0:34:40.392054 INFO: Initializing FDRManager
0:34:40.392143 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:34:45.027955 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:34:48.288646 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:34:48.290329 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:34:48.290557 PROGRESS: Starting initial search for precursors.
0:34:48.290715 INFO: Starting optimization step 0.
0:34:48.290822 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:34:48.290926 INFO: Using rust extraction backend
0:34:48.291041 PROGRESS: Extracting batch of 1976 precursors
0:34:48.305972 INFO: === Search parameters used ===
0:34:48.306858 INFO: rt_error       : 805.6019897460938
0:34:48.306944 INFO: mobility_error : 0.1
0:34:48.307014 INFO: num_candidates : 1
0:34:48.307082 INFO: ms1_error      : 3
0:34:48.307132 INFO: ms2_error      : 10
0:34:48.307175 INFO: fwhm_rt        : 5
0:34:48.307226 INFO: quant_window   : 3
0:34:48.307279 INFO: ==============================================
0:34:48.448207 INFO: performing precursor FDR with 40 features
0:34:48.448683 INFO: Decoy channel: -1
0:34:48.448811 INFO: competitive: True
0:34:48.457225 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:48.468977 INFO: Estimating optimal hyperparameters - samples: 1,577, batch_size: 128, learning_rate: 1.77e-04
0:34:48.474346 INFO: Using random state 459083 for train-test-split
0:34:49.352292 INFO: Test AUC: 0.480
0:34:49.352562 INFO: Train AUC: 0.525
0:34:49.352596 INFO: AUC difference: 8.58%
0:34:49.352623 WARNING: AUC difference > 5%. This may indicate overfitting.
0:34:49.773415 INFO: Resetting torch num_threads to 24
0:34:49.778687 PROGRESS: === Extracted 1972 precursors and 10876 fragments ===
0:34:49.780072 INFO: === FDR correction performed with classifier version -1 ===
0:34:49.782172 PROGRESS: ============================= Precursor FDR =============================
0:34:49.782604 PROGRESS: Total precursors accumulated: 1
0:34:49.782748 PROGRESS: Target precursors: 1 (100.00%)
0:34:49.782812 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:49.782880 PROGRESS: 
0:34:49.782942 PROGRESS: Precursor Summary:
0:34:49.785657 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:34:49.786012 PROGRESS: 
0:34:49.786109 PROGRESS: Protein Summary:
0:34:49.788310 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:34:49.788561 PROGRESS: =========================================================================
0:34:49.789860 INFO: Target number of precursors not reached yet.
0:34:49.902708 INFO: Starting optimization step 1.
0:34:49.903399 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:34:49.903568 INFO: Using rust extraction backend
0:34:49.903711 PROGRESS: Extracting batch of 3939 precursors
0:34:49.937122 INFO: === Search parameters used ===
0:34:49.937849 INFO: rt_error       : 805.6019897460938
0:34:49.937937 INFO: mobility_error : 0.1
0:34:49.937989 INFO: num_candidates : 1
0:34:49.938035 INFO: ms1_error      : 3
0:34:49.938078 INFO: ms2_error      : 10
0:34:49.938121 INFO: fwhm_rt        : 5
0:34:49.938166 INFO: quant_window   : 3
0:34:49.938205 INFO: ==============================================
0:34:50.056878 INFO: performing precursor FDR with 40 features
0:34:50.057157 INFO: Decoy channel: -1
0:34:50.057185 INFO: competitive: True
0:34:50.069174 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:50.077044 INFO: Estimating optimal hyperparameters - samples: 4,724, batch_size: 128, learning_rate: 1.77e-04
0:34:50.077402 INFO: Using random state 342354 for train-test-split
0:34:51.066440 INFO: Test AUC: 0.538
0:34:51.066815 INFO: Train AUC: 0.553
0:34:51.066877 INFO: AUC difference: 2.70%
0:34:51.578623 INFO: Resetting torch num_threads to 24
0:34:51.594209 PROGRESS: === Extracted 5905 precursors and 32834 fragments ===
0:34:51.595968 INFO: === FDR correction performed with classifier version -1 ===
0:34:51.598129 PROGRESS: ============================= Precursor FDR =============================
0:34:51.598429 PROGRESS: Total precursors accumulated: 16
0:34:51.598526 PROGRESS: Target precursors: 16 (100.00%)
0:34:51.598601 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:51.598657 PROGRESS: 
0:34:51.598707 PROGRESS: Precursor Summary:
0:34:51.600981 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
0:34:51.601337 PROGRESS: 
0:34:51.601418 PROGRESS: Protein Summary:
0:34:51.603475 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
0:34:51.603781 PROGRESS: =========================================================================
0:34:51.605567 INFO: Target number of precursors not reached yet.
0:34:51.769733 INFO: Starting optimization step 2.
0:34:51.770502 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:34:51.770657 INFO: Using rust extraction backend
0:34:51.770765 PROGRESS: Extracting batch of 7882 precursors
0:34:51.812181 INFO: === Search parameters used ===
0:34:51.812944 INFO: rt_error       : 805.6019897460938
0:34:51.813011 INFO: mobility_error : 0.1
0:34:51.813066 INFO: num_candidates : 1
0:34:51.813125 INFO: ms1_error      : 3
0:34:51.813175 INFO: ms2_error      : 10
0:34:51.813222 INFO: fwhm_rt        : 5
0:34:51.813274 INFO: quant_window   : 3
0:34:51.813321 INFO: ==============================================
0:34:52.184282 INFO: performing precursor FDR with 40 features
0:34:52.184747 INFO: Decoy channel: -1
0:34:52.184844 INFO: competitive: True
0:34:52.262998 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:52.303567 INFO: Estimating optimal hyperparameters - samples: 11,015, batch_size: 128, learning_rate: 1.77e-04
0:34:52.304487 INFO: Using random state 497648 for train-test-split
0:34:54.536074 INFO: Test AUC: 0.548
0:34:54.536345 INFO: Train AUC: 0.577
0:34:54.536385 INFO: AUC difference: 5.09%
0:34:54.536411 WARNING: AUC difference > 5%. This may indicate overfitting.
0:34:55.006757 INFO: Resetting torch num_threads to 24
0:34:55.027069 PROGRESS: === Extracted 13769 precursors and 76681 fragments ===
0:34:55.028568 INFO: === FDR correction performed with classifier version -1 ===
0:34:55.030635 PROGRESS: ============================= Precursor FDR =============================
0:34:55.030966 PROGRESS: Total precursors accumulated: 63
0:34:55.031102 PROGRESS: Target precursors: 63 (100.00%)
0:34:55.031194 PROGRESS: Decoy precursors: 0 (0.00%)
0:34:55.031248 PROGRESS: 
0:34:55.031300 PROGRESS: Precursor Summary:
0:34:55.033737 PROGRESS: Channel   0:	 0.050 FDR:    63; 0.010 FDR:    63; 0.001 FDR:    63
0:34:55.034032 PROGRESS: 
0:34:55.034108 PROGRESS: Protein Summary:
0:34:55.036376 PROGRESS: Channel   0:	 0.050 FDR:    63; 0.010 FDR:    63; 0.001 FDR:    63
0:34:55.036628 PROGRESS: =========================================================================
0:34:55.038699 INFO: Target number of precursors not reached yet.
0:34:55.206333 INFO: Starting optimization step 3.
0:34:55.207634 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:34:55.207824 INFO: Using rust extraction backend
0:34:55.207937 PROGRESS: Extracting batch of 15793 precursors
0:34:55.285736 INFO: === Search parameters used ===
0:34:55.286552 INFO: rt_error       : 805.6019897460938
0:34:55.286612 INFO: mobility_error : 0.1
0:34:55.286662 INFO: num_candidates : 1
0:34:55.286710 INFO: ms1_error      : 3
0:34:55.286758 INFO: ms2_error      : 10
0:34:55.286846 INFO: fwhm_rt        : 5
0:34:55.286891 INFO: quant_window   : 3
0:34:55.286938 INFO: ==============================================
0:34:55.671853 INFO: performing precursor FDR with 40 features
0:34:55.672141 INFO: Decoy channel: -1
0:34:55.672172 INFO: competitive: True
0:34:55.725912 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:55.760910 INFO: Estimating optimal hyperparameters - samples: 23,620, batch_size: 128, learning_rate: 1.77e-04
0:34:55.761472 INFO: Using random state 17460 for train-test-split
0:34:59.530499 INFO: Test AUC: 0.569
0:34:59.530794 INFO: Train AUC: 0.587
0:34:59.530840 INFO: AUC difference: 3.19%
0:35:00.014365 INFO: Resetting torch num_threads to 24
0:35:00.049742 PROGRESS: === Extracted 29526 precursors and 164554 fragments ===
0:35:00.051140 INFO: === FDR correction performed with classifier version -1 ===
0:35:00.053063 PROGRESS: ============================= Precursor FDR =============================
0:35:00.053333 PROGRESS: Total precursors accumulated: 153
0:35:00.053421 PROGRESS: Target precursors: 152 (99.35%)
0:35:00.053478 PROGRESS: Decoy precursors: 1 (0.65%)
0:35:00.053530 PROGRESS: 
0:35:00.053581 PROGRESS: Precursor Summary:
0:35:00.056385 PROGRESS: Channel   0:	 0.050 FDR:   152; 0.010 FDR:   152; 0.001 FDR:   112
0:35:00.056710 PROGRESS: 
0:35:00.056793 PROGRESS: Protein Summary:
0:35:00.059566 PROGRESS: Channel   0:	 0.050 FDR:   148; 0.010 FDR:   148; 0.001 FDR:   111
0:35:00.059875 PROGRESS: =========================================================================
0:35:00.062622 INFO: Target number of precursors not reached yet.
0:35:00.360332 INFO: Starting optimization step 4.
0:35:00.361181 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:35:00.361388 INFO: Using rust extraction backend
0:35:00.361499 PROGRESS: Extracting batch of 31556 precursors
0:35:00.608257 INFO: === Search parameters used ===
0:35:00.608988 INFO: rt_error       : 805.6019897460938
0:35:00.609086 INFO: mobility_error : 0.1
0:35:00.609147 INFO: num_candidates : 1
0:35:00.609231 INFO: ms1_error      : 3
0:35:00.609279 INFO: ms2_error      : 10
0:35:00.609327 INFO: fwhm_rt        : 5
0:35:00.609370 INFO: quant_window   : 3
0:35:00.609418 INFO: ==============================================
0:35:01.396096 INFO: performing precursor FDR with 40 features
0:35:01.396344 INFO: Decoy channel: -1
0:35:01.396372 INFO: competitive: True
0:35:01.503609 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:01.571729 INFO: Estimating optimal hyperparameters - samples: 48,788, batch_size: 199, learning_rate: 2.20e-04
0:35:01.572403 INFO: Using random state 601918 for train-test-split
0:35:07.383669 INFO: Test AUC: 0.573
0:35:07.384071 INFO: Train AUC: 0.603
0:35:07.384130 INFO: AUC difference: 5.01%
0:35:07.384158 WARNING: AUC difference > 5%. This may indicate overfitting.
0:35:07.926467 INFO: Resetting torch num_threads to 24
0:35:07.981048 PROGRESS: === Extracted 60985 precursors and 339883 fragments ===
0:35:07.982382 INFO: === FDR correction performed with classifier version -1 ===
0:35:07.984463 PROGRESS: ============================= Precursor FDR =============================
0:35:07.984794 PROGRESS: Total precursors accumulated: 306
0:35:07.984897 PROGRESS: Target precursors: 303 (99.02%)
0:35:07.984970 PROGRESS: Decoy precursors: 3 (0.98%)
0:35:07.985021 PROGRESS: 
0:35:07.985073 PROGRESS: Precursor Summary:
0:35:07.987994 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   239
0:35:07.988544 PROGRESS: 
0:35:07.988629 PROGRESS: Protein Summary:
0:35:07.991635 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   291; 0.001 FDR:   230
0:35:07.991897 PROGRESS: =========================================================================
0:35:07.996804 INFO: Target number of precursors not reached yet.
0:35:08.370991 INFO: Starting optimization step 5.
0:35:08.371611 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:35:08.371909 INFO: Using rust extraction backend
0:35:08.372088 PROGRESS: Extracting batch of 63064 precursors
0:35:08.783533 INFO: === Search parameters used ===
0:35:08.784559 INFO: rt_error       : 805.6019897460938
0:35:08.784679 INFO: mobility_error : 0.1
0:35:08.784738 INFO: num_candidates : 1
0:35:08.784789 INFO: ms1_error      : 3
0:35:08.784837 INFO: ms2_error      : 10
0:35:08.784883 INFO: fwhm_rt        : 5
0:35:08.784927 INFO: quant_window   : 3
0:35:08.784972 INFO: ==============================================
0:35:10.131659 INFO: performing precursor FDR with 40 features
0:35:10.131928 INFO: Decoy channel: -1
0:35:10.131964 INFO: competitive: True
0:35:10.348095 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:10.534588 INFO: Estimating optimal hyperparameters - samples: 99,105, batch_size: 405, learning_rate: 3.14e-04
0:35:10.535508 INFO: Using random state 533214 for train-test-split
0:35:16.839559 INFO: Test AUC: 0.586
0:35:16.839836 INFO: Train AUC: 0.607
0:35:16.839870 INFO: AUC difference: 3.40%
0:35:17.200624 INFO: Resetting torch num_threads to 24
0:35:17.243409 PROGRESS: === Extracted 123882 precursors and 689717 fragments ===
0:35:17.244226 INFO: === FDR correction performed with classifier version -1 ===
0:35:17.245024 PROGRESS: ============================= Precursor FDR =============================
0:35:17.245119 PROGRESS: Total precursors accumulated: 658
0:35:17.245189 PROGRESS: Target precursors: 652 (99.09%)
0:35:17.245245 PROGRESS: Decoy precursors: 6 (0.91%)
0:35:17.245296 PROGRESS: 
0:35:17.245384 PROGRESS: Precursor Summary:
0:35:17.246616 PROGRESS: Channel   0:	 0.050 FDR:   652; 0.010 FDR:   652; 0.001 FDR:   284
0:35:17.246710 PROGRESS: 
0:35:17.246768 PROGRESS: Protein Summary:
0:35:17.248185 PROGRESS: Channel   0:	 0.050 FDR:   606; 0.010 FDR:   606; 0.001 FDR:   268
0:35:17.248281 PROGRESS: =========================================================================
0:35:17.250855 INFO: Target number of precursors not reached yet.
0:35:17.607187 INFO: Starting optimization step 6.
0:35:17.607755 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:35:17.608004 INFO: Using rust extraction backend
0:35:17.608202 PROGRESS: Extracting batch of 126165 precursors
0:35:18.026360 INFO: === Search parameters used ===
0:35:18.026968 INFO: rt_error       : 805.6019897460938
0:35:18.027113 INFO: mobility_error : 0.1
0:35:18.027232 INFO: num_candidates : 1
0:35:18.027309 INFO: ms1_error      : 3
0:35:18.027405 INFO: ms2_error      : 10
0:35:18.027471 INFO: fwhm_rt        : 5
0:35:18.027539 INFO: quant_window   : 3
0:35:18.027616 INFO: ==============================================
0:35:20.892103 INFO: performing precursor FDR with 40 features
0:35:20.892413 INFO: Decoy channel: -1
0:35:20.892455 INFO: competitive: True
0:35:21.343438 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:21.667852 INFO: Estimating optimal hyperparameters - samples: 199,796, batch_size: 818, learning_rate: 4.47e-04
0:35:21.668836 INFO: Using random state 555635 for train-test-split
0:35:32.437401 INFO: Test AUC: 0.592
0:35:32.437759 INFO: Train AUC: 0.609
0:35:32.437805 INFO: AUC difference: 2.70%
0:35:33.064125 INFO: Resetting torch num_threads to 24
0:35:33.215918 PROGRESS: === Extracted 249745 precursors and 1390205 fragments ===
0:35:33.216948 INFO: === FDR correction performed with classifier version -1 ===
0:35:33.218019 PROGRESS: ============================= Precursor FDR =============================
0:35:33.218128 PROGRESS: Total precursors accumulated: 1,396
0:35:33.218204 PROGRESS: Target precursors: 1,383 (99.07%)
0:35:33.218256 PROGRESS: Decoy precursors: 13 (0.93%)
0:35:33.218305 PROGRESS: 
0:35:33.218352 PROGRESS: Precursor Summary:
0:35:33.219909 PROGRESS: Channel   0:	 0.050 FDR: 1,383; 0.010 FDR: 1,383; 0.001 FDR:   635
0:35:33.220014 PROGRESS: 
0:35:33.220068 PROGRESS: Protein Summary:
0:35:33.221879 PROGRESS: Channel   0:	 0.050 FDR: 1,190; 0.010 FDR: 1,190; 0.001 FDR:   570
0:35:33.221975 PROGRESS: =========================================================================
0:35:33.228329 INFO: Target number of precursors reached.
0:35:33.412562 INFO: fragments_df: keeping 5000 of 1390205 [sum(precursor_idx_mask)=14351 sum(mass_error_mask)=1390205 stop_rank=5000
0:35:34.306710 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:34.680864 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:35.643719 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:35:35.644851 INFO: Using score_cutoff 10.672783193778992 (fac=0.99, q=1)
0:35:35.645843 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:35:35.646080 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:35:35.646152 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.672783193778992
0:35:35.646271 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:35.842873 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:36.281436 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:35:36.281947 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:35:36.282117 INFO: Starting optimization step 7.
0:35:36.282210 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:35:36.282307 INFO: Using rust extraction backend
0:35:36.282394 PROGRESS: Extracting batch of 250375 precursors
0:35:37.006744 INFO: === Search parameters used ===
0:35:37.007169 INFO: rt_error       : 805.6019897460938
0:35:37.007228 INFO: mobility_error : 0.1
0:35:37.007277 INFO: num_candidates : 3
0:35:37.007325 INFO: ms1_error      : 3
0:35:37.007368 INFO: ms2_error      : 10
0:35:37.007410 INFO: fwhm_rt        : 3.0
0:35:37.007450 INFO: quant_window   : 3
0:35:37.007490 INFO: ==============================================
0:35:44.655581 INFO: performing precursor FDR with 40 features
0:35:44.655917 INFO: Decoy channel: -1
0:35:44.655947 INFO: competitive: True
0:35:45.291760 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:46.410809 INFO: Estimating optimal hyperparameters - samples: 599,461, batch_size: 2,455, learning_rate: 7.74e-04
0:35:46.420287 INFO: Using random state 300688 for train-test-split
0:36:13.806060 INFO: Test AUC: 0.598
0:36:13.806450 INFO: Train AUC: 0.606
0:36:13.806501 INFO: AUC difference: 1.35%
0:36:14.621894 INFO: Resetting torch num_threads to 24
0:36:14.702690 PROGRESS: === Extracted 749327 precursors and 4008069 fragments ===
0:36:14.704218 INFO: === FDR correction performed with classifier version 6 ===
0:36:14.707037 PROGRESS: ============================= Precursor FDR =============================
0:36:14.707483 PROGRESS: Total precursors accumulated: 1,532
0:36:14.707621 PROGRESS: Target precursors: 1,517 (99.02%)
0:36:14.707685 PROGRESS: Decoy precursors: 15 (0.98%)
0:36:14.707742 PROGRESS: 
0:36:14.707791 PROGRESS: Precursor Summary:
0:36:14.712305 PROGRESS: Channel   0:	 0.050 FDR: 1,517; 0.010 FDR: 1,517; 0.001 FDR:   690
0:36:14.712773 PROGRESS: 
0:36:14.712862 PROGRESS: Protein Summary:
0:36:14.716085 PROGRESS: Channel   0:	 0.050 FDR: 1,287; 0.010 FDR: 1,287; 0.001 FDR:   616
0:36:14.716400 PROGRESS: =========================================================================
0:36:14.763632 INFO: Target number of precursors reached.
0:36:15.273809 INFO: fragments_df: keeping 5000 of 4008069 [sum(precursor_idx_mask)=36038 sum(mass_error_mask)=4008069 stop_rank=5000
0:36:16.693113 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:17.179347 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:18.047634 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:18.048527 INFO: Using score_cutoff 11.025961135482788 (fac=0.99, q=1)
0:36:18.048998 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:18.049078 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:18.049132 INFO: Updating optimization_manager: score_cutoff        : 10.672783193778992 -> 11.025961135482788
0:36:18.049197 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:18.227799 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:18.727752 INFO: === checking if optimization conditions were reached ===
0:36:18.732825 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:36:18.733264 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:36:18.733423 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:36:18.733526 INFO: ==============================================
0:36:18.733638 INFO: Starting optimization step 8.
0:36:18.733733 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:36:18.733854 INFO: Using rust extraction backend
0:36:18.733959 PROGRESS: Extracting batch of 250375 precursors
0:36:19.940115 INFO: === Search parameters used ===
0:36:19.940807 INFO: rt_error       : 805.6019897460938
0:36:19.940938 INFO: mobility_error : 0.1
0:36:19.941004 INFO: num_candidates : 3
0:36:19.941061 INFO: ms1_error      : 3
0:36:19.941111 INFO: ms2_error      : 10.0
0:36:19.941155 INFO: fwhm_rt        : 3.0
0:36:19.941200 INFO: quant_window   : 3
0:36:19.941246 INFO: ==============================================
0:36:28.798003 INFO: performing precursor FDR with 40 features
0:36:28.798325 INFO: Decoy channel: -1
0:36:28.798355 INFO: competitive: True
0:36:29.402817 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:30.374719 INFO: Estimating optimal hyperparameters - samples: 599,464, batch_size: 2,455, learning_rate: 7.74e-04
0:36:30.380813 INFO: Using random state 896462 for train-test-split
0:37:03.473285 INFO: Test AUC: 0.604
0:37:03.473669 INFO: Train AUC: 0.612
0:37:03.473711 INFO: AUC difference: 1.26%
0:37:04.261176 INFO: Resetting torch num_threads to 24
0:37:04.331320 PROGRESS: === Extracted 749330 precursors and 4008364 fragments ===
0:37:04.332746 INFO: === FDR correction performed with classifier version 7 ===
0:37:04.335792 PROGRESS: ============================= Precursor FDR =============================
0:37:04.336205 PROGRESS: Total precursors accumulated: 1,793
0:37:04.336346 PROGRESS: Target precursors: 1,776 (99.05%)
0:37:04.336407 PROGRESS: Decoy precursors: 17 (0.95%)
0:37:04.336462 PROGRESS: 
0:37:04.336513 PROGRESS: Precursor Summary:
0:37:04.341638 PROGRESS: Channel   0:	 0.050 FDR: 1,776; 0.010 FDR: 1,776; 0.001 FDR: 1,189
0:37:04.341947 PROGRESS: 
0:37:04.342030 PROGRESS: Protein Summary:
0:37:04.347242 PROGRESS: Channel   0:	 0.050 FDR: 1,484; 0.010 FDR: 1,484; 0.001 FDR: 1,024
0:37:04.347544 PROGRESS: =========================================================================
0:37:04.396481 INFO: Target number of precursors reached.
0:37:04.874998 INFO: fragments_df: keeping 5000 of 4008364 [sum(precursor_idx_mask)=41226 sum(mass_error_mask)=4008364 stop_rank=5000
0:37:06.260919 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:06.795296 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:07.764598 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:07.765834 INFO: Using score_cutoff 10.463674442768097 (fac=0.99, q=1)
0:37:07.767072 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:07.767357 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:07.767453 INFO: Updating optimization_manager: score_cutoff        : 11.025961135482788 -> 10.463674442768097
0:37:07.767588 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:07.979307 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:08.584789 INFO: === checking if optimization conditions were reached ===
0:37:08.592221 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:37:08.593066 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:37:08.593411 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:37:08.593714 INFO: ==============================================
0:37:08.594001 INFO: Starting optimization step 9.
0:37:08.594219 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:37:08.594422 INFO: Using rust extraction backend
0:37:08.594608 PROGRESS: Extracting batch of 250375 precursors
0:37:10.145456 INFO: === Search parameters used ===
0:37:10.146112 INFO: rt_error       : 805.6019897460938
0:37:10.146253 INFO: mobility_error : 0.1
0:37:10.146338 INFO: num_candidates : 3
0:37:10.146410 INFO: ms1_error      : 3
0:37:10.146463 INFO: ms2_error      : 10.0
0:37:10.146511 INFO: fwhm_rt        : 3.0
0:37:10.146557 INFO: quant_window   : 3
0:37:10.146601 INFO: ==============================================
0:37:18.809289 INFO: performing precursor FDR with 40 features
0:37:18.809605 INFO: Decoy channel: -1
0:37:18.809635 INFO: competitive: True
0:37:19.424477 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:20.668678 INFO: Estimating optimal hyperparameters - samples: 599,466, batch_size: 2,455, learning_rate: 7.74e-04
0:37:20.677754 INFO: Using random state 740270 for train-test-split
0:37:48.670832 INFO: Test AUC: 0.605
0:37:48.671222 INFO: Train AUC: 0.618
0:37:48.671262 INFO: AUC difference: 2.01%
0:37:49.451286 INFO: Resetting torch num_threads to 24
0:37:49.583987 PROGRESS: === Extracted 749333 precursors and 4008991 fragments ===
0:37:49.586255 INFO: === FDR correction performed with classifier version 8 ===
0:37:49.588464 PROGRESS: ============================= Precursor FDR =============================
0:37:49.588651 PROGRESS: Total precursors accumulated: 1,831
0:37:49.588720 PROGRESS: Target precursors: 1,813 (99.02%)
0:37:49.588775 PROGRESS: Decoy precursors: 18 (0.98%)
0:37:49.588833 PROGRESS: 
0:37:49.588891 PROGRESS: Precursor Summary:
0:37:49.591801 PROGRESS: Channel   0:	 0.050 FDR: 1,813; 0.010 FDR: 1,813; 0.001 FDR: 1,446
0:37:49.592060 PROGRESS: 
0:37:49.592125 PROGRESS: Protein Summary:
0:37:49.594958 PROGRESS: Channel   0:	 0.050 FDR: 1,514; 0.010 FDR: 1,514; 0.001 FDR: 1,229
0:37:49.595145 PROGRESS: =========================================================================
0:37:49.656331 INFO: Target number of precursors reached.
0:37:50.200798 INFO: fragments_df: keeping 5000 of 4008991 [sum(precursor_idx_mask)=42131 sum(mass_error_mask)=4008991 stop_rank=5000
0:37:51.430052 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:53.915568 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:55.214498 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:55.220378 INFO: Using score_cutoff 10.383732095718385 (fac=0.99, q=1)
0:37:55.220983 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:55.221076 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:55.221157 INFO: Updating optimization_manager: score_cutoff        : 10.463674442768097 -> 10.383732095718385
0:37:55.221233 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:55.679143 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:59.665552 INFO: === checking if optimization conditions were reached ===
0:37:59.745202 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:37:59.745478 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:37:59.745560 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:37:59.745628 INFO: ==============================================
0:37:59.745705 INFO: Starting optimization step 10.
0:37:59.745775 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:37:59.745854 INFO: Using rust extraction backend
0:37:59.745928 PROGRESS: Extracting batch of 250375 precursors
0:38:06.019119 INFO: === Search parameters used ===
0:38:06.019545 INFO: rt_error       : 805.6019897460938
0:38:06.019619 INFO: mobility_error : 0.1
0:38:06.019677 INFO: num_candidates : 3
0:38:06.019732 INFO: ms1_error      : 3
0:38:06.019786 INFO: ms2_error      : 10.0
0:38:06.019838 INFO: fwhm_rt        : 3.0
0:38:06.019894 INFO: quant_window   : 3
0:38:06.019944 INFO: ==============================================
0:39:22.915116 INFO: performing precursor FDR with 40 features
0:39:22.915382 INFO: Decoy channel: -1
0:39:22.915422 INFO: competitive: True
0:39:26.558849 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:31.455562 INFO: Estimating optimal hyperparameters - samples: 599,482, batch_size: 2,455, learning_rate: 7.74e-04
0:39:31.457171 INFO: Using random state 436524 for train-test-split
0:51:05.896203 INFO: Test AUC: 0.608
0:51:05.896741 INFO: Train AUC: 0.620
0:51:05.896832 INFO: AUC difference: 1.91%
0:51:06.742260 INFO: Resetting torch num_threads to 24
0:51:06.827624 PROGRESS: === Extracted 749353 precursors and 4009116 fragments ===
0:51:06.829576 INFO: === FDR correction performed with classifier version 9 ===
0:51:06.832377 PROGRESS: ============================= Precursor FDR =============================
0:51:06.832619 PROGRESS: Total precursors accumulated: 1,852
0:51:06.832707 PROGRESS: Target precursors: 1,834 (99.03%)
0:51:06.832800 PROGRESS: Decoy precursors: 18 (0.97%)
0:51:06.832863 PROGRESS: 
0:51:06.832934 PROGRESS: Precursor Summary:
0:51:06.835914 PROGRESS: Channel   0:	 0.050 FDR: 1,834; 0.010 FDR: 1,834; 0.001 FDR: 1,244
0:51:06.836145 PROGRESS: 
0:51:06.836232 PROGRESS: Protein Summary:
0:51:06.839510 PROGRESS: Channel   0:	 0.050 FDR: 1,539; 0.010 FDR: 1,539; 0.001 FDR: 1,056
0:51:06.839742 PROGRESS: =========================================================================
0:51:06.887206 INFO: Target number of precursors reached.
0:51:07.543625 INFO: fragments_df: keeping 5000 of 4009116 [sum(precursor_idx_mask)=42233 sum(mass_error_mask)=4009116 stop_rank=5000
0:51:09.151975 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:09.809968 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:11.252922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:11.254611 INFO: Using score_cutoff 9.83260065279007 (fac=0.99, q=1)
0:51:11.255908 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:11.256221 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:11.256403 INFO: Updating optimization_manager: score_cutoff        : 10.383732095718385 -> 9.83260065279007
0:51:11.256605 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:11.517192 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:12.214196 INFO: === checking if optimization conditions were reached ===
0:51:12.222491 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:51:12.223402 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:51:12.223800 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:51:12.224131 INFO: ==============================================
0:51:12.224447 INFO: Starting optimization step 11.
0:51:12.224713 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:12.224988 INFO: Using rust extraction backend
0:51:12.225222 PROGRESS: Extracting batch of 250375 precursors
0:51:14.716815 INFO: === Search parameters used ===
0:51:14.717937 INFO: rt_error       : 805.6019897460938
0:51:14.718186 INFO: mobility_error : 0.1
0:51:14.718384 INFO: num_candidates : 3
0:51:14.718542 INFO: ms1_error      : 3
0:51:14.718636 INFO: ms2_error      : 10.0
0:51:14.718712 INFO: fwhm_rt        : 3.0
0:51:14.718784 INFO: quant_window   : 3
0:51:14.718897 INFO: ==============================================
0:51:22.797520 INFO: performing precursor FDR with 40 features
0:51:22.797838 INFO: Decoy channel: -1
0:51:22.797872 INFO: competitive: True
0:51:23.303255 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:24.349029 INFO: Estimating optimal hyperparameters - samples: 599,486, batch_size: 2,455, learning_rate: 7.74e-04
0:51:24.354261 INFO: Using random state 578517 for train-test-split
0:52:00.268605 INFO: Test AUC: 0.609
0:52:00.269132 INFO: Train AUC: 0.621
0:52:00.269179 INFO: AUC difference: 1.95%
0:52:01.238227 INFO: Resetting torch num_threads to 24
0:52:01.346399 PROGRESS: === Extracted 749358 precursors and 4009074 fragments ===
0:52:01.347962 INFO: === FDR correction performed with classifier version 10 ===
0:52:01.350607 PROGRESS: ============================= Precursor FDR =============================
0:52:01.350830 PROGRESS: Total precursors accumulated: 2,056
0:52:01.350914 PROGRESS: Target precursors: 2,036 (99.03%)
0:52:01.350994 PROGRESS: Decoy precursors: 20 (0.97%)
0:52:01.351059 PROGRESS: 
0:52:01.351116 PROGRESS: Precursor Summary:
0:52:01.354093 PROGRESS: Channel   0:	 0.050 FDR: 2,036; 0.010 FDR: 2,036; 0.001 FDR: 1,387
0:52:01.354257 PROGRESS: 
0:52:01.354325 PROGRESS: Protein Summary:
0:52:01.357733 PROGRESS: Channel   0:	 0.050 FDR: 1,714; 0.010 FDR: 1,714; 0.001 FDR: 1,175
0:52:01.358000 PROGRESS: =========================================================================
0:52:01.430875 INFO: Target number of precursors reached.
0:52:02.123192 INFO: fragments_df: keeping 5000 of 4009074 [sum(precursor_idx_mask)=45712 sum(mass_error_mask)=4009074 stop_rank=5000
0:52:02.810902 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:03.445628 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:04.695832 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:04.697173 INFO: Using score_cutoff 8.805521972179413 (fac=0.99, q=1)
0:52:04.697870 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:04.697971 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:04.698034 INFO: Updating optimization_manager: score_cutoff        : 9.83260065279007 -> 8.805521972179413
0:52:04.698120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:04.801747 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:05.088856 INFO: === checking if optimization conditions were reached ===
0:52:05.095569 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:52:05.096341 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:52:05.096648 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:52:05.096778 INFO: ==============================================
0:52:05.096927 PROGRESS: Optimization finished for ms2_error.
0:52:05.903738 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:06.009738 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:06.289280 INFO: Starting optimization step 0.
0:52:06.290049 PROGRESS: === Extracting elution groups 0 to 63000 ===
0:52:06.290259 INFO: Using rust extraction backend
0:52:06.290381 PROGRESS: Extracting batch of 124210 precursors
0:52:07.248042 INFO: === Search parameters used ===
0:52:07.248985 INFO: rt_error       : 805.6019897460938
0:52:07.249208 INFO: mobility_error : 0.1
0:52:07.249363 INFO: num_candidates : 3
0:52:07.249440 INFO: ms1_error      : 3
0:52:07.249496 INFO: ms2_error      : 10.0
0:52:07.249568 INFO: fwhm_rt        : 3.0
0:52:07.249633 INFO: quant_window   : 3
0:52:07.249686 INFO: ==============================================
0:52:11.870838 INFO: performing precursor FDR with 40 features
0:52:11.871145 INFO: Decoy channel: -1
0:52:11.871192 INFO: competitive: True
0:52:12.165782 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:12.743152 INFO: Estimating optimal hyperparameters - samples: 297,384, batch_size: 1,218, learning_rate: 5.45e-04
0:52:12.744715 INFO: Using random state 440105 for train-test-split
0:52:31.009248 INFO: Test AUC: 0.612
0:52:31.009820 INFO: Train AUC: 0.630
0:52:31.009895 INFO: AUC difference: 2.90%
0:52:31.826448 INFO: Resetting torch num_threads to 24
0:52:31.884042 PROGRESS: === Extracted 371730 precursors and 1989257 fragments ===
0:52:31.886068 INFO: === FDR correction performed with classifier version 11 ===
0:52:31.889028 PROGRESS: ============================= Precursor FDR =============================
0:52:31.889608 PROGRESS: Total precursors accumulated: 1,014
0:52:31.889845 PROGRESS: Target precursors: 1,004 (99.01%)
0:52:31.889977 PROGRESS: Decoy precursors: 10 (0.99%)
0:52:31.890050 PROGRESS: 
0:52:31.890116 PROGRESS: Precursor Summary:
0:52:31.895520 PROGRESS: Channel   0:	 0.050 FDR: 1,004; 0.010 FDR: 1,004; 0.001 FDR:   514
0:52:31.896394 PROGRESS: 
0:52:31.896583 PROGRESS: Protein Summary:
0:52:31.902779 PROGRESS: Channel   0:	 0.050 FDR:   908; 0.010 FDR:   908; 0.001 FDR:   480
0:52:31.903721 PROGRESS: =========================================================================
0:52:31.953263 INFO: Target number of precursors reached.
0:52:32.282570 INFO: fragments_df: keeping 5000 of 1989257 [sum(precursor_idx_mask)=22728 sum(mass_error_mask)=1989257 stop_rank=5000
0:52:33.082218 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:33.554032 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:34.668066 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:34.669498 INFO: Using score_cutoff 8.5973175822258 (fac=0.99, q=1)
0:52:34.670655 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:34.670946 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:34.671073 INFO: Updating optimization_manager: score_cutoff        : 8.805521972179413 -> 8.5973175822258
0:52:34.671169 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:34.772867 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:35.046288 INFO: === checking if optimization conditions were reached ===
0:52:35.047053 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:52:35.053213 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 720.9689671696176
0:52:35.053871 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 720.9690.
0:52:35.054029 INFO: ==============================================
0:52:35.054201 INFO: Starting optimization step 1.
0:52:35.054324 PROGRESS: === Extracting elution groups 0 to 63000 ===
0:52:35.054457 INFO: Using rust extraction backend
0:52:35.054578 PROGRESS: Extracting batch of 124210 precursors
0:52:35.725442 INFO: === Search parameters used ===
0:52:35.726244 INFO: rt_error       : 720.9689671696176
0:52:35.726388 INFO: mobility_error : 0.1
0:52:35.726449 INFO: num_candidates : 3
0:52:35.726499 INFO: ms1_error      : 3
0:52:35.726553 INFO: ms2_error      : 10.0
0:52:35.726604 INFO: fwhm_rt        : 3.0
0:52:35.726647 INFO: quant_window   : 3
0:52:35.726688 INFO: ==============================================
0:52:39.409711 INFO: performing precursor FDR with 40 features
0:52:39.409955 INFO: Decoy channel: -1
0:52:39.409984 INFO: competitive: True
0:52:39.759246 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:40.487777 INFO: Estimating optimal hyperparameters - samples: 297,383, batch_size: 1,218, learning_rate: 5.45e-04
0:52:40.489829 INFO: Using random state 440105 for train-test-split
0:52:59.799850 INFO: Test AUC: 0.613
0:52:59.800233 INFO: Train AUC: 0.630
0:52:59.800279 INFO: AUC difference: 2.68%
0:53:00.824443 INFO: Resetting torch num_threads to 24
0:53:00.897715 PROGRESS: === Extracted 371729 precursors and 1988890 fragments ===
0:53:00.899724 INFO: === FDR correction performed with classifier version 11 ===
0:53:00.902966 PROGRESS: ============================= Precursor FDR =============================
0:53:00.903534 PROGRESS: Total precursors accumulated: 855
0:53:00.903741 PROGRESS: Target precursors: 847 (99.06%)
0:53:00.903857 PROGRESS: Decoy precursors: 8 (0.94%)
0:53:00.903926 PROGRESS: 
0:53:00.903984 PROGRESS: Precursor Summary:
0:53:00.909542 PROGRESS: Channel   0:	 0.050 FDR:   847; 0.010 FDR:   847; 0.001 FDR:   506
0:53:00.910131 PROGRESS: 
0:53:00.910321 PROGRESS: Protein Summary:
0:53:00.916427 PROGRESS: Channel   0:	 0.050 FDR:   774; 0.010 FDR:   774; 0.001 FDR:   470
0:53:00.917052 PROGRESS: =========================================================================
0:53:00.953732 INFO: Target number of precursors not reached yet.
0:53:01.689903 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:01.811741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:02.110490 INFO: === skipping optimization until target number of precursors are found ===
0:53:02.111413 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:53:02.111715 INFO: Starting optimization step 2.
0:53:02.111864 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:53:02.112027 INFO: Using rust extraction backend
0:53:02.112183 PROGRESS: Extracting batch of 126165 precursors
0:53:03.147441 INFO: === Search parameters used ===
0:53:03.148373 INFO: rt_error       : 720.9689671696176
0:53:03.148573 INFO: mobility_error : 0.1
0:53:03.148776 INFO: num_candidates : 3
0:53:03.148963 INFO: ms1_error      : 3
0:53:03.149127 INFO: ms2_error      : 10.0
0:53:03.149290 INFO: fwhm_rt        : 3.0
0:53:03.149402 INFO: quant_window   : 3
0:53:03.149472 INFO: ==============================================
0:53:07.420104 INFO: performing precursor FDR with 40 features
0:53:07.420366 INFO: Decoy channel: -1
0:53:07.420404 INFO: competitive: True
0:53:08.162741 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:09.097378 INFO: Estimating optimal hyperparameters - samples: 599,472, batch_size: 2,455, learning_rate: 7.74e-04
0:53:09.100498 INFO: Using random state 440105 for train-test-split
0:53:36.867101 INFO: Test AUC: 0.614
0:53:36.867586 INFO: Train AUC: 0.625
0:53:36.867641 INFO: AUC difference: 1.79%
0:53:38.329824 INFO: Resetting torch num_threads to 24
0:53:39.132859 PROGRESS: === Extracted 749341 precursors and 4008670 fragments ===
0:53:39.136059 INFO: === FDR correction performed with classifier version 11 ===
0:53:39.142338 PROGRESS: ============================= Precursor FDR =============================
0:53:39.143340 PROGRESS: Total precursors accumulated: 1,999
0:53:39.143688 PROGRESS: Target precursors: 1,980 (99.05%)
0:53:39.143973 PROGRESS: Decoy precursors: 19 (0.95%)
0:53:39.144263 PROGRESS: 
0:53:39.144540 PROGRESS: Precursor Summary:
0:53:39.156331 PROGRESS: Channel   0:	 0.050 FDR: 1,980; 0.010 FDR: 1,980; 0.001 FDR: 1,227
0:53:39.157122 PROGRESS: 
0:53:39.157437 PROGRESS: Protein Summary:
0:53:39.171922 PROGRESS: Channel   0:	 0.050 FDR: 1,664; 0.010 FDR: 1,664; 0.001 FDR: 1,044
0:53:39.172834 PROGRESS: =========================================================================
0:53:39.218753 INFO: Target number of precursors reached.
0:53:39.853229 INFO: fragments_df: keeping 5000 of 4008670 [sum(precursor_idx_mask)=44275 sum(mass_error_mask)=4008670 stop_rank=5000
0:53:41.057319 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:53:41.760319 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:42.858442 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:42.859630 INFO: Using score_cutoff 8.183131236076354 (fac=0.99, q=1)
0:53:42.860352 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:42.860462 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:42.860537 INFO: Updating optimization_manager: score_cutoff        : 8.5973175822258 -> 8.183131236076354
0:53:42.860638 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:43.072540 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:43.566416 INFO: === checking if optimization conditions were reached ===
0:53:43.567370 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:53:43.574837 INFO: Updating optimization_manager: rt_error            : 720.9689671696176 -> 841.27320809359
0:53:43.575664 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 841.2732.
0:53:43.575899 INFO: ==============================================
0:53:43.576105 INFO: Starting optimization step 3.
0:53:43.576272 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:53:43.576526 INFO: Using rust extraction backend
0:53:43.576721 PROGRESS: Extracting batch of 250375 precursors
0:53:45.907507 INFO: === Search parameters used ===
0:53:45.908781 INFO: rt_error       : 841.27320809359
0:53:45.909012 INFO: mobility_error : 0.1
0:53:45.909171 INFO: num_candidates : 3
0:53:45.909321 INFO: ms1_error      : 3
0:53:45.909492 INFO: ms2_error      : 10.0
0:53:45.909663 INFO: fwhm_rt        : 3.0
0:53:45.909791 INFO: quant_window   : 3
0:53:45.909960 INFO: ==============================================
0:53:57.650890 INFO: performing precursor FDR with 40 features
0:53:57.651384 INFO: Decoy channel: -1
0:53:57.651451 INFO: competitive: True
0:53:58.600692 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:00.071855 INFO: Estimating optimal hyperparameters - samples: 599,476, batch_size: 2,455, learning_rate: 7.74e-04
0:54:00.079777 INFO: Using random state 440105 for train-test-split
0:54:54.445765 INFO: Test AUC: 0.614
0:54:54.445937 INFO: Train AUC: 0.624
0:54:54.445977 INFO: AUC difference: 1.65%
0:54:55.082470 INFO: Resetting torch num_threads to 24
0:54:55.167436 PROGRESS: === Extracted 749346 precursors and 4009340 fragments ===
0:54:55.168106 INFO: === FDR correction performed with classifier version 11 ===
0:54:55.169417 PROGRESS: ============================= Precursor FDR =============================
0:54:55.169526 PROGRESS: Total precursors accumulated: 2,122
0:54:55.169605 PROGRESS: Target precursors: 2,101 (99.01%)
0:54:55.169672 PROGRESS: Decoy precursors: 21 (0.99%)
0:54:55.169733 PROGRESS: 
0:54:55.169793 PROGRESS: Precursor Summary:
0:54:55.172010 PROGRESS: Channel   0:	 0.050 FDR: 2,101; 0.010 FDR: 2,101; 0.001 FDR: 1,361
0:54:55.172127 PROGRESS: 
0:54:55.172202 PROGRESS: Protein Summary:
0:54:55.175133 PROGRESS: Channel   0:	 0.050 FDR: 1,758; 0.010 FDR: 1,758; 0.001 FDR: 1,151
0:54:55.175256 PROGRESS: =========================================================================
0:54:55.202962 INFO: Target number of precursors reached.
0:54:55.857948 INFO: fragments_df: keeping 5000 of 4009340 [sum(precursor_idx_mask)=46829 sum(mass_error_mask)=4009340 stop_rank=5000
0:54:56.241784 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:54:56.776738 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:54:57.952727 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:54:57.953312 INFO: Using score_cutoff 8.696832618713378 (fac=0.99, q=1)
0:54:57.953725 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:54:57.953815 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:54:57.953897 INFO: Updating optimization_manager: score_cutoff        : 8.183131236076354 -> 8.696832618713378
0:54:57.953973 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:58.038632 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:58.226696 INFO: === checking if optimization conditions were reached ===
0:54:58.227071 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:54:58.231208 INFO: Updating optimization_manager: rt_error            : 841.27320809359 -> 771.4977426156273
0:54:58.231347 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 771.4977.
0:54:58.231435 INFO: ==============================================
0:54:58.231539 INFO: Starting optimization step 4.
0:54:58.231621 PROGRESS: === Extracting elution groups 0 to 63000 ===
0:54:58.231724 INFO: Using rust extraction backend
0:54:58.231820 PROGRESS: Extracting batch of 124210 precursors
0:54:58.477022 INFO: === Search parameters used ===
0:54:58.477330 INFO: rt_error       : 771.4977426156273
0:54:58.477439 INFO: mobility_error : 0.1
0:54:58.477516 INFO: num_candidates : 3
0:54:58.477574 INFO: ms1_error      : 3
0:54:58.477641 INFO: ms2_error      : 10.0
0:54:58.477700 INFO: fwhm_rt        : 3.0
0:54:58.477760 INFO: quant_window   : 3
0:54:58.477823 INFO: ==============================================
0:55:01.261429 INFO: performing precursor FDR with 40 features
0:55:01.261563 INFO: Decoy channel: -1
0:55:01.261596 INFO: competitive: True
0:55:01.382244 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:01.578237 INFO: Estimating optimal hyperparameters - samples: 297,383, batch_size: 1,218, learning_rate: 5.45e-04
0:55:01.579136 INFO: Using random state 440105 for train-test-split
0:55:12.135898 INFO: Test AUC: 0.609
0:55:12.136078 INFO: Train AUC: 0.630
0:55:12.136118 INFO: AUC difference: 3.33%
0:55:12.658267 INFO: Resetting torch num_threads to 24
0:55:12.684041 PROGRESS: === Extracted 371729 precursors and 1989621 fragments ===
0:55:12.684678 INFO: === FDR correction performed with classifier version 11 ===
0:55:12.685638 PROGRESS: ============================= Precursor FDR =============================
0:55:12.685777 PROGRESS: Total precursors accumulated: 1,047
0:55:12.685852 PROGRESS: Target precursors: 1,037 (99.04%)
0:55:12.685921 PROGRESS: Decoy precursors: 10 (0.96%)
0:55:12.685992 PROGRESS: 
0:55:12.686049 PROGRESS: Precursor Summary:
0:55:12.687899 PROGRESS: Channel   0:	 0.050 FDR: 1,037; 0.010 FDR: 1,037; 0.001 FDR:   457
0:55:12.688025 PROGRESS: 
0:55:12.688099 PROGRESS: Protein Summary:
0:55:12.690297 PROGRESS: Channel   0:	 0.050 FDR:   945; 0.010 FDR:   945; 0.001 FDR:   424
0:55:12.690409 PROGRESS: =========================================================================
0:55:12.706027 INFO: Target number of precursors reached.
0:55:12.959025 INFO: fragments_df: keeping 5000 of 1989621 [sum(precursor_idx_mask)=23248 sum(mass_error_mask)=1989621 stop_rank=5000
0:55:13.288552 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:13.659381 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:14.700505 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:14.701068 INFO: Using score_cutoff 8.312030430221556 (fac=0.99, q=1)
0:55:14.701565 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:14.701689 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:14.701760 INFO: Updating optimization_manager: score_cutoff        : 8.696832618713378 -> 8.312030430221556
0:55:14.701835 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:14.790629 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:14.993973 INFO: === checking if optimization conditions were reached ===
0:55:14.994272 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:55:14.997515 INFO: Updating optimization_manager: rt_error            : 771.4977426156273 -> 734.6039739016281
0:55:14.997642 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 734.6040.
0:55:14.997720 INFO: ==============================================
0:55:14.997813 INFO: Starting optimization step 5.
0:55:14.997885 PROGRESS: === Extracting elution groups 0 to 63000 ===
0:55:14.997973 INFO: Using rust extraction backend
0:55:14.998052 PROGRESS: Extracting batch of 124210 precursors
0:55:15.244899 INFO: === Search parameters used ===
0:55:15.245210 INFO: rt_error       : 734.6039739016281
0:55:15.245295 INFO: mobility_error : 0.1
0:55:15.245356 INFO: num_candidates : 3
0:55:15.245419 INFO: ms1_error      : 3
0:55:15.245487 INFO: ms2_error      : 10.0
0:55:15.245559 INFO: fwhm_rt        : 3.0
0:55:15.245625 INFO: quant_window   : 3
0:55:15.245682 INFO: ==============================================
0:55:17.845819 INFO: performing precursor FDR with 40 features
0:55:17.845963 INFO: Decoy channel: -1
0:55:17.845999 INFO: competitive: True
0:55:17.979563 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:18.191833 INFO: Estimating optimal hyperparameters - samples: 297,391, batch_size: 1,218, learning_rate: 5.45e-04
0:55:18.192595 INFO: Using random state 440105 for train-test-split
0:55:28.262190 INFO: Test AUC: 0.609
0:55:28.262340 INFO: Train AUC: 0.631
0:55:28.262380 INFO: AUC difference: 3.50%
0:55:28.767687 INFO: Resetting torch num_threads to 24
0:55:28.798249 PROGRESS: === Extracted 371739 precursors and 1989333 fragments ===
0:55:28.798961 INFO: === FDR correction performed with classifier version 11 ===
0:55:28.800094 PROGRESS: ============================= Precursor FDR =============================
0:55:28.800267 PROGRESS: Total precursors accumulated: 765
0:55:28.800355 PROGRESS: Target precursors: 758 (99.08%)
0:55:28.800429 PROGRESS: Decoy precursors: 7 (0.92%)
0:55:28.800497 PROGRESS: 
0:55:28.800561 PROGRESS: Precursor Summary:
0:55:28.801850 PROGRESS: Channel   0:	 0.050 FDR:   758; 0.010 FDR:   758; 0.001 FDR:   413
0:55:28.801948 PROGRESS: 
0:55:28.802009 PROGRESS: Protein Summary:
0:55:28.803479 PROGRESS: Channel   0:	 0.050 FDR:   706; 0.010 FDR:   706; 0.001 FDR:   391
0:55:28.803578 PROGRESS: =========================================================================
0:55:28.814161 INFO: Target number of precursors not reached yet.
0:55:29.157340 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:29.242477 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:29.438922 INFO: === skipping optimization until target number of precursors are found ===
0:55:29.439299 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:55:29.439456 INFO: Starting optimization step 6.
0:55:29.439553 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:55:29.439670 INFO: Using rust extraction backend
0:55:29.439776 PROGRESS: Extracting batch of 126165 precursors
0:55:29.683385 INFO: === Search parameters used ===
0:55:29.683694 INFO: rt_error       : 734.6039739016281
0:55:29.683783 INFO: mobility_error : 0.1
0:55:29.683848 INFO: num_candidates : 3
0:55:29.683914 INFO: ms1_error      : 3
0:55:29.683973 INFO: ms2_error      : 10.0
0:55:29.684029 INFO: fwhm_rt        : 3.0
0:55:29.684085 INFO: quant_window   : 3
0:55:29.684142 INFO: ==============================================
0:55:32.578373 INFO: performing precursor FDR with 40 features
0:55:32.578496 INFO: Decoy channel: -1
0:55:32.578530 INFO: competitive: True
0:55:33.000555 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:33.434916 INFO: Estimating optimal hyperparameters - samples: 599,489, batch_size: 2,455, learning_rate: 7.74e-04
0:55:33.436221 INFO: Using random state 440105 for train-test-split
0:55:49.930359 INFO: Test AUC: 0.611
0:55:49.930482 INFO: Train AUC: 0.624
0:55:49.930514 INFO: AUC difference: 2.11%
0:55:50.570469 INFO: Resetting torch num_threads to 24
0:55:50.713059 PROGRESS: === Extracted 749362 precursors and 4009894 fragments ===
0:55:50.713707 INFO: === FDR correction performed with classifier version 11 ===
0:55:50.714711 PROGRESS: ============================= Precursor FDR =============================
0:55:50.714805 PROGRESS: Total precursors accumulated: 2,135
0:55:50.714869 PROGRESS: Target precursors: 2,114 (99.02%)
0:55:50.714925 PROGRESS: Decoy precursors: 21 (0.98%)
0:55:50.714993 PROGRESS: 
0:55:50.715048 PROGRESS: Precursor Summary:
0:55:50.716623 PROGRESS: Channel   0:	 0.050 FDR: 2,114; 0.010 FDR: 2,114; 0.001 FDR: 1,514
0:55:50.716732 PROGRESS: 
0:55:50.716793 PROGRESS: Protein Summary:
0:55:50.718890 PROGRESS: Channel   0:	 0.050 FDR: 1,760; 0.010 FDR: 1,760; 0.001 FDR: 1,275
0:55:50.718995 PROGRESS: =========================================================================
0:55:50.727528 INFO: Target number of precursors reached.
0:55:51.349396 INFO: fragments_df: keeping 5000 of 4009894 [sum(precursor_idx_mask)=47176 sum(mass_error_mask)=4009894 stop_rank=5000
0:55:51.694434 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:52.256977 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:53.357856 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:53.358403 INFO: Using score_cutoff 8.503052630424499 (fac=0.99, q=1)
0:55:53.358818 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:53.358907 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:53.358988 INFO: Updating optimization_manager: score_cutoff        : 8.312030430221556 -> 8.503052630424499
0:55:53.359065 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:53.442801 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:53.626213 INFO: === checking if optimization conditions were reached ===
0:55:53.626516 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:55:53.627715 INFO: Updating optimization_manager: rt_error            : 734.6039739016281 -> 734.6039739016281
0:55:53.627869 INFO: Updating optimization_manager: classifier_version  : 11 -> 18
0:55:53.628016 INFO: Updating optimization_manager: score_cutoff        : 8.503052630424499 -> 8.503052630424499
0:55:53.628132 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:53.628254 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:53.628374 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 734.6040 found after 5 searches.
0:55:53.628455 INFO: ==============================================
0:55:53.628550 PROGRESS: Optimization finished for rt_error.
0:55:53.944185 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:54.026753 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:54.225929 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:55:54.226214 PROGRESS: ==============================================
0:55:54.226312 PROGRESS: ms2_error      : 10.0000
0:55:54.226388 PROGRESS: rt_error       : 734.6040
0:55:54.226475 PROGRESS: ==============================================
0:55:54.241280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:02.455417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:21.967014 INFO: Using rust extraction backend
0:56:21.967720 PROGRESS: Extracting batch of 11997144 precursors
0:56:40.164130 INFO: === Search parameters used ===
0:56:40.164692 INFO: rt_error       : 734.6039739016281
0:56:40.164782 INFO: mobility_error : 0.1
0:56:40.164844 INFO: num_candidates : 3
0:56:40.164896 INFO: ms1_error      : 3
0:56:40.164946 INFO: ms2_error      : 10.0
0:56:40.164998 INFO: fwhm_rt        : 3.0
0:56:40.165043 INFO: quant_window   : 3
0:56:40.165093 INFO: ==============================================
0:58:16.972189 INFO: Removed 4241324 precursors with score below cutoff 8.503052630424499
0:59:02.414040 INFO: performing precursor FDR with 40 features
0:59:02.414296 INFO: Decoy channel: -1
0:59:02.414335 INFO: competitive: True
0:59:06.455404 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:27.473191 INFO: Estimating optimal hyperparameters - samples: 25,399,767, batch_size: 4,096, learning_rate: 1.00e-03
0:59:27.567138 INFO: Using random state 730466 for train-test-split
1:08:55.647747 INFO: Test AUC: 0.621
1:08:55.648023 INFO: Train AUC: 0.622
1:08:55.648066 INFO: AUC difference: 0.07%
1:09:04.007425 INFO: Resetting torch num_threads to 24
1:09:06.720567 PROGRESS: ============================= Precursor FDR =============================
1:09:06.720881 PROGRESS: Total precursors accumulated: 90,941
1:09:06.720953 PROGRESS: Target precursors: 90,041 (99.01%)
1:09:06.721010 PROGRESS: Decoy precursors: 900 (0.99%)
1:09:06.721060 PROGRESS: 
1:09:06.721106 PROGRESS: Precursor Summary:
1:09:06.749089 PROGRESS: Channel   0:	 0.050 FDR: 90,041; 0.010 FDR: 90,041; 0.001 FDR: 54,333
1:09:06.749308 PROGRESS: 
1:09:06.749373 PROGRESS: Protein Summary:
1:09:06.785743 PROGRESS: Channel   0:	 0.050 FDR: 14,404; 0.010 FDR: 14,404; 0.001 FDR: 9,260
1:09:06.785985 PROGRESS: =========================================================================
1:09:06.960266 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
1:09:07.146466 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
1:09:07.453247 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:09:08.079324 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
1:09:08.079488 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:09:08.079617 INFO: Initializing TimingManager
1:09:08.080353 INFO: Initializing RawFileManager
1:09:26.846367 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.
1:09:26.858843 INFO: Determining DIA cycle
1:09:26.879007 INFO: Found cycle with start 0.00 min and length 300.
1:09:27.070342 INFO: RT (min)            : 0.0 - 26.9
1:09:27.070449 INFO: RT duration (sec)   : 1611.2
1:09:27.070484 INFO: RT duration (min)   : 26.9
1:09:27.070516 INFO: Cycle len (scans)   : 300
1:09:27.070543 INFO: Cycle len (sec)     : 1.65
1:09:27.070571 INFO: Number of cycles    : 977
1:09:27.070596 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:09:27.070639 INFO: Creating DIA data object took: 18.99017071723938
1:09:29.144617 INFO: Creating DIA data NG object took: 2.073823928833008
1:09:30.783670 INFO: Initializing CalibrationManager
1:09:30.784040 INFO: Setting up calibration estimators ..
1:09:30.784119 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:09:30.784226 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'}' ..
1:09:30.784355 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:09:30.784428 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:09:30.784499 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}}' ..
1:09:30.784566 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:09:30.784649 INFO: Done setting up calibration estimators.
1:09:30.784866 INFO: Initializing OptimizationManager
1:09:30.785036 INFO: initial parameter: ms1_error = 3
1:09:30.785108 INFO: initial parameter: ms2_error = 10
1:09:30.785167 INFO: initial parameter: rt_error = 805.6004638671875
1:09:30.785225 INFO: initial parameter: mobility_error = 0.1
1:09:30.785281 INFO: initial parameter: num_candidates = 1
1:09:30.785331 INFO: initial parameter: fwhm_rt = 5
1:09:30.785382 INFO: initial parameter: fwhm_mobility = 0.01
1:09:30.785439 INFO: initial parameter: score_cutoff = 0
1:09:30.785491 INFO: initial parameter: classifier_version = -1
1:09:30.785576 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:09:30.785894 INFO: FDRManager: loading saved state not requested, will be initialized.
1:09:30.785935 INFO: Initializing FDRManager
1:09:30.785985 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:09:32.675205 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:09:33.737554 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:09:33.738045 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
1:09:33.738192 PROGRESS: Starting initial search for precursors.
1:09:33.738308 INFO: Starting optimization step 0.
1:09:33.738387 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:09:33.738469 INFO: Using rust extraction backend
1:09:33.738574 PROGRESS: Extracting batch of 1976 precursors
1:09:33.744445 INFO: === Search parameters used ===
1:09:33.744603 INFO: rt_error       : 805.6004638671875
1:09:33.744678 INFO: mobility_error : 0.1
1:09:33.744745 INFO: num_candidates : 1
1:09:33.744805 INFO: ms1_error      : 3
1:09:33.744861 INFO: ms2_error      : 10
1:09:33.744920 INFO: fwhm_rt        : 5
1:09:33.744975 INFO: quant_window   : 3
1:09:33.745033 INFO: ==============================================
1:09:33.820818 INFO: performing precursor FDR with 40 features
1:09:33.820925 INFO: Decoy channel: -1
1:09:33.820961 INFO: competitive: True
1:09:33.822638 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:33.825119 INFO: Estimating optimal hyperparameters - samples: 1,577, batch_size: 128, learning_rate: 1.77e-04
1:09:33.826292 INFO: Using random state 276760 for train-test-split
1:09:34.026922 INFO: Test AUC: 0.523
1:09:34.027041 INFO: Train AUC: 0.538
1:09:34.027081 INFO: AUC difference: 2.79%
1:09:34.381583 INFO: Resetting torch num_threads to 24
1:09:34.384334 PROGRESS: === Extracted 1972 precursors and 11008 fragments ===
1:09:34.384870 INFO: === FDR correction performed with classifier version -1 ===
1:09:34.385550 PROGRESS: ============================= Precursor FDR =============================
1:09:34.385663 PROGRESS: Total precursors accumulated: 3
1:09:34.385737 PROGRESS: Target precursors: 3 (100.00%)
1:09:34.385802 PROGRESS: Decoy precursors: 0 (0.00%)
1:09:34.385863 PROGRESS: 
1:09:34.385917 PROGRESS: Precursor Summary:
1:09:34.387403 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1:09:34.387518 PROGRESS: 
1:09:34.387591 PROGRESS: Protein Summary:
1:09:34.389286 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1:09:34.389391 PROGRESS: =========================================================================
1:09:34.389857 INFO: Target number of precursors not reached yet.
1:09:34.491332 INFO: Starting optimization step 1.
1:09:34.491569 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:09:34.491678 INFO: Using rust extraction backend
1:09:34.491789 PROGRESS: Extracting batch of 3939 precursors
1:09:34.502357 INFO: === Search parameters used ===
1:09:34.502710 INFO: rt_error       : 805.6004638671875
1:09:34.502784 INFO: mobility_error : 0.1
1:09:34.502844 INFO: num_candidates : 1
1:09:34.502898 INFO: ms1_error      : 3
1:09:34.502951 INFO: ms2_error      : 10
1:09:34.503027 INFO: fwhm_rt        : 5
1:09:34.503080 INFO: quant_window   : 3
1:09:34.503133 INFO: ==============================================
1:09:34.607508 INFO: performing precursor FDR with 40 features
1:09:34.607629 INFO: Decoy channel: -1
1:09:34.607662 INFO: competitive: True
1:09:34.613996 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:34.617482 INFO: Estimating optimal hyperparameters - samples: 4,720, batch_size: 128, learning_rate: 1.77e-04
1:09:34.617592 INFO: Using random state 92399 for train-test-split
1:09:35.229001 INFO: Test AUC: 0.531
1:09:35.229120 INFO: Train AUC: 0.572
1:09:35.229153 INFO: AUC difference: 7.13%
1:09:35.229178 WARNING: AUC difference > 5%. This may indicate overfitting.
1:09:35.546520 INFO: Resetting torch num_threads to 24
1:09:35.549984 PROGRESS: === Extracted 5901 precursors and 33050 fragments ===
1:09:35.550447 INFO: === FDR correction performed with classifier version -1 ===
1:09:35.550968 PROGRESS: ============================= Precursor FDR =============================
1:09:35.551078 PROGRESS: Total precursors accumulated: 0
1:09:35.551136 PROGRESS: Target precursors: 0 (0.00%)
1:09:35.551186 PROGRESS: Decoy precursors: 0 (0.00%)
1:09:35.551231 PROGRESS: 
1:09:35.551276 PROGRESS: Precursor Summary:
1:09:35.551405 PROGRESS: 
1:09:35.551468 PROGRESS: Protein Summary:
1:09:35.551543 PROGRESS: =========================================================================
1:09:35.551834 INFO: Target number of precursors not reached yet.
1:09:35.653469 INFO: Starting optimization step 2.
1:09:35.654191 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:09:35.654320 INFO: Using rust extraction backend
1:09:35.654392 PROGRESS: Extracting batch of 7882 precursors
1:09:35.669588 INFO: === Search parameters used ===
1:09:35.669789 INFO: rt_error       : 805.6004638671875
1:09:35.669843 INFO: mobility_error : 0.1
1:09:35.669890 INFO: num_candidates : 1
1:09:35.669932 INFO: ms1_error      : 3
1:09:35.669973 INFO: ms2_error      : 10
1:09:35.670024 INFO: fwhm_rt        : 5
1:09:35.670079 INFO: quant_window   : 3
1:09:35.670139 INFO: ==============================================
1:09:35.804897 INFO: performing precursor FDR with 40 features
1:09:35.805002 INFO: Decoy channel: -1
1:09:35.805026 INFO: competitive: True
1:09:35.811594 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:35.817546 INFO: Estimating optimal hyperparameters - samples: 11,014, batch_size: 128, learning_rate: 1.77e-04
1:09:35.817722 INFO: Using random state 639479 for train-test-split
1:09:36.816927 INFO: Test AUC: 0.561
1:09:36.817023 INFO: Train AUC: 0.594
1:09:36.817055 INFO: AUC difference: 5.61%
1:09:36.817080 WARNING: AUC difference > 5%. This may indicate overfitting.
1:09:38.120061 INFO: Resetting torch num_threads to 24
1:09:38.127973 PROGRESS: === Extracted 13768 precursors and 77379 fragments ===
1:09:38.128608 INFO: === FDR correction performed with classifier version -1 ===
1:09:38.129275 PROGRESS: ============================= Precursor FDR =============================
1:09:38.129375 PROGRESS: Total precursors accumulated: 0
1:09:38.129479 PROGRESS: Target precursors: 0 (0.00%)
1:09:38.129546 PROGRESS: Decoy precursors: 0 (0.00%)
1:09:38.129602 PROGRESS: 
1:09:38.129659 PROGRESS: Precursor Summary:
1:09:38.129809 PROGRESS: 
1:09:38.129882 PROGRESS: Protein Summary:
1:09:38.129982 PROGRESS: =========================================================================
1:09:38.130730 INFO: Target number of precursors not reached yet.
1:09:38.259684 INFO: Starting optimization step 3.
1:09:38.259956 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:09:38.260051 INFO: Using rust extraction backend
1:09:38.260125 PROGRESS: Extracting batch of 15793 precursors
1:09:38.290284 INFO: === Search parameters used ===
1:09:38.290581 INFO: rt_error       : 805.6004638671875
1:09:38.290650 INFO: mobility_error : 0.1
1:09:38.290713 INFO: num_candidates : 1
1:09:38.290777 INFO: ms1_error      : 3
1:09:38.290830 INFO: ms2_error      : 10
1:09:38.290882 INFO: fwhm_rt        : 5
1:09:38.290940 INFO: quant_window   : 3
1:09:38.291020 INFO: ==============================================
1:09:38.536521 INFO: performing precursor FDR with 40 features
1:09:38.536641 INFO: Decoy channel: -1
1:09:38.536671 INFO: competitive: True
1:09:38.552167 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:38.563241 INFO: Estimating optimal hyperparameters - samples: 23,614, batch_size: 128, learning_rate: 1.77e-04
1:09:38.563455 INFO: Using random state 47871 for train-test-split
1:09:41.044981 INFO: Test AUC: 0.578
1:09:41.045104 INFO: Train AUC: 0.607
1:09:41.045141 INFO: AUC difference: 4.79%
1:09:41.399714 INFO: Resetting torch num_threads to 24
1:09:41.412023 PROGRESS: === Extracted 29518 precursors and 165821 fragments ===
1:09:41.412690 INFO: === FDR correction performed with classifier version -1 ===
1:09:41.413469 PROGRESS: ============================= Precursor FDR =============================
1:09:41.413577 PROGRESS: Total precursors accumulated: 7
1:09:41.413655 PROGRESS: Target precursors: 7 (100.00%)
1:09:41.413720 PROGRESS: Decoy precursors: 0 (0.00%)
1:09:41.413776 PROGRESS: 
1:09:41.413839 PROGRESS: Precursor Summary:
1:09:41.415228 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
1:09:41.415333 PROGRESS: 
1:09:41.415412 PROGRESS: Protein Summary:
1:09:41.416930 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
1:09:41.417025 PROGRESS: =========================================================================
1:09:41.417935 INFO: Target number of precursors not reached yet.
1:09:41.566882 INFO: Starting optimization step 4.
1:09:41.567130 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:09:41.567211 INFO: Using rust extraction backend
1:09:41.567273 PROGRESS: Extracting batch of 31556 precursors
1:09:41.623030 INFO: === Search parameters used ===
1:09:41.623259 INFO: rt_error       : 805.6004638671875
1:09:41.623315 INFO: mobility_error : 0.1
1:09:41.623362 INFO: num_candidates : 1
1:09:41.623407 INFO: ms1_error      : 3
1:09:41.623466 INFO: ms2_error      : 10
1:09:41.623509 INFO: fwhm_rt        : 5
1:09:41.623550 INFO: quant_window   : 3
1:09:41.623589 INFO: ==============================================
1:09:42.063666 INFO: performing precursor FDR with 40 features
1:09:42.063764 INFO: Decoy channel: -1
1:09:42.063788 INFO: competitive: True
1:09:42.087325 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:42.103235 INFO: Estimating optimal hyperparameters - samples: 48,803, batch_size: 199, learning_rate: 2.20e-04
1:09:42.103456 INFO: Using random state 785334 for train-test-split
1:09:45.432092 INFO: Test AUC: 0.579
1:09:45.432204 INFO: Train AUC: 0.610
1:09:45.432235 INFO: AUC difference: 5.16%
1:09:45.432259 WARNING: AUC difference > 5%. This may indicate overfitting.
1:09:45.788032 INFO: Resetting torch num_threads to 24
1:09:45.810983 PROGRESS: === Extracted 61004 precursors and 342567 fragments ===
1:09:45.811693 INFO: === FDR correction performed with classifier version -1 ===
1:09:45.812589 PROGRESS: ============================= Precursor FDR =============================
1:09:45.812725 PROGRESS: Total precursors accumulated: 349
1:09:45.812805 PROGRESS: Target precursors: 346 (99.14%)
1:09:45.812870 PROGRESS: Decoy precursors: 3 (0.86%)
1:09:45.812926 PROGRESS: 
1:09:45.812989 PROGRESS: Precursor Summary:
1:09:45.814508 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   346; 0.001 FDR:   269
1:09:45.814629 PROGRESS: 
1:09:45.814704 PROGRESS: Protein Summary:
1:09:45.816399 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:   255
1:09:45.816518 PROGRESS: =========================================================================
1:09:45.818545 INFO: Target number of precursors not reached yet.
1:09:46.038534 INFO: Starting optimization step 5.
1:09:46.038784 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:09:46.038868 INFO: Using rust extraction backend
1:09:46.038954 PROGRESS: Extracting batch of 63064 precursors
1:09:46.153500 INFO: === Search parameters used ===
1:09:46.153790 INFO: rt_error       : 805.6004638671875
1:09:46.153870 INFO: mobility_error : 0.1
1:09:46.153930 INFO: num_candidates : 1
1:09:46.153990 INFO: ms1_error      : 3
1:09:46.154057 INFO: ms2_error      : 10
1:09:46.154125 INFO: fwhm_rt        : 5
1:09:46.154185 INFO: quant_window   : 3
1:09:46.154243 INFO: ==============================================
1:09:46.952531 INFO: performing precursor FDR with 40 features
1:09:46.952656 INFO: Decoy channel: -1
1:09:46.952686 INFO: competitive: True
1:09:47.028158 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:47.077288 INFO: Estimating optimal hyperparameters - samples: 99,117, batch_size: 405, learning_rate: 3.14e-04
1:09:47.077640 INFO: Using random state 445593 for train-test-split
1:09:52.808412 INFO: Test AUC: 0.590
1:09:52.808553 INFO: Train AUC: 0.611
1:09:52.808590 INFO: AUC difference: 3.45%
1:09:53.194144 INFO: Resetting torch num_threads to 24
1:09:53.234531 PROGRESS: === Extracted 123897 precursors and 693983 fragments ===
1:09:53.235300 INFO: === FDR correction performed with classifier version -1 ===
1:09:53.236246 PROGRESS: ============================= Precursor FDR =============================
1:09:53.236380 PROGRESS: Total precursors accumulated: 689
1:09:53.236452 PROGRESS: Target precursors: 683 (99.13%)
1:09:53.236516 PROGRESS: Decoy precursors: 6 (0.87%)
1:09:53.236583 PROGRESS: 
1:09:53.236640 PROGRESS: Precursor Summary:
1:09:53.238196 PROGRESS: Channel   0:	 0.050 FDR:   683; 0.010 FDR:   683; 0.001 FDR:   257
1:09:53.238311 PROGRESS: 
1:09:53.238379 PROGRESS: Protein Summary:
1:09:53.240258 PROGRESS: Channel   0:	 0.050 FDR:   628; 0.010 FDR:   628; 0.001 FDR:   243
1:09:53.240379 PROGRESS: =========================================================================
1:09:53.243685 INFO: Target number of precursors not reached yet.
1:09:53.571051 INFO: Starting optimization step 6.
1:09:53.571339 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:09:53.571437 INFO: Using rust extraction backend
1:09:53.571522 PROGRESS: Extracting batch of 126165 precursors
1:09:53.797652 INFO: === Search parameters used ===
1:09:53.797912 INFO: rt_error       : 805.6004638671875
1:09:53.797982 INFO: mobility_error : 0.1
1:09:53.798035 INFO: num_candidates : 1
1:09:53.798086 INFO: ms1_error      : 3
1:09:53.798133 INFO: ms2_error      : 10
1:09:53.798178 INFO: fwhm_rt        : 5
1:09:53.798222 INFO: quant_window   : 3
1:09:53.798265 INFO: ==============================================
1:09:55.322441 INFO: performing precursor FDR with 40 features
1:09:55.322562 INFO: Decoy channel: -1
1:09:55.322597 INFO: competitive: True
1:09:55.466468 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:55.589407 INFO: Estimating optimal hyperparameters - samples: 199,806, batch_size: 818, learning_rate: 4.47e-04
1:09:55.589918 INFO: Using random state 60791 for train-test-split
1:10:03.139328 INFO: Test AUC: 0.590
1:10:03.139463 INFO: Train AUC: 0.611
1:10:03.139498 INFO: AUC difference: 3.51%
1:10:03.576484 INFO: Resetting torch num_threads to 24
1:10:03.644010 PROGRESS: === Extracted 249758 precursors and 1399839 fragments ===
1:10:03.644813 INFO: === FDR correction performed with classifier version -1 ===
1:10:03.645889 PROGRESS: ============================= Precursor FDR =============================
1:10:03.645997 PROGRESS: Total precursors accumulated: 1,180
1:10:03.646072 PROGRESS: Target precursors: 1,169 (99.07%)
1:10:03.646133 PROGRESS: Decoy precursors: 11 (0.93%)
1:10:03.646201 PROGRESS: 
1:10:03.646264 PROGRESS: Precursor Summary:
1:10:03.647844 PROGRESS: Channel   0:	 0.050 FDR: 1,169; 0.010 FDR: 1,169; 0.001 FDR:     2
1:10:03.647950 PROGRESS: 
1:10:03.648021 PROGRESS: Protein Summary:
1:10:03.649996 PROGRESS: Channel   0:	 0.050 FDR:   999; 0.010 FDR:   999; 0.001 FDR:     2
1:10:03.650104 PROGRESS: =========================================================================
1:10:03.656228 INFO: Target number of precursors reached.
1:10:03.898151 INFO: fragments_df: keeping 5000 of 1399839 [sum(precursor_idx_mask)=12445 sum(mass_error_mask)=1399839 stop_rank=5000
1:10:04.393371 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:04.691021 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:05.622251 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:10:05.622773 INFO: Using score_cutoff 12.505772419738769 (fac=0.99, q=1)
1:10:05.623147 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:10:05.623239 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:10:05.623311 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.505772419738769
1:10:05.623382 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:05.786018 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:06.145805 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:10:06.146094 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:10:06.146229 INFO: Starting optimization step 7.
1:10:06.146310 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:10:06.146391 INFO: Using rust extraction backend
1:10:06.146467 PROGRESS: Extracting batch of 250375 precursors
1:10:06.602410 INFO: === Search parameters used ===
1:10:06.602733 INFO: rt_error       : 805.6004638671875
1:10:06.602842 INFO: mobility_error : 0.1
1:10:06.602911 INFO: num_candidates : 3
1:10:06.602992 INFO: ms1_error      : 3
1:10:06.603060 INFO: ms2_error      : 10
1:10:06.603118 INFO: fwhm_rt        : 3.0
1:10:06.603175 INFO: quant_window   : 3
1:10:06.603231 INFO: ==============================================
1:10:11.623563 INFO: performing precursor FDR with 40 features
1:10:11.623702 INFO: Decoy channel: -1
1:10:11.623734 INFO: competitive: True
1:10:11.870939 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:12.332128 INFO: Estimating optimal hyperparameters - samples: 599,426, batch_size: 2,455, learning_rate: 7.74e-04
1:10:12.333383 INFO: Using random state 304482 for train-test-split
1:10:28.185998 INFO: Test AUC: 0.594
1:10:28.186179 INFO: Train AUC: 0.606
1:10:28.186220 INFO: AUC difference: 1.98%
1:10:28.819397 INFO: Resetting torch num_threads to 24
1:10:28.864336 PROGRESS: === Extracted 749283 precursors and 4024319 fragments ===
1:10:28.864969 INFO: === FDR correction performed with classifier version 6 ===
1:10:28.865991 PROGRESS: ============================= Precursor FDR =============================
1:10:28.866120 PROGRESS: Total precursors accumulated: 1,391
1:10:28.866193 PROGRESS: Target precursors: 1,378 (99.07%)
1:10:28.866252 PROGRESS: Decoy precursors: 13 (0.93%)
1:10:28.866318 PROGRESS: 
1:10:28.866376 PROGRESS: Precursor Summary:
1:10:28.868297 PROGRESS: Channel   0:	 0.050 FDR: 1,378; 0.010 FDR: 1,378; 0.001 FDR: 1,166
1:10:28.868433 PROGRESS: 
1:10:28.868507 PROGRESS: Protein Summary:
1:10:28.870884 PROGRESS: Channel   0:	 0.050 FDR: 1,160; 0.010 FDR: 1,160; 0.001 FDR:   995
1:10:28.871010 PROGRESS: =========================================================================
1:10:28.896877 INFO: Target number of precursors reached.
1:10:29.481428 INFO: fragments_df: keeping 5000 of 4024319 [sum(precursor_idx_mask)=33109 sum(mass_error_mask)=4024319 stop_rank=5000
1:10:30.019408 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:30.386177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:31.390687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:31.391258 INFO: Using score_cutoff 12.980202418899536 (fac=0.99, q=1)
1:10:31.391692 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:31.391794 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:31.391864 INFO: Updating optimization_manager: score_cutoff        : 12.505772419738769 -> 12.980202418899536
1:10:31.391931 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:31.553781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:31.908658 INFO: === checking if optimization conditions were reached ===
1:10:31.911194 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:10:31.911313 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:10:31.911398 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:10:31.911488 INFO: ==============================================
1:10:31.911580 INFO: Starting optimization step 8.
1:10:31.911650 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:10:31.911731 INFO: Using rust extraction backend
1:10:31.911807 PROGRESS: Extracting batch of 250375 precursors
1:10:32.356406 INFO: === Search parameters used ===
1:10:32.356736 INFO: rt_error       : 805.6004638671875
1:10:32.356827 INFO: mobility_error : 0.1
1:10:32.356900 INFO: num_candidates : 3
1:10:32.356962 INFO: ms1_error      : 3
1:10:32.357022 INFO: ms2_error      : 10.0
1:10:32.357082 INFO: fwhm_rt        : 3.0
1:10:32.357139 INFO: quant_window   : 3
1:10:32.357197 INFO: ==============================================
1:10:37.261648 INFO: performing precursor FDR with 40 features
1:10:37.261781 INFO: Decoy channel: -1
1:10:37.261818 INFO: competitive: True
1:10:37.523482 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:37.971617 INFO: Estimating optimal hyperparameters - samples: 599,448, batch_size: 2,455, learning_rate: 7.74e-04
1:10:37.972777 INFO: Using random state 116305 for train-test-split
1:10:52.103723 INFO: Test AUC: 0.600
1:10:52.104007 INFO: Train AUC: 0.613
1:10:52.104055 INFO: AUC difference: 2.18%
1:10:52.740126 INFO: Resetting torch num_threads to 24
1:10:52.785416 PROGRESS: === Extracted 749310 precursors and 4024099 fragments ===
1:10:52.786048 INFO: === FDR correction performed with classifier version 7 ===
1:10:52.787142 PROGRESS: ============================= Precursor FDR =============================
1:10:52.787279 PROGRESS: Total precursors accumulated: 1,573
1:10:52.787358 PROGRESS: Target precursors: 1,558 (99.05%)
1:10:52.787429 PROGRESS: Decoy precursors: 15 (0.95%)
1:10:52.787498 PROGRESS: 
1:10:52.787578 PROGRESS: Precursor Summary:
1:10:52.789727 PROGRESS: Channel   0:	 0.050 FDR: 1,558; 0.010 FDR: 1,558; 0.001 FDR: 1,243
1:10:52.789838 PROGRESS: 
1:10:52.789909 PROGRESS: Protein Summary:
1:10:52.792401 PROGRESS: Channel   0:	 0.050 FDR: 1,309; 0.010 FDR: 1,309; 0.001 FDR: 1,060
1:10:52.792523 PROGRESS: =========================================================================
1:10:52.818422 INFO: Target number of precursors reached.
1:10:53.473454 INFO: fragments_df: keeping 5000 of 4024099 [sum(precursor_idx_mask)=37101 sum(mass_error_mask)=4024099 stop_rank=5000
1:10:54.056493 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:54.503707 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:55.385777 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:55.386223 INFO: Using score_cutoff 11.446742320346832 (fac=0.99, q=1)
1:10:55.386565 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:55.386645 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:55.386700 INFO: Updating optimization_manager: score_cutoff        : 12.980202418899536 -> 11.446742320346832
1:10:55.386755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:55.549386 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:55.907969 INFO: === checking if optimization conditions were reached ===
1:10:55.910608 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:10:55.910730 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:10:55.910837 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:10:55.910913 INFO: ==============================================
1:10:55.911036 INFO: Starting optimization step 9.
1:10:55.911118 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:10:55.911211 INFO: Using rust extraction backend
1:10:55.911291 PROGRESS: Extracting batch of 250375 precursors
1:10:56.393857 INFO: === Search parameters used ===
1:10:56.394433 INFO: rt_error       : 805.6004638671875
1:10:56.394565 INFO: mobility_error : 0.1
1:10:56.394667 INFO: num_candidates : 3
1:10:56.394757 INFO: ms1_error      : 3
1:10:56.394850 INFO: ms2_error      : 10.0
1:10:56.394939 INFO: fwhm_rt        : 3.0
1:10:56.395037 INFO: quant_window   : 3
1:10:56.395123 INFO: ==============================================
1:11:01.828702 INFO: performing precursor FDR with 40 features
1:11:01.828836 INFO: Decoy channel: -1
1:11:01.828873 INFO: competitive: True
1:11:02.085352 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:02.514240 INFO: Estimating optimal hyperparameters - samples: 599,450, batch_size: 2,455, learning_rate: 7.74e-04
1:11:02.515472 INFO: Using random state 844153 for train-test-split
1:11:18.643442 INFO: Test AUC: 0.605
1:11:18.643710 INFO: Train AUC: 0.619
1:11:18.643768 INFO: AUC difference: 2.21%
1:11:19.282308 INFO: Resetting torch num_threads to 24
1:11:19.327603 PROGRESS: === Extracted 749313 precursors and 4024310 fragments ===
1:11:19.328239 INFO: === FDR correction performed with classifier version 8 ===
1:11:19.329279 PROGRESS: ============================= Precursor FDR =============================
1:11:19.329411 PROGRESS: Total precursors accumulated: 1,578
1:11:19.329490 PROGRESS: Target precursors: 1,563 (99.05%)
1:11:19.329553 PROGRESS: Decoy precursors: 15 (0.95%)
1:11:19.329642 PROGRESS: 
1:11:19.329714 PROGRESS: Precursor Summary:
1:11:19.331665 PROGRESS: Channel   0:	 0.050 FDR: 1,563; 0.010 FDR: 1,563; 0.001 FDR: 1,204
1:11:19.331789 PROGRESS: 
1:11:19.331868 PROGRESS: Protein Summary:
1:11:19.334320 PROGRESS: Channel   0:	 0.050 FDR: 1,330; 0.010 FDR: 1,330; 0.001 FDR: 1,029
1:11:19.334429 PROGRESS: =========================================================================
1:11:19.364055 INFO: Target number of precursors reached.
1:11:20.006047 INFO: fragments_df: keeping 5000 of 4024310 [sum(precursor_idx_mask)=36281 sum(mass_error_mask)=4024310 stop_rank=5000
1:11:20.460973 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:20.874321 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:21.765079 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:11:21.765530 INFO: Using score_cutoff 8.926184595108031 (fac=0.99, q=1)
1:11:21.765857 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:11:21.765935 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:11:21.765990 INFO: Updating optimization_manager: score_cutoff        : 11.446742320346832 -> 8.926184595108031
1:11:21.766049 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:21.925636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:22.274616 INFO: === checking if optimization conditions were reached ===
1:11:22.277375 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:11:22.277557 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:11:22.277646 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:11:22.277722 INFO: ==============================================
1:11:22.277818 INFO: Starting optimization step 10.
1:11:22.277902 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:11:22.278003 INFO: Using rust extraction backend
1:11:22.278100 PROGRESS: Extracting batch of 250375 precursors
1:11:22.721394 INFO: === Search parameters used ===
1:11:22.721642 INFO: rt_error       : 805.6004638671875
1:11:22.721706 INFO: mobility_error : 0.1
1:11:22.721764 INFO: num_candidates : 3
1:11:22.721813 INFO: ms1_error      : 3
1:11:22.721862 INFO: ms2_error      : 10.0
1:11:22.721907 INFO: fwhm_rt        : 3.0
1:11:22.721951 INFO: quant_window   : 3
1:11:22.721997 INFO: ==============================================
1:11:27.756949 INFO: performing precursor FDR with 40 features
1:11:27.757079 INFO: Decoy channel: -1
1:11:27.757111 INFO: competitive: True
1:11:27.999516 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:28.349380 INFO: Estimating optimal hyperparameters - samples: 599,462, batch_size: 2,455, learning_rate: 7.74e-04
1:11:28.350738 INFO: Using random state 376771 for train-test-split
1:11:42.674670 INFO: Test AUC: 0.609
1:11:42.674931 INFO: Train AUC: 0.622
1:11:42.675013 INFO: AUC difference: 2.00%
1:11:43.303375 INFO: Resetting torch num_threads to 24
1:11:43.345560 PROGRESS: === Extracted 749328 precursors and 4024926 fragments ===
1:11:43.346218 INFO: === FDR correction performed with classifier version 9 ===
1:11:43.347389 PROGRESS: ============================= Precursor FDR =============================
1:11:43.347521 PROGRESS: Total precursors accumulated: 1,597
1:11:43.347616 PROGRESS: Target precursors: 1,582 (99.06%)
1:11:43.347688 PROGRESS: Decoy precursors: 15 (0.94%)
1:11:43.347749 PROGRESS: 
1:11:43.347804 PROGRESS: Precursor Summary:
1:11:43.349837 PROGRESS: Channel   0:	 0.050 FDR: 1,582; 0.010 FDR: 1,582; 0.001 FDR: 1,195
1:11:43.349950 PROGRESS: 
1:11:43.350023 PROGRESS: Protein Summary:
1:11:43.352548 PROGRESS: Channel   0:	 0.050 FDR: 1,334; 0.010 FDR: 1,334; 0.001 FDR: 1,020
1:11:43.352668 PROGRESS: =========================================================================
1:11:43.389726 INFO: Target number of precursors reached.
1:11:44.064593 INFO: fragments_df: keeping 5000 of 4024926 [sum(precursor_idx_mask)=37203 sum(mass_error_mask)=4024926 stop_rank=5000
1:11:44.623001 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:45.068360 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:46.039703 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:11:46.040511 INFO: Using score_cutoff 9.755234460639953 (fac=0.99, q=1)
1:11:46.040993 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:11:46.041087 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:11:46.041170 INFO: Updating optimization_manager: score_cutoff        : 8.926184595108031 -> 9.755234460639953
1:11:46.041263 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:46.213848 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:46.580183 INFO: === checking if optimization conditions were reached ===
1:11:46.582897 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:11:46.583111 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:11:46.583210 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:11:46.583295 INFO: ==============================================
1:11:46.583394 INFO: Starting optimization step 11.
1:11:46.583484 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:11:46.583589 INFO: Using rust extraction backend
1:11:46.583690 PROGRESS: Extracting batch of 250375 precursors
1:11:47.043655 INFO: === Search parameters used ===
1:11:47.044018 INFO: rt_error       : 805.6004638671875
1:11:47.044105 INFO: mobility_error : 0.1
1:11:47.044166 INFO: num_candidates : 3
1:11:47.044229 INFO: ms1_error      : 3
1:11:47.044288 INFO: ms2_error      : 10.0
1:11:47.044354 INFO: fwhm_rt        : 3.0
1:11:47.044417 INFO: quant_window   : 3
1:11:47.044481 INFO: ==============================================
1:11:51.762931 INFO: performing precursor FDR with 40 features
1:11:51.763078 INFO: Decoy channel: -1
1:11:51.763109 INFO: competitive: True
1:11:52.010120 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:52.439411 INFO: Estimating optimal hyperparameters - samples: 599,452, batch_size: 2,455, learning_rate: 7.74e-04
1:11:52.440501 INFO: Using random state 745392 for train-test-split
1:12:08.843071 INFO: Test AUC: 0.610
1:12:08.843354 INFO: Train AUC: 0.625
1:12:08.843394 INFO: AUC difference: 2.39%
1:12:09.469019 INFO: Resetting torch num_threads to 24
1:12:09.513712 PROGRESS: === Extracted 749316 precursors and 4024969 fragments ===
1:12:09.514346 INFO: === FDR correction performed with classifier version 10 ===
1:12:09.515421 PROGRESS: ============================= Precursor FDR =============================
1:12:09.515577 PROGRESS: Total precursors accumulated: 1,641
1:12:09.515661 PROGRESS: Target precursors: 1,625 (99.02%)
1:12:09.515723 PROGRESS: Decoy precursors: 16 (0.98%)
1:12:09.515786 PROGRESS: 
1:12:09.515845 PROGRESS: Precursor Summary:
1:12:09.517898 PROGRESS: Channel   0:	 0.050 FDR: 1,625; 0.010 FDR: 1,625; 0.001 FDR: 1,083
1:12:09.518021 PROGRESS: 
1:12:09.518097 PROGRESS: Protein Summary:
1:12:09.520800 PROGRESS: Channel   0:	 0.050 FDR: 1,382; 0.010 FDR: 1,382; 0.001 FDR:   926
1:12:09.520914 PROGRESS: =========================================================================
1:12:09.547050 INFO: Target number of precursors reached.
1:12:10.202998 INFO: fragments_df: keeping 5000 of 4024969 [sum(precursor_idx_mask)=37518 sum(mass_error_mask)=4024969 stop_rank=5000
1:12:10.728162 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:11.230130 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:12.390749 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:12:12.391335 INFO: Using score_cutoff 9.224999831771852 (fac=0.99, q=1)
1:12:12.391837 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:12:12.391949 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:12:12.392024 INFO: Updating optimization_manager: score_cutoff        : 9.755234460639953 -> 9.224999831771852
1:12:12.392097 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:12.557741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:12.902317 INFO: === checking if optimization conditions were reached ===
1:12:12.905176 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:12:12.905367 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:12:12.905456 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:12:12.905531 INFO: ==============================================
1:12:12.905639 PROGRESS: Optimization finished for ms2_error.
1:12:13.375271 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:13.534116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:13.882838 INFO: Starting optimization step 0.
1:12:13.883143 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:13.883274 INFO: Using rust extraction backend
1:12:13.883382 PROGRESS: Extracting batch of 250375 precursors
1:12:14.345971 INFO: === Search parameters used ===
1:12:14.346300 INFO: rt_error       : 805.6004638671875
1:12:14.346412 INFO: mobility_error : 0.1
1:12:14.346481 INFO: num_candidates : 3
1:12:14.346542 INFO: ms1_error      : 3
1:12:14.346607 INFO: ms2_error      : 10.0
1:12:14.346666 INFO: fwhm_rt        : 3.0
1:12:14.346722 INFO: quant_window   : 3
1:12:14.346791 INFO: ==============================================
1:12:19.082291 INFO: performing precursor FDR with 40 features
1:12:19.082418 INFO: Decoy channel: -1
1:12:19.082453 INFO: competitive: True
1:12:19.295655 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:19.705426 INFO: Estimating optimal hyperparameters - samples: 599,466, batch_size: 2,455, learning_rate: 7.74e-04
1:12:19.706761 INFO: Using random state 41357 for train-test-split
1:12:35.934704 INFO: Test AUC: 0.613
1:12:35.934989 INFO: Train AUC: 0.626
1:12:35.935035 INFO: AUC difference: 2.12%
1:12:36.497819 INFO: Resetting torch num_threads to 24
1:12:36.542559 PROGRESS: === Extracted 749333 precursors and 4024788 fragments ===
1:12:36.543261 INFO: === FDR correction performed with classifier version 11 ===
1:12:36.544335 PROGRESS: ============================= Precursor FDR =============================
1:12:36.544469 PROGRESS: Total precursors accumulated: 1,603
1:12:36.544549 PROGRESS: Target precursors: 1,588 (99.06%)
1:12:36.544614 PROGRESS: Decoy precursors: 15 (0.94%)
1:12:36.544680 PROGRESS: 
1:12:36.544738 PROGRESS: Precursor Summary:
1:12:36.546689 PROGRESS: Channel   0:	 0.050 FDR: 1,588; 0.010 FDR: 1,588; 0.001 FDR: 1,161
1:12:36.546804 PROGRESS: 
1:12:36.546870 PROGRESS: Protein Summary:
1:12:36.549327 PROGRESS: Channel   0:	 0.050 FDR: 1,331; 0.010 FDR: 1,331; 0.001 FDR:   992
1:12:36.549449 PROGRESS: =========================================================================
1:12:36.575602 INFO: Target number of precursors reached.
1:12:37.230060 INFO: fragments_df: keeping 5000 of 4024788 [sum(precursor_idx_mask)=37667 sum(mass_error_mask)=4024788 stop_rank=5000
1:12:37.749700 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:38.197535 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:39.237435 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:12:39.238007 INFO: Using score_cutoff 11.000571737194061 (fac=0.99, q=1)
1:12:39.238465 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:12:39.238560 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:12:39.238630 INFO: Updating optimization_manager: score_cutoff        : 9.224999831771852 -> 11.000571737194061
1:12:39.238708 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:39.401723 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:39.756112 INFO: === checking if optimization conditions were reached ===
1:12:39.756412 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:12:39.759784 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 605.283385858314
1:12:39.759911 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 605.2834.
1:12:39.759989 INFO: ==============================================
1:12:39.760085 INFO: Starting optimization step 1.
1:12:39.760190 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:39.760285 INFO: Using rust extraction backend
1:12:39.760370 PROGRESS: Extracting batch of 250375 precursors
1:12:40.222022 INFO: === Search parameters used ===
1:12:40.222306 INFO: rt_error       : 605.283385858314
1:12:40.222382 INFO: mobility_error : 0.1
1:12:40.222443 INFO: num_candidates : 3
1:12:40.222496 INFO: ms1_error      : 3
1:12:40.222557 INFO: ms2_error      : 10.0
1:12:40.222623 INFO: fwhm_rt        : 3.0
1:12:40.222673 INFO: quant_window   : 3
1:12:40.222727 INFO: ==============================================
1:12:44.695702 INFO: performing precursor FDR with 40 features
1:12:44.695847 INFO: Decoy channel: -1
1:12:44.695880 INFO: competitive: True
1:12:44.960715 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:45.390954 INFO: Estimating optimal hyperparameters - samples: 599,190, batch_size: 2,454, learning_rate: 7.74e-04
1:12:45.392239 INFO: Using random state 41357 for train-test-split
1:13:00.710383 INFO: Test AUC: 0.611
1:13:00.710601 INFO: Train AUC: 0.625
1:13:00.710646 INFO: AUC difference: 2.22%
1:13:01.346072 INFO: Resetting torch num_threads to 24
1:13:01.389577 PROGRESS: === Extracted 748988 precursors and 4009153 fragments ===
1:13:01.390259 INFO: === FDR correction performed with classifier version 11 ===
1:13:01.391483 PROGRESS: ============================= Precursor FDR =============================
1:13:01.391638 PROGRESS: Total precursors accumulated: 1,678
1:13:01.391724 PROGRESS: Target precursors: 1,662 (99.05%)
1:13:01.391788 PROGRESS: Decoy precursors: 16 (0.95%)
1:13:01.391855 PROGRESS: 
1:13:01.391912 PROGRESS: Precursor Summary:
1:13:01.394101 PROGRESS: Channel   0:	 0.050 FDR: 1,662; 0.010 FDR: 1,662; 0.001 FDR: 1,216
1:13:01.394234 PROGRESS: 
1:13:01.394303 PROGRESS: Protein Summary:
1:13:01.396892 PROGRESS: Channel   0:	 0.050 FDR: 1,417; 0.010 FDR: 1,417; 0.001 FDR: 1,040
1:13:01.397023 PROGRESS: =========================================================================
1:13:01.423509 INFO: Target number of precursors reached.
1:13:02.080529 INFO: fragments_df: keeping 5000 of 4009153 [sum(precursor_idx_mask)=38207 sum(mass_error_mask)=4009153 stop_rank=5000
1:13:02.728496 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:03.176714 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:04.274236 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:04.274765 INFO: Using score_cutoff 8.479439636421205 (fac=0.99, q=1)
1:13:04.275188 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:04.275295 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:04.275356 INFO: Updating optimization_manager: score_cutoff        : 11.000571737194061 -> 8.479439636421205
1:13:04.275422 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:04.437910 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:04.781202 INFO: === checking if optimization conditions were reached ===
1:13:04.781493 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:13:04.784985 INFO: Updating optimization_manager: rt_error            : 605.283385858314 -> 628.8415253284393
1:13:04.785103 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 628.8415.
1:13:04.785181 INFO: ==============================================
1:13:04.785280 INFO: Starting optimization step 2.
1:13:04.785367 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:04.785460 INFO: Using rust extraction backend
1:13:04.785552 PROGRESS: Extracting batch of 250375 precursors
1:13:05.237549 INFO: === Search parameters used ===
1:13:05.237846 INFO: rt_error       : 628.8415253284393
1:13:05.237913 INFO: mobility_error : 0.1
1:13:05.237964 INFO: num_candidates : 3
1:13:05.238023 INFO: ms1_error      : 3
1:13:05.238068 INFO: ms2_error      : 10.0
1:13:05.238110 INFO: fwhm_rt        : 3.0
1:13:05.238151 INFO: quant_window   : 3
1:13:05.238200 INFO: ==============================================
1:13:09.784195 INFO: performing precursor FDR with 40 features
1:13:09.784331 INFO: Decoy channel: -1
1:13:09.784358 INFO: competitive: True
1:13:09.982826 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:10.400562 INFO: Estimating optimal hyperparameters - samples: 599,383, batch_size: 2,455, learning_rate: 7.74e-04
1:13:10.401737 INFO: Using random state 41357 for train-test-split
1:13:21.499071 INFO: Test AUC: 0.612
1:13:21.499269 INFO: Train AUC: 0.626
1:13:21.499304 INFO: AUC difference: 2.21%
1:13:22.116843 INFO: Resetting torch num_threads to 24
1:13:22.161164 PROGRESS: === Extracted 749229 precursors and 4020870 fragments ===
1:13:22.161781 INFO: === FDR correction performed with classifier version 11 ===
1:13:22.162858 PROGRESS: ============================= Precursor FDR =============================
1:13:22.163001 PROGRESS: Total precursors accumulated: 1,522
1:13:22.163091 PROGRESS: Target precursors: 1,507 (99.01%)
1:13:22.163161 PROGRESS: Decoy precursors: 15 (0.99%)
1:13:22.163226 PROGRESS: 
1:13:22.163295 PROGRESS: Precursor Summary:
1:13:22.165367 PROGRESS: Channel   0:	 0.050 FDR: 1,507; 0.010 FDR: 1,507; 0.001 FDR: 1,107
1:13:22.165485 PROGRESS: 
1:13:22.165555 PROGRESS: Protein Summary:
1:13:22.167982 PROGRESS: Channel   0:	 0.050 FDR: 1,275; 0.010 FDR: 1,275; 0.001 FDR:   940
1:13:22.168097 PROGRESS: =========================================================================
1:13:22.191320 INFO: Target number of precursors reached.
1:13:22.859149 INFO: fragments_df: keeping 5000 of 4020870 [sum(precursor_idx_mask)=35638 sum(mass_error_mask)=4020870 stop_rank=5000
1:13:23.395197 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:23.829618 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:24.836291 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:24.836815 INFO: Using score_cutoff 10.589276132583619 (fac=0.99, q=1)
1:13:24.837221 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:24.837319 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:24.837388 INFO: Updating optimization_manager: score_cutoff        : 8.479439636421205 -> 10.589276132583619
1:13:24.837459 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:25.001517 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:25.357971 INFO: === checking if optimization conditions were reached ===
1:13:25.358256 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:13:25.361856 INFO: Updating optimization_manager: rt_error            : 628.8415253284393 -> 476.1939385288106
1:13:25.362025 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 476.1939.
1:13:25.362109 INFO: ==============================================
1:13:25.362211 INFO: Starting optimization step 3.
1:13:25.362291 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:25.362387 INFO: Using rust extraction backend
1:13:25.362477 PROGRESS: Extracting batch of 250375 precursors
1:13:25.802388 INFO: === Search parameters used ===
1:13:25.802633 INFO: rt_error       : 476.1939385288106
1:13:25.802711 INFO: mobility_error : 0.1
1:13:25.802765 INFO: num_candidates : 3
1:13:25.802813 INFO: ms1_error      : 3
1:13:25.802860 INFO: ms2_error      : 10.0
1:13:25.802904 INFO: fwhm_rt        : 3.0
1:13:25.802946 INFO: quant_window   : 3
1:13:25.803035 INFO: ==============================================
1:13:30.099686 INFO: performing precursor FDR with 40 features
1:13:30.099832 INFO: Decoy channel: -1
1:13:30.099865 INFO: competitive: True
1:13:30.336134 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:30.763027 INFO: Estimating optimal hyperparameters - samples: 598,665, batch_size: 2,452, learning_rate: 7.74e-04
1:13:30.764153 INFO: Using random state 41357 for train-test-split
1:13:44.997861 INFO: Test AUC: 0.608
1:13:44.998030 INFO: Train AUC: 0.624
1:13:44.998095 INFO: AUC difference: 2.52%
1:13:45.633337 INFO: Resetting torch num_threads to 24
1:13:45.674473 PROGRESS: === Extracted 748332 precursors and 3968342 fragments ===
1:13:45.675075 INFO: === FDR correction performed with classifier version 11 ===
1:13:45.676062 PROGRESS: ============================= Precursor FDR =============================
1:13:45.676165 PROGRESS: Total precursors accumulated: 1,665
1:13:45.676246 PROGRESS: Target precursors: 1,649 (99.04%)
1:13:45.676308 PROGRESS: Decoy precursors: 16 (0.96%)
1:13:45.676364 PROGRESS: 
1:13:45.676427 PROGRESS: Precursor Summary:
1:13:45.678258 PROGRESS: Channel   0:	 0.050 FDR: 1,649; 0.010 FDR: 1,649; 0.001 FDR: 1,218
1:13:45.678358 PROGRESS: 
1:13:45.678429 PROGRESS: Protein Summary:
1:13:45.680870 PROGRESS: Channel   0:	 0.050 FDR: 1,391; 0.010 FDR: 1,391; 0.001 FDR: 1,035
1:13:45.680979 PROGRESS: =========================================================================
1:13:45.705101 INFO: Target number of precursors reached.
1:13:46.352119 INFO: fragments_df: keeping 5000 of 3968342 [sum(precursor_idx_mask)=38562 sum(mass_error_mask)=3968342 stop_rank=5000
1:13:46.897807 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:47.307521 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:48.209239 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:48.209831 INFO: Using score_cutoff 9.918917231369019 (fac=0.99, q=1)
1:13:48.210346 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:48.210462 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:48.210530 INFO: Updating optimization_manager: score_cutoff        : 10.589276132583619 -> 9.918917231369019
1:13:48.210613 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:48.373705 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:48.739642 INFO: === checking if optimization conditions were reached ===
1:13:48.739996 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:13:48.743761 INFO: Updating optimization_manager: rt_error            : 476.1939385288106 -> 608.7370208869334
1:13:48.743885 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 608.7370.
1:13:48.743967 INFO: ==============================================
1:13:48.744072 INFO: Starting optimization step 4.
1:13:48.744163 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:48.744275 INFO: Using rust extraction backend
1:13:48.744378 PROGRESS: Extracting batch of 250375 precursors
1:13:49.205976 INFO: === Search parameters used ===
1:13:49.206260 INFO: rt_error       : 608.7370208869334
1:13:49.206340 INFO: mobility_error : 0.1
1:13:49.206407 INFO: num_candidates : 3
1:13:49.206467 INFO: ms1_error      : 3
1:13:49.206521 INFO: ms2_error      : 10.0
1:13:49.206581 INFO: fwhm_rt        : 3.0
1:13:49.206636 INFO: quant_window   : 3
1:13:49.206692 INFO: ==============================================
1:13:53.957141 INFO: performing precursor FDR with 40 features
1:13:53.957291 INFO: Decoy channel: -1
1:13:53.957324 INFO: competitive: True
1:13:54.201609 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:54.601248 INFO: Estimating optimal hyperparameters - samples: 599,280, batch_size: 2,454, learning_rate: 7.74e-04
1:13:54.602279 INFO: Using random state 41357 for train-test-split
1:14:06.953126 INFO: Test AUC: 0.613
1:14:06.953338 INFO: Train AUC: 0.626
1:14:06.953384 INFO: AUC difference: 2.08%
1:14:07.587575 INFO: Resetting torch num_threads to 24
1:14:07.634307 PROGRESS: === Extracted 749101 precursors and 4014819 fragments ===
1:14:07.634903 INFO: === FDR correction performed with classifier version 11 ===
1:14:07.636096 PROGRESS: ============================= Precursor FDR =============================
1:14:07.636243 PROGRESS: Total precursors accumulated: 1,653
1:14:07.636324 PROGRESS: Target precursors: 1,637 (99.03%)
1:14:07.636386 PROGRESS: Decoy precursors: 16 (0.97%)
1:14:07.636469 PROGRESS: 
1:14:07.636526 PROGRESS: Precursor Summary:
1:14:07.638603 PROGRESS: Channel   0:	 0.050 FDR: 1,637; 0.010 FDR: 1,637; 0.001 FDR: 1,137
1:14:07.638722 PROGRESS: 
1:14:07.638793 PROGRESS: Protein Summary:
1:14:07.641297 PROGRESS: Channel   0:	 0.050 FDR: 1,396; 0.010 FDR: 1,396; 0.001 FDR:   973
1:14:07.641415 PROGRESS: =========================================================================
1:14:07.668511 INFO: Target number of precursors reached.
1:14:08.321536 INFO: fragments_df: keeping 5000 of 4014819 [sum(precursor_idx_mask)=37637 sum(mass_error_mask)=4014819 stop_rank=5000
1:14:08.873949 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:09.411743 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:10.564346 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:10.564960 INFO: Using score_cutoff 8.182697442626953 (fac=0.99, q=1)
1:14:10.565437 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:10.565548 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:10.565620 INFO: Updating optimization_manager: score_cutoff        : 9.918917231369019 -> 8.182697442626953
1:14:10.565700 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:10.737607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:11.100621 INFO: === checking if optimization conditions were reached ===
1:14:11.100903 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:14:11.104629 INFO: Updating optimization_manager: rt_error            : 608.7370208869334 -> 736.0886979427069
1:14:11.104757 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 736.0887.
1:14:11.104832 INFO: ==============================================
1:14:11.104934 INFO: Starting optimization step 5.
1:14:11.105013 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:11.105127 INFO: Using rust extraction backend
1:14:11.105216 PROGRESS: Extracting batch of 250375 precursors
1:14:11.565481 INFO: === Search parameters used ===
1:14:11.565760 INFO: rt_error       : 736.0886979427069
1:14:11.565842 INFO: mobility_error : 0.1
1:14:11.565903 INFO: num_candidates : 3
1:14:11.565959 INFO: ms1_error      : 3
1:14:11.566017 INFO: ms2_error      : 10.0
1:14:11.566077 INFO: fwhm_rt        : 3.0
1:14:11.566132 INFO: quant_window   : 3
1:14:11.566187 INFO: ==============================================
1:14:16.340594 INFO: performing precursor FDR with 40 features
1:14:16.340736 INFO: Decoy channel: -1
1:14:16.340768 INFO: competitive: True
1:14:16.581910 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:17.013004 INFO: Estimating optimal hyperparameters - samples: 599,466, batch_size: 2,455, learning_rate: 7.74e-04
1:14:17.014294 INFO: Using random state 41357 for train-test-split
1:14:27.966945 INFO: Test AUC: 0.613
1:14:27.967132 INFO: Train AUC: 0.626
1:14:27.967174 INFO: AUC difference: 2.18%
1:14:29.693059 INFO: Resetting torch num_threads to 24
1:14:29.739542 PROGRESS: === Extracted 749333 precursors and 4025362 fragments ===
1:14:29.740129 INFO: === FDR correction performed with classifier version 11 ===
1:14:29.741164 PROGRESS: ============================= Precursor FDR =============================
1:14:29.741287 PROGRESS: Total precursors accumulated: 1,554
1:14:29.741368 PROGRESS: Target precursors: 1,539 (99.03%)
1:14:29.741434 PROGRESS: Decoy precursors: 15 (0.97%)
1:14:29.741494 PROGRESS: 
1:14:29.741559 PROGRESS: Precursor Summary:
1:14:29.743422 PROGRESS: Channel   0:	 0.050 FDR: 1,539; 0.010 FDR: 1,539; 0.001 FDR:   273
1:14:29.743538 PROGRESS: 
1:14:29.743610 PROGRESS: Protein Summary:
1:14:29.745907 PROGRESS: Channel   0:	 0.050 FDR: 1,311; 0.010 FDR: 1,311; 0.001 FDR:   255
1:14:29.746023 PROGRESS: =========================================================================
1:14:29.770688 INFO: Target number of precursors reached.
1:14:30.441098 INFO: fragments_df: keeping 5000 of 4025362 [sum(precursor_idx_mask)=35927 sum(mass_error_mask)=4025362 stop_rank=5000
1:14:30.907180 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:31.404327 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:32.451334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:32.451790 INFO: Using score_cutoff 8.598336202812193 (fac=0.99, q=1)
1:14:32.452101 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:32.452180 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:32.452238 INFO: Updating optimization_manager: score_cutoff        : 8.182697442626953 -> 8.598336202812193
1:14:32.452293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:32.613744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:32.973380 INFO: === checking if optimization conditions were reached ===
1:14:32.973665 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:14:32.977195 INFO: Updating optimization_manager: rt_error            : 736.0886979427069 -> 865.4054298347098
1:14:32.977322 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 865.4054.
1:14:32.977405 INFO: ==============================================
1:14:32.977496 INFO: Starting optimization step 6.
1:14:32.977585 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:32.977668 INFO: Using rust extraction backend
1:14:32.977741 PROGRESS: Extracting batch of 250375 precursors
1:14:33.426428 INFO: === Search parameters used ===
1:14:33.426795 INFO: rt_error       : 865.4054298347098
1:14:33.426907 INFO: mobility_error : 0.1
1:14:33.426997 INFO: num_candidates : 3
1:14:33.427063 INFO: ms1_error      : 3
1:14:33.427119 INFO: ms2_error      : 10.0
1:14:33.427175 INFO: fwhm_rt        : 3.0
1:14:33.427229 INFO: quant_window   : 3
1:14:33.427283 INFO: ==============================================
1:14:38.371680 INFO: performing precursor FDR with 40 features
1:14:38.371819 INFO: Decoy channel: -1
1:14:38.371852 INFO: competitive: True
1:14:38.603362 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:39.012688 INFO: Estimating optimal hyperparameters - samples: 599,453, batch_size: 2,455, learning_rate: 7.74e-04
1:14:39.013930 INFO: Using random state 41357 for train-test-split
1:14:55.379967 INFO: Test AUC: 0.614
1:14:55.380133 INFO: Train AUC: 0.626
1:14:55.380173 INFO: AUC difference: 1.86%
1:14:56.009821 INFO: Resetting torch num_threads to 24
1:14:56.051685 PROGRESS: === Extracted 749317 precursors and 4024025 fragments ===
1:14:56.052289 INFO: === FDR correction performed with classifier version 11 ===
1:14:56.053474 PROGRESS: ============================= Precursor FDR =============================
1:14:56.053622 PROGRESS: Total precursors accumulated: 1,634
1:14:56.053696 PROGRESS: Target precursors: 1,618 (99.02%)
1:14:56.053763 PROGRESS: Decoy precursors: 16 (0.98%)
1:14:56.053838 PROGRESS: 
1:14:56.053899 PROGRESS: Precursor Summary:
1:14:56.056066 PROGRESS: Channel   0:	 0.050 FDR: 1,618; 0.010 FDR: 1,618; 0.001 FDR: 1,104
1:14:56.056211 PROGRESS: 
1:14:56.056286 PROGRESS: Protein Summary:
1:14:56.058916 PROGRESS: Channel   0:	 0.050 FDR: 1,377; 0.010 FDR: 1,377; 0.001 FDR:   952
1:14:56.059052 PROGRESS: =========================================================================
1:14:56.087415 INFO: Target number of precursors reached.
1:14:56.753340 INFO: fragments_df: keeping 5000 of 4024025 [sum(precursor_idx_mask)=37486 sum(mass_error_mask)=4024025 stop_rank=5000
1:14:57.305428 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:57.814600 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:58.938987 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:58.939544 INFO: Using score_cutoff 9.060542830467224 (fac=0.99, q=1)
1:14:58.939973 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:58.940071 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:58.940154 INFO: Updating optimization_manager: score_cutoff        : 8.598336202812193 -> 9.060542830467224
1:14:58.940231 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:59.101554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:59.458263 INFO: === checking if optimization conditions were reached ===
1:14:59.458549 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:14:59.462033 INFO: Updating optimization_manager: rt_error            : 865.4054298347098 -> 857.4195580573179
1:14:59.462162 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 857.4196.
1:14:59.462262 INFO: ==============================================
1:14:59.462357 INFO: Starting optimization step 7.
1:14:59.462433 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:59.462516 INFO: Using rust extraction backend
1:14:59.462594 PROGRESS: Extracting batch of 250375 precursors
1:14:59.909256 INFO: === Search parameters used ===
1:14:59.909544 INFO: rt_error       : 857.4195580573179
1:14:59.909616 INFO: mobility_error : 0.1
1:14:59.909683 INFO: num_candidates : 3
1:14:59.909742 INFO: ms1_error      : 3
1:14:59.909794 INFO: ms2_error      : 10.0
1:14:59.909850 INFO: fwhm_rt        : 3.0
1:14:59.909905 INFO: quant_window   : 3
1:14:59.909957 INFO: ==============================================
1:15:04.733552 INFO: performing precursor FDR with 40 features
1:15:04.733680 INFO: Decoy channel: -1
1:15:04.733711 INFO: competitive: True
1:15:04.962569 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:05.364520 INFO: Estimating optimal hyperparameters - samples: 599,452, batch_size: 2,455, learning_rate: 7.74e-04
1:15:05.365670 INFO: Using random state 41357 for train-test-split
1:15:21.064679 INFO: Test AUC: 0.616
1:15:21.064849 INFO: Train AUC: 0.625
1:15:21.064888 INFO: AUC difference: 1.55%
1:15:21.687297 INFO: Resetting torch num_threads to 24
1:15:21.727432 PROGRESS: === Extracted 749316 precursors and 4024544 fragments ===
1:15:21.728020 INFO: === FDR correction performed with classifier version 11 ===
1:15:21.729056 PROGRESS: ============================= Precursor FDR =============================
1:15:21.729177 PROGRESS: Total precursors accumulated: 1,658
1:15:21.729250 PROGRESS: Target precursors: 1,642 (99.03%)
1:15:21.729319 PROGRESS: Decoy precursors: 16 (0.97%)
1:15:21.729378 PROGRESS: 
1:15:21.729433 PROGRESS: Precursor Summary:
1:15:21.731392 PROGRESS: Channel   0:	 0.050 FDR: 1,642; 0.010 FDR: 1,642; 0.001 FDR: 1,125
1:15:21.731515 PROGRESS: 
1:15:21.731586 PROGRESS: Protein Summary:
1:15:21.734055 PROGRESS: Channel   0:	 0.050 FDR: 1,377; 0.010 FDR: 1,377; 0.001 FDR:   964
1:15:21.734166 PROGRESS: =========================================================================
1:15:21.757865 INFO: Target number of precursors reached.
1:15:22.332365 INFO: fragments_df: keeping 5000 of 4024544 [sum(precursor_idx_mask)=38734 sum(mass_error_mask)=4024544 stop_rank=5000
1:15:22.840723 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:23.299955 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:24.232218 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:24.232667 INFO: Using score_cutoff 10.148922881412506 (fac=0.99, q=1)
1:15:24.232991 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:24.233069 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:24.233126 INFO: Updating optimization_manager: score_cutoff        : 9.060542830467224 -> 10.148922881412506
1:15:24.233182 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:24.389522 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:24.753667 INFO: === checking if optimization conditions were reached ===
1:15:24.753982 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:15:24.755333 INFO: Updating optimization_manager: rt_error            : 857.4195580573179 -> 605.283385858314
1:15:24.755523 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
1:15:24.755654 INFO: Updating optimization_manager: score_cutoff        : 10.148922881412506 -> 8.479439636421205
1:15:24.755773 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:24.755888 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:24.756013 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 605.2834 found after 8 searches.
1:15:24.756102 INFO: ==============================================
1:15:24.756191 PROGRESS: Optimization finished for rt_error.
1:15:25.302703 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:25.464539 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:25.812543 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:15:25.812816 PROGRESS: ==============================================
1:15:25.812912 PROGRESS: ms2_error      : 10.0000
1:15:25.812986 PROGRESS: rt_error       : 605.2834
1:15:25.813051 PROGRESS: ==============================================
1:15:25.814550 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:33.858269 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:52.170303 INFO: Using rust extraction backend
1:15:52.170650 PROGRESS: Extracting batch of 11997144 precursors
1:16:09.215567 INFO: === Search parameters used ===
1:16:09.215894 INFO: rt_error       : 605.283385858314
1:16:09.215978 INFO: mobility_error : 0.1
1:16:09.216053 INFO: num_candidates : 3
1:16:09.216114 INFO: ms1_error      : 3
1:16:09.216170 INFO: ms2_error      : 10.0
1:16:09.216231 INFO: fwhm_rt        : 3.0
1:16:09.216292 INFO: quant_window   : 3
1:16:09.216347 INFO: ==============================================
1:17:30.207400 INFO: Removed 4375370 precursors with score below cutoff 8.479439636421205
1:18:13.774883 INFO: performing precursor FDR with 40 features
1:18:13.775025 INFO: Decoy channel: -1
1:18:13.775058 INFO: competitive: True
1:18:17.404186 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:37.207507 INFO: Estimating optimal hyperparameters - samples: 25,292,110, batch_size: 4,096, learning_rate: 1.00e-03
1:18:37.295842 INFO: Using random state 294699 for train-test-split
1:27:20.471176 INFO: Test AUC: 0.622
1:27:20.471397 INFO: Train AUC: 0.622
1:27:20.471447 INFO: AUC difference: 0.05%
1:27:28.642606 INFO: Resetting torch num_threads to 24
1:27:31.434138 PROGRESS: ============================= Precursor FDR =============================
1:27:31.434506 PROGRESS: Total precursors accumulated: 91,481
1:27:31.434590 PROGRESS: Target precursors: 90,576 (99.01%)
1:27:31.434663 PROGRESS: Decoy precursors: 905 (0.99%)
1:27:31.434727 PROGRESS: 
1:27:31.434783 PROGRESS: Precursor Summary:
1:27:31.475732 PROGRESS: Channel   0:	 0.050 FDR: 90,576; 0.010 FDR: 90,576; 0.001 FDR: 58,429
1:27:31.475994 PROGRESS: 
1:27:31.476072 PROGRESS: Protein Summary:
1:27:31.525489 PROGRESS: Channel   0:	 0.050 FDR: 13,188; 0.010 FDR: 13,188; 0.001 FDR: 9,317
1:27:31.525759 PROGRESS: =========================================================================
1:27:31.733904 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
1:27:31.935169 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
1:27:32.228177 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:27:32.903356 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
1:27:32.903521 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:27:32.903644 INFO: Initializing TimingManager
1:27:32.904463 INFO: Initializing RawFileManager
1:27:51.495896 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.
1:27:51.506122 INFO: Determining DIA cycle
1:27:51.522992 INFO: Found cycle with start 0.00 min and length 300.
1:27:51.701875 INFO: RT (min)            : 0.0 - 26.9
1:27:51.701979 INFO: RT duration (sec)   : 1611.2
1:27:51.702020 INFO: RT duration (min)   : 26.9
1:27:51.702058 INFO: Cycle len (scans)   : 300
1:27:51.702087 INFO: Cycle len (sec)     : 1.65
1:27:51.702117 INFO: Number of cycles    : 977
1:27:51.702150 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:27:51.702191 INFO: Creating DIA data object took: 18.797609567642212
1:27:53.772028 INFO: Creating DIA data NG object took: 2.069701671600342
1:27:55.065825 INFO: Initializing CalibrationManager
1:27:55.066210 INFO: Setting up calibration estimators ..
1:27:55.066302 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:27:55.066417 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'}' ..
1:27:55.066530 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:27:55.066590 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:27:55.066652 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}}' ..
1:27:55.066726 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:27:55.066802 INFO: Done setting up calibration estimators.
1:27:55.067014 INFO: Initializing OptimizationManager
1:27:55.067169 INFO: initial parameter: ms1_error = 3
1:27:55.067225 INFO: initial parameter: ms2_error = 10
1:27:55.067280 INFO: initial parameter: rt_error = 805.5982666015625
1:27:55.067329 INFO: initial parameter: mobility_error = 0.1
1:27:55.067374 INFO: initial parameter: num_candidates = 1
1:27:55.067419 INFO: initial parameter: fwhm_rt = 5
1:27:55.067464 INFO: initial parameter: fwhm_mobility = 0.01
1:27:55.067508 INFO: initial parameter: score_cutoff = 0
1:27:55.067550 INFO: initial parameter: classifier_version = -1
1:27:55.067619 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:27:55.067878 INFO: FDRManager: loading saved state not requested, will be initialized.
1:27:55.067912 INFO: Initializing FDRManager
1:27:55.067958 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:27:56.699741 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:27:57.873923 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:27:57.874464 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
1:27:57.874589 PROGRESS: Starting initial search for precursors.
1:27:57.874698 INFO: Starting optimization step 0.
1:27:57.874778 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:27:57.874856 INFO: Using rust extraction backend
1:27:57.874940 PROGRESS: Extracting batch of 1976 precursors
1:27:57.880224 INFO: === Search parameters used ===
1:27:57.880343 INFO: rt_error       : 805.5982666015625
1:27:57.880408 INFO: mobility_error : 0.1
1:27:57.880463 INFO: num_candidates : 1
1:27:57.880525 INFO: ms1_error      : 3
1:27:57.880579 INFO: ms2_error      : 10
1:27:57.880631 INFO: fwhm_rt        : 5
1:27:57.880681 INFO: quant_window   : 3
1:27:57.880740 INFO: ==============================================
1:27:57.970060 INFO: performing precursor FDR with 40 features
1:27:57.970163 INFO: Decoy channel: -1
1:27:57.970193 INFO: competitive: True
1:27:57.971847 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:57.974353 INFO: Estimating optimal hyperparameters - samples: 1,578, batch_size: 128, learning_rate: 1.77e-04
1:27:57.975533 INFO: Using random state 710652 for train-test-split
1:27:58.187312 INFO: Test AUC: 0.491
1:27:58.187413 INFO: Train AUC: 0.524
1:27:58.187451 INFO: AUC difference: 6.46%
1:27:58.187477 WARNING: AUC difference > 5%. This may indicate overfitting.
1:27:58.528331 INFO: Resetting torch num_threads to 24
1:27:58.530418 PROGRESS: === Extracted 1973 precursors and 11031 fragments ===
1:27:58.530890 INFO: === FDR correction performed with classifier version -1 ===
1:27:58.531542 PROGRESS: ============================= Precursor FDR =============================
1:27:58.531643 PROGRESS: Total precursors accumulated: 2
1:27:58.531714 PROGRESS: Target precursors: 2 (100.00%)
1:27:58.531777 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:58.531829 PROGRESS: 
1:27:58.531880 PROGRESS: Precursor Summary:
1:27:58.533273 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:27:58.533364 PROGRESS: 
1:27:58.533430 PROGRESS: Protein Summary:
1:27:58.534935 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:27:58.535043 PROGRESS: =========================================================================
1:27:58.535389 INFO: Target number of precursors not reached yet.
1:27:58.629934 INFO: Starting optimization step 1.
1:27:58.630180 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:27:58.630268 INFO: Using rust extraction backend
1:27:58.630336 PROGRESS: Extracting batch of 3939 precursors
1:27:58.639033 INFO: === Search parameters used ===
1:27:58.639190 INFO: rt_error       : 805.5982666015625
1:27:58.639256 INFO: mobility_error : 0.1
1:27:58.639310 INFO: num_candidates : 1
1:27:58.639369 INFO: ms1_error      : 3
1:27:58.639421 INFO: ms2_error      : 10
1:27:58.639472 INFO: fwhm_rt        : 5
1:27:58.639522 INFO: quant_window   : 3
1:27:58.639579 INFO: ==============================================
1:27:58.750735 INFO: performing precursor FDR with 40 features
1:27:58.750844 INFO: Decoy channel: -1
1:27:58.750872 INFO: competitive: True
1:27:58.756575 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:58.760029 INFO: Estimating optimal hyperparameters - samples: 4,724, batch_size: 128, learning_rate: 1.77e-04
1:27:58.760147 INFO: Using random state 234903 for train-test-split
1:27:59.363137 INFO: Test AUC: 0.530
1:27:59.363251 INFO: Train AUC: 0.573
1:27:59.363286 INFO: AUC difference: 7.53%
1:27:59.363312 WARNING: AUC difference > 5%. This may indicate overfitting.
1:27:59.698856 INFO: Resetting torch num_threads to 24
1:27:59.703397 PROGRESS: === Extracted 5906 precursors and 33329 fragments ===
1:27:59.703903 INFO: === FDR correction performed with classifier version -1 ===
1:27:59.704620 PROGRESS: ============================= Precursor FDR =============================
1:27:59.704738 PROGRESS: Total precursors accumulated: 18
1:27:59.704815 PROGRESS: Target precursors: 18 (100.00%)
1:27:59.704883 PROGRESS: Decoy precursors: 0 (0.00%)
1:27:59.704942 PROGRESS: 
1:27:59.704998 PROGRESS: Precursor Summary:
1:27:59.706441 PROGRESS: Channel   0:	 0.050 FDR:    18; 0.010 FDR:    18; 0.001 FDR:    18
1:27:59.706546 PROGRESS: 
1:27:59.706612 PROGRESS: Protein Summary:
1:27:59.708162 PROGRESS: Channel   0:	 0.050 FDR:    18; 0.010 FDR:    18; 0.001 FDR:    18
1:27:59.708270 PROGRESS: =========================================================================
1:27:59.708683 INFO: Target number of precursors not reached yet.
1:27:59.812201 INFO: Starting optimization step 2.
1:27:59.812439 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:27:59.812529 INFO: Using rust extraction backend
1:27:59.812605 PROGRESS: Extracting batch of 7882 precursors
1:27:59.829113 INFO: === Search parameters used ===
1:27:59.829309 INFO: rt_error       : 805.5982666015625
1:27:59.829381 INFO: mobility_error : 0.1
1:27:59.829439 INFO: num_candidates : 1
1:27:59.829494 INFO: ms1_error      : 3
1:27:59.829556 INFO: ms2_error      : 10
1:27:59.829608 INFO: fwhm_rt        : 5
1:27:59.829661 INFO: quant_window   : 3
1:27:59.829741 INFO: ==============================================
1:27:59.974542 INFO: performing precursor FDR with 40 features
1:27:59.974653 INFO: Decoy channel: -1
1:27:59.974682 INFO: competitive: True
1:27:59.982896 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:59.987597 INFO: Estimating optimal hyperparameters - samples: 11,017, batch_size: 128, learning_rate: 1.77e-04
1:27:59.987738 INFO: Using random state 285948 for train-test-split
1:28:01.437414 INFO: Test AUC: 0.574
1:28:01.437519 INFO: Train AUC: 0.579
1:28:01.437558 INFO: AUC difference: 1.00%
1:28:01.779210 INFO: Resetting torch num_threads to 24
1:28:01.786111 PROGRESS: === Extracted 13772 precursors and 77770 fragments ===
1:28:01.786667 INFO: === FDR correction performed with classifier version -1 ===
1:28:01.787350 PROGRESS: ============================= Precursor FDR =============================
1:28:01.787463 PROGRESS: Total precursors accumulated: 0
1:28:01.787533 PROGRESS: Target precursors: 0 (0.00%)
1:28:01.787610 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:01.787675 PROGRESS: 
1:28:01.787730 PROGRESS: Precursor Summary:
1:28:01.787873 PROGRESS: 
1:28:01.787947 PROGRESS: Protein Summary:
1:28:01.788037 PROGRESS: =========================================================================
1:28:01.788586 INFO: Target number of precursors not reached yet.
1:28:01.900544 INFO: Starting optimization step 3.
1:28:01.900798 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:28:01.900888 INFO: Using rust extraction backend
1:28:01.900964 PROGRESS: Extracting batch of 15793 precursors
1:28:01.930961 INFO: === Search parameters used ===
1:28:01.931226 INFO: rt_error       : 805.5982666015625
1:28:01.931293 INFO: mobility_error : 0.1
1:28:01.931355 INFO: num_candidates : 1
1:28:01.931412 INFO: ms1_error      : 3
1:28:01.931465 INFO: ms2_error      : 10
1:28:01.931515 INFO: fwhm_rt        : 5
1:28:01.931574 INFO: quant_window   : 3
1:28:01.931644 INFO: ==============================================
1:28:02.197675 INFO: performing precursor FDR with 40 features
1:28:02.197810 INFO: Decoy channel: -1
1:28:02.197839 INFO: competitive: True
1:28:02.212182 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:02.221387 INFO: Estimating optimal hyperparameters - samples: 23,624, batch_size: 128, learning_rate: 1.77e-04
1:28:02.221590 INFO: Using random state 490606 for train-test-split
1:28:05.245801 INFO: Test AUC: 0.575
1:28:05.246022 INFO: Train AUC: 0.603
1:28:05.246063 INFO: AUC difference: 4.63%
1:28:05.587307 INFO: Resetting torch num_threads to 24
1:28:05.598817 PROGRESS: === Extracted 29531 precursors and 166453 fragments ===
1:28:05.599593 INFO: === FDR correction performed with classifier version -1 ===
1:28:05.600343 PROGRESS: ============================= Precursor FDR =============================
1:28:05.600450 PROGRESS: Total precursors accumulated: 90
1:28:05.600526 PROGRESS: Target precursors: 90 (100.00%)
1:28:05.600599 PROGRESS: Decoy precursors: 0 (0.00%)
1:28:05.600657 PROGRESS: 
1:28:05.600713 PROGRESS: Precursor Summary:
1:28:05.602150 PROGRESS: Channel   0:	 0.050 FDR:    90; 0.010 FDR:    90; 0.001 FDR:    90
1:28:05.602252 PROGRESS: 
1:28:05.602325 PROGRESS: Protein Summary:
1:28:05.603954 PROGRESS: Channel   0:	 0.050 FDR:    89; 0.010 FDR:    89; 0.001 FDR:    89
1:28:05.604065 PROGRESS: =========================================================================
1:28:05.604965 INFO: Target number of precursors not reached yet.
1:28:05.778562 INFO: Starting optimization step 4.
1:28:05.778871 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:28:05.779017 INFO: Using rust extraction backend
1:28:05.779126 PROGRESS: Extracting batch of 31556 precursors
1:28:05.836974 INFO: === Search parameters used ===
1:28:05.837257 INFO: rt_error       : 805.5982666015625
1:28:05.837349 INFO: mobility_error : 0.1
1:28:05.837414 INFO: num_candidates : 1
1:28:05.837484 INFO: ms1_error      : 3
1:28:05.837538 INFO: ms2_error      : 10
1:28:05.837589 INFO: fwhm_rt        : 5
1:28:05.837646 INFO: quant_window   : 3
1:28:05.837706 INFO: ==============================================
1:28:06.331433 INFO: performing precursor FDR with 40 features
1:28:06.331549 INFO: Decoy channel: -1
1:28:06.331577 INFO: competitive: True
1:28:06.366479 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:06.388876 INFO: Estimating optimal hyperparameters - samples: 48,800, batch_size: 199, learning_rate: 2.20e-04
1:28:06.389124 INFO: Using random state 401790 for train-test-split
1:28:11.077399 INFO: Test AUC: 0.586
1:28:11.077533 INFO: Train AUC: 0.611
1:28:11.077572 INFO: AUC difference: 4.01%
1:28:11.397634 INFO: Resetting torch num_threads to 24
1:28:11.416208 PROGRESS: === Extracted 61001 precursors and 344353 fragments ===
1:28:11.416802 INFO: === FDR correction performed with classifier version -1 ===
1:28:11.417403 PROGRESS: ============================= Precursor FDR =============================
1:28:11.417496 PROGRESS: Total precursors accumulated: 327
1:28:11.417563 PROGRESS: Target precursors: 324 (99.08%)
1:28:11.417618 PROGRESS: Decoy precursors: 3 (0.92%)
1:28:11.417668 PROGRESS: 
1:28:11.417717 PROGRESS: Precursor Summary:
1:28:11.418776 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   230
1:28:11.418864 PROGRESS: 
1:28:11.418923 PROGRESS: Protein Summary:
1:28:11.420183 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:   220
1:28:11.420276 PROGRESS: =========================================================================
1:28:11.421355 INFO: Target number of precursors not reached yet.
1:28:11.629529 INFO: Starting optimization step 5.
1:28:11.629795 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:28:11.629879 INFO: Using rust extraction backend
1:28:11.629946 PROGRESS: Extracting batch of 63064 precursors
1:28:11.742224 INFO: === Search parameters used ===
1:28:11.742477 INFO: rt_error       : 805.5982666015625
1:28:11.742543 INFO: mobility_error : 0.1
1:28:11.742597 INFO: num_candidates : 1
1:28:11.742646 INFO: ms1_error      : 3
1:28:11.742691 INFO: ms2_error      : 10
1:28:11.742736 INFO: fwhm_rt        : 5
1:28:11.742781 INFO: quant_window   : 3
1:28:11.742827 INFO: ==============================================
1:28:12.525412 INFO: performing precursor FDR with 40 features
1:28:12.525515 INFO: Decoy channel: -1
1:28:12.525541 INFO: competitive: True
1:28:12.578056 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:12.611447 INFO: Estimating optimal hyperparameters - samples: 99,136, batch_size: 406, learning_rate: 3.15e-04
1:28:12.611741 INFO: Using random state 879533 for train-test-split
1:28:18.054073 INFO: Test AUC: 0.585
1:28:18.054201 INFO: Train AUC: 0.610
1:28:18.054240 INFO: AUC difference: 4.01%
1:28:18.439796 INFO: Resetting torch num_threads to 24
1:28:18.474901 PROGRESS: === Extracted 123920 precursors and 697826 fragments ===
1:28:18.475640 INFO: === FDR correction performed with classifier version -1 ===
1:28:18.476498 PROGRESS: ============================= Precursor FDR =============================
1:28:18.476599 PROGRESS: Total precursors accumulated: 659
1:28:18.476672 PROGRESS: Target precursors: 653 (99.09%)
1:28:18.476742 PROGRESS: Decoy precursors: 6 (0.91%)
1:28:18.476800 PROGRESS: 
1:28:18.476855 PROGRESS: Precursor Summary:
1:28:18.478375 PROGRESS: Channel   0:	 0.050 FDR:   653; 0.010 FDR:   653; 0.001 FDR:   395
1:28:18.478499 PROGRESS: 
1:28:18.478566 PROGRESS: Protein Summary:
1:28:18.480375 PROGRESS: Channel   0:	 0.050 FDR:   604; 0.010 FDR:   604; 0.001 FDR:   374
1:28:18.480476 PROGRESS: =========================================================================
1:28:18.483948 INFO: Target number of precursors not reached yet.
1:28:18.819157 INFO: Starting optimization step 6.
1:28:18.819444 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:28:18.819536 INFO: Using rust extraction backend
1:28:18.819609 PROGRESS: Extracting batch of 126165 precursors
1:28:19.045427 INFO: === Search parameters used ===
1:28:19.045715 INFO: rt_error       : 805.5982666015625
1:28:19.045790 INFO: mobility_error : 0.1
1:28:19.045869 INFO: num_candidates : 1
1:28:19.045927 INFO: ms1_error      : 3
1:28:19.045981 INFO: ms2_error      : 10
1:28:19.046030 INFO: fwhm_rt        : 5
1:28:19.046078 INFO: quant_window   : 3
1:28:19.046132 INFO: ==============================================
1:28:20.409561 INFO: performing precursor FDR with 40 features
1:28:20.409699 INFO: Decoy channel: -1
1:28:20.409727 INFO: competitive: True
1:28:20.533934 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:20.659263 INFO: Estimating optimal hyperparameters - samples: 199,848, batch_size: 818, learning_rate: 4.47e-04
1:28:20.659695 INFO: Using random state 524448 for train-test-split
1:28:29.168549 INFO: Test AUC: 0.594
1:28:29.168688 INFO: Train AUC: 0.610
1:28:29.168726 INFO: AUC difference: 2.61%
1:28:29.600976 INFO: Resetting torch num_threads to 24
1:28:29.666009 PROGRESS: === Extracted 249811 precursors and 1406560 fragments ===
1:28:29.666784 INFO: === FDR correction performed with classifier version -1 ===
1:28:29.667799 PROGRESS: ============================= Precursor FDR =============================
1:28:29.667905 PROGRESS: Total precursors accumulated: 1,232
1:28:29.668005 PROGRESS: Target precursors: 1,220 (99.03%)
1:28:29.668069 PROGRESS: Decoy precursors: 12 (0.97%)
1:28:29.668126 PROGRESS: 
1:28:29.668190 PROGRESS: Precursor Summary:
1:28:29.669874 PROGRESS: Channel   0:	 0.050 FDR: 1,220; 0.010 FDR: 1,220; 0.001 FDR:   736
1:28:29.669989 PROGRESS: 
1:28:29.670057 PROGRESS: Protein Summary:
1:28:29.672263 PROGRESS: Channel   0:	 0.050 FDR: 1,037; 0.010 FDR: 1,037; 0.001 FDR:   654
1:28:29.672375 PROGRESS: =========================================================================
1:28:29.678695 INFO: Target number of precursors reached.
1:28:29.922216 INFO: fragments_df: keeping 5000 of 1406560 [sum(precursor_idx_mask)=13023 sum(mass_error_mask)=1406560 stop_rank=5000
1:28:30.544508 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:30.945124 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:31.978831 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:28:31.979482 INFO: Using score_cutoff 12.567937581539153 (fac=0.99, q=1)
1:28:31.979905 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:28:31.979996 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:28:31.980068 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.567937581539153
1:28:31.980146 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:32.141379 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:32.498928 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:28:32.499257 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:28:32.499382 INFO: Starting optimization step 7.
1:28:32.499459 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:28:32.499553 INFO: Using rust extraction backend
1:28:32.499632 PROGRESS: Extracting batch of 250375 precursors
1:28:32.946070 INFO: === Search parameters used ===
1:28:32.946347 INFO: rt_error       : 805.5982666015625
1:28:32.946428 INFO: mobility_error : 0.1
1:28:32.946492 INFO: num_candidates : 3
1:28:32.946550 INFO: ms1_error      : 3
1:28:32.946609 INFO: ms2_error      : 10
1:28:32.946668 INFO: fwhm_rt        : 3.0
1:28:32.946721 INFO: quant_window   : 3
1:28:32.946771 INFO: ==============================================
1:28:37.321604 INFO: performing precursor FDR with 40 features
1:28:37.321745 INFO: Decoy channel: -1
1:28:37.321781 INFO: competitive: True
1:28:37.538014 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:37.866536 INFO: Estimating optimal hyperparameters - samples: 599,742, batch_size: 2,456, learning_rate: 7.74e-04
1:28:37.867691 INFO: Using random state 290970 for train-test-split
1:28:51.415998 INFO: Test AUC: 0.597
1:28:51.416198 INFO: Train AUC: 0.606
1:28:51.416232 INFO: AUC difference: 1.51%
1:28:51.928643 INFO: Resetting torch num_threads to 24
1:28:51.960208 PROGRESS: === Extracted 749678 precursors and 4054661 fragments ===
1:28:51.960743 INFO: === FDR correction performed with classifier version 6 ===
1:28:51.961487 PROGRESS: ============================= Precursor FDR =============================
1:28:51.961593 PROGRESS: Total precursors accumulated: 1,365
1:28:51.961658 PROGRESS: Target precursors: 1,352 (99.05%)
1:28:51.961712 PROGRESS: Decoy precursors: 13 (0.95%)
1:28:51.961768 PROGRESS: 
1:28:51.961817 PROGRESS: Precursor Summary:
1:28:51.963265 PROGRESS: Channel   0:	 0.050 FDR: 1,352; 0.010 FDR: 1,352; 0.001 FDR:   989
1:28:51.963377 PROGRESS: 
1:28:51.963435 PROGRESS: Protein Summary:
1:28:51.965247 PROGRESS: Channel   0:	 0.050 FDR: 1,150; 0.010 FDR: 1,150; 0.001 FDR:   843
1:28:51.965342 PROGRESS: =========================================================================
1:28:51.986132 INFO: Target number of precursors reached.
1:28:52.443305 INFO: fragments_df: keeping 5000 of 4054661 [sum(precursor_idx_mask)=32684 sum(mass_error_mask)=4054661 stop_rank=5000
1:28:53.011992 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:53.428253 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:54.523466 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:54.524071 INFO: Using score_cutoff 12.335606917190551 (fac=0.99, q=1)
1:28:54.524545 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:54.524655 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:54.524720 INFO: Updating optimization_manager: score_cutoff        : 12.567937581539153 -> 12.335606917190551
1:28:54.524808 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:54.690013 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:55.048628 INFO: === checking if optimization conditions were reached ===
1:28:55.051271 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:28:55.051461 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:28:55.051554 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:28:55.051624 INFO: ==============================================
1:28:55.051714 INFO: Starting optimization step 8.
1:28:55.051786 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:28:55.051870 INFO: Using rust extraction backend
1:28:55.051953 PROGRESS: Extracting batch of 250375 precursors
1:28:55.504452 INFO: === Search parameters used ===
1:28:55.504749 INFO: rt_error       : 805.5982666015625
1:28:55.504841 INFO: mobility_error : 0.1
1:28:55.504915 INFO: num_candidates : 3
1:28:55.504971 INFO: ms1_error      : 3
1:28:55.505025 INFO: ms2_error      : 10.0
1:28:55.505079 INFO: fwhm_rt        : 3.0
1:28:55.505138 INFO: quant_window   : 3
1:28:55.505189 INFO: ==============================================
1:29:00.054949 INFO: performing precursor FDR with 40 features
1:29:00.055077 INFO: Decoy channel: -1
1:29:00.055104 INFO: competitive: True
1:29:00.286469 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:00.693790 INFO: Estimating optimal hyperparameters - samples: 599,722, batch_size: 2,456, learning_rate: 7.74e-04
1:29:00.695651 INFO: Using random state 998232 for train-test-split
1:29:15.305919 INFO: Test AUC: 0.605
1:29:15.306203 INFO: Train AUC: 0.613
1:29:15.306423 INFO: AUC difference: 1.30%
1:29:15.921889 INFO: Resetting torch num_threads to 24
1:29:15.969095 PROGRESS: === Extracted 749653 precursors and 4054178 fragments ===
1:29:15.969716 INFO: === FDR correction performed with classifier version 7 ===
1:29:15.970702 PROGRESS: ============================= Precursor FDR =============================
1:29:15.970820 PROGRESS: Total precursors accumulated: 1,462
1:29:15.970894 PROGRESS: Target precursors: 1,448 (99.04%)
1:29:15.970998 PROGRESS: Decoy precursors: 14 (0.96%)
1:29:15.971063 PROGRESS: 
1:29:15.971123 PROGRESS: Precursor Summary:
1:29:15.972938 PROGRESS: Channel   0:	 0.050 FDR: 1,448; 0.010 FDR: 1,448; 0.001 FDR: 1,029
1:29:15.973047 PROGRESS: 
1:29:15.973111 PROGRESS: Protein Summary:
1:29:15.975471 PROGRESS: Channel   0:	 0.050 FDR: 1,220; 0.010 FDR: 1,220; 0.001 FDR:   881
1:29:15.975582 PROGRESS: =========================================================================
1:29:16.010514 INFO: Target number of precursors reached.
1:29:16.676069 INFO: fragments_df: keeping 5000 of 4054178 [sum(precursor_idx_mask)=34958 sum(mass_error_mask)=4054178 stop_rank=5000
1:29:17.343474 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:29:17.765980 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:29:18.694253 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:29:18.694699 INFO: Using score_cutoff 12.608228491973877 (fac=0.99, q=1)
1:29:18.695043 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:29:18.695129 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:29:18.695189 INFO: Updating optimization_manager: score_cutoff        : 12.335606917190551 -> 12.608228491973877
1:29:18.695247 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:29:18.853503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:29:19.218553 INFO: === checking if optimization conditions were reached ===
1:29:19.221185 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:29:19.221309 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:29:19.221394 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:29:19.221470 INFO: ==============================================
1:29:19.221556 INFO: Starting optimization step 9.
1:29:19.221633 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:29:19.221710 INFO: Using rust extraction backend
1:29:19.221785 PROGRESS: Extracting batch of 250375 precursors
1:29:19.657983 INFO: === Search parameters used ===
1:29:19.658221 INFO: rt_error       : 805.5982666015625
1:29:19.658287 INFO: mobility_error : 0.1
1:29:19.658339 INFO: num_candidates : 3
1:29:19.658386 INFO: ms1_error      : 3
1:29:19.658430 INFO: ms2_error      : 10.0
1:29:19.658474 INFO: fwhm_rt        : 3.0
1:29:19.658517 INFO: quant_window   : 3
1:29:19.658562 INFO: ==============================================
1:29:24.062891 INFO: performing precursor FDR with 40 features
1:29:24.063023 INFO: Decoy channel: -1
1:29:24.063051 INFO: competitive: True
1:29:24.268081 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:24.630703 INFO: Estimating optimal hyperparameters - samples: 599,717, batch_size: 2,456, learning_rate: 7.74e-04
1:29:24.631927 INFO: Using random state 996803 for train-test-split
1:29:39.196418 INFO: Test AUC: 0.608
1:29:39.196584 INFO: Train AUC: 0.617
1:29:39.196623 INFO: AUC difference: 1.39%
1:29:39.838833 INFO: Resetting torch num_threads to 24
1:29:39.884732 PROGRESS: === Extracted 749647 precursors and 4054402 fragments ===
1:29:39.885320 INFO: === FDR correction performed with classifier version 8 ===
1:29:39.886265 PROGRESS: ============================= Precursor FDR =============================
1:29:39.886409 PROGRESS: Total precursors accumulated: 1,470
1:29:39.886481 PROGRESS: Target precursors: 1,456 (99.05%)
1:29:39.886549 PROGRESS: Decoy precursors: 14 (0.95%)
1:29:39.886606 PROGRESS: 
1:29:39.886661 PROGRESS: Precursor Summary:
1:29:39.888535 PROGRESS: Channel   0:	 0.050 FDR: 1,456; 0.010 FDR: 1,456; 0.001 FDR: 1,058
1:29:39.888650 PROGRESS: 
1:29:39.888719 PROGRESS: Protein Summary:
1:29:39.891092 PROGRESS: Channel   0:	 0.050 FDR: 1,232; 0.010 FDR: 1,232; 0.001 FDR:   913
1:29:39.891207 PROGRESS: =========================================================================
1:29:39.919128 INFO: Target number of precursors reached.
1:29:40.586063 INFO: fragments_df: keeping 5000 of 4054402 [sum(precursor_idx_mask)=35186 sum(mass_error_mask)=4054402 stop_rank=5000
1:29:41.187111 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:29:41.639432 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:29:42.660859 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:29:42.661307 INFO: Using score_cutoff 12.621783588409423 (fac=0.99, q=1)
1:29:42.661641 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:29:42.661721 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:29:42.661776 INFO: Updating optimization_manager: score_cutoff        : 12.608228491973877 -> 12.621783588409423
1:29:42.661831 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:29:42.817760 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:29:43.167348 INFO: === checking if optimization conditions were reached ===
1:29:43.170221 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:29:43.170397 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:29:43.170482 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:29:43.170556 INFO: ==============================================
1:29:43.170642 INFO: Starting optimization step 10.
1:29:43.170719 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:29:43.170805 INFO: Using rust extraction backend
1:29:43.170888 PROGRESS: Extracting batch of 250375 precursors
1:29:43.621217 INFO: === Search parameters used ===
1:29:43.621509 INFO: rt_error       : 805.5982666015625
1:29:43.621588 INFO: mobility_error : 0.1
1:29:43.621647 INFO: num_candidates : 3
1:29:43.621699 INFO: ms1_error      : 3
1:29:43.621752 INFO: ms2_error      : 10.0
1:29:43.621816 INFO: fwhm_rt        : 3.0
1:29:43.621878 INFO: quant_window   : 3
1:29:43.621937 INFO: ==============================================
1:29:48.644275 INFO: performing precursor FDR with 40 features
1:29:48.644415 INFO: Decoy channel: -1
1:29:48.644449 INFO: competitive: True
1:29:48.873855 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:49.302265 INFO: Estimating optimal hyperparameters - samples: 599,716, batch_size: 2,456, learning_rate: 7.74e-04
1:29:49.304066 INFO: Using random state 946263 for train-test-split
1:30:03.463547 INFO: Test AUC: 0.611
1:30:03.463687 INFO: Train AUC: 0.620
1:30:03.463729 INFO: AUC difference: 1.54%
1:30:04.084644 INFO: Resetting torch num_threads to 24
1:30:04.163295 PROGRESS: === Extracted 749646 precursors and 4054151 fragments ===
1:30:04.163864 INFO: === FDR correction performed with classifier version 9 ===
1:30:04.164554 PROGRESS: ============================= Precursor FDR =============================
1:30:04.164667 PROGRESS: Total precursors accumulated: 1
1:30:04.164739 PROGRESS: Target precursors: 1 (100.00%)
1:30:04.164804 PROGRESS: Decoy precursors: 0 (0.00%)
1:30:04.164859 PROGRESS: 
1:30:04.164913 PROGRESS: Precursor Summary:
1:30:04.166310 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:30:04.166406 PROGRESS: 
1:30:04.166469 PROGRESS: Protein Summary:
1:30:04.167974 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:30:04.168077 PROGRESS: =========================================================================
1:30:04.193644 INFO: Target number of precursors not reached yet.
1:30:04.736549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:30:04.909671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:30:05.284099 INFO: === skipping optimization until target number of precursors are found ===
1:30:05.284419 INFO: Starting optimization step 11.
1:30:05.284512 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:30:05.284601 INFO: Using rust extraction backend
1:30:05.284680 PROGRESS: Extracting batch of 252219 precursors
1:30:05.750119 INFO: === Search parameters used ===
1:30:05.750410 INFO: rt_error       : 805.5982666015625
1:30:05.750506 INFO: mobility_error : 0.1
1:30:05.750578 INFO: num_candidates : 3
1:30:05.750634 INFO: ms1_error      : 3
1:30:05.750687 INFO: ms2_error      : 10.0
1:30:05.750744 INFO: fwhm_rt        : 3.0
1:30:05.750798 INFO: quant_window   : 3
1:30:05.750848 INFO: ==============================================
1:30:10.766636 INFO: performing precursor FDR with 40 features
1:30:10.766784 INFO: Decoy channel: -1
1:30:10.766811 INFO: competitive: True
1:30:11.444887 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:12.268537 INFO: Estimating optimal hyperparameters - samples: 1,203,877, batch_size: 4,096, learning_rate: 1.00e-03
1:30:12.271219 INFO: Using random state 946263 for train-test-split
1:30:38.986617 INFO: Test AUC: 0.608
1:30:38.986784 INFO: Train AUC: 0.614
1:30:38.986819 INFO: AUC difference: 0.98%
1:30:39.860207 INFO: Resetting torch num_threads to 24
1:30:40.246674 PROGRESS: === Extracted 1504847 precursors and 8128702 fragments ===
1:30:40.247481 INFO: === FDR correction performed with classifier version 9 ===
1:30:40.249024 PROGRESS: ============================= Precursor FDR =============================
1:30:40.249141 PROGRESS: Total precursors accumulated: 3,483
1:30:40.249216 PROGRESS: Target precursors: 3,449 (99.02%)
1:30:40.249279 PROGRESS: Decoy precursors: 34 (0.98%)
1:30:40.249336 PROGRESS: 
1:30:40.249402 PROGRESS: Precursor Summary:
1:30:40.251820 PROGRESS: Channel   0:	 0.050 FDR: 3,449; 0.010 FDR: 3,449; 0.001 FDR: 2,084
1:30:40.251936 PROGRESS: 
1:30:40.252006 PROGRESS: Protein Summary:
1:30:40.255501 PROGRESS: Channel   0:	 0.050 FDR: 2,536; 0.010 FDR: 2,536; 0.001 FDR: 1,594
1:30:40.255607 PROGRESS: =========================================================================
1:30:40.279463 INFO: Target number of precursors reached.
1:30:41.625169 INFO: fragments_df: keeping 5000 of 8128702 [sum(precursor_idx_mask)=80515 sum(mass_error_mask)=8128702 stop_rank=5000
1:30:42.352451 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:30:43.036131 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:30:44.059545 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:30:44.060072 INFO: Using score_cutoff 9.552552501296997 (fac=0.99, q=1)
1:30:44.060448 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:30:44.060535 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:30:44.060597 INFO: Updating optimization_manager: score_cutoff        : 12.621783588409423 -> 9.552552501296997
1:30:44.060669 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:30:44.221419 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:30:44.602377 INFO: === checking if optimization conditions were reached ===
1:30:44.604939 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:30:44.605073 INFO: Updating optimization_manager: classifier_version  : 9 -> 11
1:30:44.605159 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:30:44.605242 INFO: ==============================================
1:30:44.605329 INFO: Starting optimization step 12.
1:30:44.605408 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:30:44.605491 INFO: Using rust extraction backend
1:30:44.605573 PROGRESS: Extracting batch of 250375 precursors
1:30:45.052524 INFO: === Search parameters used ===
1:30:45.052827 INFO: rt_error       : 805.5982666015625
1:30:45.052914 INFO: mobility_error : 0.1
1:30:45.052984 INFO: num_candidates : 3
1:30:45.053046 INFO: ms1_error      : 3
1:30:45.053106 INFO: ms2_error      : 10.0
1:30:45.053165 INFO: fwhm_rt        : 3.0
1:30:45.053223 INFO: quant_window   : 3
1:30:45.053281 INFO: ==============================================
1:30:50.127270 INFO: performing precursor FDR with 40 features
1:30:50.127412 INFO: Decoy channel: -1
1:30:50.127444 INFO: competitive: True
1:30:50.369398 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:50.789261 INFO: Estimating optimal hyperparameters - samples: 599,784, batch_size: 2,456, learning_rate: 7.74e-04
1:30:50.790509 INFO: Using random state 839658 for train-test-split
1:31:05.596211 INFO: Test AUC: 0.612
1:31:05.596360 INFO: Train AUC: 0.621
1:31:05.596399 INFO: AUC difference: 1.38%
1:31:06.126910 INFO: Resetting torch num_threads to 24
1:31:06.153996 PROGRESS: === Extracted 749730 precursors and 4054238 fragments ===
1:31:06.154472 INFO: === FDR correction performed with classifier version 11 ===
1:31:06.155258 PROGRESS: ============================= Precursor FDR =============================
1:31:06.155362 PROGRESS: Total precursors accumulated: 1,632
1:31:06.155423 PROGRESS: Target precursors: 1,616 (99.02%)
1:31:06.155475 PROGRESS: Decoy precursors: 16 (0.98%)
1:31:06.155523 PROGRESS: 
1:31:06.155577 PROGRESS: Precursor Summary:
1:31:06.157024 PROGRESS: Channel   0:	 0.050 FDR: 1,616; 0.010 FDR: 1,616; 0.001 FDR: 1,217
1:31:06.157117 PROGRESS: 
1:31:06.157173 PROGRESS: Protein Summary:
1:31:06.159051 PROGRESS: Channel   0:	 0.050 FDR: 1,384; 0.010 FDR: 1,384; 0.001 FDR: 1,051
1:31:06.159147 PROGRESS: =========================================================================
1:31:06.173084 INFO: Target number of precursors reached.
1:31:06.818538 INFO: fragments_df: keeping 5000 of 4054238 [sum(precursor_idx_mask)=37724 sum(mass_error_mask)=4054238 stop_rank=5000
1:31:07.345155 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:07.837829 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:10.123569 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:10.124093 INFO: Using score_cutoff 9.390905867099761 (fac=0.99, q=1)
1:31:10.124525 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:10.124635 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:10.124702 INFO: Updating optimization_manager: score_cutoff        : 9.552552501296997 -> 9.390905867099761
1:31:10.124772 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:10.286515 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:10.647622 INFO: === checking if optimization conditions were reached ===
1:31:10.650263 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:31:10.650425 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:31:10.650502 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:31:10.650573 INFO: ==============================================
1:31:10.650654 PROGRESS: Optimization finished for ms2_error.
1:31:11.143372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:11.305893 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:11.669278 INFO: Starting optimization step 0.
1:31:11.669555 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:31:11.669663 INFO: Using rust extraction backend
1:31:11.669744 PROGRESS: Extracting batch of 250375 precursors
1:31:12.124508 INFO: === Search parameters used ===
1:31:12.124793 INFO: rt_error       : 805.5982666015625
1:31:12.124887 INFO: mobility_error : 0.1
1:31:12.124955 INFO: num_candidates : 3
1:31:12.125011 INFO: ms1_error      : 3
1:31:12.125065 INFO: ms2_error      : 10.0
1:31:12.125117 INFO: fwhm_rt        : 3.0
1:31:12.125178 INFO: quant_window   : 3
1:31:12.125236 INFO: ==============================================
1:31:17.030279 INFO: performing precursor FDR with 40 features
1:31:17.030410 INFO: Decoy channel: -1
1:31:17.030441 INFO: competitive: True
1:31:17.270341 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:17.695890 INFO: Estimating optimal hyperparameters - samples: 599,757, batch_size: 2,456, learning_rate: 7.74e-04
1:31:17.697294 INFO: Using random state 27491 for train-test-split
1:31:30.937832 INFO: Test AUC: 0.610
1:31:30.938002 INFO: Train AUC: 0.623
1:31:30.938043 INFO: AUC difference: 2.04%
1:31:31.571966 INFO: Resetting torch num_threads to 24
1:31:31.611034 PROGRESS: === Extracted 749697 precursors and 4054555 fragments ===
1:31:31.611620 INFO: === FDR correction performed with classifier version 12 ===
1:31:31.612631 PROGRESS: ============================= Precursor FDR =============================
1:31:31.612751 PROGRESS: Total precursors accumulated: 1,729
1:31:31.612827 PROGRESS: Target precursors: 1,712 (99.02%)
1:31:31.612889 PROGRESS: Decoy precursors: 17 (0.98%)
1:31:31.612951 PROGRESS: 
1:31:31.613008 PROGRESS: Precursor Summary:
1:31:31.615221 PROGRESS: Channel   0:	 0.050 FDR: 1,712; 0.010 FDR: 1,712; 0.001 FDR: 1,203
1:31:31.615368 PROGRESS: 
1:31:31.615443 PROGRESS: Protein Summary:
1:31:31.618024 PROGRESS: Channel   0:	 0.050 FDR: 1,454; 0.010 FDR: 1,454; 0.001 FDR: 1,038
1:31:31.618127 PROGRESS: =========================================================================
1:31:31.640017 INFO: Target number of precursors reached.
1:31:32.297264 INFO: fragments_df: keeping 5000 of 4054555 [sum(precursor_idx_mask)=39554 sum(mass_error_mask)=4054555 stop_rank=5000
1:31:32.824260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:33.250211 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:34.358797 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:34.359454 INFO: Using score_cutoff 8.473563314723968 (fac=0.99, q=1)
1:31:34.359908 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:34.360006 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:34.360076 INFO: Updating optimization_manager: score_cutoff        : 9.390905867099761 -> 8.473563314723968
1:31:34.360154 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:34.521661 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:34.874575 INFO: === checking if optimization conditions were reached ===
1:31:34.874848 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:31:34.878439 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 662.8791818368542
1:31:34.878633 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 662.8792.
1:31:34.878721 INFO: ==============================================
1:31:34.878819 INFO: Starting optimization step 1.
1:31:34.878898 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:31:34.879008 INFO: Using rust extraction backend
1:31:34.879102 PROGRESS: Extracting batch of 250375 precursors
1:31:35.320464 INFO: === Search parameters used ===
1:31:35.320765 INFO: rt_error       : 662.8791818368542
1:31:35.320832 INFO: mobility_error : 0.1
1:31:35.320885 INFO: num_candidates : 3
1:31:35.320933 INFO: ms1_error      : 3
1:31:35.320978 INFO: ms2_error      : 10.0
1:31:35.321022 INFO: fwhm_rt        : 3.0
1:31:35.321065 INFO: quant_window   : 3
1:31:35.321107 INFO: ==============================================
1:31:39.652904 INFO: performing precursor FDR with 40 features
1:31:39.653055 INFO: Decoy channel: -1
1:31:39.653087 INFO: competitive: True
1:31:39.875216 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:40.266467 INFO: Estimating optimal hyperparameters - samples: 599,743, batch_size: 2,456, learning_rate: 7.74e-04
1:31:40.267562 INFO: Using random state 27491 for train-test-split
1:31:50.790473 INFO: Test AUC: 0.611
1:31:50.790645 INFO: Train AUC: 0.624
1:31:50.790683 INFO: AUC difference: 2.09%
1:31:51.337679 INFO: Resetting torch num_threads to 24
1:31:51.366148 PROGRESS: === Extracted 749679 precursors and 4052511 fragments ===
1:31:51.366691 INFO: === FDR correction performed with classifier version 12 ===
1:31:51.367522 PROGRESS: ============================= Precursor FDR =============================
1:31:51.367636 PROGRESS: Total precursors accumulated: 1,669
1:31:51.367702 PROGRESS: Target precursors: 1,653 (99.04%)
1:31:51.367761 PROGRESS: Decoy precursors: 16 (0.96%)
1:31:51.367834 PROGRESS: 
1:31:51.367887 PROGRESS: Precursor Summary:
1:31:51.369503 PROGRESS: Channel   0:	 0.050 FDR: 1,653; 0.010 FDR: 1,653; 0.001 FDR: 1,141
1:31:51.369611 PROGRESS: 
1:31:51.369671 PROGRESS: Protein Summary:
1:31:51.371649 PROGRESS: Channel   0:	 0.050 FDR: 1,395; 0.010 FDR: 1,395; 0.001 FDR:   982
1:31:51.371758 PROGRESS: =========================================================================
1:31:51.386101 INFO: Target number of precursors reached.
1:31:52.011259 INFO: fragments_df: keeping 5000 of 4052511 [sum(precursor_idx_mask)=39322 sum(mass_error_mask)=4052511 stop_rank=5000
1:31:52.530240 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:53.019535 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:53.888378 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:53.888830 INFO: Using score_cutoff 12.0358953540802 (fac=0.99, q=1)
1:31:53.889166 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:53.889245 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:53.889302 INFO: Updating optimization_manager: score_cutoff        : 8.473563314723968 -> 12.0358953540802
1:31:53.889356 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:54.045834 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:54.401627 INFO: === checking if optimization conditions were reached ===
1:31:54.401911 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:31:54.405641 INFO: Updating optimization_manager: rt_error            : 662.8791818368542 -> 573.5094772651445
1:31:54.405825 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 573.5095.
1:31:54.405913 INFO: ==============================================
1:31:54.406007 INFO: Starting optimization step 2.
1:31:54.406083 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:31:54.406173 INFO: Using rust extraction backend
1:31:54.406256 PROGRESS: Extracting batch of 250375 precursors
1:31:54.850522 INFO: === Search parameters used ===
1:31:54.850809 INFO: rt_error       : 573.5094772651445
1:31:54.850890 INFO: mobility_error : 0.1
1:31:54.850953 INFO: num_candidates : 3
1:31:54.851031 INFO: ms1_error      : 3
1:31:54.851087 INFO: ms2_error      : 10.0
1:31:54.851142 INFO: fwhm_rt        : 3.0
1:31:54.851197 INFO: quant_window   : 3
1:31:54.851257 INFO: ==============================================
1:31:59.372231 INFO: performing precursor FDR with 40 features
1:31:59.372349 INFO: Decoy channel: -1
1:31:59.372375 INFO: competitive: True
1:31:59.560666 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:59.874054 INFO: Estimating optimal hyperparameters - samples: 599,401, batch_size: 2,455, learning_rate: 7.74e-04
1:31:59.875048 INFO: Using random state 27491 for train-test-split
1:32:14.744343 INFO: Test AUC: 0.613
1:32:14.744490 INFO: Train AUC: 0.623
1:32:14.744524 INFO: AUC difference: 1.60%
1:32:15.243642 INFO: Resetting torch num_threads to 24
1:32:15.272675 PROGRESS: === Extracted 749252 precursors and 4028571 fragments ===
1:32:15.273174 INFO: === FDR correction performed with classifier version 12 ===
1:32:15.274055 PROGRESS: ============================= Precursor FDR =============================
1:32:15.274161 PROGRESS: Total precursors accumulated: 1,717
1:32:15.274224 PROGRESS: Target precursors: 1,700 (99.01%)
1:32:15.274287 PROGRESS: Decoy precursors: 17 (0.99%)
1:32:15.274338 PROGRESS: 
1:32:15.274385 PROGRESS: Precursor Summary:
1:32:15.275970 PROGRESS: Channel   0:	 0.050 FDR: 1,700; 0.010 FDR: 1,678; 0.001 FDR: 1,287
1:32:15.276076 PROGRESS: 
1:32:15.276135 PROGRESS: Protein Summary:
1:32:15.278090 PROGRESS: Channel   0:	 0.050 FDR: 1,432; 0.010 FDR: 1,416; 0.001 FDR: 1,101
1:32:15.278187 PROGRESS: =========================================================================
1:32:15.294060 INFO: Target number of precursors reached.
1:32:15.906676 INFO: fragments_df: keeping 5000 of 4028571 [sum(precursor_idx_mask)=39337 sum(mass_error_mask)=4028571 stop_rank=5000
1:32:16.431010 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:32:16.917703 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:32:17.816042 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:32:17.816506 INFO: Using score_cutoff 9.866110087394715 (fac=0.99, q=1)
1:32:17.816838 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:32:17.816919 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:32:17.816977 INFO: Updating optimization_manager: score_cutoff        : 12.0358953540802 -> 9.866110087394715
1:32:17.817044 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:32:17.977508 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:32:18.329314 INFO: === checking if optimization conditions were reached ===
1:32:18.329622 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:32:18.333281 INFO: Updating optimization_manager: rt_error            : 573.5094772651445 -> 673.4503668091279
1:32:18.333442 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 673.4504.
1:32:18.333524 INFO: ==============================================
1:32:18.333616 INFO: Starting optimization step 3.
1:32:18.333688 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:32:18.333767 INFO: Using rust extraction backend
1:32:18.333842 PROGRESS: Extracting batch of 250375 precursors
1:32:18.770122 INFO: === Search parameters used ===
1:32:18.770378 INFO: rt_error       : 673.4503668091279
1:32:18.770441 INFO: mobility_error : 0.1
1:32:18.770493 INFO: num_candidates : 3
1:32:18.770539 INFO: ms1_error      : 3
1:32:18.770587 INFO: ms2_error      : 10.0
1:32:18.770630 INFO: fwhm_rt        : 3.0
1:32:18.770672 INFO: quant_window   : 3
1:32:18.770713 INFO: ==============================================
1:32:23.099946 INFO: performing precursor FDR with 40 features
1:32:23.100074 INFO: Decoy channel: -1
1:32:23.100103 INFO: competitive: True
1:32:23.292591 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:23.600401 INFO: Estimating optimal hyperparameters - samples: 599,712, batch_size: 2,456, learning_rate: 7.74e-04
1:32:23.601517 INFO: Using random state 27491 for train-test-split
1:32:36.293823 INFO: Test AUC: 0.611
1:32:36.293981 INFO: Train AUC: 0.622
1:32:36.294021 INFO: AUC difference: 1.78%
1:32:36.933487 INFO: Resetting torch num_threads to 24
1:32:36.973784 PROGRESS: === Extracted 749641 precursors and 4050419 fragments ===
1:32:36.974372 INFO: === FDR correction performed with classifier version 12 ===
1:32:36.975399 PROGRESS: ============================= Precursor FDR =============================
1:32:36.975535 PROGRESS: Total precursors accumulated: 1,730
1:32:36.975613 PROGRESS: Target precursors: 1,713 (99.02%)
1:32:36.975676 PROGRESS: Decoy precursors: 17 (0.98%)
1:32:36.975734 PROGRESS: 
1:32:36.975794 PROGRESS: Precursor Summary:
1:32:36.977783 PROGRESS: Channel   0:	 0.050 FDR: 1,713; 0.010 FDR: 1,713; 0.001 FDR: 1,230
1:32:36.977900 PROGRESS: 
1:32:36.977969 PROGRESS: Protein Summary:
1:32:36.980467 PROGRESS: Channel   0:	 0.050 FDR: 1,449; 0.010 FDR: 1,449; 0.001 FDR: 1,072
1:32:36.980576 PROGRESS: =========================================================================
1:32:37.001822 INFO: Target number of precursors reached.
1:32:37.534615 INFO: fragments_df: keeping 5000 of 4050419 [sum(precursor_idx_mask)=40465 sum(mass_error_mask)=4050419 stop_rank=5000
1:32:37.971670 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:32:38.346406 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:32:39.507348 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:32:39.507868 INFO: Using score_cutoff 11.279825302505493 (fac=0.99, q=1)
1:32:39.508238 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:32:39.508329 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:32:39.508393 INFO: Updating optimization_manager: score_cutoff        : 9.866110087394715 -> 11.279825302505493
1:32:39.508464 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:32:39.669746 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:32:40.017151 INFO: === checking if optimization conditions were reached ===
1:32:40.017462 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:32:40.020914 INFO: Updating optimization_manager: rt_error            : 673.4503668091279 -> 671.6475653336271
1:32:40.021038 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 671.6476.
1:32:40.021135 INFO: ==============================================
1:32:40.021231 INFO: Starting optimization step 4.
1:32:40.021302 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:32:40.021384 INFO: Using rust extraction backend
1:32:40.021456 PROGRESS: Extracting batch of 250375 precursors
1:32:40.466981 INFO: === Search parameters used ===
1:32:40.467260 INFO: rt_error       : 671.6475653336271
1:32:40.467338 INFO: mobility_error : 0.1
1:32:40.467396 INFO: num_candidates : 3
1:32:40.467455 INFO: ms1_error      : 3
1:32:40.467515 INFO: ms2_error      : 10.0
1:32:40.467572 INFO: fwhm_rt        : 3.0
1:32:40.467622 INFO: quant_window   : 3
1:32:40.467680 INFO: ==============================================
1:32:44.817940 INFO: performing precursor FDR with 40 features
1:32:44.818079 INFO: Decoy channel: -1
1:32:44.818105 INFO: competitive: True
1:32:45.026232 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:45.419863 INFO: Estimating optimal hyperparameters - samples: 599,689, batch_size: 2,456, learning_rate: 7.74e-04
1:32:45.420899 INFO: Using random state 27491 for train-test-split
1:32:59.618267 INFO: Test AUC: 0.613
1:32:59.618431 INFO: Train AUC: 0.624
1:32:59.618470 INFO: AUC difference: 1.76%
1:33:00.233000 INFO: Resetting torch num_threads to 24
1:33:00.274542 PROGRESS: === Extracted 749612 precursors and 4049069 fragments ===
1:33:00.275140 INFO: === FDR correction performed with classifier version 12 ===
1:33:00.276099 PROGRESS: ============================= Precursor FDR =============================
1:33:00.276217 PROGRESS: Total precursors accumulated: 1,633
1:33:00.276287 PROGRESS: Target precursors: 1,617 (99.02%)
1:33:00.276353 PROGRESS: Decoy precursors: 16 (0.98%)
1:33:00.276414 PROGRESS: 
1:33:00.276469 PROGRESS: Precursor Summary:
1:33:00.278381 PROGRESS: Channel   0:	 0.050 FDR: 1,617; 0.010 FDR: 1,617; 0.001 FDR: 1,214
1:33:00.278490 PROGRESS: 
1:33:00.278554 PROGRESS: Protein Summary:
1:33:00.280983 PROGRESS: Channel   0:	 0.050 FDR: 1,370; 0.010 FDR: 1,370; 0.001 FDR: 1,046
1:33:00.281091 PROGRESS: =========================================================================
1:33:00.303148 INFO: Target number of precursors reached.
1:33:00.956673 INFO: fragments_df: keeping 5000 of 4049069 [sum(precursor_idx_mask)=38459 sum(mass_error_mask)=4049069 stop_rank=5000
1:33:01.472926 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:33:01.944468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:33:02.860497 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:33:02.860938 INFO: Using score_cutoff 11.768939775466919 (fac=0.99, q=1)
1:33:02.861243 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:33:02.861321 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:33:02.861384 INFO: Updating optimization_manager: score_cutoff        : 11.279825302505493 -> 11.768939775466919
1:33:02.861443 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:03.017410 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:03.381268 INFO: === checking if optimization conditions were reached ===
1:33:03.381551 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:33:03.382859 INFO: Updating optimization_manager: rt_error            : 671.6475653336271 -> 673.4503668091279
1:33:03.383082 INFO: Updating optimization_manager: classifier_version  : 12 -> 16
1:33:03.383209 INFO: Updating optimization_manager: score_cutoff        : 11.768939775466919 -> 11.279825302505493
1:33:03.383319 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:33:03.383425 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:33:03.383538 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 673.4504 found after 5 searches.
1:33:03.383619 INFO: ==============================================
1:33:03.383708 PROGRESS: Optimization finished for rt_error.
1:33:03.824613 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:03.985734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:04.365032 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:33:04.365307 PROGRESS: ==============================================
1:33:04.365404 PROGRESS: ms2_error      : 10.0000
1:33:04.365477 PROGRESS: rt_error       : 673.4504
1:33:04.365544 PROGRESS: ==============================================
1:33:04.366677 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:12.318506 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:31.829747 INFO: Using rust extraction backend
1:33:31.830028 PROGRESS: Extracting batch of 11997144 precursors
1:33:48.551117 INFO: === Search parameters used ===
1:33:48.551431 INFO: rt_error       : 673.4503668091279
1:33:48.551512 INFO: mobility_error : 0.1
1:33:48.551574 INFO: num_candidates : 3
1:33:48.551632 INFO: ms1_error      : 3
1:33:48.551692 INFO: ms2_error      : 10.0
1:33:48.551746 INFO: fwhm_rt        : 3.0
1:33:48.551797 INFO: quant_window   : 3
1:33:48.551855 INFO: ==============================================
1:35:30.503472 INFO: Removed 9671517 precursors with score below cutoff 11.279825302505493
1:36:10.029440 INFO: performing precursor FDR with 40 features
1:36:10.029579 INFO: Decoy channel: -1
1:36:10.029612 INFO: competitive: True
1:36:13.073268 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:25.770131 INFO: Estimating optimal hyperparameters - samples: 21,055,452, batch_size: 4,096, learning_rate: 1.00e-03
1:36:25.836243 INFO: Using random state 258007 for train-test-split
1:48:40.329974 INFO: Test AUC: 0.620
1:48:40.330485 INFO: Train AUC: 0.621
1:48:40.330555 INFO: AUC difference: 0.06%
1:48:48.976795 INFO: Resetting torch num_threads to 24
1:48:54.476217 PROGRESS: ============================= Precursor FDR =============================
1:48:54.476946 PROGRESS: Total precursors accumulated: 94,747
1:48:54.477034 PROGRESS: Target precursors: 93,809 (99.01%)
1:48:54.477095 PROGRESS: Decoy precursors: 938 (0.99%)
1:48:54.477186 PROGRESS: 
1:48:54.477237 PROGRESS: Precursor Summary:
1:48:54.569816 PROGRESS: Channel   0:	 0.050 FDR: 93,809; 0.010 FDR: 93,809; 0.001 FDR: 60,925
1:48:54.570625 PROGRESS: 
1:48:54.570698 PROGRESS: Protein Summary:
1:48:54.705690 PROGRESS: Channel   0:	 0.050 FDR: 13,395; 0.010 FDR: 13,395; 0.001 FDR: 9,220
1:48:54.706462 PROGRESS: =========================================================================
1:48:55.047630 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
1:48:55.793083 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
1:48:56.871801 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:48:58.660968 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
1:48:58.661327 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:48:58.661546 INFO: Initializing TimingManager
1:48:58.663597 INFO: Initializing RawFileManager
1:49:30.963414 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.
1:49:30.976637 INFO: Determining DIA cycle
1:49:30.995163 INFO: Found cycle with start 0.00 min and length 300.
1:49:31.745616 INFO: RT (min)            : 0.0 - 26.9
1:49:31.745817 INFO: RT duration (sec)   : 1611.2
1:49:31.745850 INFO: RT duration (min)   : 26.9
1:49:31.745881 INFO: Cycle len (scans)   : 300
1:49:31.745903 INFO: Cycle len (sec)     : 1.65
1:49:31.745924 INFO: Number of cycles    : 977
1:49:31.745944 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:49:31.746025 INFO: Creating DIA data object took: 33.08219122886658
1:49:35.811316 INFO: Creating DIA data NG object took: 4.0649847984313965
1:49:40.105103 INFO: Initializing CalibrationManager
1:49:40.105950 INFO: Setting up calibration estimators ..
1:49:40.106024 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:49:40.106140 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'}' ..
1:49:40.106238 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:49:40.106344 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:49:40.106400 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}}' ..
1:49:40.106451 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:49:40.106497 INFO: Done setting up calibration estimators.
1:49:40.107258 INFO: Initializing OptimizationManager
1:49:40.107461 INFO: initial parameter: ms1_error = 3
1:49:40.107516 INFO: initial parameter: ms2_error = 10
1:49:40.107566 INFO: initial parameter: rt_error = 805.6002197265625
1:49:40.107610 INFO: initial parameter: mobility_error = 0.1
1:49:40.107653 INFO: initial parameter: num_candidates = 1
1:49:40.107694 INFO: initial parameter: fwhm_rt = 5
1:49:40.107736 INFO: initial parameter: fwhm_mobility = 0.01
1:49:40.107780 INFO: initial parameter: score_cutoff = 0
1:49:40.107821 INFO: initial parameter: classifier_version = -1
1:49:40.107910 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:49:40.108560 INFO: FDRManager: loading saved state not requested, will be initialized.
1:49:40.108603 INFO: Initializing FDRManager
1:49:40.108656 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:49:44.332671 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:49:47.599973 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:49:47.601338 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
1:49:47.601508 PROGRESS: Starting initial search for precursors.
1:49:47.601689 INFO: Starting optimization step 0.
1:49:47.601775 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:49:47.601863 INFO: Using rust extraction backend
1:49:47.601954 PROGRESS: Extracting batch of 1976 precursors
1:49:47.616569 INFO: === Search parameters used ===
1:49:47.617208 INFO: rt_error       : 805.6002197265625
1:49:47.617270 INFO: mobility_error : 0.1
1:49:47.617325 INFO: num_candidates : 1
1:49:47.617372 INFO: ms1_error      : 3
1:49:47.617416 INFO: ms2_error      : 10
1:49:47.617460 INFO: fwhm_rt        : 5
1:49:47.617503 INFO: quant_window   : 3
1:49:47.617547 INFO: ==============================================
1:49:47.705134 INFO: performing precursor FDR with 40 features
1:49:47.705392 INFO: Decoy channel: -1
1:49:47.705424 INFO: competitive: True
1:49:47.708568 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:47.712847 INFO: Estimating optimal hyperparameters - samples: 1,577, batch_size: 128, learning_rate: 1.77e-04
1:49:47.715091 INFO: Using random state 47304 for train-test-split
1:49:47.973494 INFO: Test AUC: 0.498
1:49:47.973766 INFO: Train AUC: 0.506
1:49:47.973802 INFO: AUC difference: 1.66%
1:49:48.402880 INFO: Resetting torch num_threads to 24
1:49:48.406912 PROGRESS: === Extracted 1972 precursors and 11084 fragments ===
1:49:48.408204 INFO: === FDR correction performed with classifier version -1 ===
1:49:48.409706 PROGRESS: ============================= Precursor FDR =============================
1:49:48.410004 PROGRESS: Total precursors accumulated: 1
1:49:48.410099 PROGRESS: Target precursors: 1 (100.00%)
1:49:48.410217 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:48.410279 PROGRESS: 
1:49:48.410327 PROGRESS: Precursor Summary:
1:49:48.412428 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:49:48.412666 PROGRESS: 
1:49:48.412746 PROGRESS: Protein Summary:
1:49:48.414727 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:49:48.414965 PROGRESS: =========================================================================
1:49:48.415980 INFO: Target number of precursors not reached yet.
1:49:48.522692 INFO: Starting optimization step 1.
1:49:48.523253 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:49:48.523430 INFO: Using rust extraction backend
1:49:48.523529 PROGRESS: Extracting batch of 3939 precursors
1:49:48.555259 INFO: === Search parameters used ===
1:49:48.555809 INFO: rt_error       : 805.6002197265625
1:49:48.555869 INFO: mobility_error : 0.1
1:49:48.555918 INFO: num_candidates : 1
1:49:48.555963 INFO: ms1_error      : 3
1:49:48.556005 INFO: ms2_error      : 10
1:49:48.556047 INFO: fwhm_rt        : 5
1:49:48.556093 INFO: quant_window   : 3
1:49:48.556134 INFO: ==============================================
1:49:48.715878 INFO: performing precursor FDR with 40 features
1:49:48.716316 INFO: Decoy channel: -1
1:49:48.716438 INFO: competitive: True
1:49:48.746935 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:48.762653 INFO: Estimating optimal hyperparameters - samples: 4,720, batch_size: 128, learning_rate: 1.77e-04
1:49:48.763118 INFO: Using random state 798328 for train-test-split
1:49:49.541971 INFO: Test AUC: 0.511
1:49:49.542246 INFO: Train AUC: 0.563
1:49:49.542280 INFO: AUC difference: 9.27%
1:49:49.542304 WARNING: AUC difference > 5%. This may indicate overfitting.
1:49:49.950784 INFO: Resetting torch num_threads to 24
1:49:49.963459 PROGRESS: === Extracted 5900 precursors and 33198 fragments ===
1:49:49.964900 INFO: === FDR correction performed with classifier version -1 ===
1:49:49.966624 PROGRESS: ============================= Precursor FDR =============================
1:49:49.966928 PROGRESS: Total precursors accumulated: 18
1:49:49.967049 PROGRESS: Target precursors: 18 (100.00%)
1:49:49.967125 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:49.967175 PROGRESS: 
1:49:49.967226 PROGRESS: Precursor Summary:
1:49:49.969507 PROGRESS: Channel   0:	 0.050 FDR:    18; 0.010 FDR:    18; 0.001 FDR:    18
1:49:49.969742 PROGRESS: 
1:49:49.969809 PROGRESS: Protein Summary:
1:49:49.971805 PROGRESS: Channel   0:	 0.050 FDR:    18; 0.010 FDR:    18; 0.001 FDR:    18
1:49:49.972039 PROGRESS: =========================================================================
1:49:49.973463 INFO: Target number of precursors not reached yet.
1:49:50.120172 INFO: Starting optimization step 2.
1:49:50.120780 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:49:50.120890 INFO: Using rust extraction backend
1:49:50.120970 PROGRESS: Extracting batch of 7882 precursors
1:49:50.159206 INFO: === Search parameters used ===
1:49:50.159815 INFO: rt_error       : 805.6002197265625
1:49:50.159874 INFO: mobility_error : 0.1
1:49:50.159924 INFO: num_candidates : 1
1:49:50.159968 INFO: ms1_error      : 3
1:49:50.160014 INFO: ms2_error      : 10
1:49:50.160060 INFO: fwhm_rt        : 5
1:49:50.160108 INFO: quant_window   : 3
1:49:50.160152 INFO: ==============================================
1:49:50.368664 INFO: performing precursor FDR with 40 features
1:49:50.368930 INFO: Decoy channel: -1
1:49:50.368962 INFO: competitive: True
1:49:50.395825 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:50.409147 INFO: Estimating optimal hyperparameters - samples: 11,013, batch_size: 128, learning_rate: 1.77e-04
1:49:50.409567 INFO: Using random state 425976 for train-test-split
1:49:51.919888 INFO: Test AUC: 0.556
1:49:51.920148 INFO: Train AUC: 0.577
1:49:51.920190 INFO: AUC difference: 3.65%
1:49:52.381171 INFO: Resetting torch num_threads to 24
1:49:52.401652 PROGRESS: === Extracted 13767 precursors and 77505 fragments ===
1:49:52.403116 INFO: === FDR correction performed with classifier version -1 ===
1:49:52.405041 PROGRESS: ============================= Precursor FDR =============================
1:49:52.405361 PROGRESS: Total precursors accumulated: 57
1:49:52.405452 PROGRESS: Target precursors: 57 (100.00%)
1:49:52.405514 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:52.405566 PROGRESS: 
1:49:52.405616 PROGRESS: Precursor Summary:
1:49:52.407933 PROGRESS: Channel   0:	 0.050 FDR:    57; 0.010 FDR:    57; 0.001 FDR:    57
1:49:52.408228 PROGRESS: 
1:49:52.408300 PROGRESS: Protein Summary:
1:49:52.410430 PROGRESS: Channel   0:	 0.050 FDR:    57; 0.010 FDR:    57; 0.001 FDR:    57
1:49:52.410667 PROGRESS: =========================================================================
1:49:52.412566 INFO: Target number of precursors not reached yet.
1:49:52.572588 INFO: Starting optimization step 3.
1:49:52.573198 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:49:52.573333 INFO: Using rust extraction backend
1:49:52.573428 PROGRESS: Extracting batch of 15793 precursors
1:49:52.640618 INFO: === Search parameters used ===
1:49:52.641383 INFO: rt_error       : 805.6002197265625
1:49:52.641488 INFO: mobility_error : 0.1
1:49:52.641543 INFO: num_candidates : 1
1:49:52.641590 INFO: ms1_error      : 3
1:49:52.641637 INFO: ms2_error      : 10
1:49:52.641721 INFO: fwhm_rt        : 5
1:49:52.641769 INFO: quant_window   : 3
1:49:52.641815 INFO: ==============================================
1:49:53.009689 INFO: performing precursor FDR with 40 features
1:49:53.009991 INFO: Decoy channel: -1
1:49:53.010024 INFO: competitive: True
1:49:53.050579 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:53.075269 INFO: Estimating optimal hyperparameters - samples: 23,623, batch_size: 128, learning_rate: 1.77e-04
1:49:53.075778 INFO: Using random state 93964 for train-test-split
1:49:56.523207 INFO: Test AUC: 0.586
1:49:56.523498 INFO: Train AUC: 0.583
1:49:56.523541 INFO: AUC difference: 0.56%
1:49:56.981131 INFO: Resetting torch num_threads to 24
1:49:57.017037 PROGRESS: === Extracted 29529 precursors and 165816 fragments ===
1:49:57.018603 INFO: === FDR correction performed with classifier version -1 ===
1:49:57.020503 PROGRESS: ============================= Precursor FDR =============================
1:49:57.020856 PROGRESS: Total precursors accumulated: 153
1:49:57.020977 PROGRESS: Target precursors: 152 (99.35%)
1:49:57.021046 PROGRESS: Decoy precursors: 1 (0.65%)
1:49:57.021100 PROGRESS: 
1:49:57.021150 PROGRESS: Precursor Summary:
1:49:57.023561 PROGRESS: Channel   0:	 0.050 FDR:   152; 0.010 FDR:   152; 0.001 FDR:   141
1:49:57.023844 PROGRESS: 
1:49:57.023910 PROGRESS: Protein Summary:
1:49:57.026255 PROGRESS: Channel   0:	 0.050 FDR:   150; 0.010 FDR:   150; 0.001 FDR:   139
1:49:57.026506 PROGRESS: =========================================================================
1:49:57.029495 INFO: Target number of precursors not reached yet.
1:49:57.270126 INFO: Starting optimization step 4.
1:49:57.270720 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:49:57.270854 INFO: Using rust extraction backend
1:49:57.270938 PROGRESS: Extracting batch of 31556 precursors
1:49:57.417031 INFO: === Search parameters used ===
1:49:57.417737 INFO: rt_error       : 805.6002197265625
1:49:57.417841 INFO: mobility_error : 0.1
1:49:57.417902 INFO: num_candidates : 1
1:49:57.417951 INFO: ms1_error      : 3
1:49:57.417995 INFO: ms2_error      : 10
1:49:57.418039 INFO: fwhm_rt        : 5
1:49:57.418080 INFO: quant_window   : 3
1:49:57.418121 INFO: ==============================================
1:49:58.108860 INFO: performing precursor FDR with 40 features
1:49:58.109137 INFO: Decoy channel: -1
1:49:58.109168 INFO: competitive: True
1:49:58.214188 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:58.282149 INFO: Estimating optimal hyperparameters - samples: 48,809, batch_size: 199, learning_rate: 2.20e-04
1:49:58.282792 INFO: Using random state 848522 for train-test-split
1:50:03.404536 INFO: Test AUC: 0.582
1:50:03.404841 INFO: Train AUC: 0.603
1:50:03.404923 INFO: AUC difference: 3.52%
1:50:03.861479 INFO: Resetting torch num_threads to 24
1:50:03.920400 PROGRESS: === Extracted 61012 precursors and 342574 fragments ===
1:50:03.922064 INFO: === FDR correction performed with classifier version -1 ===
1:50:03.924430 PROGRESS: ============================= Precursor FDR =============================
1:50:03.924742 PROGRESS: Total precursors accumulated: 323
1:50:03.924861 PROGRESS: Target precursors: 320 (99.07%)
1:50:03.924925 PROGRESS: Decoy precursors: 3 (0.93%)
1:50:03.924978 PROGRESS: 
1:50:03.925028 PROGRESS: Precursor Summary:
1:50:03.928156 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   320; 0.001 FDR:     0
1:50:03.928466 PROGRESS: 
1:50:03.928546 PROGRESS: Protein Summary:
1:50:03.931715 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:     0
1:50:03.932007 PROGRESS: =========================================================================
1:50:03.937582 INFO: Target number of precursors not reached yet.
1:50:04.286260 INFO: Starting optimization step 5.
1:50:04.287038 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:50:04.287308 INFO: Using rust extraction backend
1:50:04.287439 PROGRESS: Extracting batch of 63064 precursors
1:50:04.689010 INFO: === Search parameters used ===
1:50:04.689853 INFO: rt_error       : 805.6002197265625
1:50:04.689991 INFO: mobility_error : 0.1
1:50:04.690052 INFO: num_candidates : 1
1:50:04.690106 INFO: ms1_error      : 3
1:50:04.690154 INFO: ms2_error      : 10
1:50:04.690200 INFO: fwhm_rt        : 5
1:50:04.690243 INFO: quant_window   : 3
1:50:04.690287 INFO: ==============================================
1:50:05.961072 INFO: performing precursor FDR with 40 features
1:50:05.961333 INFO: Decoy channel: -1
1:50:05.961366 INFO: competitive: True
1:50:06.149493 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:06.338024 INFO: Estimating optimal hyperparameters - samples: 99,129, batch_size: 406, learning_rate: 3.15e-04
1:50:06.338912 INFO: Using random state 302922 for train-test-split
1:50:11.938786 INFO: Test AUC: 0.583
1:50:11.939165 INFO: Train AUC: 0.606
1:50:11.939217 INFO: AUC difference: 3.90%
1:50:12.392273 INFO: Resetting torch num_threads to 24
1:50:12.510030 PROGRESS: === Extracted 123912 precursors and 694735 fragments ===
1:50:12.511655 INFO: === FDR correction performed with classifier version -1 ===
1:50:12.514095 PROGRESS: ============================= Precursor FDR =============================
1:50:12.514449 PROGRESS: Total precursors accumulated: 523
1:50:12.514529 PROGRESS: Target precursors: 518 (99.04%)
1:50:12.514589 PROGRESS: Decoy precursors: 5 (0.96%)
1:50:12.514641 PROGRESS: 
1:50:12.514749 PROGRESS: Precursor Summary:
1:50:12.517650 PROGRESS: Channel   0:	 0.050 FDR:   518; 0.010 FDR:   518; 0.001 FDR:     0
1:50:12.518132 PROGRESS: 
1:50:12.518195 PROGRESS: Protein Summary:
1:50:12.520467 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   487; 0.001 FDR:     0
1:50:12.520830 PROGRESS: =========================================================================
1:50:12.527905 INFO: Target number of precursors not reached yet.
1:50:13.154249 INFO: Starting optimization step 6.
1:50:13.154829 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:50:13.155006 INFO: Using rust extraction backend
1:50:13.155132 PROGRESS: Extracting batch of 126165 precursors
1:50:13.838120 INFO: === Search parameters used ===
1:50:13.838798 INFO: rt_error       : 805.6002197265625
1:50:13.838914 INFO: mobility_error : 0.1
1:50:13.838994 INFO: num_candidates : 1
1:50:13.839052 INFO: ms1_error      : 3
1:50:13.839098 INFO: ms2_error      : 10
1:50:13.839142 INFO: fwhm_rt        : 5
1:50:13.839186 INFO: quant_window   : 3
1:50:13.839226 INFO: ==============================================
1:50:16.279681 INFO: performing precursor FDR with 40 features
1:50:16.280018 INFO: Decoy channel: -1
1:50:16.280051 INFO: competitive: True
1:50:16.611399 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:16.994390 INFO: Estimating optimal hyperparameters - samples: 199,820, batch_size: 818, learning_rate: 4.47e-04
1:50:16.996174 INFO: Using random state 900201 for train-test-split
1:50:24.992877 INFO: Test AUC: 0.595
1:50:24.993264 INFO: Train AUC: 0.605
1:50:24.993308 INFO: AUC difference: 1.80%
1:50:25.503486 INFO: Resetting torch num_threads to 24
1:50:25.686662 PROGRESS: === Extracted 249775 precursors and 1400905 fragments ===
1:50:25.688469 INFO: === FDR correction performed with classifier version -1 ===
1:50:25.690462 PROGRESS: ============================= Precursor FDR =============================
1:50:25.690618 PROGRESS: Total precursors accumulated: 1,358
1:50:25.690688 PROGRESS: Target precursors: 1,345 (99.04%)
1:50:25.690746 PROGRESS: Decoy precursors: 13 (0.96%)
1:50:25.690799 PROGRESS: 
1:50:25.690848 PROGRESS: Precursor Summary:
1:50:25.692929 PROGRESS: Channel   0:	 0.050 FDR: 1,345; 0.010 FDR: 1,345; 0.001 FDR: 1,018
1:50:25.693103 PROGRESS: 
1:50:25.693162 PROGRESS: Protein Summary:
1:50:25.695366 PROGRESS: Channel   0:	 0.050 FDR: 1,142; 0.010 FDR: 1,142; 0.001 FDR:   883
1:50:25.695521 PROGRESS: =========================================================================
1:50:25.707025 INFO: Target number of precursors reached.
1:50:25.920709 INFO: fragments_df: keeping 5000 of 1400905 [sum(precursor_idx_mask)=14069 sum(mass_error_mask)=1400905 stop_rank=5000
1:50:27.096889 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:27.646660 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:28.621410 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:50:28.623343 INFO: Using score_cutoff 12.068186558532714 (fac=0.99, q=1)
1:50:28.624626 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:50:28.624871 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:50:28.624958 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.068186558532714
1:50:28.625120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:28.843643 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:29.456949 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:50:29.457687 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:50:29.457950 INFO: Starting optimization step 7.
1:50:29.458080 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:50:29.458219 INFO: Using rust extraction backend
1:50:29.458331 PROGRESS: Extracting batch of 250375 precursors
1:50:30.818945 INFO: === Search parameters used ===
1:50:30.819731 INFO: rt_error       : 805.6002197265625
1:50:30.819855 INFO: mobility_error : 0.1
1:50:30.819938 INFO: num_candidates : 3
1:50:30.819991 INFO: ms1_error      : 3
1:50:30.820047 INFO: ms2_error      : 10
1:50:30.820093 INFO: fwhm_rt        : 3.0
1:50:30.820138 INFO: quant_window   : 3
1:50:30.820181 INFO: ==============================================
1:50:39.967545 INFO: performing precursor FDR with 40 features
1:50:39.967852 INFO: Decoy channel: -1
1:50:39.967881 INFO: competitive: True
1:50:40.730163 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:41.913823 INFO: Estimating optimal hyperparameters - samples: 599,644, batch_size: 2,456, learning_rate: 7.74e-04
1:50:41.920099 INFO: Using random state 817150 for train-test-split
1:51:09.465197 INFO: Test AUC: 0.599
1:51:09.465652 INFO: Train AUC: 0.606
1:51:09.465698 INFO: AUC difference: 1.13%
1:51:10.220413 INFO: Resetting torch num_threads to 24
1:51:10.302378 PROGRESS: === Extracted 749556 precursors and 4036046 fragments ===
1:51:10.303835 INFO: === FDR correction performed with classifier version 6 ===
1:51:10.306846 PROGRESS: ============================= Precursor FDR =============================
1:51:10.307269 PROGRESS: Total precursors accumulated: 1,556
1:51:10.307432 PROGRESS: Target precursors: 1,541 (99.04%)
1:51:10.307498 PROGRESS: Decoy precursors: 15 (0.96%)
1:51:10.307549 PROGRESS: 
1:51:10.307598 PROGRESS: Precursor Summary:
1:51:10.312765 PROGRESS: Channel   0:	 0.050 FDR: 1,541; 0.010 FDR: 1,541; 0.001 FDR: 1,178
1:51:10.313129 PROGRESS: 
1:51:10.313217 PROGRESS: Protein Summary:
1:51:10.318498 PROGRESS: Channel   0:	 0.050 FDR: 1,299; 0.010 FDR: 1,299; 0.001 FDR: 1,006
1:51:10.318808 PROGRESS: =========================================================================
1:51:10.371718 INFO: Target number of precursors reached.
1:51:10.859381 INFO: fragments_df: keeping 5000 of 4036046 [sum(precursor_idx_mask)=36703 sum(mass_error_mask)=4036046 stop_rank=5000
1:51:12.127577 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:12.647072 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:13.602894 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:13.604348 INFO: Using score_cutoff 12.17486775970459 (fac=0.99, q=1)
1:51:13.605488 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:13.605737 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:13.605824 INFO: Updating optimization_manager: score_cutoff        : 12.068186558532714 -> 12.17486775970459
1:51:13.605924 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:13.828742 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:14.454832 INFO: === checking if optimization conditions were reached ===
1:51:14.460607 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:51:14.461047 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:51:14.461172 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:51:14.461267 INFO: ==============================================
1:51:14.461367 INFO: Starting optimization step 8.
1:51:14.461454 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:51:14.461561 INFO: Using rust extraction backend
1:51:14.461663 PROGRESS: Extracting batch of 250375 precursors
1:51:15.832205 INFO: === Search parameters used ===
1:51:15.832870 INFO: rt_error       : 805.6002197265625
1:51:15.832994 INFO: mobility_error : 0.1
1:51:15.833120 INFO: num_candidates : 3
1:51:15.833167 INFO: ms1_error      : 3
1:51:15.833213 INFO: ms2_error      : 10.0
1:51:15.833256 INFO: fwhm_rt        : 3.0
1:51:15.833300 INFO: quant_window   : 3
1:51:15.833342 INFO: ==============================================
1:51:24.143373 INFO: performing precursor FDR with 40 features
1:51:24.143674 INFO: Decoy channel: -1
1:51:24.143705 INFO: competitive: True
1:51:24.945943 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:26.061029 INFO: Estimating optimal hyperparameters - samples: 599,620, batch_size: 2,456, learning_rate: 7.74e-04
1:51:26.069317 INFO: Using random state 321909 for train-test-split
1:51:56.653250 INFO: Test AUC: 0.601
1:51:56.653879 INFO: Train AUC: 0.613
1:51:56.653930 INFO: AUC difference: 1.92%
1:51:58.220191 INFO: Resetting torch num_threads to 24
1:51:58.343534 PROGRESS: === Extracted 749526 precursors and 4035199 fragments ===
1:51:58.344981 INFO: === FDR correction performed with classifier version 7 ===
1:51:58.347979 PROGRESS: ============================= Precursor FDR =============================
1:51:58.348381 PROGRESS: Total precursors accumulated: 1,720
1:51:58.348512 PROGRESS: Target precursors: 1,703 (99.01%)
1:51:58.348578 PROGRESS: Decoy precursors: 17 (0.99%)
1:51:58.348632 PROGRESS: 
1:51:58.348682 PROGRESS: Precursor Summary:
1:51:58.352274 PROGRESS: Channel   0:	 0.050 FDR: 1,703; 0.010 FDR: 1,703; 0.001 FDR: 1,063
1:51:58.352666 PROGRESS: 
1:51:58.352731 PROGRESS: Protein Summary:
1:51:58.355240 PROGRESS: Channel   0:	 0.050 FDR: 1,421; 0.010 FDR: 1,421; 0.001 FDR:   909
1:51:58.355475 PROGRESS: =========================================================================
1:51:58.402659 INFO: Target number of precursors reached.
1:51:58.875992 INFO: fragments_df: keeping 5000 of 4035199 [sum(precursor_idx_mask)=40567 sum(mass_error_mask)=4035199 stop_rank=5000
1:52:00.082686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:00.600165 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:01.673315 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:52:01.674515 INFO: Using score_cutoff 12.105400420761109 (fac=0.99, q=1)
1:52:01.675595 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:52:01.675841 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:52:01.675933 INFO: Updating optimization_manager: score_cutoff        : 12.17486775970459 -> 12.105400420761109
1:52:01.676049 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:01.895426 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:02.522709 INFO: === checking if optimization conditions were reached ===
1:52:02.526806 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:52:02.527309 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:52:02.527388 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:52:02.527465 INFO: ==============================================
1:52:02.527555 INFO: Starting optimization step 9.
1:52:02.527625 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:02.527721 INFO: Using rust extraction backend
1:52:02.527850 PROGRESS: Extracting batch of 250375 precursors
1:52:03.924019 INFO: === Search parameters used ===
1:52:03.924714 INFO: rt_error       : 805.6002197265625
1:52:03.924834 INFO: mobility_error : 0.1
1:52:03.924891 INFO: num_candidates : 3
1:52:03.924936 INFO: ms1_error      : 3
1:52:03.924984 INFO: ms2_error      : 10.0
1:52:03.925026 INFO: fwhm_rt        : 3.0
1:52:03.925067 INFO: quant_window   : 3
1:52:03.925109 INFO: ==============================================
1:52:12.937225 INFO: performing precursor FDR with 40 features
1:52:12.937511 INFO: Decoy channel: -1
1:52:12.937540 INFO: competitive: True
1:52:13.643702 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:14.800578 INFO: Estimating optimal hyperparameters - samples: 599,632, batch_size: 2,456, learning_rate: 7.74e-04
1:52:14.810074 INFO: Using random state 413322 for train-test-split
1:52:40.047412 INFO: Test AUC: 0.605
1:52:40.047808 INFO: Train AUC: 0.615
1:52:40.047855 INFO: AUC difference: 1.68%
1:52:40.776173 INFO: Resetting torch num_threads to 24
1:52:40.851242 PROGRESS: === Extracted 749540 precursors and 4035449 fragments ===
1:52:40.852498 INFO: === FDR correction performed with classifier version 8 ===
1:52:40.854341 PROGRESS: ============================= Precursor FDR =============================
1:52:40.854493 PROGRESS: Total precursors accumulated: 1,747
1:52:40.854569 PROGRESS: Target precursors: 1,730 (99.03%)
1:52:40.854625 PROGRESS: Decoy precursors: 17 (0.97%)
1:52:40.854675 PROGRESS: 
1:52:40.854725 PROGRESS: Precursor Summary:
1:52:40.856622 PROGRESS: Channel   0:	 0.050 FDR: 1,730; 0.010 FDR: 1,730; 0.001 FDR: 1,131
1:52:40.856755 PROGRESS: 
1:52:40.856813 PROGRESS: Protein Summary:
1:52:40.859204 PROGRESS: Channel   0:	 0.050 FDR: 1,450; 0.010 FDR: 1,450; 0.001 FDR:   965
1:52:40.859374 PROGRESS: =========================================================================
1:52:40.902723 INFO: Target number of precursors reached.
1:52:41.377226 INFO: fragments_df: keeping 5000 of 4035449 [sum(precursor_idx_mask)=40759 sum(mass_error_mask)=4035449 stop_rank=5000
1:52:42.512014 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:43.399173 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:44.378215 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:52:44.379486 INFO: Using score_cutoff 11.13350139799118 (fac=0.99, q=1)
1:52:44.380569 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:52:44.380825 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:52:44.380931 INFO: Updating optimization_manager: score_cutoff        : 12.105400420761109 -> 11.13350139799118
1:52:44.381050 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:44.594623 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:45.200264 INFO: === checking if optimization conditions were reached ===
1:52:45.204254 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:52:45.204565 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:52:45.204646 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:52:45.204721 INFO: ==============================================
1:52:45.204823 INFO: Starting optimization step 10.
1:52:45.204896 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:45.204990 INFO: Using rust extraction backend
1:52:45.205079 PROGRESS: Extracting batch of 250375 precursors
1:52:46.589012 INFO: === Search parameters used ===
1:52:46.589675 INFO: rt_error       : 805.6002197265625
1:52:46.589789 INFO: mobility_error : 0.1
1:52:46.589843 INFO: num_candidates : 3
1:52:46.589886 INFO: ms1_error      : 3
1:52:46.589928 INFO: ms2_error      : 10.0
1:52:46.589970 INFO: fwhm_rt        : 3.0
1:52:46.590010 INFO: quant_window   : 3
1:52:46.590050 INFO: ==============================================
1:52:55.327008 INFO: performing precursor FDR with 40 features
1:52:55.327292 INFO: Decoy channel: -1
1:52:55.327322 INFO: competitive: True
1:52:56.252417 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:57.527737 INFO: Estimating optimal hyperparameters - samples: 599,644, batch_size: 2,456, learning_rate: 7.74e-04
1:52:57.535824 INFO: Using random state 22055 for train-test-split
1:53:21.843583 INFO: Test AUC: 0.607
1:53:21.844020 INFO: Train AUC: 0.618
1:53:21.844071 INFO: AUC difference: 1.88%
1:53:22.627478 INFO: Resetting torch num_threads to 24
1:53:22.711160 PROGRESS: === Extracted 749555 precursors and 4035381 fragments ===
1:53:22.713050 INFO: === FDR correction performed with classifier version 9 ===
1:53:22.716763 PROGRESS: ============================= Precursor FDR =============================
1:53:22.717296 PROGRESS: Total precursors accumulated: 1,652
1:53:22.717478 PROGRESS: Target precursors: 1,636 (99.03%)
1:53:22.717549 PROGRESS: Decoy precursors: 16 (0.97%)
1:53:22.717617 PROGRESS: 
1:53:22.717674 PROGRESS: Precursor Summary:
1:53:22.723301 PROGRESS: Channel   0:	 0.050 FDR: 1,636; 0.010 FDR: 1,636; 0.001 FDR: 1,182
1:53:22.723643 PROGRESS: 
1:53:22.723709 PROGRESS: Protein Summary:
1:53:22.727327 PROGRESS: Channel   0:	 0.050 FDR: 1,375; 0.010 FDR: 1,375; 0.001 FDR: 1,015
1:53:22.727547 PROGRESS: =========================================================================
1:53:22.775932 INFO: Target number of precursors reached.
1:53:23.241494 INFO: fragments_df: keeping 5000 of 4035381 [sum(precursor_idx_mask)=38892 sum(mass_error_mask)=4035381 stop_rank=5000
1:53:24.388895 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:24.836034 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:25.738728 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:25.740021 INFO: Using score_cutoff 11.889313964366913 (fac=0.99, q=1)
1:53:25.741262 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:25.741560 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:25.741649 INFO: Updating optimization_manager: score_cutoff        : 11.13350139799118 -> 11.889313964366913
1:53:25.741735 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:25.964224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:26.567319 INFO: === checking if optimization conditions were reached ===
1:53:26.572434 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:53:26.573088 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:53:26.573233 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:53:26.573321 INFO: ==============================================
1:53:26.573431 INFO: Starting optimization step 11.
1:53:26.573529 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:53:26.573635 INFO: Using rust extraction backend
1:53:26.573733 PROGRESS: Extracting batch of 250375 precursors
1:53:27.934574 INFO: === Search parameters used ===
1:53:27.935658 INFO: rt_error       : 805.6002197265625
1:53:27.935825 INFO: mobility_error : 0.1
1:53:27.935894 INFO: num_candidates : 3
1:53:27.935946 INFO: ms1_error      : 3
1:53:27.935994 INFO: ms2_error      : 10.0
1:53:27.936041 INFO: fwhm_rt        : 3.0
1:53:27.936086 INFO: quant_window   : 3
1:53:27.936142 INFO: ==============================================
1:53:36.502147 INFO: performing precursor FDR with 40 features
1:53:36.502494 INFO: Decoy channel: -1
1:53:36.502524 INFO: competitive: True
1:53:37.254189 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:38.354789 INFO: Estimating optimal hyperparameters - samples: 599,632, batch_size: 2,456, learning_rate: 7.74e-04
1:53:38.362907 INFO: Using random state 661677 for train-test-split
1:54:04.442171 INFO: Test AUC: 0.609
1:54:04.442761 INFO: Train AUC: 0.620
1:54:04.442811 INFO: AUC difference: 1.72%
1:54:05.227262 INFO: Resetting torch num_threads to 24
1:54:05.300196 PROGRESS: === Extracted 749541 precursors and 4035046 fragments ===
1:54:05.301691 INFO: === FDR correction performed with classifier version 10 ===
1:54:05.304603 PROGRESS: ============================= Precursor FDR =============================
1:54:05.304959 PROGRESS: Total precursors accumulated: 1,841
1:54:05.305060 PROGRESS: Target precursors: 1,823 (99.02%)
1:54:05.305119 PROGRESS: Decoy precursors: 18 (0.98%)
1:54:05.305174 PROGRESS: 
1:54:05.305225 PROGRESS: Precursor Summary:
1:54:05.309008 PROGRESS: Channel   0:	 0.050 FDR: 1,823; 0.010 FDR: 1,823; 0.001 FDR: 1,185
1:54:05.309496 PROGRESS: 
1:54:05.309563 PROGRESS: Protein Summary:
1:54:05.312520 PROGRESS: Channel   0:	 0.050 FDR: 1,520; 0.010 FDR: 1,520; 0.001 FDR: 1,007
1:54:05.312870 PROGRESS: =========================================================================
1:54:05.362238 INFO: Target number of precursors reached.
1:54:05.841949 INFO: fragments_df: keeping 5000 of 4035046 [sum(precursor_idx_mask)=42925 sum(mass_error_mask)=4035046 stop_rank=5000
1:54:06.987169 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:08.103836 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:09.193391 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:09.194617 INFO: Using score_cutoff 11.221124493026732 (fac=0.99, q=1)
1:54:09.195742 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:09.195989 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:09.196067 INFO: Updating optimization_manager: score_cutoff        : 11.889313964366913 -> 11.221124493026732
1:54:09.196153 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:09.424075 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:10.106488 INFO: === checking if optimization conditions were reached ===
1:54:10.111924 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:10.112367 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:54:10.112497 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:54:10.112588 INFO: ==============================================
1:54:10.112695 PROGRESS: Optimization finished for ms2_error.
1:54:11.255068 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:11.466338 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:12.045148 INFO: Starting optimization step 0.
1:54:12.046072 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:12.046328 INFO: Using rust extraction backend
1:54:12.046493 PROGRESS: Extracting batch of 250375 precursors
1:54:13.461992 INFO: === Search parameters used ===
1:54:13.462713 INFO: rt_error       : 805.6002197265625
1:54:13.462847 INFO: mobility_error : 0.1
1:54:13.462960 INFO: num_candidates : 3
1:54:13.463046 INFO: ms1_error      : 3
1:54:13.463095 INFO: ms2_error      : 10.0
1:54:13.463154 INFO: fwhm_rt        : 3.0
1:54:13.463203 INFO: quant_window   : 3
1:54:13.463248 INFO: ==============================================
1:54:21.947163 INFO: performing precursor FDR with 40 features
1:54:21.947486 INFO: Decoy channel: -1
1:54:21.947528 INFO: competitive: True
1:54:22.672718 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:23.822053 INFO: Estimating optimal hyperparameters - samples: 599,641, batch_size: 2,456, learning_rate: 7.74e-04
1:54:23.828366 INFO: Using random state 953524 for train-test-split
1:54:51.018250 INFO: Test AUC: 0.612
1:54:51.018843 INFO: Train AUC: 0.623
1:54:51.018891 INFO: AUC difference: 1.81%
1:54:51.757842 INFO: Resetting torch num_threads to 24
1:54:51.831138 PROGRESS: === Extracted 749552 precursors and 4035238 fragments ===
1:54:51.832675 INFO: === FDR correction performed with classifier version 11 ===
1:54:51.835938 PROGRESS: ============================= Precursor FDR =============================
1:54:51.836332 PROGRESS: Total precursors accumulated: 1,818
1:54:51.836440 PROGRESS: Target precursors: 1,800 (99.01%)
1:54:51.836503 PROGRESS: Decoy precursors: 18 (0.99%)
1:54:51.836561 PROGRESS: 
1:54:51.836613 PROGRESS: Precursor Summary:
1:54:51.841833 PROGRESS: Channel   0:	 0.050 FDR: 1,800; 0.010 FDR: 1,792; 0.001 FDR: 1,287
1:54:51.842413 PROGRESS: 
1:54:51.842479 PROGRESS: Protein Summary:
1:54:51.846406 PROGRESS: Channel   0:	 0.050 FDR: 1,505; 0.010 FDR: 1,497; 0.001 FDR: 1,094
1:54:51.846921 PROGRESS: =========================================================================
1:54:51.890064 INFO: Target number of precursors reached.
1:54:52.370001 INFO: fragments_df: keeping 5000 of 4035238 [sum(precursor_idx_mask)=41623 sum(mass_error_mask)=4035238 stop_rank=5000
1:54:53.499924 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:58.698165 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:59.666567 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:59.667982 INFO: Using score_cutoff 10.028680522441864 (fac=0.99, q=1)
1:54:59.669327 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:59.669678 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:59.669790 INFO: Updating optimization_manager: score_cutoff        : 11.221124493026732 -> 10.028680522441864
1:54:59.669889 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:59.884153 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:00.489337 INFO: === checking if optimization conditions were reached ===
1:55:00.490236 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:55:00.496154 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 753.2223201310176
1:55:00.496645 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 753.2223.
1:55:00.496766 INFO: ==============================================
1:55:00.496886 INFO: Starting optimization step 1.
1:55:00.496974 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:00.497102 INFO: Using rust extraction backend
1:55:00.497190 PROGRESS: Extracting batch of 250375 precursors
1:55:01.820468 INFO: === Search parameters used ===
1:55:01.821264 INFO: rt_error       : 753.2223201310176
1:55:01.821393 INFO: mobility_error : 0.1
1:55:01.821454 INFO: num_candidates : 3
1:55:01.821505 INFO: ms1_error      : 3
1:55:01.821551 INFO: ms2_error      : 10.0
1:55:01.821594 INFO: fwhm_rt        : 3.0
1:55:01.821640 INFO: quant_window   : 3
1:55:01.821688 INFO: ==============================================
1:55:10.679777 INFO: performing precursor FDR with 40 features
1:55:10.680075 INFO: Decoy channel: -1
1:55:10.680107 INFO: competitive: True
1:55:11.414327 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:12.531732 INFO: Estimating optimal hyperparameters - samples: 599,637, batch_size: 2,456, learning_rate: 7.74e-04
1:55:12.539578 INFO: Using random state 953524 for train-test-split
1:55:42.886470 INFO: Test AUC: 0.611
1:55:42.886823 INFO: Train AUC: 0.623
1:55:42.886867 INFO: AUC difference: 1.88%
1:55:43.647942 INFO: Resetting torch num_threads to 24
1:55:43.720525 PROGRESS: === Extracted 749547 precursors and 4035062 fragments ===
1:55:43.721994 INFO: === FDR correction performed with classifier version 11 ===
1:55:43.725069 PROGRESS: ============================= Precursor FDR =============================
1:55:43.725419 PROGRESS: Total precursors accumulated: 1,768
1:55:43.725530 PROGRESS: Target precursors: 1,751 (99.04%)
1:55:43.725593 PROGRESS: Decoy precursors: 17 (0.96%)
1:55:43.725647 PROGRESS: 
1:55:43.725703 PROGRESS: Precursor Summary:
1:55:43.730145 PROGRESS: Channel   0:	 0.050 FDR: 1,751; 0.010 FDR: 1,751; 0.001 FDR: 1,334
1:55:43.730441 PROGRESS: 
1:55:43.730503 PROGRESS: Protein Summary:
1:55:43.733053 PROGRESS: Channel   0:	 0.050 FDR: 1,472; 0.010 FDR: 1,472; 0.001 FDR: 1,136
1:55:43.733234 PROGRESS: =========================================================================
1:55:43.782526 INFO: Target number of precursors reached.
1:55:44.256980 INFO: fragments_df: keeping 5000 of 4035062 [sum(precursor_idx_mask)=40951 sum(mass_error_mask)=4035062 stop_rank=5000
1:55:45.356654 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:55:45.789677 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:55:46.769580 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:55:46.770789 INFO: Using score_cutoff 10.07095546245575 (fac=0.99, q=1)
1:55:46.771929 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:55:46.772186 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:55:46.772261 INFO: Updating optimization_manager: score_cutoff        : 10.028680522441864 -> 10.07095546245575
1:55:46.772342 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:47.008505 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:47.638525 INFO: === checking if optimization conditions were reached ===
1:55:47.639243 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:55:47.645166 INFO: Updating optimization_manager: rt_error            : 753.2223201310176 -> 774.5052103543159
1:55:47.645686 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 774.5052.
1:55:47.645835 INFO: ==============================================
1:55:47.645957 INFO: Starting optimization step 2.
1:55:47.646049 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:47.646170 INFO: Using rust extraction backend
1:55:47.646314 PROGRESS: Extracting batch of 250375 precursors
1:55:48.963843 INFO: === Search parameters used ===
1:55:48.964699 INFO: rt_error       : 774.5052103543159
1:55:48.964828 INFO: mobility_error : 0.1
1:55:48.964889 INFO: num_candidates : 3
1:55:48.964940 INFO: ms1_error      : 3
1:55:48.964986 INFO: ms2_error      : 10.0
1:55:48.965039 INFO: fwhm_rt        : 3.0
1:55:48.965084 INFO: quant_window   : 3
1:55:48.965126 INFO: ==============================================
1:56:00.626691 INFO: performing precursor FDR with 40 features
1:56:00.627117 INFO: Decoy channel: -1
1:56:00.627175 INFO: competitive: True
1:56:01.805179 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:03.878989 INFO: Estimating optimal hyperparameters - samples: 599,652, batch_size: 2,456, learning_rate: 7.74e-04
1:56:03.890025 INFO: Using random state 953524 for train-test-split
1:56:40.513391 INFO: Test AUC: 0.612
1:56:40.514040 INFO: Train AUC: 0.623
1:56:40.514157 INFO: AUC difference: 1.73%
1:56:42.237619 INFO: Resetting torch num_threads to 24
1:56:42.388363 PROGRESS: === Extracted 749566 precursors and 4036121 fragments ===
1:56:42.391053 INFO: === FDR correction performed with classifier version 11 ===
1:56:42.396073 PROGRESS: ============================= Precursor FDR =============================
1:56:42.396853 PROGRESS: Total precursors accumulated: 1,929
1:56:42.397069 PROGRESS: Target precursors: 1,910 (99.02%)
1:56:42.397148 PROGRESS: Decoy precursors: 19 (0.98%)
1:56:42.397256 PROGRESS: 
1:56:42.397461 PROGRESS: Precursor Summary:
1:56:42.407616 PROGRESS: Channel   0:	 0.050 FDR: 1,910; 0.010 FDR: 1,910; 0.001 FDR: 1,137
1:56:42.408510 PROGRESS: 
1:56:42.408775 PROGRESS: Protein Summary:
1:56:42.422470 PROGRESS: Channel   0:	 0.050 FDR: 1,605; 0.010 FDR: 1,605; 0.001 FDR:   981
1:56:42.423342 PROGRESS: =========================================================================
1:56:42.520210 INFO: Target number of precursors reached.
1:56:43.649137 INFO: fragments_df: keeping 5000 of 4036121 [sum(precursor_idx_mask)=43081 sum(mass_error_mask)=4036121 stop_rank=5000
1:56:45.343149 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:56:45.936456 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:56:46.752098 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:56:46.752923 INFO: Using score_cutoff 8.184149781131744 (fac=0.99, q=1)
1:56:46.753686 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:46.753841 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:46.753901 INFO: Updating optimization_manager: score_cutoff        : 10.07095546245575 -> 8.184149781131744
1:56:46.753964 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:46.927357 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:47.441588 INFO: === checking if optimization conditions were reached ===
1:56:47.442378 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:56:47.449957 INFO: Updating optimization_manager: rt_error            : 774.5052103543159 -> 941.0827556536594
1:56:47.450514 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 941.0828.
1:56:47.450658 INFO: ==============================================
1:56:47.450786 INFO: Starting optimization step 3.
1:56:47.450891 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:56:47.451071 INFO: Using rust extraction backend
1:56:47.451201 PROGRESS: Extracting batch of 250375 precursors
1:56:48.813102 INFO: === Search parameters used ===
1:56:48.813735 INFO: rt_error       : 941.0827556536594
1:56:48.813801 INFO: mobility_error : 0.1
1:56:48.813855 INFO: num_candidates : 3
1:56:48.813903 INFO: ms1_error      : 3
1:56:48.813950 INFO: ms2_error      : 10.0
1:56:48.813994 INFO: fwhm_rt        : 3.0
1:56:48.814043 INFO: quant_window   : 3
1:56:48.814090 INFO: ==============================================
1:56:56.437743 INFO: performing precursor FDR with 40 features
1:56:56.438339 INFO: Decoy channel: -1
1:56:56.438389 INFO: competitive: True
1:56:57.021125 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:58.151998 INFO: Estimating optimal hyperparameters - samples: 599,656, batch_size: 2,456, learning_rate: 7.74e-04
1:56:58.159430 INFO: Using random state 953524 for train-test-split
1:57:18.596821 INFO: Test AUC: 0.610
1:57:18.597317 INFO: Train AUC: 0.622
1:57:18.597363 INFO: AUC difference: 1.95%
1:57:19.338444 INFO: Resetting torch num_threads to 24
1:57:19.412813 PROGRESS: === Extracted 749570 precursors and 4036455 fragments ===
1:57:19.414117 INFO: === FDR correction performed with classifier version 11 ===
1:57:19.415885 PROGRESS: ============================= Precursor FDR =============================
1:57:19.416034 PROGRESS: Total precursors accumulated: 1,787
1:57:19.416105 PROGRESS: Target precursors: 1,770 (99.05%)
1:57:19.416195 PROGRESS: Decoy precursors: 17 (0.95%)
1:57:19.416246 PROGRESS: 
1:57:19.416294 PROGRESS: Precursor Summary:
1:57:19.418547 PROGRESS: Channel   0:	 0.050 FDR: 1,770; 0.010 FDR: 1,770; 0.001 FDR: 1,079
1:57:19.418709 PROGRESS: 
1:57:19.418787 PROGRESS: Protein Summary:
1:57:19.421288 PROGRESS: Channel   0:	 0.050 FDR: 1,470; 0.010 FDR: 1,470; 0.001 FDR:   927
1:57:19.421439 PROGRESS: =========================================================================
1:57:19.464079 INFO: Target number of precursors reached.
1:57:19.931128 INFO: fragments_df: keeping 5000 of 4036455 [sum(precursor_idx_mask)=41151 sum(mass_error_mask)=4036455 stop_rank=5000
1:57:21.027976 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:57:21.597283 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:57:24.082771 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:57:24.084902 INFO: Using score_cutoff 10.318958272361757 (fac=0.99, q=1)
1:57:24.086652 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:57:24.087148 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:57:24.087389 INFO: Updating optimization_manager: score_cutoff        : 8.184149781131744 -> 10.318958272361757
1:57:24.087599 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:57:24.389156 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:57:25.181404 INFO: === checking if optimization conditions were reached ===
1:57:25.182318 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:57:25.192714 INFO: Updating optimization_manager: rt_error            : 941.0827556536594 -> 827.4519044769127
1:57:25.193513 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 827.4519.
1:57:25.193769 INFO: ==============================================
1:57:25.194109 INFO: Starting optimization step 4.
1:57:25.194327 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:57:25.194573 INFO: Using rust extraction backend
1:57:25.194805 PROGRESS: Extracting batch of 250375 precursors
1:57:26.428495 INFO: === Search parameters used ===
1:57:26.429857 INFO: rt_error       : 827.4519044769127
1:57:26.430063 INFO: mobility_error : 0.1
1:57:26.430152 INFO: num_candidates : 3
1:57:26.430210 INFO: ms1_error      : 3
1:57:26.430273 INFO: ms2_error      : 10.0
1:57:26.430320 INFO: fwhm_rt        : 3.0
1:57:26.430400 INFO: quant_window   : 3
1:57:26.430456 INFO: ==============================================
1:57:34.881506 INFO: performing precursor FDR with 40 features
1:57:34.881710 INFO: Decoy channel: -1
1:57:34.881745 INFO: competitive: True
1:57:35.400610 INFO: Setting torch num_threads to 2 for FDR classification task
1:57:36.342167 INFO: Estimating optimal hyperparameters - samples: 599,666, batch_size: 2,456, learning_rate: 7.74e-04
1:57:36.345727 INFO: Using random state 953524 for train-test-split
1:58:11.311276 INFO: Test AUC: 0.609
1:58:11.311603 INFO: Train AUC: 0.623
1:58:11.311644 INFO: AUC difference: 2.27%
1:58:12.083304 INFO: Resetting torch num_threads to 24
1:58:12.160494 PROGRESS: === Extracted 749583 precursors and 4036786 fragments ===
1:58:12.161912 INFO: === FDR correction performed with classifier version 11 ===
1:58:12.165026 PROGRESS: ============================= Precursor FDR =============================
1:58:12.165390 PROGRESS: Total precursors accumulated: 1,628
1:58:12.165499 PROGRESS: Target precursors: 1,612 (99.02%)
1:58:12.165566 PROGRESS: Decoy precursors: 16 (0.98%)
1:58:12.165618 PROGRESS: 
1:58:12.165670 PROGRESS: Precursor Summary:
1:58:12.170248 PROGRESS: Channel   0:	 0.050 FDR: 1,612; 0.010 FDR: 1,612; 0.001 FDR:   579
1:58:12.170600 PROGRESS: 
1:58:12.170688 PROGRESS: Protein Summary:
1:58:12.175644 PROGRESS: Channel   0:	 0.050 FDR: 1,348; 0.010 FDR: 1,348; 0.001 FDR:   527
1:58:12.176016 PROGRESS: =========================================================================
1:58:12.226820 INFO: Target number of precursors reached.
1:58:12.690179 INFO: fragments_df: keeping 5000 of 4036786 [sum(precursor_idx_mask)=37948 sum(mass_error_mask)=4036786 stop_rank=5000
1:58:13.658399 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:58:14.163756 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:58:15.162012 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:58:15.163322 INFO: Using score_cutoff 10.46335917634964 (fac=0.99, q=1)
1:58:15.164427 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:58:15.164683 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:58:15.164771 INFO: Updating optimization_manager: score_cutoff        : 10.318958272361757 -> 10.46335917634964
1:58:15.164886 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:58:15.379701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:58:15.972335 INFO: === checking if optimization conditions were reached ===
1:58:15.973019 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:58:15.979313 INFO: Updating optimization_manager: rt_error            : 827.4519044769127 -> 938.2945095514909
1:58:15.979727 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 938.2945.
1:58:15.979866 INFO: ==============================================
1:58:15.979988 INFO: Starting optimization step 5.
1:58:15.980070 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:58:15.980175 INFO: Using rust extraction backend
1:58:15.980260 PROGRESS: Extracting batch of 250375 precursors
1:58:17.086275 INFO: === Search parameters used ===
1:58:17.086960 INFO: rt_error       : 938.2945095514909
1:58:17.087178 INFO: mobility_error : 0.1
1:58:17.087251 INFO: num_candidates : 3
1:58:17.087305 INFO: ms1_error      : 3
1:58:17.087356 INFO: ms2_error      : 10.0
1:58:17.087402 INFO: fwhm_rt        : 3.0
1:58:17.087447 INFO: quant_window   : 3
1:58:17.087492 INFO: ==============================================
1:58:25.461134 INFO: performing precursor FDR with 40 features
1:58:25.461478 INFO: Decoy channel: -1
1:58:25.461527 INFO: competitive: True
1:58:26.064106 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:27.176589 INFO: Estimating optimal hyperparameters - samples: 599,649, batch_size: 2,456, learning_rate: 7.74e-04
1:58:27.181993 INFO: Using random state 953524 for train-test-split
1:58:46.427041 INFO: Test AUC: 0.613
1:58:46.427359 INFO: Train AUC: 0.623
1:58:46.427403 INFO: AUC difference: 1.58%
1:58:47.241563 INFO: Resetting torch num_threads to 24
1:58:47.325881 PROGRESS: === Extracted 749562 precursors and 4036108 fragments ===
1:58:47.327252 INFO: === FDR correction performed with classifier version 11 ===
1:58:47.329117 PROGRESS: ============================= Precursor FDR =============================
1:58:47.329304 PROGRESS: Total precursors accumulated: 1,832
1:58:47.329377 PROGRESS: Target precursors: 1,814 (99.02%)
1:58:47.329443 PROGRESS: Decoy precursors: 18 (0.98%)
1:58:47.329508 PROGRESS: 
1:58:47.329583 PROGRESS: Precursor Summary:
1:58:47.331978 PROGRESS: Channel   0:	 0.050 FDR: 1,814; 0.010 FDR: 1,814; 0.001 FDR: 1,192
1:58:47.332128 PROGRESS: 
1:58:47.332194 PROGRESS: Protein Summary:
1:58:47.334854 PROGRESS: Channel   0:	 0.050 FDR: 1,527; 0.010 FDR: 1,527; 0.001 FDR: 1,022
1:58:47.335091 PROGRESS: =========================================================================
1:58:47.384606 INFO: Target number of precursors reached.
1:58:47.844763 INFO: fragments_df: keeping 5000 of 4036108 [sum(precursor_idx_mask)=41709 sum(mass_error_mask)=4036108 stop_rank=5000
1:58:48.947684 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:58:49.504653 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:58:50.358262 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:58:50.359335 INFO: Using score_cutoff 9.321627346229555 (fac=0.99, q=1)
1:58:50.360331 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:58:50.360548 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:58:50.360629 INFO: Updating optimization_manager: score_cutoff        : 10.46335917634964 -> 9.321627346229555
1:58:50.360709 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:58:50.545711 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:58:51.046022 INFO: === checking if optimization conditions were reached ===
1:58:51.046681 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:58:51.052963 INFO: Updating optimization_manager: rt_error            : 938.2945095514909 -> 1056.7747021901955
1:58:51.053435 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 1056.7747.
1:58:51.053616 INFO: ==============================================
1:58:51.053740 INFO: Starting optimization step 6.
1:58:51.053827 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:58:51.053925 INFO: Using rust extraction backend
1:58:51.054014 PROGRESS: Extracting batch of 250375 precursors
1:58:52.104503 INFO: === Search parameters used ===
1:58:52.105184 INFO: rt_error       : 1056.7747021901955
1:58:52.105343 INFO: mobility_error : 0.1
1:58:52.105415 INFO: num_candidates : 3
1:58:52.105468 INFO: ms1_error      : 3
1:58:52.105520 INFO: ms2_error      : 10.0
1:58:52.105574 INFO: fwhm_rt        : 3.0
1:58:52.105622 INFO: quant_window   : 3
1:58:52.105880 INFO: ==============================================
1:58:59.092437 INFO: performing precursor FDR with 40 features
1:58:59.092785 INFO: Decoy channel: -1
1:58:59.092816 INFO: competitive: True
1:58:59.509197 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:00.241029 INFO: Estimating optimal hyperparameters - samples: 599,629, batch_size: 2,456, learning_rate: 7.74e-04
1:59:00.243889 INFO: Using random state 953524 for train-test-split
1:59:20.006316 INFO: Test AUC: 0.610
1:59:20.006670 INFO: Train AUC: 0.621
1:59:20.006711 INFO: AUC difference: 1.85%
1:59:20.738949 INFO: Resetting torch num_threads to 24
1:59:20.810355 PROGRESS: === Extracted 749537 precursors and 4036141 fragments ===
1:59:20.811687 INFO: === FDR correction performed with classifier version 11 ===
1:59:20.814327 PROGRESS: ============================= Precursor FDR =============================
1:59:20.814688 PROGRESS: Total precursors accumulated: 1,881
1:59:20.814788 PROGRESS: Target precursors: 1,863 (99.04%)
1:59:20.814894 PROGRESS: Decoy precursors: 18 (0.96%)
1:59:20.814953 PROGRESS: 
1:59:20.815021 PROGRESS: Precursor Summary:
1:59:20.819502 PROGRESS: Channel   0:	 0.050 FDR: 1,863; 0.010 FDR: 1,863; 0.001 FDR: 1,206
1:59:20.819761 PROGRESS: 
1:59:20.819848 PROGRESS: Protein Summary:
1:59:20.824694 PROGRESS: Channel   0:	 0.050 FDR: 1,553; 0.010 FDR: 1,553; 0.001 FDR: 1,028
1:59:20.824942 PROGRESS: =========================================================================
1:59:20.880426 INFO: Target number of precursors reached.
1:59:21.343421 INFO: fragments_df: keeping 5000 of 4036141 [sum(precursor_idx_mask)=43718 sum(mass_error_mask)=4036141 stop_rank=5000
1:59:22.461952 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:59:22.983077 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:59:23.903523 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:59:23.904504 INFO: Using score_cutoff 10.78431157836914 (fac=0.99, q=1)
1:59:23.904997 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:59:23.905085 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:59:23.905143 INFO: Updating optimization_manager: score_cutoff        : 9.321627346229555 -> 10.78431157836914
1:59:23.905226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:59:24.096563 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:59:24.521594 INFO: === checking if optimization conditions were reached ===
1:59:24.522131 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:59:24.526453 INFO: Updating optimization_manager: rt_error            : 1056.7747021901955 -> 936.0309535148448
1:59:24.526858 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 936.0310.
1:59:24.526944 INFO: ==============================================
1:59:24.527075 INFO: Starting optimization step 7.
1:59:24.527155 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:59:24.527248 INFO: Using rust extraction backend
1:59:24.527335 PROGRESS: Extracting batch of 250375 precursors
1:59:25.392806 INFO: === Search parameters used ===
1:59:25.393227 INFO: rt_error       : 936.0309535148448
1:59:25.393289 INFO: mobility_error : 0.1
1:59:25.393339 INFO: num_candidates : 3
1:59:25.393407 INFO: ms1_error      : 3
1:59:25.393453 INFO: ms2_error      : 10.0
1:59:25.393502 INFO: fwhm_rt        : 3.0
1:59:25.393546 INFO: quant_window   : 3
1:59:25.393591 INFO: ==============================================
1:59:32.106835 INFO: performing precursor FDR with 40 features
1:59:32.107121 INFO: Decoy channel: -1
1:59:32.107151 INFO: competitive: True
1:59:32.669156 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:34.244978 INFO: Estimating optimal hyperparameters - samples: 599,654, batch_size: 2,456, learning_rate: 7.74e-04
1:59:34.248162 INFO: Using random state 953524 for train-test-split
1:59:55.207057 INFO: Test AUC: 0.613
1:59:55.207371 INFO: Train AUC: 0.623
1:59:55.207414 INFO: AUC difference: 1.62%
1:59:56.065927 INFO: Resetting torch num_threads to 24
1:59:56.135799 PROGRESS: === Extracted 749568 precursors and 4036386 fragments ===
1:59:56.136849 INFO: === FDR correction performed with classifier version 11 ===
1:59:56.139230 PROGRESS: ============================= Precursor FDR =============================
1:59:56.139477 PROGRESS: Total precursors accumulated: 1,915
1:59:56.139560 PROGRESS: Target precursors: 1,897 (99.06%)
1:59:56.139615 PROGRESS: Decoy precursors: 18 (0.94%)
1:59:56.139664 PROGRESS: 
1:59:56.139712 PROGRESS: Precursor Summary:
1:59:56.142661 PROGRESS: Channel   0:	 0.050 FDR: 1,897; 0.010 FDR: 1,897; 0.001 FDR: 1,168
1:59:56.142906 PROGRESS: 
1:59:56.143013 PROGRESS: Protein Summary:
1:59:56.145797 PROGRESS: Channel   0:	 0.050 FDR: 1,581; 0.010 FDR: 1,581; 0.001 FDR:   995
1:59:56.146053 PROGRESS: =========================================================================
1:59:56.192127 INFO: Target number of precursors reached.
1:59:56.661413 INFO: fragments_df: keeping 5000 of 4036386 [sum(precursor_idx_mask)=44561 sum(mass_error_mask)=4036386 stop_rank=5000
1:59:57.595447 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:59:58.141949 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:59:59.193328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:59:59.194541 INFO: Using score_cutoff 10.88447974090576 (fac=0.99, q=1)
1:59:59.195677 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:59:59.195946 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:59:59.196046 INFO: Updating optimization_manager: score_cutoff        : 10.78431157836914 -> 10.88447974090576
1:59:59.196137 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:59:59.401156 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:59:59.886465 INFO: === checking if optimization conditions were reached ===
1:59:59.887191 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:59:59.893764 INFO: Updating optimization_manager: rt_error            : 936.0309535148448 -> 560.0007727070711
1:59:59.894382 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 560.0008.
1:59:59.894506 INFO: ==============================================
1:59:59.894621 INFO: Starting optimization step 8.
1:59:59.894713 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:59:59.894820 INFO: Using rust extraction backend
1:59:59.894907 PROGRESS: Extracting batch of 250375 precursors
2:00:01.293479 INFO: === Search parameters used ===
2:00:01.294288 INFO: rt_error       : 560.0007727070711
2:00:01.294434 INFO: mobility_error : 0.1
2:00:01.294491 INFO: num_candidates : 3
2:00:01.294544 INFO: ms1_error      : 3
2:00:01.294603 INFO: ms2_error      : 10.0
2:00:01.294668 INFO: fwhm_rt        : 3.0
2:00:01.294714 INFO: quant_window   : 3
2:00:01.294762 INFO: ==============================================
2:00:08.484910 INFO: performing precursor FDR with 40 features
2:00:08.485289 INFO: Decoy channel: -1
2:00:08.485332 INFO: competitive: True
2:00:09.220561 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:10.383238 INFO: Estimating optimal hyperparameters - samples: 599,297, batch_size: 2,454, learning_rate: 7.74e-04
2:00:10.388498 INFO: Using random state 953524 for train-test-split
2:00:35.843756 INFO: Test AUC: 0.611
2:00:35.844055 INFO: Train AUC: 0.621
2:00:35.844092 INFO: AUC difference: 1.70%
2:00:36.578080 INFO: Resetting torch num_threads to 24
2:00:36.649167 PROGRESS: === Extracted 749122 precursors and 4006597 fragments ===
2:00:36.650166 INFO: === FDR correction performed with classifier version 11 ===
2:00:36.651763 PROGRESS: ============================= Precursor FDR =============================
2:00:36.651920 PROGRESS: Total precursors accumulated: 1,828
2:00:36.651986 PROGRESS: Target precursors: 1,810 (99.02%)
2:00:36.652041 PROGRESS: Decoy precursors: 18 (0.98%)
2:00:36.652090 PROGRESS: 
2:00:36.652141 PROGRESS: Precursor Summary:
2:00:36.654172 PROGRESS: Channel   0:	 0.050 FDR: 1,810; 0.010 FDR: 1,810; 0.001 FDR: 1,094
2:00:36.654309 PROGRESS: 
2:00:36.654369 PROGRESS: Protein Summary:
2:00:36.656735 PROGRESS: Channel   0:	 0.050 FDR: 1,523; 0.010 FDR: 1,523; 0.001 FDR:   943
2:00:36.656918 PROGRESS: =========================================================================
2:00:36.703928 INFO: Target number of precursors reached.
2:00:37.176459 INFO: fragments_df: keeping 5000 of 4006597 [sum(precursor_idx_mask)=41726 sum(mass_error_mask)=4006597 stop_rank=5000
2:00:38.322946 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:00:38.686327 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:00:39.719677 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:00:39.720873 INFO: Using score_cutoff 9.374817139720916 (fac=0.99, q=1)
2:00:39.721927 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:00:39.722174 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:00:39.722256 INFO: Updating optimization_manager: score_cutoff        : 10.88447974090576 -> 9.374817139720916
2:00:39.722348 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:00:39.939748 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:00:40.530017 INFO: === checking if optimization conditions were reached ===
2:00:40.530625 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:00:40.537546 INFO: Updating optimization_manager: rt_error            : 560.0007727070711 -> 704.4421652938636
2:00:40.537931 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 704.4422.
2:00:40.538049 INFO: ==============================================
2:00:40.538160 INFO: Starting optimization step 9.
2:00:40.538239 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:00:40.538332 INFO: Using rust extraction backend
2:00:40.538415 PROGRESS: Extracting batch of 250375 precursors
2:00:41.838345 INFO: === Search parameters used ===
2:00:41.839089 INFO: rt_error       : 704.4421652938636
2:00:41.839277 INFO: mobility_error : 0.1
2:00:41.839339 INFO: num_candidates : 3
2:00:41.839392 INFO: ms1_error      : 3
2:00:41.839435 INFO: ms2_error      : 10.0
2:00:41.839482 INFO: fwhm_rt        : 3.0
2:00:41.839524 INFO: quant_window   : 3
2:00:41.839576 INFO: ==============================================
2:00:49.054285 INFO: performing precursor FDR with 40 features
2:00:49.054727 INFO: Decoy channel: -1
2:00:49.054762 INFO: competitive: True
2:00:49.694258 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:50.816365 INFO: Estimating optimal hyperparameters - samples: 599,638, batch_size: 2,456, learning_rate: 7.74e-04
2:00:50.822963 INFO: Using random state 953524 for train-test-split
2:01:15.125512 INFO: Test AUC: 0.610
2:01:15.125717 INFO: Train AUC: 0.623
2:01:15.125754 INFO: AUC difference: 1.99%
2:01:15.776114 INFO: Resetting torch num_threads to 24
2:01:15.873175 PROGRESS: === Extracted 749548 precursors and 4033940 fragments ===
2:01:15.874623 INFO: === FDR correction performed with classifier version 11 ===
2:01:15.878545 PROGRESS: ============================= Precursor FDR =============================
2:01:15.878959 PROGRESS: Total precursors accumulated: 1,904
2:01:15.879122 PROGRESS: Target precursors: 1,886 (99.05%)
2:01:15.879204 PROGRESS: Decoy precursors: 18 (0.95%)
2:01:15.879274 PROGRESS: 
2:01:15.879342 PROGRESS: Precursor Summary:
2:01:15.885613 PROGRESS: Channel   0:	 0.050 FDR: 1,886; 0.010 FDR: 1,886; 0.001 FDR: 1,015
2:01:15.885914 PROGRESS: 
2:01:15.885995 PROGRESS: Protein Summary:
2:01:15.891355 PROGRESS: Channel   0:	 0.050 FDR: 1,573; 0.010 FDR: 1,573; 0.001 FDR:   875
2:01:15.891626 PROGRESS: =========================================================================
2:01:15.966700 INFO: Target number of precursors reached.
2:01:16.595562 INFO: fragments_df: keeping 5000 of 4033940 [sum(precursor_idx_mask)=43829 sum(mass_error_mask)=4033940 stop_rank=5000
2:01:17.655288 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:18.153543 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:19.251410 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:19.252561 INFO: Using score_cutoff 10.457771080970764 (fac=0.99, q=1)
2:01:19.253141 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:19.253259 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:19.253320 INFO: Updating optimization_manager: score_cutoff        : 9.374817139720916 -> 10.457771080970764
2:01:19.253393 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:19.442356 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:19.919685 INFO: === checking if optimization conditions were reached ===
2:01:19.920182 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:01:19.923998 INFO: Updating optimization_manager: rt_error            : 704.4421652938636 -> 690.5671026381824
2:01:19.924205 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 690.5671.
2:01:19.924278 INFO: ==============================================
2:01:19.924386 INFO: Starting optimization step 10.
2:01:19.924449 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:01:19.924519 INFO: Using rust extraction backend
2:01:19.924585 PROGRESS: Extracting batch of 250375 precursors
2:01:20.956924 INFO: === Search parameters used ===
2:01:20.957563 INFO: rt_error       : 690.5671026381824
2:01:20.957624 INFO: mobility_error : 0.1
2:01:20.957675 INFO: num_candidates : 3
2:01:20.957719 INFO: ms1_error      : 3
2:01:20.957761 INFO: ms2_error      : 10.0
2:01:20.957800 INFO: fwhm_rt        : 3.0
2:01:20.957840 INFO: quant_window   : 3
2:01:20.957906 INFO: ==============================================
2:01:27.330922 INFO: performing precursor FDR with 40 features
2:01:27.331110 INFO: Decoy channel: -1
2:01:27.331138 INFO: competitive: True
2:01:27.618538 INFO: Setting torch num_threads to 2 for FDR classification task
2:01:28.195429 INFO: Estimating optimal hyperparameters - samples: 599,621, batch_size: 2,456, learning_rate: 7.74e-04
2:01:28.198155 INFO: Using random state 953524 for train-test-split
2:01:50.427430 INFO: Test AUC: 0.611
2:01:50.427670 INFO: Train AUC: 0.623
2:01:50.427709 INFO: AUC difference: 1.79%
2:01:51.163596 INFO: Resetting torch num_threads to 24
2:01:51.256702 PROGRESS: === Extracted 749527 precursors and 4031918 fragments ===
2:01:51.257934 INFO: === FDR correction performed with classifier version 11 ===
2:01:51.260013 PROGRESS: ============================= Precursor FDR =============================
2:01:51.260167 PROGRESS: Total precursors accumulated: 1,865
2:01:51.260250 PROGRESS: Target precursors: 1,847 (99.03%)
2:01:51.260320 PROGRESS: Decoy precursors: 18 (0.97%)
2:01:51.260385 PROGRESS: 
2:01:51.260446 PROGRESS: Precursor Summary:
2:01:51.262837 PROGRESS: Channel   0:	 0.050 FDR: 1,847; 0.010 FDR: 1,847; 0.001 FDR:   942
2:01:51.263000 PROGRESS: 
2:01:51.263081 PROGRESS: Protein Summary:
2:01:51.266242 PROGRESS: Channel   0:	 0.050 FDR: 1,551; 0.010 FDR: 1,551; 0.001 FDR:   828
2:01:51.266409 PROGRESS: =========================================================================
2:01:51.328125 INFO: Target number of precursors reached.
2:01:51.807566 INFO: fragments_df: keeping 5000 of 4031918 [sum(precursor_idx_mask)=42780 sum(mass_error_mask)=4031918 stop_rank=5000
2:01:52.498601 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:01:52.850463 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:01:53.861170 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:01:53.862216 INFO: Using score_cutoff 9.971357823371887 (fac=0.99, q=1)
2:01:53.862844 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:53.862956 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:53.863044 INFO: Updating optimization_manager: score_cutoff        : 10.457771080970764 -> 9.971357823371887
2:01:53.863114 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:54.056890 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:54.552944 INFO: === checking if optimization conditions were reached ===
2:01:54.553490 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:01:54.556398 INFO: Updating optimization_manager: rt_error            : 690.5671026381824 -> 774.5052103543159
2:01:54.556927 INFO: Updating optimization_manager: classifier_version  : 11 -> 14
2:01:54.557260 INFO: Updating optimization_manager: score_cutoff        : 9.971357823371887 -> 8.184149781131744
2:01:54.557534 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:01:54.557752 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:01:54.557952 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 774.5052 found after 11 searches.
2:01:54.558069 INFO: ==============================================
2:01:54.558202 PROGRESS: Optimization finished for rt_error.
2:01:55.710810 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:01:55.914406 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:01:56.441673 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:01:56.442295 PROGRESS: ==============================================
2:01:56.442471 PROGRESS: ms2_error      : 10.0000
2:01:56.442581 PROGRESS: rt_error       : 774.5052
2:01:56.442647 PROGRESS: ==============================================
2:01:56.456853 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:02:05.816658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:02:27.916850 INFO: Using rust extraction backend
2:02:27.917343 PROGRESS: Extracting batch of 11997144 precursors
2:02:43.993125 INFO: === Search parameters used ===
2:02:43.993712 INFO: rt_error       : 774.5052103543159
2:02:43.993783 INFO: mobility_error : 0.1
2:02:43.993846 INFO: num_candidates : 3
2:02:43.993896 INFO: ms1_error      : 3
2:02:43.993944 INFO: ms2_error      : 10.0
2:02:43.993989 INFO: fwhm_rt        : 3.0
2:02:43.994037 INFO: quant_window   : 3
2:02:43.994086 INFO: ==============================================
2:03:45.481532 INFO: Removed 3469209 precursors with score below cutoff 8.184149781131744
2:04:21.454474 INFO: performing precursor FDR with 40 features
2:04:21.454690 INFO: Decoy channel: -1
2:04:21.454722 INFO: competitive: True
2:04:24.905906 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:38.353234 INFO: Estimating optimal hyperparameters - samples: 26,017,490, batch_size: 4,096, learning_rate: 1.00e-03
2:04:38.436744 INFO: Using random state 243885 for train-test-split
2:15:40.438682 INFO: Test AUC: 0.621
2:15:40.439124 INFO: Train AUC: 0.622
2:15:40.439172 INFO: AUC difference: 0.07%
2:15:48.014028 INFO: Resetting torch num_threads to 24
2:15:50.791396 PROGRESS: ============================= Precursor FDR =============================
2:15:50.791764 PROGRESS: Total precursors accumulated: 92,116
2:15:50.791840 PROGRESS: Target precursors: 91,204 (99.01%)
2:15:50.791896 PROGRESS: Decoy precursors: 912 (0.99%)
2:15:50.791960 PROGRESS: 
2:15:50.792007 PROGRESS: Precursor Summary:
2:15:50.822082 PROGRESS: Channel   0:	 0.050 FDR: 91,204; 0.010 FDR: 91,204; 0.001 FDR: 60,750
2:15:50.822335 PROGRESS: 
2:15:50.822403 PROGRESS: Protein Summary:
2:15:50.861213 PROGRESS: Channel   0:	 0.050 FDR: 12,701; 0.010 FDR: 12,701; 0.001 FDR: 9,156
2:15:50.861469 PROGRESS: =========================================================================
2:15:51.038574 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
2:15:51.243664 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
2:15:51.490389 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:15:52.147446 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:15:52.147629 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
2:15:52.147761 INFO: Initializing TimingManager
2:15:52.148623 INFO: Initializing RawFileManager
2:16:05.626859 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.
2:16:05.634639 INFO: Determining DIA cycle
2:16:05.652192 INFO: Found cycle with start 0.00 min and length 300.
2:16:05.826510 INFO: RT (min)            : 0.0 - 26.9
2:16:05.826614 INFO: RT duration (sec)   : 1611.2
2:16:05.826656 INFO: RT duration (min)   : 26.9
2:16:05.826682 INFO: Cycle len (scans)   : 300
2:16:05.826702 INFO: Cycle len (sec)     : 1.65
2:16:05.826721 INFO: Number of cycles    : 978
2:16:05.826740 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:16:05.826794 INFO: Creating DIA data object took: 13.678066968917847
2:16:07.728897 INFO: Creating DIA data NG object took: 1.9019510746002197
2:16:09.193491 INFO: Initializing CalibrationManager
2:16:09.193802 INFO: Setting up calibration estimators ..
2:16:09.193868 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:16:09.193991 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'}' ..
2:16:09.194096 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:16:09.194154 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:16:09.194215 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}}' ..
2:16:09.194267 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:16:09.194312 INFO: Done setting up calibration estimators.
2:16:09.194582 INFO: Initializing OptimizationManager
2:16:09.194759 INFO: initial parameter: ms1_error = 3
2:16:09.194818 INFO: initial parameter: ms2_error = 10
2:16:09.194868 INFO: initial parameter: rt_error = 805.611083984375
2:16:09.194913 INFO: initial parameter: mobility_error = 0.1
2:16:09.194956 INFO: initial parameter: num_candidates = 1
2:16:09.195055 INFO: initial parameter: fwhm_rt = 5
2:16:09.195100 INFO: initial parameter: fwhm_mobility = 0.01
2:16:09.195141 INFO: initial parameter: score_cutoff = 0
2:16:09.195181 INFO: initial parameter: classifier_version = -1
2:16:09.195259 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:16:09.195610 INFO: FDRManager: loading saved state not requested, will be initialized.
2:16:09.195646 INFO: Initializing FDRManager
2:16:09.195688 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:16:10.740461 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
2:16:11.741585 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:16:11.742031 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:16:11.742152 PROGRESS: Starting initial search for precursors.
2:16:11.742249 INFO: Starting optimization step 0.
2:16:11.742315 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:16:11.742383 INFO: Using rust extraction backend
2:16:11.742470 PROGRESS: Extracting batch of 1976 precursors
2:16:11.748396 INFO: === Search parameters used ===
2:16:11.748506 INFO: rt_error       : 805.611083984375
2:16:11.748558 INFO: mobility_error : 0.1
2:16:11.748604 INFO: num_candidates : 1
2:16:11.748647 INFO: ms1_error      : 3
2:16:11.748698 INFO: ms2_error      : 10
2:16:11.748739 INFO: fwhm_rt        : 5
2:16:11.748780 INFO: quant_window   : 3
2:16:11.748821 INFO: ==============================================
2:16:11.784115 INFO: performing precursor FDR with 40 features
2:16:11.784196 INFO: Decoy channel: -1
2:16:11.784220 INFO: competitive: True
2:16:11.785634 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:11.787964 INFO: Estimating optimal hyperparameters - samples: 1,578, batch_size: 128, learning_rate: 1.77e-04
2:16:11.789081 INFO: Using random state 383095 for train-test-split
2:16:11.980637 INFO: Test AUC: 0.506
2:16:11.980720 INFO: Train AUC: 0.518
2:16:11.980760 INFO: AUC difference: 2.36%
2:16:12.234411 INFO: Resetting torch num_threads to 24
2:16:12.236207 PROGRESS: === Extracted 1973 precursors and 11026 fragments ===
2:16:12.236589 INFO: === FDR correction performed with classifier version -1 ===
2:16:12.237095 PROGRESS: ============================= Precursor FDR =============================
2:16:12.237180 PROGRESS: Total precursors accumulated: 1
2:16:12.237236 PROGRESS: Target precursors: 1 (100.00%)
2:16:12.237283 PROGRESS: Decoy precursors: 0 (0.00%)
2:16:12.237327 PROGRESS: 
2:16:12.237369 PROGRESS: Precursor Summary:
2:16:12.238443 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2:16:12.238524 PROGRESS: 
2:16:12.238578 PROGRESS: Protein Summary:
2:16:12.239768 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2:16:12.239858 PROGRESS: =========================================================================
2:16:12.240148 INFO: Target number of precursors not reached yet.
2:16:12.327512 INFO: Starting optimization step 1.
2:16:12.327745 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:16:12.327829 INFO: Using rust extraction backend
2:16:12.327892 PROGRESS: Extracting batch of 3939 precursors
2:16:12.337385 INFO: === Search parameters used ===
2:16:12.337536 INFO: rt_error       : 805.611083984375
2:16:12.337589 INFO: mobility_error : 0.1
2:16:12.337634 INFO: num_candidates : 1
2:16:12.337676 INFO: ms1_error      : 3
2:16:12.337719 INFO: ms2_error      : 10
2:16:12.337762 INFO: fwhm_rt        : 5
2:16:12.337802 INFO: quant_window   : 3
2:16:12.337842 INFO: ==============================================
2:16:12.401764 INFO: performing precursor FDR with 40 features
2:16:12.401859 INFO: Decoy channel: -1
2:16:12.401882 INFO: competitive: True
2:16:12.409323 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:12.412318 INFO: Estimating optimal hyperparameters - samples: 4,719, batch_size: 128, learning_rate: 1.77e-04
2:16:12.412409 INFO: Using random state 617920 for train-test-split
2:16:12.947647 INFO: Test AUC: 0.548
2:16:12.947743 INFO: Train AUC: 0.561
2:16:12.947771 INFO: AUC difference: 2.35%
2:16:13.191641 INFO: Resetting torch num_threads to 24
2:16:13.194951 PROGRESS: === Extracted 5899 precursors and 33318 fragments ===
2:16:13.195391 INFO: === FDR correction performed with classifier version -1 ===
2:16:13.195897 PROGRESS: ============================= Precursor FDR =============================
2:16:13.195980 PROGRESS: Total precursors accumulated: 11
2:16:13.196037 PROGRESS: Target precursors: 11 (100.00%)
2:16:13.196086 PROGRESS: Decoy precursors: 0 (0.00%)
2:16:13.196146 PROGRESS: 
2:16:13.196189 PROGRESS: Precursor Summary:
2:16:13.197395 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2:16:13.197476 PROGRESS: 
2:16:13.197530 PROGRESS: Protein Summary:
2:16:13.198711 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2:16:13.198792 PROGRESS: =========================================================================
2:16:13.199149 INFO: Target number of precursors not reached yet.
2:16:13.294108 INFO: Starting optimization step 2.
2:16:13.294330 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:16:13.294410 INFO: Using rust extraction backend
2:16:13.294471 PROGRESS: Extracting batch of 7882 precursors
2:16:13.310838 INFO: === Search parameters used ===
2:16:13.310995 INFO: rt_error       : 805.611083984375
2:16:13.311051 INFO: mobility_error : 0.1
2:16:13.311097 INFO: num_candidates : 1
2:16:13.311141 INFO: ms1_error      : 3
2:16:13.311182 INFO: ms2_error      : 10
2:16:13.311223 INFO: fwhm_rt        : 5
2:16:13.311262 INFO: quant_window   : 3
2:16:13.311302 INFO: ==============================================
2:16:13.422158 INFO: performing precursor FDR with 40 features
2:16:13.422268 INFO: Decoy channel: -1
2:16:13.422292 INFO: competitive: True
2:16:13.431573 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:13.437197 INFO: Estimating optimal hyperparameters - samples: 11,009, batch_size: 128, learning_rate: 1.77e-04
2:16:13.437330 INFO: Using random state 412894 for train-test-split
2:16:14.665569 INFO: Test AUC: 0.560
2:16:14.665683 INFO: Train AUC: 0.579
2:16:14.665712 INFO: AUC difference: 3.28%
2:16:14.923457 INFO: Resetting torch num_threads to 24
2:16:14.928255 PROGRESS: === Extracted 13762 precursors and 77600 fragments ===
2:16:14.928663 INFO: === FDR correction performed with classifier version -1 ===
2:16:14.929188 PROGRESS: ============================= Precursor FDR =============================
2:16:14.929276 PROGRESS: Total precursors accumulated: 66
2:16:14.929336 PROGRESS: Target precursors: 66 (100.00%)
2:16:14.929388 PROGRESS: Decoy precursors: 0 (0.00%)
2:16:14.929439 PROGRESS: 
2:16:14.929486 PROGRESS: Precursor Summary:
2:16:14.930573 PROGRESS: Channel   0:	 0.050 FDR:    66; 0.010 FDR:    66; 0.001 FDR:    66
2:16:14.930660 PROGRESS: 
2:16:14.930716 PROGRESS: Protein Summary:
2:16:14.931943 PROGRESS: Channel   0:	 0.050 FDR:    66; 0.010 FDR:    66; 0.001 FDR:    66
2:16:14.932033 PROGRESS: =========================================================================
2:16:14.932433 INFO: Target number of precursors not reached yet.
2:16:15.038802 INFO: Starting optimization step 3.
2:16:15.039104 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:16:15.039218 INFO: Using rust extraction backend
2:16:15.039286 PROGRESS: Extracting batch of 15793 precursors
2:16:15.069813 INFO: === Search parameters used ===
2:16:15.069985 INFO: rt_error       : 805.611083984375
2:16:15.070040 INFO: mobility_error : 0.1
2:16:15.070089 INFO: num_candidates : 1
2:16:15.070138 INFO: ms1_error      : 3
2:16:15.070184 INFO: ms2_error      : 10
2:16:15.070240 INFO: fwhm_rt        : 5
2:16:15.070287 INFO: quant_window   : 3
2:16:15.070336 INFO: ==============================================
2:16:15.247118 INFO: performing precursor FDR with 40 features
2:16:15.247235 INFO: Decoy channel: -1
2:16:15.247262 INFO: competitive: True
2:16:15.262193 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:15.270104 INFO: Estimating optimal hyperparameters - samples: 23,608, batch_size: 128, learning_rate: 1.77e-04
2:16:15.270289 INFO: Using random state 686785 for train-test-split
2:16:17.839519 INFO: Test AUC: 0.561
2:16:17.839638 INFO: Train AUC: 0.594
2:16:17.839667 INFO: AUC difference: 5.54%
2:16:17.839689 WARNING: AUC difference > 5%. This may indicate overfitting.
2:16:18.108871 INFO: Resetting torch num_threads to 24
2:16:18.116858 PROGRESS: === Extracted 29510 precursors and 166120 fragments ===
2:16:18.117347 INFO: === FDR correction performed with classifier version -1 ===
2:16:18.117877 PROGRESS: ============================= Precursor FDR =============================
2:16:18.117961 PROGRESS: Total precursors accumulated: 131
2:16:18.118017 PROGRESS: Target precursors: 130 (99.24%)
2:16:18.118065 PROGRESS: Decoy precursors: 1 (0.76%)
2:16:18.118108 PROGRESS: 
2:16:18.118150 PROGRESS: Precursor Summary:
2:16:18.119182 PROGRESS: Channel   0:	 0.050 FDR:   130; 0.010 FDR:   130; 0.001 FDR:   113
2:16:18.119268 PROGRESS: 
2:16:18.119322 PROGRESS: Protein Summary:
2:16:18.120450 PROGRESS: Channel   0:	 0.050 FDR:   127; 0.010 FDR:   127; 0.001 FDR:   110
2:16:18.120533 PROGRESS: =========================================================================
2:16:18.121224 INFO: Target number of precursors not reached yet.
2:16:18.251637 INFO: Starting optimization step 4.
2:16:18.251897 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:16:18.251983 INFO: Using rust extraction backend
2:16:18.252046 PROGRESS: Extracting batch of 31556 precursors
2:16:18.310564 INFO: === Search parameters used ===
2:16:18.310841 INFO: rt_error       : 805.611083984375
2:16:18.310894 INFO: mobility_error : 0.1
2:16:18.310942 INFO: num_candidates : 1
2:16:18.310994 INFO: ms1_error      : 3
2:16:18.311040 INFO: ms2_error      : 10
2:16:18.311081 INFO: fwhm_rt        : 5
2:16:18.311121 INFO: quant_window   : 3
2:16:18.311161 INFO: ==============================================
2:16:18.602573 INFO: performing precursor FDR with 40 features
2:16:18.602680 INFO: Decoy channel: -1
2:16:18.602705 INFO: competitive: True
2:16:18.639832 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:18.661466 INFO: Estimating optimal hyperparameters - samples: 48,796, batch_size: 199, learning_rate: 2.20e-04
2:16:18.661755 INFO: Using random state 120758 for train-test-split
2:16:22.859812 INFO: Test AUC: 0.579
2:16:22.859938 INFO: Train AUC: 0.600
2:16:22.859970 INFO: AUC difference: 3.50%
2:16:23.133609 INFO: Resetting torch num_threads to 24
2:16:23.147021 PROGRESS: === Extracted 60996 precursors and 342247 fragments ===
2:16:23.147625 INFO: === FDR correction performed with classifier version -1 ===
2:16:23.148221 PROGRESS: ============================= Precursor FDR =============================
2:16:23.148312 PROGRESS: Total precursors accumulated: 292
2:16:23.148374 PROGRESS: Target precursors: 290 (99.32%)
2:16:23.148438 PROGRESS: Decoy precursors: 2 (0.68%)
2:16:23.148485 PROGRESS: 
2:16:23.148531 PROGRESS: Precursor Summary:
2:16:23.149667 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:   290; 0.001 FDR:   201
2:16:23.149756 PROGRESS: 
2:16:23.149813 PROGRESS: Protein Summary:
2:16:23.151067 PROGRESS: Channel   0:	 0.050 FDR:   275; 0.010 FDR:   275; 0.001 FDR:   195
2:16:23.151160 PROGRESS: =========================================================================
2:16:23.152371 INFO: Target number of precursors not reached yet.
2:16:23.324979 INFO: Starting optimization step 5.
2:16:23.325259 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:16:23.325346 INFO: Using rust extraction backend
2:16:23.325410 PROGRESS: Extracting batch of 63064 precursors
2:16:23.435710 INFO: === Search parameters used ===
2:16:23.436008 INFO: rt_error       : 805.611083984375
2:16:23.436067 INFO: mobility_error : 0.1
2:16:23.436117 INFO: num_candidates : 1
2:16:23.436163 INFO: ms1_error      : 3
2:16:23.436207 INFO: ms2_error      : 10
2:16:23.436248 INFO: fwhm_rt        : 5
2:16:23.436290 INFO: quant_window   : 3
2:16:23.436331 INFO: ==============================================
2:16:23.996405 INFO: performing precursor FDR with 40 features
2:16:23.996534 INFO: Decoy channel: -1
2:16:23.996560 INFO: competitive: True
2:16:24.054759 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:24.105601 INFO: Estimating optimal hyperparameters - samples: 99,125, batch_size: 406, learning_rate: 3.15e-04
2:16:24.105931 INFO: Using random state 724418 for train-test-split
2:16:29.176618 INFO: Test AUC: 0.581
2:16:29.176741 INFO: Train AUC: 0.609
2:16:29.176772 INFO: AUC difference: 4.61%
2:16:29.471460 INFO: Resetting torch num_threads to 24
2:16:29.497514 PROGRESS: === Extracted 123907 precursors and 694254 fragments ===
2:16:29.498193 INFO: === FDR correction performed with classifier version -1 ===
2:16:29.498870 PROGRESS: ============================= Precursor FDR =============================
2:16:29.498963 PROGRESS: Total precursors accumulated: 612
2:16:29.499049 PROGRESS: Target precursors: 606 (99.02%)
2:16:29.499104 PROGRESS: Decoy precursors: 6 (0.98%)
2:16:29.499151 PROGRESS: 
2:16:29.499206 PROGRESS: Precursor Summary:
2:16:29.500389 PROGRESS: Channel   0:	 0.050 FDR:   606; 0.010 FDR:   606; 0.001 FDR:   319
2:16:29.500479 PROGRESS: 
2:16:29.500535 PROGRESS: Protein Summary:
2:16:29.501931 PROGRESS: Channel   0:	 0.050 FDR:   568; 0.010 FDR:   568; 0.001 FDR:   302
2:16:29.502028 PROGRESS: =========================================================================
2:16:29.504438 INFO: Target number of precursors not reached yet.
2:16:29.767950 INFO: Starting optimization step 6.
2:16:29.768238 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:16:29.768327 INFO: Using rust extraction backend
2:16:29.768396 PROGRESS: Extracting batch of 126165 precursors
2:16:29.987528 INFO: === Search parameters used ===
2:16:29.987805 INFO: rt_error       : 805.611083984375
2:16:29.987865 INFO: mobility_error : 0.1
2:16:29.987915 INFO: num_candidates : 1
2:16:29.987978 INFO: ms1_error      : 3
2:16:29.988023 INFO: ms2_error      : 10
2:16:29.988066 INFO: fwhm_rt        : 5
2:16:29.988108 INFO: quant_window   : 3
2:16:29.988149 INFO: ==============================================
2:16:31.115025 INFO: performing precursor FDR with 40 features
2:16:31.115147 INFO: Decoy channel: -1
2:16:31.115173 INFO: competitive: True
2:16:31.252196 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:31.371295 INFO: Estimating optimal hyperparameters - samples: 199,848, batch_size: 818, learning_rate: 4.47e-04
2:16:31.371746 INFO: Using random state 235428 for train-test-split
2:16:39.320259 INFO: Test AUC: 0.588
2:16:39.320382 INFO: Train AUC: 0.609
2:16:39.320413 INFO: AUC difference: 3.50%
2:16:39.651288 INFO: Resetting torch num_threads to 24
2:16:39.714125 PROGRESS: === Extracted 249811 precursors and 1399366 fragments ===
2:16:39.714843 INFO: === FDR correction performed with classifier version -1 ===
2:16:39.715767 PROGRESS: ============================= Precursor FDR =============================
2:16:39.715862 PROGRESS: Total precursors accumulated: 1,242
2:16:39.715923 PROGRESS: Target precursors: 1,230 (99.03%)
2:16:39.715975 PROGRESS: Decoy precursors: 12 (0.97%)
2:16:39.716022 PROGRESS: 
2:16:39.716068 PROGRESS: Precursor Summary:
2:16:39.717375 PROGRESS: Channel   0:	 0.050 FDR: 1,230; 0.010 FDR: 1,230; 0.001 FDR:   664
2:16:39.717466 PROGRESS: 
2:16:39.717524 PROGRESS: Protein Summary:
2:16:39.719292 PROGRESS: Channel   0:	 0.050 FDR: 1,051; 0.010 FDR: 1,051; 0.001 FDR:   594
2:16:39.719387 PROGRESS: =========================================================================
2:16:39.724798 INFO: Target number of precursors reached.
2:16:39.890659 INFO: fragments_df: keeping 5000 of 1399366 [sum(precursor_idx_mask)=13115 sum(mass_error_mask)=1399366 stop_rank=5000
2:16:40.333841 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:40.523480 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:41.183099 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:16:41.183679 INFO: Using score_cutoff 12.177603643798829 (fac=0.99, q=1)
2:16:41.184078 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:16:41.184157 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:16:41.184213 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.177603643798829
2:16:41.184297 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:41.346516 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:41.705879 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
2:16:41.706162 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:16:41.706277 INFO: Starting optimization step 7.
2:16:41.706351 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:16:41.706445 INFO: Using rust extraction backend
2:16:41.706518 PROGRESS: Extracting batch of 250375 precursors
2:16:42.138137 INFO: === Search parameters used ===
2:16:42.138428 INFO: rt_error       : 805.611083984375
2:16:42.138486 INFO: mobility_error : 0.1
2:16:42.138535 INFO: num_candidates : 3
2:16:42.138591 INFO: ms1_error      : 3
2:16:42.138633 INFO: ms2_error      : 10
2:16:42.138673 INFO: fwhm_rt        : 3.0
2:16:42.138712 INFO: quant_window   : 3
2:16:42.138750 INFO: ==============================================
2:16:45.900069 INFO: performing precursor FDR with 40 features
2:16:45.900199 INFO: Decoy channel: -1
2:16:45.900226 INFO: competitive: True
2:16:46.128065 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:46.450501 INFO: Estimating optimal hyperparameters - samples: 599,739, batch_size: 2,456, learning_rate: 7.74e-04
2:16:46.451872 INFO: Using random state 442983 for train-test-split
2:17:01.991811 INFO: Test AUC: 0.597
2:17:01.991972 INFO: Train AUC: 0.606
2:17:01.992006 INFO: AUC difference: 1.56%
2:17:02.508633 INFO: Resetting torch num_threads to 24
2:17:02.749659 PROGRESS: === Extracted 749674 precursors and 4036001 fragments ===
2:17:02.750204 INFO: === FDR correction performed with classifier version 6 ===
2:17:02.750878 PROGRESS: ============================= Precursor FDR =============================
2:17:02.750989 PROGRESS: Total precursors accumulated: 1,352
2:17:02.751061 PROGRESS: Target precursors: 1,339 (99.04%)
2:17:02.751119 PROGRESS: Decoy precursors: 13 (0.96%)
2:17:02.751167 PROGRESS: 
2:17:02.751213 PROGRESS: Precursor Summary:
2:17:02.752534 PROGRESS: Channel   0:	 0.050 FDR: 1,339; 0.010 FDR: 1,339; 0.001 FDR:   789
2:17:02.752640 PROGRESS: 
2:17:02.752697 PROGRESS: Protein Summary:
2:17:02.754395 PROGRESS: Channel   0:	 0.050 FDR: 1,143; 0.010 FDR: 1,143; 0.001 FDR:   695
2:17:02.754489 PROGRESS: =========================================================================
2:17:02.773161 INFO: Target number of precursors reached.
2:17:03.220615 INFO: fragments_df: keeping 5000 of 4036001 [sum(precursor_idx_mask)=32410 sum(mass_error_mask)=4036001 stop_rank=5000
2:17:03.834504 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:04.031474 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:04.686804 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:04.687371 INFO: Using score_cutoff 12.422621789360047 (fac=0.99, q=1)
2:17:04.687729 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:04.687810 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:04.687867 INFO: Updating optimization_manager: score_cutoff        : 12.177603643798829 -> 12.422621789360047
2:17:04.687923 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:04.840078 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:05.204404 INFO: === checking if optimization conditions were reached ===
2:17:05.206858 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:17:05.206978 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
2:17:05.207055 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:17:05.207118 INFO: ==============================================
2:17:05.207209 INFO: Starting optimization step 8.
2:17:05.207275 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:17:05.207350 INFO: Using rust extraction backend
2:17:05.207419 PROGRESS: Extracting batch of 250375 precursors
2:17:05.632707 INFO: === Search parameters used ===
2:17:05.633004 INFO: rt_error       : 805.611083984375
2:17:05.633064 INFO: mobility_error : 0.1
2:17:05.633113 INFO: num_candidates : 3
2:17:05.633158 INFO: ms1_error      : 3
2:17:05.633199 INFO: ms2_error      : 10.0
2:17:05.633254 INFO: fwhm_rt        : 3.0
2:17:05.633294 INFO: quant_window   : 3
2:17:05.633333 INFO: ==============================================
2:17:09.388526 INFO: performing precursor FDR with 40 features
2:17:09.388689 INFO: Decoy channel: -1
2:17:09.388718 INFO: competitive: True
2:17:09.615368 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:09.938487 INFO: Estimating optimal hyperparameters - samples: 599,732, batch_size: 2,456, learning_rate: 7.74e-04
2:17:09.940148 INFO: Using random state 650010 for train-test-split
2:17:23.960727 INFO: Test AUC: 0.603
2:17:23.960930 INFO: Train AUC: 0.613
2:17:23.960964 INFO: AUC difference: 1.65%
2:17:24.434133 INFO: Resetting torch num_threads to 24
2:17:24.473551 PROGRESS: === Extracted 749666 precursors and 4035540 fragments ===
2:17:24.474041 INFO: === FDR correction performed with classifier version 7 ===
2:17:24.474838 PROGRESS: ============================= Precursor FDR =============================
2:17:24.474935 PROGRESS: Total precursors accumulated: 1,476
2:17:24.475031 PROGRESS: Target precursors: 1,462 (99.05%)
2:17:24.475088 PROGRESS: Decoy precursors: 14 (0.95%)
2:17:24.475136 PROGRESS: 
2:17:24.475181 PROGRESS: Precursor Summary:
2:17:24.476588 PROGRESS: Channel   0:	 0.050 FDR: 1,462; 0.010 FDR: 1,462; 0.001 FDR:   753
2:17:24.476681 PROGRESS: 
2:17:24.476738 PROGRESS: Protein Summary:
2:17:24.478498 PROGRESS: Channel   0:	 0.050 FDR: 1,246; 0.010 FDR: 1,246; 0.001 FDR:   672
2:17:24.478595 PROGRESS: =========================================================================
2:17:24.496194 INFO: Target number of precursors reached.
2:17:24.933087 INFO: fragments_df: keeping 5000 of 4035540 [sum(precursor_idx_mask)=34556 sum(mass_error_mask)=4035540 stop_rank=5000
2:17:25.384708 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:25.591011 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:26.252281 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:26.252736 INFO: Using score_cutoff 9.774137567710877 (fac=0.99, q=1)
2:17:26.253066 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:26.253144 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:26.253197 INFO: Updating optimization_manager: score_cutoff        : 12.422621789360047 -> 9.774137567710877
2:17:26.253256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:26.412198 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:26.765601 INFO: === checking if optimization conditions were reached ===
2:17:26.768446 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:17:26.768552 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
2:17:26.768618 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:17:26.768678 INFO: ==============================================
2:17:26.768755 INFO: Starting optimization step 9.
2:17:26.768819 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:17:26.768886 INFO: Using rust extraction backend
2:17:26.768957 PROGRESS: Extracting batch of 250375 precursors
2:17:27.198154 INFO: === Search parameters used ===
2:17:27.198442 INFO: rt_error       : 805.611083984375
2:17:27.198500 INFO: mobility_error : 0.1
2:17:27.198547 INFO: num_candidates : 3
2:17:27.198591 INFO: ms1_error      : 3
2:17:27.198633 INFO: ms2_error      : 10.0
2:17:27.198674 INFO: fwhm_rt        : 3.0
2:17:27.198713 INFO: quant_window   : 3
2:17:27.198752 INFO: ==============================================
2:17:30.870193 INFO: performing precursor FDR with 40 features
2:17:30.870317 INFO: Decoy channel: -1
2:17:30.870343 INFO: competitive: True
2:17:31.086065 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:31.402131 INFO: Estimating optimal hyperparameters - samples: 599,756, batch_size: 2,456, learning_rate: 7.74e-04
2:17:31.403286 INFO: Using random state 41259 for train-test-split
2:17:45.128092 INFO: Test AUC: 0.608
2:17:45.128227 INFO: Train AUC: 0.616
2:17:45.128271 INFO: AUC difference: 1.23%
2:17:45.612043 INFO: Resetting torch num_threads to 24
2:17:45.643999 PROGRESS: === Extracted 749695 precursors and 4037623 fragments ===
2:17:45.644466 INFO: === FDR correction performed with classifier version 8 ===
2:17:45.645205 PROGRESS: ============================= Precursor FDR =============================
2:17:45.645301 PROGRESS: Total precursors accumulated: 1,425
2:17:45.645361 PROGRESS: Target precursors: 1,411 (99.02%)
2:17:45.645412 PROGRESS: Decoy precursors: 14 (0.98%)
2:17:45.645458 PROGRESS: 
2:17:45.645500 PROGRESS: Precursor Summary:
2:17:45.646876 PROGRESS: Channel   0:	 0.050 FDR: 1,411; 0.010 FDR: 1,411; 0.001 FDR:   831
2:17:45.646966 PROGRESS: 
2:17:45.647046 PROGRESS: Protein Summary:
2:17:45.648745 PROGRESS: Channel   0:	 0.050 FDR: 1,206; 0.010 FDR: 1,206; 0.001 FDR:   733
2:17:45.648831 PROGRESS: =========================================================================
2:17:45.664357 INFO: Target number of precursors reached.
2:17:46.111076 INFO: fragments_df: keeping 5000 of 4037623 [sum(precursor_idx_mask)=33390 sum(mass_error_mask)=4037623 stop_rank=5000
2:17:46.580536 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:46.775881 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:47.428125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:47.428583 INFO: Using score_cutoff 9.661819676399231 (fac=0.99, q=1)
2:17:47.428880 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:47.428955 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:47.429015 INFO: Updating optimization_manager: score_cutoff        : 9.774137567710877 -> 9.661819676399231
2:17:47.429071 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:47.582575 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:47.915078 INFO: === checking if optimization conditions were reached ===
2:17:47.917300 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:17:47.917416 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:17:47.917481 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:17:47.917539 INFO: ==============================================
2:17:47.917603 INFO: Starting optimization step 10.
2:17:47.917659 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:17:47.917717 INFO: Using rust extraction backend
2:17:47.917773 PROGRESS: Extracting batch of 250375 precursors
2:17:48.342960 INFO: === Search parameters used ===
2:17:48.343246 INFO: rt_error       : 805.611083984375
2:17:48.343305 INFO: mobility_error : 0.1
2:17:48.343352 INFO: num_candidates : 3
2:17:48.343394 INFO: ms1_error      : 3
2:17:48.343434 INFO: ms2_error      : 10.0
2:17:48.343473 INFO: fwhm_rt        : 3.0
2:17:48.343512 INFO: quant_window   : 3
2:17:48.343552 INFO: ==============================================
2:17:51.931842 INFO: performing precursor FDR with 40 features
2:17:51.931968 INFO: Decoy channel: -1
2:17:51.931994 INFO: competitive: True
2:17:52.136955 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:52.438766 INFO: Estimating optimal hyperparameters - samples: 599,752, batch_size: 2,456, learning_rate: 7.74e-04
2:17:52.440135 INFO: Using random state 986631 for train-test-split
2:18:06.103001 INFO: Test AUC: 0.610
2:18:06.103135 INFO: Train AUC: 0.619
2:18:06.103168 INFO: AUC difference: 1.57%
2:18:08.550948 INFO: Resetting torch num_threads to 24
2:18:08.582803 PROGRESS: === Extracted 749691 precursors and 4037204 fragments ===
2:18:08.583289 INFO: === FDR correction performed with classifier version 9 ===
2:18:08.584018 PROGRESS: ============================= Precursor FDR =============================
2:18:08.584116 PROGRESS: Total precursors accumulated: 1,167
2:18:08.584177 PROGRESS: Target precursors: 1,156 (99.06%)
2:18:08.584229 PROGRESS: Decoy precursors: 11 (0.94%)
2:18:08.584276 PROGRESS: 
2:18:08.584322 PROGRESS: Precursor Summary:
2:18:08.585620 PROGRESS: Channel   0:	 0.050 FDR: 1,156; 0.010 FDR: 1,156; 0.001 FDR:   218
2:18:08.585728 PROGRESS: 
2:18:08.585786 PROGRESS: Protein Summary:
2:18:08.587431 PROGRESS: Channel   0:	 0.050 FDR:   998; 0.010 FDR:   998; 0.001 FDR:   205
2:18:08.587528 PROGRESS: =========================================================================
2:18:08.603444 INFO: Target number of precursors reached.
2:18:09.040469 INFO: fragments_df: keeping 5000 of 4037204 [sum(precursor_idx_mask)=28244 sum(mass_error_mask)=4037204 stop_rank=5000
2:18:09.471085 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:09.645887 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:10.315263 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:10.315726 INFO: Using score_cutoff 12.473093014240265 (fac=0.99, q=1)
2:18:10.316033 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:10.316117 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:10.316174 INFO: Updating optimization_manager: score_cutoff        : 9.661819676399231 -> 12.473093014240265
2:18:10.316228 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:10.466903 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:10.795070 INFO: === checking if optimization conditions were reached ===
2:18:10.797434 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:18:10.797536 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:18:10.797602 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:18:10.797662 INFO: ==============================================
2:18:10.797727 INFO: Starting optimization step 11.
2:18:10.797786 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:18:10.797847 INFO: Using rust extraction backend
2:18:10.797906 PROGRESS: Extracting batch of 250375 precursors
2:18:11.220857 INFO: === Search parameters used ===
2:18:11.221139 INFO: rt_error       : 805.611083984375
2:18:11.221200 INFO: mobility_error : 0.1
2:18:11.221250 INFO: num_candidates : 3
2:18:11.221295 INFO: ms1_error      : 3
2:18:11.221335 INFO: ms2_error      : 10.0
2:18:11.221378 INFO: fwhm_rt        : 3.0
2:18:11.221418 INFO: quant_window   : 3
2:18:11.221473 INFO: ==============================================
2:18:14.735593 INFO: performing precursor FDR with 40 features
2:18:14.735717 INFO: Decoy channel: -1
2:18:14.735743 INFO: competitive: True
2:18:14.940384 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:15.247728 INFO: Estimating optimal hyperparameters - samples: 599,724, batch_size: 2,456, learning_rate: 7.74e-04
2:18:15.249256 INFO: Using random state 366369 for train-test-split
2:18:29.445678 INFO: Test AUC: 0.610
2:18:29.445834 INFO: Train AUC: 0.621
2:18:29.445867 INFO: AUC difference: 1.65%
2:18:29.951276 INFO: Resetting torch num_threads to 24
2:18:29.982074 PROGRESS: === Extracted 749655 precursors and 4036428 fragments ===
2:18:29.982566 INFO: === FDR correction performed with classifier version 10 ===
2:18:29.983388 PROGRESS: ============================= Precursor FDR =============================
2:18:29.983492 PROGRESS: Total precursors accumulated: 1,632
2:18:29.983556 PROGRESS: Target precursors: 1,616 (99.02%)
2:18:29.983611 PROGRESS: Decoy precursors: 16 (0.98%)
2:18:29.983659 PROGRESS: 
2:18:29.983706 PROGRESS: Precursor Summary:
2:18:29.985198 PROGRESS: Channel   0:	 0.050 FDR: 1,616; 0.010 FDR: 1,616; 0.001 FDR:   800
2:18:29.985297 PROGRESS: 
2:18:29.985356 PROGRESS: Protein Summary:
2:18:29.987264 PROGRESS: Channel   0:	 0.050 FDR: 1,352; 0.010 FDR: 1,352; 0.001 FDR:   708
2:18:29.987362 PROGRESS: =========================================================================
2:18:30.003934 INFO: Target number of precursors reached.
2:18:30.436429 INFO: fragments_df: keeping 5000 of 4036428 [sum(precursor_idx_mask)=38134 sum(mass_error_mask)=4036428 stop_rank=5000
2:18:30.912629 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:31.136058 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:31.795989 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:31.796451 INFO: Using score_cutoff 11.431920899391175 (fac=0.99, q=1)
2:18:31.796783 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:31.796862 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:31.796923 INFO: Updating optimization_manager: score_cutoff        : 12.473093014240265 -> 11.431920899391175
2:18:31.796975 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:31.947832 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:32.300876 INFO: === checking if optimization conditions were reached ===
2:18:32.303190 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:18:32.303297 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:18:32.303364 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:18:32.303421 INFO: ==============================================
2:18:32.303487 PROGRESS: Optimization finished for ms2_error.
2:18:32.714692 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:32.865846 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:33.212020 INFO: Starting optimization step 0.
2:18:33.212287 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:18:33.212372 INFO: Using rust extraction backend
2:18:33.212440 PROGRESS: Extracting batch of 250375 precursors
2:18:33.636008 INFO: === Search parameters used ===
2:18:33.636282 INFO: rt_error       : 805.611083984375
2:18:33.636339 INFO: mobility_error : 0.1
2:18:33.636402 INFO: num_candidates : 3
2:18:33.636447 INFO: ms1_error      : 3
2:18:33.636489 INFO: ms2_error      : 10.0
2:18:33.636528 INFO: fwhm_rt        : 3.0
2:18:33.636568 INFO: quant_window   : 3
2:18:33.636606 INFO: ==============================================
2:18:37.226379 INFO: performing precursor FDR with 40 features
2:18:37.226505 INFO: Decoy channel: -1
2:18:37.226531 INFO: competitive: True
2:18:37.434063 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:37.742321 INFO: Estimating optimal hyperparameters - samples: 599,746, batch_size: 2,456, learning_rate: 7.74e-04
2:18:37.743759 INFO: Using random state 96290 for train-test-split
2:18:51.465521 INFO: Test AUC: 0.613
2:18:51.465681 INFO: Train AUC: 0.624
2:18:51.465714 INFO: AUC difference: 1.79%
2:18:51.953984 INFO: Resetting torch num_threads to 24
2:18:51.985622 PROGRESS: === Extracted 749683 precursors and 4036569 fragments ===
2:18:51.986103 INFO: === FDR correction performed with classifier version 11 ===
2:18:51.986915 PROGRESS: ============================= Precursor FDR =============================
2:18:51.987025 PROGRESS: Total precursors accumulated: 1,588
2:18:51.987091 PROGRESS: Target precursors: 1,573 (99.06%)
2:18:51.987144 PROGRESS: Decoy precursors: 15 (0.94%)
2:18:51.987193 PROGRESS: 
2:18:51.987242 PROGRESS: Precursor Summary:
2:18:51.988773 PROGRESS: Channel   0:	 0.050 FDR: 1,573; 0.010 FDR: 1,573; 0.001 FDR: 1,110
2:18:51.988877 PROGRESS: 
2:18:51.988934 PROGRESS: Protein Summary:
2:18:51.990800 PROGRESS: Channel   0:	 0.050 FDR: 1,334; 0.010 FDR: 1,334; 0.001 FDR:   953
2:18:51.990894 PROGRESS: =========================================================================
2:18:52.006616 INFO: Target number of precursors reached.
2:18:52.460133 INFO: fragments_df: keeping 5000 of 4036569 [sum(precursor_idx_mask)=37252 sum(mass_error_mask)=4036569 stop_rank=5000
2:18:52.917279 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:53.134756 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:53.794295 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:53.794781 INFO: Using score_cutoff 11.3545820022583 (fac=0.99, q=1)
2:18:53.795113 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:53.795195 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:53.795251 INFO: Updating optimization_manager: score_cutoff        : 11.431920899391175 -> 11.3545820022583
2:18:53.795314 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:53.944791 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:54.297229 INFO: === checking if optimization conditions were reached ===
2:18:54.297528 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:18:54.300380 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 896.7887802743533
2:18:54.300488 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 896.7888.
2:18:54.300551 INFO: ==============================================
2:18:54.300623 INFO: Starting optimization step 1.
2:18:54.300684 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:18:54.300750 INFO: Using rust extraction backend
2:18:54.300809 PROGRESS: Extracting batch of 250375 precursors
2:18:54.725757 INFO: === Search parameters used ===
2:18:54.726041 INFO: rt_error       : 896.7887802743533
2:18:54.726100 INFO: mobility_error : 0.1
2:18:54.726148 INFO: num_candidates : 3
2:18:54.726190 INFO: ms1_error      : 3
2:18:54.726231 INFO: ms2_error      : 10.0
2:18:54.726271 INFO: fwhm_rt        : 3.0
2:18:54.726312 INFO: quant_window   : 3
2:18:54.726355 INFO: ==============================================
2:18:58.473841 INFO: performing precursor FDR with 40 features
2:18:58.473971 INFO: Decoy channel: -1
2:18:58.473999 INFO: competitive: True
2:18:58.688298 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:59.002867 INFO: Estimating optimal hyperparameters - samples: 599,722, batch_size: 2,456, learning_rate: 7.74e-04
2:18:59.004271 INFO: Using random state 96290 for train-test-split
2:19:12.443175 INFO: Test AUC: 0.612
2:19:12.443337 INFO: Train AUC: 0.622
2:19:12.443370 INFO: AUC difference: 1.60%
2:19:12.934997 INFO: Resetting torch num_threads to 24
2:19:12.969114 PROGRESS: === Extracted 749653 precursors and 4036827 fragments ===
2:19:12.969601 INFO: === FDR correction performed with classifier version 11 ===
2:19:12.970444 PROGRESS: ============================= Precursor FDR =============================
2:19:12.970542 PROGRESS: Total precursors accumulated: 1,554
2:19:12.970606 PROGRESS: Target precursors: 1,539 (99.03%)
2:19:12.970658 PROGRESS: Decoy precursors: 15 (0.97%)
2:19:12.970706 PROGRESS: 
2:19:12.970751 PROGRESS: Precursor Summary:
2:19:12.972323 PROGRESS: Channel   0:	 0.050 FDR: 1,539; 0.010 FDR: 1,539; 0.001 FDR: 1,153
2:19:12.972426 PROGRESS: 
2:19:12.972484 PROGRESS: Protein Summary:
2:19:12.974376 PROGRESS: Channel   0:	 0.050 FDR: 1,320; 0.010 FDR: 1,320; 0.001 FDR:   988
2:19:12.974479 PROGRESS: =========================================================================
2:19:12.990308 INFO: Target number of precursors reached.
2:19:13.436125 INFO: fragments_df: keeping 5000 of 4036827 [sum(precursor_idx_mask)=34905 sum(mass_error_mask)=4036827 stop_rank=5000
2:19:13.890069 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:19:14.099998 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:19:14.766477 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:19:14.766943 INFO: Using score_cutoff 7.56101343126297 (fac=0.99, q=1)
2:19:14.767320 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:19:14.767400 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:19:14.767454 INFO: Updating optimization_manager: score_cutoff        : 11.3545820022583 -> 7.56101343126297
2:19:14.767509 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:14.921865 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:15.270923 INFO: === checking if optimization conditions were reached ===
2:19:15.271224 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:19:15.274272 INFO: Updating optimization_manager: rt_error            : 896.7887802743533 -> 836.0290487723775
2:19:15.274406 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 836.0290.
2:19:15.274492 INFO: ==============================================
2:19:15.274569 INFO: Starting optimization step 2.
2:19:15.274632 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:19:15.274701 INFO: Using rust extraction backend
2:19:15.274768 PROGRESS: Extracting batch of 250375 precursors
2:19:15.700247 INFO: === Search parameters used ===
2:19:15.700588 INFO: rt_error       : 836.0290487723775
2:19:15.700645 INFO: mobility_error : 0.1
2:19:15.700696 INFO: num_candidates : 3
2:19:15.700741 INFO: ms1_error      : 3
2:19:15.700782 INFO: ms2_error      : 10.0
2:19:15.700822 INFO: fwhm_rt        : 3.0
2:19:15.700864 INFO: quant_window   : 3
2:19:15.700914 INFO: ==============================================
2:19:19.395256 INFO: performing precursor FDR with 40 features
2:19:19.395408 INFO: Decoy channel: -1
2:19:19.395440 INFO: competitive: True
2:19:19.606324 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:19.921097 INFO: Estimating optimal hyperparameters - samples: 599,744, batch_size: 2,456, learning_rate: 7.74e-04
2:19:19.922456 INFO: Using random state 96290 for train-test-split
2:19:33.388397 INFO: Test AUC: 0.612
2:19:33.388570 INFO: Train AUC: 0.621
2:19:33.388603 INFO: AUC difference: 1.47%
2:19:33.892222 INFO: Resetting torch num_threads to 24
2:19:33.923956 PROGRESS: === Extracted 749680 precursors and 4036733 fragments ===
2:19:33.924462 INFO: === FDR correction performed with classifier version 11 ===
2:19:33.925360 PROGRESS: ============================= Precursor FDR =============================
2:19:33.925463 PROGRESS: Total precursors accumulated: 1,580
2:19:33.925527 PROGRESS: Target precursors: 1,565 (99.05%)
2:19:33.925582 PROGRESS: Decoy precursors: 15 (0.95%)
2:19:33.925633 PROGRESS: 
2:19:33.925680 PROGRESS: Precursor Summary:
2:19:33.927286 PROGRESS: Channel   0:	 0.050 FDR: 1,565; 0.010 FDR: 1,565; 0.001 FDR: 1,033
2:19:33.927394 PROGRESS: 
2:19:33.927454 PROGRESS: Protein Summary:
2:19:33.929298 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR:   894
2:19:33.929401 PROGRESS: =========================================================================
2:19:33.945139 INFO: Target number of precursors reached.
2:19:34.383098 INFO: fragments_df: keeping 5000 of 4036733 [sum(precursor_idx_mask)=37093 sum(mass_error_mask)=4036733 stop_rank=5000
2:19:34.863155 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:19:35.079389 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:19:35.737912 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:19:35.738406 INFO: Using score_cutoff 11.522324168014526 (fac=0.99, q=1)
2:19:35.738776 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:19:35.738862 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:19:35.738923 INFO: Updating optimization_manager: score_cutoff        : 7.56101343126297 -> 11.522324168014526
2:19:35.738999 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:35.891966 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:36.239262 INFO: === checking if optimization conditions were reached ===
2:19:36.239561 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:19:36.242575 INFO: Updating optimization_manager: rt_error            : 836.0290487723775 -> 979.078020868767
2:19:36.242679 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 979.0780.
2:19:36.242744 INFO: ==============================================
2:19:36.242819 INFO: Starting optimization step 3.
2:19:36.242892 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:19:36.242961 INFO: Using rust extraction backend
2:19:36.243041 PROGRESS: Extracting batch of 250375 precursors
2:19:36.677891 INFO: === Search parameters used ===
2:19:36.678217 INFO: rt_error       : 979.078020868767
2:19:36.678277 INFO: mobility_error : 0.1
2:19:36.678329 INFO: num_candidates : 3
2:19:36.678384 INFO: ms1_error      : 3
2:19:36.678424 INFO: ms2_error      : 10.0
2:19:36.678463 INFO: fwhm_rt        : 3.0
2:19:36.678503 INFO: quant_window   : 3
2:19:36.678547 INFO: ==============================================
2:19:40.378393 INFO: performing precursor FDR with 40 features
2:19:40.378516 INFO: Decoy channel: -1
2:19:40.378547 INFO: competitive: True
2:19:40.591024 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:40.902506 INFO: Estimating optimal hyperparameters - samples: 599,709, batch_size: 2,456, learning_rate: 7.74e-04
2:19:40.903923 INFO: Using random state 96290 for train-test-split
2:19:55.048529 INFO: Test AUC: 0.607
2:19:55.048728 INFO: Train AUC: 0.624
2:19:55.048762 INFO: AUC difference: 2.71%
2:19:55.550993 INFO: Resetting torch num_threads to 24
2:19:55.584504 PROGRESS: === Extracted 749637 precursors and 4036364 fragments ===
2:19:55.585071 INFO: === FDR correction performed with classifier version 11 ===
2:19:55.585918 PROGRESS: ============================= Precursor FDR =============================
2:19:55.586035 PROGRESS: Total precursors accumulated: 1,567
2:19:55.586115 PROGRESS: Target precursors: 1,552 (99.04%)
2:19:55.586173 PROGRESS: Decoy precursors: 15 (0.96%)
2:19:55.586224 PROGRESS: 
2:19:55.586269 PROGRESS: Precursor Summary:
2:19:55.588194 PROGRESS: Channel   0:	 0.050 FDR: 1,552; 0.010 FDR: 1,552; 0.001 FDR: 1,040
2:19:55.588293 PROGRESS: 
2:19:55.588359 PROGRESS: Protein Summary:
2:19:55.590225 PROGRESS: Channel   0:	 0.050 FDR: 1,308; 0.010 FDR: 1,308; 0.001 FDR:   901
2:19:55.590328 PROGRESS: =========================================================================
2:19:55.605449 INFO: Target number of precursors reached.
2:19:56.056309 INFO: fragments_df: keeping 5000 of 4036364 [sum(precursor_idx_mask)=37082 sum(mass_error_mask)=4036364 stop_rank=5000
2:19:56.549580 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:19:56.807510 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:19:57.499916 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:19:57.500402 INFO: Using score_cutoff 12.0792065700531 (fac=0.99, q=1)
2:19:57.500733 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:19:57.500811 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:19:57.500870 INFO: Updating optimization_manager: score_cutoff        : 11.522324168014526 -> 12.0792065700531
2:19:57.500930 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:57.650751 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:57.999261 INFO: === checking if optimization conditions were reached ===
2:19:57.999588 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:19:58.002691 INFO: Updating optimization_manager: rt_error            : 979.078020868767 -> 689.3051415011536
2:19:58.002800 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 689.3051.
2:19:58.002878 INFO: ==============================================
2:19:58.002992 INFO: Starting optimization step 4.
2:19:58.003071 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:19:58.003184 INFO: Using rust extraction backend
2:19:58.003294 PROGRESS: Extracting batch of 250375 precursors
2:19:58.437765 INFO: === Search parameters used ===
2:19:58.438055 INFO: rt_error       : 689.3051415011536
2:19:58.438117 INFO: mobility_error : 0.1
2:19:58.438165 INFO: num_candidates : 3
2:19:58.438209 INFO: ms1_error      : 3
2:19:58.438251 INFO: ms2_error      : 10.0
2:19:58.438292 INFO: fwhm_rt        : 3.0
2:19:58.438334 INFO: quant_window   : 3
2:19:58.438374 INFO: ==============================================
2:20:01.936845 INFO: performing precursor FDR with 40 features
2:20:01.936963 INFO: Decoy channel: -1
2:20:01.936988 INFO: competitive: True
2:20:02.139008 INFO: Setting torch num_threads to 2 for FDR classification task
2:20:02.440516 INFO: Estimating optimal hyperparameters - samples: 599,632, batch_size: 2,456, learning_rate: 7.74e-04
2:20:02.441822 INFO: Using random state 96290 for train-test-split
2:20:16.182590 INFO: Test AUC: 0.610
2:20:16.182801 INFO: Train AUC: 0.623
2:20:16.182851 INFO: AUC difference: 2.10%
2:20:16.671134 INFO: Resetting torch num_threads to 24
2:20:16.701716 PROGRESS: === Extracted 749541 precursors and 4031085 fragments ===
2:20:16.702229 INFO: === FDR correction performed with classifier version 11 ===
2:20:16.703035 PROGRESS: ============================= Precursor FDR =============================
2:20:16.703140 PROGRESS: Total precursors accumulated: 1,293
2:20:16.703206 PROGRESS: Target precursors: 1,281 (99.07%)
2:20:16.703260 PROGRESS: Decoy precursors: 12 (0.93%)
2:20:16.703309 PROGRESS: 
2:20:16.703354 PROGRESS: Precursor Summary:
2:20:16.704726 PROGRESS: Channel   0:	 0.050 FDR: 1,281; 0.010 FDR: 1,281; 0.001 FDR:   525
2:20:16.704826 PROGRESS: 
2:20:16.704883 PROGRESS: Protein Summary:
2:20:16.706523 PROGRESS: Channel   0:	 0.050 FDR: 1,093; 0.010 FDR: 1,093; 0.001 FDR:   478
2:20:16.706624 PROGRESS: =========================================================================
2:20:16.720531 INFO: Target number of precursors reached.
2:20:17.164983 INFO: fragments_df: keeping 5000 of 4031085 [sum(precursor_idx_mask)=31120 sum(mass_error_mask)=4031085 stop_rank=5000
2:20:17.617703 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:20:17.801977 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:20:18.455662 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:20:18.456131 INFO: Using score_cutoff 12.630031007766723 (fac=0.99, q=1)
2:20:18.456460 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:20:18.456539 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:20:18.456597 INFO: Updating optimization_manager: score_cutoff        : 12.0792065700531 -> 12.630031007766723
2:20:18.456657 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:18.606585 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:18.953111 INFO: === checking if optimization conditions were reached ===
2:20:18.953409 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:20:18.954799 INFO: Updating optimization_manager: rt_error            : 689.3051415011536 -> 805.611083984375
2:20:18.954936 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:20:18.955050 INFO: Updating optimization_manager: score_cutoff        : 12.630031007766723 -> 11.3545820022583
2:20:18.955140 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:20:18.955223 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:20:18.955316 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 805.6111 found after 5 searches.
2:20:18.955381 INFO: ==============================================
2:20:18.955467 PROGRESS: Optimization finished for rt_error.
2:20:19.376639 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:19.526886 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:19.874156 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:20:19.874511 PROGRESS: ==============================================
2:20:19.874615 PROGRESS: ms2_error      : 10.0000
2:20:19.874697 PROGRESS: rt_error       : 805.6111
2:20:19.874748 PROGRESS: ==============================================
2:20:19.876382 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:27.436733 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:43.460585 INFO: Using rust extraction backend
2:20:43.461034 PROGRESS: Extracting batch of 11997144 precursors
2:20:59.523016 INFO: === Search parameters used ===
2:20:59.523472 INFO: rt_error       : 805.611083984375
2:20:59.523545 INFO: mobility_error : 0.1
2:20:59.523597 INFO: num_candidates : 3
2:20:59.523647 INFO: ms1_error      : 3
2:20:59.523695 INFO: ms2_error      : 10.0
2:20:59.523735 INFO: fwhm_rt        : 3.0
2:20:59.523782 INFO: quant_window   : 3
2:20:59.523820 INFO: ==============================================
2:22:03.434179 INFO: Removed 9897133 precursors with score below cutoff 11.3545820022583
2:22:32.902320 INFO: performing precursor FDR with 40 features
2:22:32.902525 INFO: Decoy channel: -1
2:22:32.902557 INFO: competitive: True
2:22:35.648133 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:46.109654 INFO: Estimating optimal hyperparameters - samples: 20,875,177, batch_size: 4,096, learning_rate: 1.00e-03
2:22:46.173424 INFO: Using random state 397787 for train-test-split
2:30:32.589828 INFO: Test AUC: 0.621
2:30:32.590267 INFO: Train AUC: 0.621
2:30:32.590318 INFO: AUC difference: 0.04%
2:30:39.036334 INFO: Resetting torch num_threads to 24
2:30:41.821290 PROGRESS: ============================= Precursor FDR =============================
2:30:41.821693 PROGRESS: Total precursors accumulated: 93,302
2:30:41.821776 PROGRESS: Target precursors: 92,379 (99.01%)
2:30:41.821834 PROGRESS: Decoy precursors: 923 (0.99%)
2:30:41.821884 PROGRESS: 
2:30:41.821931 PROGRESS: Precursor Summary:
2:30:41.849448 PROGRESS: Channel   0:	 0.050 FDR: 92,379; 0.010 FDR: 92,379; 0.001 FDR: 61,390
2:30:41.849716 PROGRESS: 
2:30:41.849777 PROGRESS: Protein Summary:
2:30:41.886906 PROGRESS: Channel   0:	 0.050 FDR: 13,389; 0.010 FDR: 13,389; 0.001 FDR: 9,338
2:30:41.887192 PROGRESS: =========================================================================
2:30:42.056165 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
2:30:42.238301 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
2:30:42.486830 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:31:11.225506 PROGRESS: Processing search outputs
2:31:11.225949 PROGRESS: === Performing protein grouping and FDR ===
2:31:11.226030 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:31:11.316350 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:31:11.377530 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:31:11.439585 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:31:11.502529 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:31:11.568881 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:31:11.682914 INFO: Performing protein inference
2:31:12.497430 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2:32:05.468947 INFO: Performing protein FDR
2:32:14.200286 INFO: Normalizing q-values using 19,872 targets and 3,935 decoys
2:32:14.205102 INFO: Test AUC: 0.858
2:32:14.205159 INFO: Train AUC: 0.854
2:32:14.205197 INFO: AUC difference: 0.37%
2:32:14.930920 INFO: ================ Protein FDR =================
2:32:14.931093 INFO: Unique protein groups in output
2:32:14.931126 INFO:   1% protein FDR: 10,534
2:32:14.931146 INFO: 
2:32:14.931177 INFO: Unique precursor in output
2:32:14.931195 INFO:   1% protein FDR: 133,585
2:32:14.931214 INFO: ================================================
2:32:15.001921 PROGRESS: Building search statistics
2:32:15.114357 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:32:15.114592 INFO: Initializing OptimizationManager
2:32:15.114882 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:32:15.114962 INFO: Initializing CalibrationManager
2:32:15.115245 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:32:15.115340 INFO: Initializing RawFileManager
2:32:15.148132 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:32:15.148320 INFO: Initializing OptimizationManager
2:32:15.148531 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:32:15.148601 INFO: Initializing CalibrationManager
2:32:15.148804 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:32:15.148885 INFO: Initializing RawFileManager
2:32:15.181384 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:32:15.181574 INFO: Initializing OptimizationManager
2:32:15.181789 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:32:15.181860 INFO: Initializing CalibrationManager
2:32:15.182057 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:32:15.182124 INFO: Initializing RawFileManager
2:32:15.216715 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:32:15.217280 INFO: Initializing OptimizationManager
2:32:15.217493 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:32:15.217563 INFO: Initializing CalibrationManager
2:32:15.217777 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:32:15.217846 INFO: Initializing RawFileManager
2:32:15.251862 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:32:15.252051 INFO: Initializing OptimizationManager
2:32:15.252260 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:32:15.252330 INFO: Initializing CalibrationManager
2:32:15.252529 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:32:15.252608 INFO: Initializing RawFileManager
2:32:15.286403 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:32:15.286587 INFO: Initializing OptimizationManager
2:32:15.286806 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:32:15.286878 INFO: Initializing CalibrationManager
2:32:15.287092 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:32:15.287166 INFO: Initializing RawFileManager
2:32:15.292171 INFO: Writing stat output to disk
2:32:15.292260 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/stat.tsv to disk
2:32:15.302635 PROGRESS: Building internal statistics
2:32:15.303385 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:32:15.303449 INFO: Initializing TimingManager
2:32:15.303920 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:32:15.303962 INFO: Initializing TimingManager
2:32:15.304197 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:32:15.304232 INFO: Initializing TimingManager
2:32:15.304440 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:32:15.304472 INFO: Initializing TimingManager
2:32:15.304673 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:32:15.304706 INFO: Initializing TimingManager
2:32:15.304910 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:32:15.304942 INFO: Initializing TimingManager
2:32:15.305417 INFO: Writing internal output to disk
2:32:15.305459 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/internal.tsv to disk
2:32:15.377786 INFO: Performing label free quantification
2:32:15.377933 INFO: Accumulating fragment data
2:32:15.377993 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:32:15.604898 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:32:16.944840 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:32:18.352631 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:32:19.924666 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:32:21.518777 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:32:23.560034 INFO: Performing label free quantification on the precursor level
2:32:23.560228 INFO: Filtering fragments by quality
2:32:23.950456 INFO: Performing label-free quantification with directlfq normalization
2:32:24.561004 INFO: 133585 lfq-groups total
2:33:05.492983 INFO: using 24 processes
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2:37:23.327161 INFO: lfq-object 119900
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2:37:23.441875 INFO: lfq-object 120000
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2:37:23.961035 INFO: lfq-object 119800
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2:37:24.002850 INFO: lfq-object 120500
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2:37:24.122936 INFO: lfq-object 120600
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2:37:24.230547 INFO: lfq-object 120700
2:37:24.329470 INFO: lfq-object 121500
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2:37:36.360055 INFO: Performing label free quantification on the pg level
2:37:36.360588 INFO: Filtering fragments by quality
2:37:36.761996 INFO: Performing label-free quantification with directlfq normalization
2:37:36.977365 INFO: 10534 lfq-groups total
2:37:50.179927 INFO: using 24 processes
2:37:50.284386 INFO: lfq-object 0
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2:37:51.687606 INFO: lfq-object 700
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2:37:52.168455 INFO: lfq-object 1500
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2:37:52.200020 INFO: lfq-object 1200
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2:37:52.332878 INFO: lfq-object 3000
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2:37:52.607504 INFO: lfq-object 2500
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2:37:52.751557 INFO: lfq-object 4000
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2:37:54.657062 INFO: lfq-object 7700
2:37:54.657069 INFO: lfq-object 7100
2:37:54.813798 INFO: lfq-object 6800
2:37:54.848613 INFO: lfq-object 6900
2:37:54.937300 INFO: lfq-object 8000
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2:37:55.112900 INFO: lfq-object 8400
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2:37:55.182554 INFO: lfq-object 8700
2:37:55.209947 INFO: lfq-object 8800
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2:37:55.589254 INFO: lfq-object 9300
2:37:55.597008 INFO: lfq-object 9600
2:37:55.615917 INFO: lfq-object 9500
2:37:55.652322 INFO: lfq-object 9400
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2:37:55.660422 INFO: lfq-object 9200
2:37:55.663332 INFO: lfq-object 9700
2:37:55.698632 INFO: lfq-object 9900
2:37:55.937634 INFO: lfq-object 9000
2:37:55.991453 INFO: lfq-object 10000
2:37:56.053332 INFO: lfq-object 10100
2:37:56.147969 INFO: lfq-object 10200
2:37:56.177900 INFO: lfq-object 10400
2:37:56.178850 INFO: lfq-object 10500
2:37:56.335531 INFO: lfq-object 10300
2:37:58.727029 INFO: Writing psm output to disk
2:37:58.810501 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/precursors.parquet to disk
2:37:59.647115 INFO: Writing precursor output to disk
2:37:59.652024 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/precursor.matrix.parquet to disk
2:37:59.749360 INFO: Writing peptide output to disk
2:37:59.755129 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/peptide.matrix.parquet to disk
2:37:59.842817 INFO: Writing pg output to disk
2:37:59.846113 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/pg.matrix.parquet to disk
2:37:59.921294 PROGRESS: Building MBR spectral library
2:37:59.921513 INFO: Running MbrLibraryBuilder
2:38:02.557653 INFO: MBR spectral library contains 133,585 precursors, 10,534 proteins
2:38:02.557795 INFO: Writing MBR spectral library to disk
2:38:04.110240 PROGRESS: =================== Search step 'library' finished ===================
2:38:06.016613 INFO: =================== Running step 'mbr' ===================
2:38:06.020624 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 10.0}})
2:38:06.020836 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
2:38:06.034060 INFO: loading additional config provided via CLI
2:38:06.034129 INFO: loading additional config provided via CLI parameters
2:38:06.034532 INFO: Updating config with 'user defined'
2:38:06.034595 INFO: Updating config with 'user defined (cli)'
2:38:06.034712 INFO: updating config with user defined values: [{'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta'], 'output_directory': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 24, 'mbr_step_enabled': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [380.0, 980.0], 'fragment_mz': [150.0, 2000.0]}, 'search': {'target_ms1_tolerance': 3, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': False}, 'search_initial': {'ms1_tolerance': 3, 'ms2_tolerance': 10}}, {'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 10.0}, 'quant_directory': None, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf', 'output_directory': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1'}]
2:38:06.034931 INFO: Updating config with 'user defined'
2:38:06.034984 INFO: Updating config with 'user defined (cli)'
2:38:06.035005 INFO: Updating config with 'multistep search'
2:38:06.035051 INFO: ├──version: None
2:38:06.035074 INFO: ├──workflow_name: None
2:38:06.035094 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1 [multistep search, default: None][0m
2:38:06.035114 INFO: [32;20m├──library_path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf [multistep search, default: None][0m
2:38:06.035134 INFO: ├──raw_paths:
2:38:06.035160 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
2:38:06.035178 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
2:38:06.035194 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
2:38:06.035211 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
2:38:06.035228 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
2:38:06.035244 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
2:38:06.035264 INFO: ├──fasta_paths:
2:38:06.035283 INFO: ├──quant_directory: None
2:38:06.035300 INFO: ├──general
2:38:06.035318 INFO: │   [32;20m├──thread_count: 24 [user defined, default: 10][0m
2:38:06.035338 INFO: │   ├──transfer_step_enabled: False
2:38:06.035357 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
2:38:06.035375 INFO: │   ├──reuse_calibration: False
2:38:06.035394 INFO: │   ├──reuse_quant: False
2:38:06.035412 INFO: │   ├──log_level: INFO
2:38:06.035429 INFO: │   ├──use_gpu: True
2:38:06.035445 INFO: │   ├──save_figures: True
2:38:06.035463 INFO: │   ├──save_library: True
2:38:06.035480 INFO: │   ├──save_flat_library: False
2:38:06.035497 INFO: │   ├──input_library_type: base
2:38:06.035515 INFO: │   ├──save_mbr_library: True
2:38:06.035536 INFO: │   ├──random_state: None
2:38:06.035554 INFO: │   └──fail_fast: False
2:38:06.035576 INFO: ├──library_loading
2:38:06.035598 INFO: │   └──drop_decoys: False
2:38:06.035615 INFO: ├──library_prediction
2:38:06.035633 INFO: │   ├──enabled: False
2:38:06.035651 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
2:38:06.035668 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
2:38:06.035686 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
2:38:06.035704 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
2:38:06.035722 INFO: │   ├──missed_cleavages: 1
2:38:06.035739 INFO: │   ├──precursor_len:
2:38:06.035756 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
2:38:06.035773 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
2:38:06.035790 INFO: │   ├──precursor_charge:
2:38:06.035807 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
2:38:06.035825 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
2:38:06.035843 INFO: │   ├──precursor_mz:
2:38:06.035861 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
2:38:06.035879 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
2:38:06.035896 INFO: │   ├──fragment_mz:
2:38:06.035913 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
2:38:06.035930 INFO: │   │   - 2000.0
2:38:06.035948 INFO: │   ├──nce: 25.0
2:38:06.035964 INFO: │   ├──fragment_types:
2:38:06.035981 INFO: │   │   - b
2:38:06.035997 INFO: │   │   - y
2:38:06.036014 INFO: │   ├──max_fragment_charge: 2
2:38:06.036031 INFO: │   ├──instrument: Lumos
2:38:06.036048 INFO: │   ├──peptdeep_model_path: None
2:38:06.036065 INFO: │   ├──peptdeep_model_type: generic
2:38:06.036082 INFO: │   ├──predict_charge: False
2:38:06.036100 INFO: │   └──min_charge_probability: 0.1
2:38:06.036117 INFO: ├──custom_modifications:
2:38:06.036135 INFO: │   ├──name: Dimethyl:d12@K
2:38:06.036151 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:38:06.036172 INFO: │   ├──name: Dimethyl:d12@Any_N-term
2:38:06.036189 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:38:06.036205 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
2:38:06.036222 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:38:06.036239 INFO: │   ├──name: mTRAQ:d12@K
2:38:06.036255 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
2:38:06.036273 INFO: │   ├──name: mTRAQ:d12@Any_N-term
2:38:06.036289 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:38:06.036306 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
2:38:06.036323 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:38:06.036340 INFO: │   ├──name: Label:13C(12)@K
2:38:06.036356 INFO: │   └──composition: C(12)
2:38:06.036372 INFO: ├──search
2:38:06.036389 INFO: │   ├──extraction_backend: rust
2:38:06.036407 INFO: │   [32;20m├──target_ms1_tolerance: 3.0 [multistep search, default: 5][0m
2:38:06.036428 INFO: │   ├──target_ms2_tolerance: 10.0
2:38:06.036446 INFO: │   ├──target_rt_tolerance: 0.0
2:38:06.036463 INFO: │   ├──target_mobility_tolerance: 0.0
2:38:06.036481 INFO: │   ├──quant_window: 3
2:38:06.036498 INFO: │   ├──target_num_candidates: 3
2:38:06.036515 INFO: │   ├──channel_filter: 
2:38:06.036532 INFO: │   ├──compete_for_fragments: True
2:38:06.036549 INFO: │   ├──top_k_fragments_selection: 12
2:38:06.036566 INFO: │   ├──top_k_fragments_scoring: 12
2:38:06.036583 INFO: │   ├──min_fragment_intensity: 0.01
2:38:06.036601 INFO: │   ├──optimized_peak_group_score: False
2:38:06.036618 INFO: │   ├──exclude_shared_ions: True
2:38:06.036635 INFO: │   ├──quant_all: True
2:38:06.036651 INFO: │   └──experimental_xic: True
2:38:06.036668 INFO: ├──calibration
2:38:06.036685 INFO: │   ├──batch_size: 1000
2:38:06.036702 INFO: │   ├──optimization_lock_target: 1000
2:38:06.036720 INFO: │   ├──max_steps: 20
2:38:06.036737 INFO: │   ├──min_steps: 5
2:38:06.036754 INFO: │   ├──max_skips: 1
2:38:06.036772 INFO: │   ├──max_fragments: 5000
2:38:06.036789 INFO: │   └──min_correlation: 0.7
2:38:06.036806 INFO: ├──search_initial
2:38:06.036823 INFO: │   ├──num_candidates: 1
2:38:06.036842 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
2:38:06.036860 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
2:38:06.036877 INFO: │   ├──mobility_tolerance: 0.1
2:38:06.036895 INFO: │   └──rt_tolerance: 0.5
2:38:06.036911 INFO: ├──library_multiplexing
2:38:06.036929 INFO: │   ├──enabled: False
2:38:06.036946 INFO: │   ├──input_channel: 0
2:38:06.036962 INFO: │   └──multiplex_mapping:
2:38:06.036979 INFO: ├──multiplexing
2:38:06.036998 INFO: │   ├──enabled: False
2:38:06.037015 INFO: │   ├──target_channels: 4,8
2:38:06.037032 INFO: │   ├──decoy_channel: 12
2:38:06.037049 INFO: │   ├──reference_channel: 0
2:38:06.037066 INFO: │   └──competitive_scoring: True
2:38:06.037082 INFO: ├──fdr
2:38:06.037100 INFO: │   ├──fdr: 0.01
2:38:06.037116 INFO: │   ├──group_level: proteins
2:38:06.037133 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
2:38:06.037151 INFO: │   ├──competitive_scoring: True
2:38:06.037168 INFO: │   ├──keep_decoys: False
2:38:06.037185 INFO: │   ├──keep_decoys_in_mbr_library: False
2:38:06.037202 INFO: │   ├──channel_wise_fdr: False
2:38:06.037220 INFO: │   └──enable_nn_hyperparameter_tuning: True
2:38:06.037236 INFO: ├──search_output
2:38:06.037253 INFO: │   ├──file_format: parquet
2:38:06.037269 INFO: │   ├──precursor_level_lfq: True
2:38:06.037286 INFO: │   ├──peptide_level_lfq: True
2:38:06.037303 INFO: │   ├──save_fragment_quant_matrix: False
2:38:06.037323 INFO: │   ├──min_k_fragments: 12
2:38:06.037341 INFO: │   ├──min_correlation: 0.9
2:38:06.037358 INFO: │   ├──num_samples_quadratic: 50
2:38:06.037375 INFO: │   ├──min_nonnan: 3
2:38:06.037392 INFO: │   ├──normalization_method: directlfq
2:38:06.037409 INFO: │   [32;20m└──normalize_directlfq: False [user defined, default: True][0m
2:38:06.037426 INFO: ├──optimization
2:38:06.037443 INFO: │   ├──order_of_optimization: None
2:38:06.037460 INFO: │   ├──ms2_error
2:38:06.037477 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:38:06.037494 INFO: │   │   ├──targeted_update_factor: 1.0
2:38:06.037511 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:38:06.037529 INFO: │   │   ├──automatic_update_factor: 1.1
2:38:06.037545 INFO: │   │   ├──try_narrower_values: True
2:38:06.037563 INFO: │   │   ├──maximal_decrease: 0.5
2:38:06.037583 INFO: │   │   ├──favour_narrower_optimum: False
2:38:06.037600 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:38:06.037617 INFO: │   ├──ms1_error
2:38:06.037634 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:38:06.037652 INFO: │   │   ├──targeted_update_factor: 1.0
2:38:06.037669 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:38:06.037686 INFO: │   │   ├──automatic_update_factor: 1.1
2:38:06.037703 INFO: │   │   ├──try_narrower_values: False
2:38:06.037720 INFO: │   │   ├──maximal_decrease: 0.2
2:38:06.037737 INFO: │   │   ├──favour_narrower_optimum: False
2:38:06.037755 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:38:06.037771 INFO: │   ├──mobility_error
2:38:06.037789 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:38:06.037806 INFO: │   │   ├──targeted_update_factor: 1.0
2:38:06.037822 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:38:06.037840 INFO: │   │   ├──automatic_update_factor: 1.1
2:38:06.037857 INFO: │   │   ├──try_narrower_values: False
2:38:06.037873 INFO: │   │   ├──maximal_decrease: 0.2
2:38:06.037891 INFO: │   │   ├──favour_narrower_optimum: False
2:38:06.037908 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:38:06.037925 INFO: │   └──rt_error
2:38:06.037943 INFO: │       ├──targeted_update_percentile_range: 0.95
2:38:06.037961 INFO: │       ├──targeted_update_factor: 1.0
2:38:06.037978 INFO: │       ├──automatic_update_percentile_range: 0.999
2:38:06.037996 INFO: │       ├──automatic_update_factor: 1.5
2:38:06.038013 INFO: │       ├──try_narrower_values: True
2:38:06.038030 INFO: │       ├──maximal_decrease: 0.1
2:38:06.038048 INFO: │       ├──favour_narrower_optimum: False
2:38:06.038065 INFO: │       └──maximum_decrease_from_maximum: 0.5
2:38:06.038082 INFO: ├──optimization_manager
2:38:06.038100 INFO: │   ├──fwhm_rt: 5
2:38:06.038117 INFO: │   ├──fwhm_mobility: 0.01
2:38:06.038134 INFO: │   └──score_cutoff: 0
2:38:06.038150 INFO: ├──transfer_library
2:38:06.038168 INFO: │   ├──enabled: False
2:38:06.038185 INFO: │   ├──fragment_types:
2:38:06.038202 INFO: │   │   - b
2:38:06.038218 INFO: │   │   - y
2:38:06.038236 INFO: │   ├──max_charge: 2
2:38:06.038253 INFO: │   ├──top_k_samples: 3
2:38:06.038270 INFO: │   ├──norm_delta_max: True
2:38:06.038288 INFO: │   ├──precursor_correlation_cutoff: 0.5
2:38:06.038306 INFO: │   └──fragment_correlation_ratio: 0.75
2:38:06.038322 INFO: └──transfer_learning
2:38:06.038339 INFO:     ├──enabled: False
2:38:06.038356 INFO:     ├──batch_size: 2000
2:38:06.038373 INFO:     ├──max_lr: 0.0001
2:38:06.038391 INFO:     ├──train_fraction: 0.7
2:38:06.038408 INFO:     ├──validation_fraction: 0.2
2:38:06.038428 INFO:     ├──test_fraction: 0.1
2:38:06.038445 INFO:     ├──test_interval: 1
2:38:06.038462 INFO:     ├──lr_patience: 3
2:38:06.038479 INFO:     ├──epochs: 51
2:38:06.038496 INFO:     ├──warmup_epochs: 5
2:38:06.038512 INFO:     ├──nce: 25
2:38:06.038529 INFO:     └──instrument: Lumos
2:38:06.043815 INFO: Moved existing config file /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/frozen_config.yaml to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/frozen_config.0.bkp.yaml
2:38:06.044549 INFO: Registering 7 custom modifications
2:38:06.067643 INFO: Searching 6 files:
2:38:06.067709 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
2:38:06.067731 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
2:38:06.067750 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
2:38:06.067768 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
2:38:06.067789 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
2:38:06.067805 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
2:38:06.067822 INFO: Using 0 fasta files:
2:38:06.067839 INFO: Using library: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:38:06.067855 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1
2:38:06.067890 PROGRESS: Loading spectral library
2:38:06.067923 PROGRESS: Loading library (type: base) from disk..
2:38:06.067981 INFO: Running DynamicLoader
2:38:06.068046 INFO: Loading .hdf library from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:38:06.727449 INFO: Running PrecursorInitializer
2:38:06.727895 INFO: Channel column already present, skipping initialization
2:38:06.727930 INFO: Elution group indices already present, skipping initialization
2:38:06.727952 INFO: Precursor indices already present, skipping initialization
2:38:06.727971 INFO: Running AnnotateFasta
2:38:06.742824 INFO: Running IsotopeGenerator
2:38:06.743181 INFO: Isotope information already present, skipping isotope generation
2:38:06.743222 INFO: Running RTNormalization
2:38:06.747528 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/speclib.hdf
2:38:07.662797 INFO: Running DecoyGenerator
2:38:15.146363 INFO: Running FlattenLibrary
2:38:16.400277 INFO: Running InitFlatColumns
2:38:16.407748 INFO: Running LogFlatLibraryStats
2:38:16.407865 INFO: ============ Library Stats ============
2:38:16.407898 INFO: Number of precursors: 267,136
2:38:16.461440 INFO: 	thereof targets:133,585
2:38:16.461580 INFO: 	thereof decoys: 133,551
2:38:16.464411 INFO: Number of elution groups: 133,585
2:38:16.464491 INFO: 	average size: 2.00
2:38:16.483294 INFO: Number of proteins: 10,534
2:38:16.484406 INFO: Number of channels: 1 ([0])
2:38:16.484651 INFO: Isotopes Distribution for 4 isotopes
2:38:16.484680 INFO: =======================================
2:38:16.484749 PROGRESS: =================== Starting Search Workflows for step mbr ===================
2:38:16.484800 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
2:38:16.484840 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:38:16.484924 INFO: Initializing TimingManager
2:38:16.485406 INFO: Initializing RawFileManager
2:38:29.956438 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.
2:38:29.966333 INFO: Determining DIA cycle
2:38:29.982921 INFO: Found cycle with start 0.00 min and length 300.
2:38:30.147191 INFO: RT (min)            : 0.0 - 26.9
2:38:30.147286 INFO: RT duration (sec)   : 1611.2
2:38:30.147314 INFO: RT duration (min)   : 26.9
2:38:30.147337 INFO: Cycle len (scans)   : 300
2:38:30.147357 INFO: Cycle len (sec)     : 1.65
2:38:30.147377 INFO: Number of cycles    : 977
2:38:30.147398 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:38:30.147428 INFO: Creating DIA data object took: 13.661929845809937
2:38:31.965209 INFO: Creating DIA data NG object took: 1.8176517486572266
2:38:32.021644 INFO: Initializing CalibrationManager
2:38:32.021942 INFO: Setting up calibration estimators ..
2:38:32.022004 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:38:32.022089 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'}' ..
2:38:32.022174 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:38:32.022228 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:38:32.022285 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}}' ..
2:38:32.022353 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:38:32.022400 INFO: Done setting up calibration estimators.
2:38:32.022599 INFO: Initializing OptimizationManager
2:38:32.022728 INFO: initial parameter: ms1_error = 3
2:38:32.022782 INFO: initial parameter: ms2_error = 10
2:38:32.022830 INFO: initial parameter: rt_error = 805.5992431640625
2:38:32.022874 INFO: initial parameter: mobility_error = 0.1
2:38:32.022915 INFO: initial parameter: num_candidates = 1
2:38:32.022956 INFO: initial parameter: fwhm_rt = 5
2:38:32.023016 INFO: initial parameter: fwhm_mobility = 0.01
2:38:32.023058 INFO: initial parameter: score_cutoff = 0
2:38:32.023099 INFO: initial parameter: classifier_version = -1
2:38:32.023167 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:38:32.023420 INFO: FDRManager: loading saved state not requested, will be initialized.
2:38:32.023453 INFO: Initializing FDRManager
2:38:32.023489 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:38:32.063236 PROGRESS: Initializing spectral library: 133,585 target precursors potentially observable (0 removed)
2:38:32.088992 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:38:32.089379 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
2:38:32.089494 PROGRESS: Starting initial search for precursors.
2:38:32.089577 INFO: Starting optimization step 0.
2:38:32.089635 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:38:32.089689 INFO: Using rust extraction backend
2:38:32.089746 PROGRESS: Extracting batch of 1974 precursors
2:38:32.094705 INFO: === Search parameters used ===
2:38:32.094802 INFO: rt_error       : 805.5992431640625
2:38:32.094851 INFO: mobility_error : 0.1
2:38:32.094895 INFO: num_candidates : 1
2:38:32.094936 INFO: ms1_error      : 3
2:38:32.094987 INFO: ms2_error      : 10
2:38:32.095031 INFO: fwhm_rt        : 5
2:38:32.095071 INFO: quant_window   : 3
2:38:32.095109 INFO: ==============================================
2:38:32.135441 INFO: performing precursor FDR with 40 features
2:38:32.135513 INFO: Decoy channel: -1
2:38:32.135535 INFO: competitive: True
2:38:32.136916 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:32.138983 INFO: Estimating optimal hyperparameters - samples: 1,579, batch_size: 128, learning_rate: 1.77e-04
2:38:32.139835 INFO: Using random state 444515 for train-test-split
2:38:32.263905 INFO: Test AUC: 0.872
2:38:32.263985 INFO: Train AUC: 0.879
2:38:32.264013 INFO: AUC difference: 0.80%
2:38:32.542552 INFO: Resetting torch num_threads to 24
2:38:32.544310 PROGRESS: === Extracted 1974 precursors and 15295 fragments ===
2:38:32.544682 INFO: === FDR correction performed with classifier version -1 ===
2:38:32.545206 PROGRESS: ============================= Precursor FDR =============================
2:38:32.545306 PROGRESS: Total precursors accumulated: 545
2:38:32.545366 PROGRESS: Target precursors: 540 (99.08%)
2:38:32.545419 PROGRESS: Decoy precursors: 5 (0.92%)
2:38:32.545468 PROGRESS: 
2:38:32.545514 PROGRESS: Precursor Summary:
2:38:32.546672 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   540; 0.001 FDR:   468
2:38:32.546767 PROGRESS: 
2:38:32.546824 PROGRESS: Protein Summary:
2:38:32.548210 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   502; 0.001 FDR:   437
2:38:32.548305 PROGRESS: =========================================================================
2:38:32.548491 INFO: Target number of precursors not reached yet.
2:38:32.556388 INFO: Starting optimization step 1.
2:38:32.556496 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:38:32.556570 INFO: Using rust extraction backend
2:38:32.556628 PROGRESS: Extracting batch of 3939 precursors
2:38:32.565329 INFO: === Search parameters used ===
2:38:32.565433 INFO: rt_error       : 805.5992431640625
2:38:32.565493 INFO: mobility_error : 0.1
2:38:32.565541 INFO: num_candidates : 1
2:38:32.565586 INFO: ms1_error      : 3
2:38:32.565628 INFO: ms2_error      : 10
2:38:32.565670 INFO: fwhm_rt        : 5
2:38:32.565712 INFO: quant_window   : 3
2:38:32.565753 INFO: ==============================================
2:38:32.626498 INFO: performing precursor FDR with 40 features
2:38:32.626595 INFO: Decoy channel: -1
2:38:32.626619 INFO: competitive: True
2:38:32.631431 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:32.633975 INFO: Estimating optimal hyperparameters - samples: 4,730, batch_size: 128, learning_rate: 1.77e-04
2:38:32.634060 INFO: Using random state 963261 for train-test-split
2:38:33.010574 INFO: Test AUC: 0.899
2:38:33.010663 INFO: Train AUC: 0.909
2:38:33.010692 INFO: AUC difference: 1.09%
2:38:33.254115 INFO: Resetting torch num_threads to 24
2:38:33.257547 PROGRESS: === Extracted 5913 precursors and 45818 fragments ===
2:38:33.257928 INFO: === FDR correction performed with classifier version -1 ===
2:38:33.258616 PROGRESS: ============================= Precursor FDR =============================
2:38:33.258701 PROGRESS: Total precursors accumulated: 2,073
2:38:33.258758 PROGRESS: Target precursors: 2,053 (99.04%)
2:38:33.258806 PROGRESS: Decoy precursors: 20 (0.96%)
2:38:33.258850 PROGRESS: 
2:38:33.258893 PROGRESS: Precursor Summary:
2:38:33.260493 PROGRESS: Channel   0:	 0.050 FDR: 2,053; 0.010 FDR: 2,053; 0.001 FDR: 1,639
2:38:33.260599 PROGRESS: 
2:38:33.260654 PROGRESS: Protein Summary:
2:38:33.262741 PROGRESS: Channel   0:	 0.050 FDR: 1,662; 0.010 FDR: 1,662; 0.001 FDR: 1,359
2:38:33.262840 PROGRESS: =========================================================================
2:38:33.263092 INFO: Target number of precursors reached.
2:38:33.273790 INFO: fragments_df: keeping 5000 of 45818 [sum(precursor_idx_mask)=20639 sum(mass_error_mask)=45818 stop_rank=5000
2:38:33.284754 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:33.604511 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:34.340915 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:38:34.341387 INFO: Using score_cutoff 11.287993943023682 (fac=0.99, q=1)
2:38:34.341709 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:38:34.341786 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:38:34.341840 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.287993943023682
2:38:34.341899 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:34.345880 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:34.354285 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:38:34.354406 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:38:34.354482 INFO: Starting optimization step 2.
2:38:34.354550 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:34.354611 INFO: Using rust extraction backend
2:38:34.354666 PROGRESS: Extracting batch of 5913 precursors
2:38:34.366448 INFO: === Search parameters used ===
2:38:34.366571 INFO: rt_error       : 805.5992431640625
2:38:34.366621 INFO: mobility_error : 0.1
2:38:34.366666 INFO: num_candidates : 3
2:38:34.366707 INFO: ms1_error      : 3
2:38:34.366749 INFO: ms2_error      : 10
2:38:34.366789 INFO: fwhm_rt        : 3.0
2:38:34.366830 INFO: quant_window   : 3
2:38:34.366869 INFO: ==============================================
2:38:34.495287 INFO: performing precursor FDR with 40 features
2:38:34.495397 INFO: Decoy channel: -1
2:38:34.495421 INFO: competitive: True
2:38:34.501086 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:34.505313 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:38:34.505457 INFO: Using random state 735553 for train-test-split
2:38:35.911922 INFO: Test AUC: 0.722
2:38:35.912035 INFO: Train AUC: 0.743
2:38:35.912064 INFO: AUC difference: 2.77%
2:38:36.169510 INFO: Resetting torch num_threads to 24
2:38:36.172125 PROGRESS: === Extracted 17731 precursors and 119385 fragments ===
2:38:36.172493 INFO: === FDR correction performed with classifier version 1 ===
2:38:36.173182 PROGRESS: ============================= Precursor FDR =============================
2:38:36.173264 PROGRESS: Total precursors accumulated: 2,259
2:38:36.173320 PROGRESS: Target precursors: 2,237 (99.03%)
2:38:36.173367 PROGRESS: Decoy precursors: 22 (0.97%)
2:38:36.173409 PROGRESS: 
2:38:36.173451 PROGRESS: Precursor Summary:
2:38:36.175020 PROGRESS: Channel   0:	 0.050 FDR: 2,237; 0.010 FDR: 2,237; 0.001 FDR: 1,782
2:38:36.175113 PROGRESS: 
2:38:36.175173 PROGRESS: Protein Summary:
2:38:36.177329 PROGRESS: Channel   0:	 0.050 FDR: 1,803; 0.010 FDR: 1,803; 0.001 FDR: 1,468
2:38:36.177419 PROGRESS: =========================================================================
2:38:36.177793 INFO: Target number of precursors reached.
2:38:36.203158 INFO: fragments_df: keeping 5000 of 119385 [sum(precursor_idx_mask)=51828 sum(mass_error_mask)=119385 stop_rank=5000
2:38:36.214252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:36.565264 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:37.291800 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:37.292261 INFO: Using score_cutoff 11.382448071670533 (fac=0.99, q=1)
2:38:37.292581 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:37.292656 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:37.292708 INFO: Updating optimization_manager: score_cutoff        : 11.287993943023682 -> 11.382448071670533
2:38:37.292759 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:37.296737 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:37.304704 INFO: === checking if optimization conditions were reached ===
2:38:37.306402 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:38:37.306497 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:38:37.306559 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:38:37.306614 INFO: ==============================================
2:38:37.306684 INFO: Starting optimization step 3.
2:38:37.306741 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:37.306798 INFO: Using rust extraction backend
2:38:37.306853 PROGRESS: Extracting batch of 5913 precursors
2:38:37.318303 INFO: === Search parameters used ===
2:38:37.318448 INFO: rt_error       : 805.5992431640625
2:38:37.318499 INFO: mobility_error : 0.1
2:38:37.318543 INFO: num_candidates : 3
2:38:37.318584 INFO: ms1_error      : 3
2:38:37.318624 INFO: ms2_error      : 10.0
2:38:37.318663 INFO: fwhm_rt        : 3.0
2:38:37.318701 INFO: quant_window   : 3
2:38:37.318739 INFO: ==============================================
2:38:37.439051 INFO: performing precursor FDR with 40 features
2:38:37.439162 INFO: Decoy channel: -1
2:38:37.439188 INFO: competitive: True
2:38:37.444423 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:37.448777 INFO: Estimating optimal hyperparameters - samples: 14,181, batch_size: 128, learning_rate: 1.77e-04
2:38:37.448914 INFO: Using random state 634915 for train-test-split
2:38:38.875369 INFO: Test AUC: 0.743
2:38:38.875478 INFO: Train AUC: 0.758
2:38:38.875505 INFO: AUC difference: 1.97%
2:38:39.138083 INFO: Resetting torch num_threads to 24
2:38:39.141001 PROGRESS: === Extracted 17727 precursors and 119345 fragments ===
2:38:39.141415 INFO: === FDR correction performed with classifier version 2 ===
2:38:39.142151 PROGRESS: ============================= Precursor FDR =============================
2:38:39.142237 PROGRESS: Total precursors accumulated: 2,367
2:38:39.142295 PROGRESS: Target precursors: 2,344 (99.03%)
2:38:39.142344 PROGRESS: Decoy precursors: 23 (0.97%)
2:38:39.142388 PROGRESS: 
2:38:39.142431 PROGRESS: Precursor Summary:
2:38:39.144043 PROGRESS: Channel   0:	 0.050 FDR: 2,344; 0.010 FDR: 2,344; 0.001 FDR: 1,728
2:38:39.144139 PROGRESS: 
2:38:39.144197 PROGRESS: Protein Summary:
2:38:39.146400 PROGRESS: Channel   0:	 0.050 FDR: 1,883; 0.010 FDR: 1,883; 0.001 FDR: 1,427
2:38:39.146497 PROGRESS: =========================================================================
2:38:39.146900 INFO: Target number of precursors reached.
2:38:39.173158 INFO: fragments_df: keeping 5000 of 119345 [sum(precursor_idx_mask)=53870 sum(mass_error_mask)=119345 stop_rank=5000
2:38:39.184717 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:39.527649 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:40.249604 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:40.250086 INFO: Using score_cutoff 11.014967843055725 (fac=0.99, q=1)
2:38:40.250437 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:40.250515 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:40.250570 INFO: Updating optimization_manager: score_cutoff        : 11.382448071670533 -> 11.014967843055725
2:38:40.250621 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:40.254740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:40.262657 INFO: === checking if optimization conditions were reached ===
2:38:40.264448 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:38:40.264550 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:38:40.264614 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:38:40.264677 INFO: ==============================================
2:38:40.264740 INFO: Starting optimization step 4.
2:38:40.264794 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:40.264862 INFO: Using rust extraction backend
2:38:40.264921 PROGRESS: Extracting batch of 5913 precursors
2:38:40.276449 INFO: === Search parameters used ===
2:38:40.276569 INFO: rt_error       : 805.5992431640625
2:38:40.276622 INFO: mobility_error : 0.1
2:38:40.276667 INFO: num_candidates : 3
2:38:40.276710 INFO: ms1_error      : 3
2:38:40.276752 INFO: ms2_error      : 10.0
2:38:40.276792 INFO: fwhm_rt        : 3.0
2:38:40.276831 INFO: quant_window   : 3
2:38:40.276871 INFO: ==============================================
2:38:40.392883 INFO: performing precursor FDR with 40 features
2:38:40.392991 INFO: Decoy channel: -1
2:38:40.393015 INFO: competitive: True
2:38:40.398439 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:40.402525 INFO: Estimating optimal hyperparameters - samples: 14,183, batch_size: 128, learning_rate: 1.77e-04
2:38:40.402657 INFO: Using random state 707352 for train-test-split
2:38:41.833802 INFO: Test AUC: 0.742
2:38:41.833909 INFO: Train AUC: 0.771
2:38:41.833937 INFO: AUC difference: 3.81%
2:38:42.090492 INFO: Resetting torch num_threads to 24
2:38:42.093335 PROGRESS: === Extracted 17729 precursors and 119366 fragments ===
2:38:42.093708 INFO: === FDR correction performed with classifier version 3 ===
2:38:42.094421 PROGRESS: ============================= Precursor FDR =============================
2:38:42.094508 PROGRESS: Total precursors accumulated: 2,474
2:38:42.094565 PROGRESS: Target precursors: 2,450 (99.03%)
2:38:42.094619 PROGRESS: Decoy precursors: 24 (0.97%)
2:38:42.094664 PROGRESS: 
2:38:42.094713 PROGRESS: Precursor Summary:
2:38:42.096383 PROGRESS: Channel   0:	 0.050 FDR: 2,450; 0.010 FDR: 2,450; 0.001 FDR: 1,844
2:38:42.096485 PROGRESS: 
2:38:42.096541 PROGRESS: Protein Summary:
2:38:42.098757 PROGRESS: Channel   0:	 0.050 FDR: 1,960; 0.010 FDR: 1,960; 0.001 FDR: 1,518
2:38:42.098850 PROGRESS: =========================================================================
2:38:42.099245 INFO: Target number of precursors reached.
2:38:42.126601 INFO: fragments_df: keeping 5000 of 119366 [sum(precursor_idx_mask)=55868 sum(mass_error_mask)=119366 stop_rank=5000
2:38:42.138044 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:42.508844 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:43.228581 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:43.229050 INFO: Using score_cutoff 10.800243578910829 (fac=0.99, q=1)
2:38:43.229389 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:43.229468 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:43.229525 INFO: Updating optimization_manager: score_cutoff        : 11.014967843055725 -> 10.800243578910829
2:38:43.229581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:43.233656 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:43.241673 INFO: === checking if optimization conditions were reached ===
2:38:43.243382 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:38:43.243492 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:38:43.243556 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:38:43.243614 INFO: ==============================================
2:38:43.243677 INFO: Starting optimization step 5.
2:38:43.243731 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:43.243788 INFO: Using rust extraction backend
2:38:43.243842 PROGRESS: Extracting batch of 5913 precursors
2:38:43.255498 INFO: === Search parameters used ===
2:38:43.255624 INFO: rt_error       : 805.5992431640625
2:38:43.255678 INFO: mobility_error : 0.1
2:38:43.255727 INFO: num_candidates : 3
2:38:43.255770 INFO: ms1_error      : 3
2:38:43.255813 INFO: ms2_error      : 10.0
2:38:43.255855 INFO: fwhm_rt        : 3.0
2:38:43.255897 INFO: quant_window   : 3
2:38:43.255939 INFO: ==============================================
2:38:43.373104 INFO: performing precursor FDR with 40 features
2:38:43.373214 INFO: Decoy channel: -1
2:38:43.373239 INFO: competitive: True
2:38:43.378912 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:43.383264 INFO: Estimating optimal hyperparameters - samples: 14,183, batch_size: 128, learning_rate: 1.77e-04
2:38:43.383400 INFO: Using random state 383310 for train-test-split
2:38:44.797050 INFO: Test AUC: 0.767
2:38:44.797158 INFO: Train AUC: 0.774
2:38:44.797185 INFO: AUC difference: 0.93%
2:38:45.051430 INFO: Resetting torch num_threads to 24
2:38:45.054037 PROGRESS: === Extracted 17729 precursors and 119368 fragments ===
2:38:45.054396 INFO: === FDR correction performed with classifier version 4 ===
2:38:45.055126 PROGRESS: ============================= Precursor FDR =============================
2:38:45.055215 PROGRESS: Total precursors accumulated: 2,512
2:38:45.055272 PROGRESS: Target precursors: 2,488 (99.04%)
2:38:45.055324 PROGRESS: Decoy precursors: 24 (0.96%)
2:38:45.055370 PROGRESS: 
2:38:45.055413 PROGRESS: Precursor Summary:
2:38:45.057035 PROGRESS: Channel   0:	 0.050 FDR: 2,488; 0.010 FDR: 2,488; 0.001 FDR: 2,033
2:38:45.057127 PROGRESS: 
2:38:45.057182 PROGRESS: Protein Summary:
2:38:45.059449 PROGRESS: Channel   0:	 0.050 FDR: 1,984; 0.010 FDR: 1,984; 0.001 FDR: 1,651
2:38:45.059542 PROGRESS: =========================================================================
2:38:45.059936 INFO: Target number of precursors reached.
2:38:45.086522 INFO: fragments_df: keeping 5000 of 119368 [sum(precursor_idx_mask)=56787 sum(mass_error_mask)=119368 stop_rank=5000
2:38:45.097934 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:45.456464 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:46.172892 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:46.173361 INFO: Using score_cutoff 10.809288228034973 (fac=0.99, q=1)
2:38:46.173680 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:46.173754 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:46.173807 INFO: Updating optimization_manager: score_cutoff        : 10.800243578910829 -> 10.809288228034973
2:38:46.173859 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:46.177845 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:46.185764 INFO: === checking if optimization conditions were reached ===
2:38:46.187464 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:38:46.187572 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:38:46.187637 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:38:46.187692 INFO: ==============================================
2:38:46.187754 INFO: Starting optimization step 6.
2:38:46.187809 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:46.187866 INFO: Using rust extraction backend
2:38:46.187919 PROGRESS: Extracting batch of 5913 precursors
2:38:46.199322 INFO: === Search parameters used ===
2:38:46.199456 INFO: rt_error       : 805.5992431640625
2:38:46.199507 INFO: mobility_error : 0.1
2:38:46.199550 INFO: num_candidates : 3
2:38:46.199592 INFO: ms1_error      : 3
2:38:46.199632 INFO: ms2_error      : 10.0
2:38:46.199671 INFO: fwhm_rt        : 3.0
2:38:46.199709 INFO: quant_window   : 3
2:38:46.199751 INFO: ==============================================
2:38:46.311202 INFO: performing precursor FDR with 40 features
2:38:46.311312 INFO: Decoy channel: -1
2:38:46.311335 INFO: competitive: True
2:38:46.316828 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:46.321111 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:38:46.321244 INFO: Using random state 962399 for train-test-split
2:38:47.738138 INFO: Test AUC: 0.768
2:38:47.738244 INFO: Train AUC: 0.779
2:38:47.738272 INFO: AUC difference: 1.38%
2:38:47.993417 INFO: Resetting torch num_threads to 24
2:38:47.996091 PROGRESS: === Extracted 17728 precursors and 119351 fragments ===
2:38:47.996455 INFO: === FDR correction performed with classifier version 5 ===
2:38:47.997300 PROGRESS: ============================= Precursor FDR =============================
2:38:47.997386 PROGRESS: Total precursors accumulated: 2,594
2:38:47.997452 PROGRESS: Target precursors: 2,569 (99.04%)
2:38:47.997506 PROGRESS: Decoy precursors: 25 (0.96%)
2:38:47.997553 PROGRESS: 
2:38:47.997598 PROGRESS: Precursor Summary:
2:38:47.999242 PROGRESS: Channel   0:	 0.050 FDR: 2,569; 0.010 FDR: 2,569; 0.001 FDR: 2,055
2:38:47.999337 PROGRESS: 
2:38:47.999393 PROGRESS: Protein Summary:
2:38:48.001673 PROGRESS: Channel   0:	 0.050 FDR: 2,042; 0.010 FDR: 2,042; 0.001 FDR: 1,673
2:38:48.001768 PROGRESS: =========================================================================
2:38:48.002152 INFO: Target number of precursors reached.
2:38:48.029181 INFO: fragments_df: keeping 5000 of 119351 [sum(precursor_idx_mask)=58089 sum(mass_error_mask)=119351 stop_rank=5000
2:38:48.040504 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:48.411613 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:49.132125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:49.132591 INFO: Using score_cutoff 9.980424961853027 (fac=0.99, q=1)
2:38:49.132920 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:49.132999 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:49.133055 INFO: Updating optimization_manager: score_cutoff        : 10.809288228034973 -> 9.980424961853027
2:38:49.133109 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:49.137131 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:49.144997 INFO: === checking if optimization conditions were reached ===
2:38:49.146693 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:38:49.146795 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:38:49.146859 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:38:49.146915 INFO: ==============================================
2:38:49.146994 PROGRESS: Optimization finished for ms2_error.
2:38:49.157579 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:49.161391 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:49.169299 INFO: Starting optimization step 0.
2:38:49.169413 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:49.169487 INFO: Using rust extraction backend
2:38:49.169558 PROGRESS: Extracting batch of 5913 precursors
2:38:49.180936 INFO: === Search parameters used ===
2:38:49.181055 INFO: rt_error       : 805.5992431640625
2:38:49.181106 INFO: mobility_error : 0.1
2:38:49.181152 INFO: num_candidates : 3
2:38:49.181196 INFO: ms1_error      : 3
2:38:49.181239 INFO: ms2_error      : 10.0
2:38:49.181285 INFO: fwhm_rt        : 3.0
2:38:49.181328 INFO: quant_window   : 3
2:38:49.181379 INFO: ==============================================
2:38:49.296659 INFO: performing precursor FDR with 40 features
2:38:49.296771 INFO: Decoy channel: -1
2:38:49.296795 INFO: competitive: True
2:38:49.302035 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:49.306155 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:38:49.306294 INFO: Using random state 615304 for train-test-split
2:38:50.726023 INFO: Test AUC: 0.769
2:38:50.726130 INFO: Train AUC: 0.794
2:38:50.726158 INFO: AUC difference: 3.10%
2:38:50.982824 INFO: Resetting torch num_threads to 24
2:38:50.985498 PROGRESS: === Extracted 17728 precursors and 119363 fragments ===
2:38:50.985871 INFO: === FDR correction performed with classifier version 6 ===
2:38:50.986586 PROGRESS: ============================= Precursor FDR =============================
2:38:50.986674 PROGRESS: Total precursors accumulated: 2,590
2:38:50.986730 PROGRESS: Target precursors: 2,565 (99.03%)
2:38:50.986779 PROGRESS: Decoy precursors: 25 (0.97%)
2:38:50.986822 PROGRESS: 
2:38:50.986865 PROGRESS: Precursor Summary:
2:38:50.988503 PROGRESS: Channel   0:	 0.050 FDR: 2,565; 0.010 FDR: 2,565; 0.001 FDR: 2,092
2:38:50.988598 PROGRESS: 
2:38:50.988652 PROGRESS: Protein Summary:
2:38:50.990903 PROGRESS: Channel   0:	 0.050 FDR: 2,039; 0.010 FDR: 2,039; 0.001 FDR: 1,698
2:38:50.991009 PROGRESS: =========================================================================
2:38:50.991387 INFO: Target number of precursors reached.
2:38:51.017713 INFO: fragments_df: keeping 5000 of 119363 [sum(precursor_idx_mask)=58116 sum(mass_error_mask)=119363 stop_rank=5000
2:38:51.028980 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:51.416894 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:52.142011 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:52.142479 INFO: Using score_cutoff 10.574502154541017 (fac=0.99, q=1)
2:38:52.142792 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:52.142872 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:52.142926 INFO: Updating optimization_manager: score_cutoff        : 9.980424961853027 -> 10.574502154541017
2:38:52.142986 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:52.146993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:52.154894 INFO: === checking if optimization conditions were reached ===
2:38:52.155036 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:38:52.157790 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 517.4354053273171
2:38:52.157890 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 517.4354.
2:38:52.157952 INFO: ==============================================
2:38:52.158017 INFO: Starting optimization step 1.
2:38:52.158073 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:52.158137 INFO: Using rust extraction backend
2:38:52.158189 PROGRESS: Extracting batch of 5913 precursors
2:38:52.170003 INFO: === Search parameters used ===
2:38:52.170153 INFO: rt_error       : 517.4354053273171
2:38:52.170204 INFO: mobility_error : 0.1
2:38:52.170248 INFO: num_candidates : 3
2:38:52.170289 INFO: ms1_error      : 3
2:38:52.170329 INFO: ms2_error      : 10.0
2:38:52.170368 INFO: fwhm_rt        : 3.0
2:38:52.170407 INFO: quant_window   : 3
2:38:52.170451 INFO: ==============================================
2:38:52.274805 INFO: performing precursor FDR with 40 features
2:38:52.274924 INFO: Decoy channel: -1
2:38:52.274948 INFO: competitive: True
2:38:52.280076 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:52.284173 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:38:52.284305 INFO: Using random state 615304 for train-test-split
2:38:53.716230 INFO: Test AUC: 0.772
2:38:53.716339 INFO: Train AUC: 0.793
2:38:53.716367 INFO: AUC difference: 2.62%
2:38:53.973553 INFO: Resetting torch num_threads to 24
2:38:53.976177 PROGRESS: === Extracted 17731 precursors and 119212 fragments ===
2:38:53.976552 INFO: === FDR correction performed with classifier version 6 ===
2:38:53.977268 PROGRESS: ============================= Precursor FDR =============================
2:38:53.977354 PROGRESS: Total precursors accumulated: 2,689
2:38:53.977411 PROGRESS: Target precursors: 2,663 (99.03%)
2:38:53.977460 PROGRESS: Decoy precursors: 26 (0.97%)
2:38:53.977504 PROGRESS: 
2:38:53.977546 PROGRESS: Precursor Summary:
2:38:53.979195 PROGRESS: Channel   0:	 0.050 FDR: 2,663; 0.010 FDR: 2,663; 0.001 FDR: 2,122
2:38:53.979289 PROGRESS: 
2:38:53.979344 PROGRESS: Protein Summary:
2:38:53.981678 PROGRESS: Channel   0:	 0.050 FDR: 2,111; 0.010 FDR: 2,111; 0.001 FDR: 1,719
2:38:53.981765 PROGRESS: =========================================================================
2:38:53.982214 INFO: Target number of precursors reached.
2:38:54.008940 INFO: fragments_df: keeping 5000 of 119212 [sum(precursor_idx_mask)=59958 sum(mass_error_mask)=119212 stop_rank=5000
2:38:54.023903 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:54.416816 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:55.137776 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:55.138243 INFO: Using score_cutoff 9.979978063774109 (fac=0.99, q=1)
2:38:55.138565 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:55.138638 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:55.138689 INFO: Updating optimization_manager: score_cutoff        : 10.574502154541017 -> 9.979978063774109
2:38:55.138743 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:55.142731 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:55.150593 INFO: === checking if optimization conditions were reached ===
2:38:55.150713 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:38:55.153615 INFO: Updating optimization_manager: rt_error            : 517.4354053273171 -> 521.8364169771885
2:38:55.153721 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 521.8364.
2:38:55.153783 INFO: ==============================================
2:38:55.153877 INFO: Starting optimization step 2.
2:38:55.153934 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:55.153991 INFO: Using rust extraction backend
2:38:55.154048 PROGRESS: Extracting batch of 5913 precursors
2:38:55.165435 INFO: === Search parameters used ===
2:38:55.165553 INFO: rt_error       : 521.8364169771885
2:38:55.165603 INFO: mobility_error : 0.1
2:38:55.165649 INFO: num_candidates : 3
2:38:55.165691 INFO: ms1_error      : 3
2:38:55.165732 INFO: ms2_error      : 10.0
2:38:55.165779 INFO: fwhm_rt        : 3.0
2:38:55.165821 INFO: quant_window   : 3
2:38:55.165860 INFO: ==============================================
2:38:55.273767 INFO: performing precursor FDR with 40 features
2:38:55.273873 INFO: Decoy channel: -1
2:38:55.273896 INFO: competitive: True
2:38:55.279050 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:55.283399 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:38:55.283534 INFO: Using random state 615304 for train-test-split
2:38:56.706656 INFO: Test AUC: 0.769
2:38:56.706826 INFO: Train AUC: 0.794
2:38:56.706892 INFO: AUC difference: 3.19%
2:38:56.966067 INFO: Resetting torch num_threads to 24
2:38:56.968639 PROGRESS: === Extracted 17728 precursors and 119212 fragments ===
2:38:56.969008 INFO: === FDR correction performed with classifier version 6 ===
2:38:56.969714 PROGRESS: ============================= Precursor FDR =============================
2:38:56.969796 PROGRESS: Total precursors accumulated: 2,642
2:38:56.969851 PROGRESS: Target precursors: 2,616 (99.02%)
2:38:56.969898 PROGRESS: Decoy precursors: 26 (0.98%)
2:38:56.969940 PROGRESS: 
2:38:56.969981 PROGRESS: Precursor Summary:
2:38:56.971623 PROGRESS: Channel   0:	 0.050 FDR: 2,616; 0.010 FDR: 2,616; 0.001 FDR: 2,106
2:38:56.971714 PROGRESS: 
2:38:56.971768 PROGRESS: Protein Summary:
2:38:56.974023 PROGRESS: Channel   0:	 0.050 FDR: 2,075; 0.010 FDR: 2,075; 0.001 FDR: 1,708
2:38:56.974111 PROGRESS: =========================================================================
2:38:56.974477 INFO: Target number of precursors reached.
2:38:57.001372 INFO: fragments_df: keeping 5000 of 119212 [sum(precursor_idx_mask)=59036 sum(mass_error_mask)=119212 stop_rank=5000
2:38:57.012641 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:57.434245 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:58.153081 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:58.153558 INFO: Using score_cutoff 10.2482889046669 (fac=0.99, q=1)
2:38:58.153874 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:38:58.153954 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:38:58.154010 INFO: Updating optimization_manager: score_cutoff        : 9.979978063774109 -> 10.2482889046669
2:38:58.154065 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:58.158002 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:58.165419 INFO: === checking if optimization conditions were reached ===
2:38:58.165534 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:38:58.168486 INFO: Updating optimization_manager: rt_error            : 521.8364169771885 -> 533.3097338842149
2:38:58.168590 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 533.3097.
2:38:58.168654 INFO: ==============================================
2:38:58.168724 INFO: Starting optimization step 3.
2:38:58.168781 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:38:58.168843 INFO: Using rust extraction backend
2:38:58.168899 PROGRESS: Extracting batch of 5913 precursors
2:38:58.180213 INFO: === Search parameters used ===
2:38:58.180336 INFO: rt_error       : 533.3097338842149
2:38:58.180390 INFO: mobility_error : 0.1
2:38:58.180439 INFO: num_candidates : 3
2:38:58.180494 INFO: ms1_error      : 3
2:38:58.180538 INFO: ms2_error      : 10.0
2:38:58.180580 INFO: fwhm_rt        : 3.0
2:38:58.180621 INFO: quant_window   : 3
2:38:58.180662 INFO: ==============================================
2:38:58.285417 INFO: performing precursor FDR with 40 features
2:38:58.285526 INFO: Decoy channel: -1
2:38:58.285550 INFO: competitive: True
2:38:58.290596 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:58.294668 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:38:58.294796 INFO: Using random state 615304 for train-test-split
2:38:59.710873 INFO: Test AUC: 0.772
2:38:59.710998 INFO: Train AUC: 0.793
2:38:59.711028 INFO: AUC difference: 2.68%
2:38:59.964475 INFO: Resetting torch num_threads to 24
2:38:59.967039 PROGRESS: === Extracted 17728 precursors and 119217 fragments ===
2:38:59.967412 INFO: === FDR correction performed with classifier version 6 ===
2:38:59.968117 PROGRESS: ============================= Precursor FDR =============================
2:38:59.968201 PROGRESS: Total precursors accumulated: 2,662
2:38:59.968259 PROGRESS: Target precursors: 2,636 (99.02%)
2:38:59.968308 PROGRESS: Decoy precursors: 26 (0.98%)
2:38:59.968354 PROGRESS: 
2:38:59.968408 PROGRESS: Precursor Summary:
2:38:59.970086 PROGRESS: Channel   0:	 0.050 FDR: 2,636; 0.010 FDR: 2,636; 0.001 FDR: 2,122
2:38:59.970177 PROGRESS: 
2:38:59.970240 PROGRESS: Protein Summary:
2:38:59.972588 PROGRESS: Channel   0:	 0.050 FDR: 2,084; 0.010 FDR: 2,084; 0.001 FDR: 1,718
2:38:59.972682 PROGRESS: =========================================================================
2:38:59.973057 INFO: Target number of precursors reached.
2:39:00.000015 INFO: fragments_df: keeping 5000 of 119217 [sum(precursor_idx_mask)=59305 sum(mass_error_mask)=119217 stop_rank=5000
2:39:00.011633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:00.417102 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:01.152748 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:01.153232 INFO: Using score_cutoff 9.986714645862579 (fac=0.99, q=1)
2:39:01.153548 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:01.153621 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:01.153673 INFO: Updating optimization_manager: score_cutoff        : 10.2482889046669 -> 9.986714645862579
2:39:01.153732 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:01.157716 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:01.165669 INFO: === checking if optimization conditions were reached ===
2:39:01.165783 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:39:01.168761 INFO: Updating optimization_manager: rt_error            : 533.3097338842149 -> 490.3447595281284
2:39:01.168865 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 490.3448.
2:39:01.168928 INFO: ==============================================
2:39:01.168992 INFO: Starting optimization step 4.
2:39:01.169046 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:01.169103 INFO: Using rust extraction backend
2:39:01.169156 PROGRESS: Extracting batch of 5913 precursors
2:39:01.180507 INFO: === Search parameters used ===
2:39:01.180620 INFO: rt_error       : 490.3447595281284
2:39:01.180678 INFO: mobility_error : 0.1
2:39:01.180725 INFO: num_candidates : 3
2:39:01.180772 INFO: ms1_error      : 3
2:39:01.180813 INFO: ms2_error      : 10.0
2:39:01.180852 INFO: fwhm_rt        : 3.0
2:39:01.180892 INFO: quant_window   : 3
2:39:01.180931 INFO: ==============================================
2:39:01.288443 INFO: performing precursor FDR with 40 features
2:39:01.288555 INFO: Decoy channel: -1
2:39:01.288579 INFO: competitive: True
2:39:01.293624 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:01.297801 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:39:01.297935 INFO: Using random state 615304 for train-test-split
2:39:02.707642 INFO: Test AUC: 0.781
2:39:02.707751 INFO: Train AUC: 0.791
2:39:02.707779 INFO: AUC difference: 1.26%
2:39:02.962883 INFO: Resetting torch num_threads to 24
2:39:02.965428 PROGRESS: === Extracted 17731 precursors and 119153 fragments ===
2:39:02.965792 INFO: === FDR correction performed with classifier version 6 ===
2:39:02.966505 PROGRESS: ============================= Precursor FDR =============================
2:39:02.966588 PROGRESS: Total precursors accumulated: 2,629
2:39:02.966645 PROGRESS: Target precursors: 2,603 (99.01%)
2:39:02.966692 PROGRESS: Decoy precursors: 26 (0.99%)
2:39:02.966734 PROGRESS: 
2:39:02.966775 PROGRESS: Precursor Summary:
2:39:02.968413 PROGRESS: Channel   0:	 0.050 FDR: 2,603; 0.010 FDR: 2,603; 0.001 FDR: 2,213
2:39:02.968507 PROGRESS: 
2:39:02.968561 PROGRESS: Protein Summary:
2:39:02.970859 PROGRESS: Channel   0:	 0.050 FDR: 2,067; 0.010 FDR: 2,067; 0.001 FDR: 1,787
2:39:02.970953 PROGRESS: =========================================================================
2:39:02.971354 INFO: Target number of precursors reached.
2:39:02.998692 INFO: fragments_df: keeping 5000 of 119153 [sum(precursor_idx_mask)=58947 sum(mass_error_mask)=119153 stop_rank=5000
2:39:03.009953 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:03.383404 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:04.098365 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:04.098847 INFO: Using score_cutoff 10.43188909778595 (fac=0.99, q=1)
2:39:04.099175 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:04.099255 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:04.099308 INFO: Updating optimization_manager: score_cutoff        : 9.986714645862579 -> 10.43188909778595
2:39:04.099362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:04.103312 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:04.111062 INFO: === checking if optimization conditions were reached ===
2:39:04.111175 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:39:04.114098 INFO: Updating optimization_manager: rt_error            : 490.3447595281284 -> 443.8052943545716
2:39:04.114197 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 443.8053.
2:39:04.114262 INFO: ==============================================
2:39:04.114330 INFO: Starting optimization step 5.
2:39:04.114388 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:04.114447 INFO: Using rust extraction backend
2:39:04.114501 PROGRESS: Extracting batch of 5913 precursors
2:39:04.125865 INFO: === Search parameters used ===
2:39:04.125983 INFO: rt_error       : 443.8052943545716
2:39:04.126035 INFO: mobility_error : 0.1
2:39:04.126080 INFO: num_candidates : 3
2:39:04.126122 INFO: ms1_error      : 3
2:39:04.126162 INFO: ms2_error      : 10.0
2:39:04.126201 INFO: fwhm_rt        : 3.0
2:39:04.126239 INFO: quant_window   : 3
2:39:04.126276 INFO: ==============================================
2:39:04.226922 INFO: performing precursor FDR with 40 features
2:39:04.227043 INFO: Decoy channel: -1
2:39:04.227068 INFO: competitive: True
2:39:04.232106 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:04.236096 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:39:04.236226 INFO: Using random state 615304 for train-test-split
2:39:05.662075 INFO: Test AUC: 0.779
2:39:05.662185 INFO: Train AUC: 0.790
2:39:05.662214 INFO: AUC difference: 1.45%
2:39:05.917873 INFO: Resetting torch num_threads to 24
2:39:05.920408 PROGRESS: === Extracted 17730 precursors and 118902 fragments ===
2:39:05.920765 INFO: === FDR correction performed with classifier version 6 ===
2:39:05.921473 PROGRESS: ============================= Precursor FDR =============================
2:39:05.921556 PROGRESS: Total precursors accumulated: 2,647
2:39:05.921612 PROGRESS: Target precursors: 2,621 (99.02%)
2:39:05.921660 PROGRESS: Decoy precursors: 26 (0.98%)
2:39:05.921704 PROGRESS: 
2:39:05.921746 PROGRESS: Precursor Summary:
2:39:05.923401 PROGRESS: Channel   0:	 0.050 FDR: 2,621; 0.010 FDR: 2,621; 0.001 FDR: 2,145
2:39:05.923498 PROGRESS: 
2:39:05.923553 PROGRESS: Protein Summary:
2:39:05.925931 PROGRESS: Channel   0:	 0.050 FDR: 2,080; 0.010 FDR: 2,080; 0.001 FDR: 1,734
2:39:05.926022 PROGRESS: =========================================================================
2:39:05.926393 INFO: Target number of precursors reached.
2:39:05.953471 INFO: fragments_df: keeping 5000 of 118902 [sum(precursor_idx_mask)=59156 sum(mass_error_mask)=118902 stop_rank=5000
2:39:05.964708 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:06.349208 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:07.065829 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:07.066304 INFO: Using score_cutoff 10.249605268478392 (fac=0.99, q=1)
2:39:07.066611 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:07.066685 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:07.066737 INFO: Updating optimization_manager: score_cutoff        : 10.43188909778595 -> 10.249605268478392
2:39:07.066789 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:07.070723 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:07.078345 INFO: === checking if optimization conditions were reached ===
2:39:07.078455 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:39:07.081405 INFO: Updating optimization_manager: rt_error            : 443.8052943545716 -> 351.9419811018874
2:39:07.081512 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 351.9420.
2:39:07.081573 INFO: ==============================================
2:39:07.081639 INFO: Starting optimization step 6.
2:39:07.081695 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:07.081751 INFO: Using rust extraction backend
2:39:07.081810 PROGRESS: Extracting batch of 5913 precursors
2:39:07.093157 INFO: === Search parameters used ===
2:39:07.093296 INFO: rt_error       : 351.9419811018874
2:39:07.093346 INFO: mobility_error : 0.1
2:39:07.093390 INFO: num_candidates : 3
2:39:07.093431 INFO: ms1_error      : 3
2:39:07.093471 INFO: ms2_error      : 10.0
2:39:07.093510 INFO: fwhm_rt        : 3.0
2:39:07.093549 INFO: quant_window   : 3
2:39:07.093588 INFO: ==============================================
2:39:07.194746 INFO: performing precursor FDR with 40 features
2:39:07.194851 INFO: Decoy channel: -1
2:39:07.194875 INFO: competitive: True
2:39:07.200024 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:07.204055 INFO: Estimating optimal hyperparameters - samples: 14,183, batch_size: 128, learning_rate: 1.77e-04
2:39:07.204187 INFO: Using random state 615304 for train-test-split
2:39:08.617990 INFO: Test AUC: 0.763
2:39:08.618099 INFO: Train AUC: 0.794
2:39:08.618131 INFO: AUC difference: 3.92%
2:39:08.875095 INFO: Resetting torch num_threads to 24
2:39:08.877658 PROGRESS: === Extracted 17729 precursors and 118110 fragments ===
2:39:08.878021 INFO: === FDR correction performed with classifier version 6 ===
2:39:08.878744 PROGRESS: ============================= Precursor FDR =============================
2:39:08.878830 PROGRESS: Total precursors accumulated: 2,716
2:39:08.878889 PROGRESS: Target precursors: 2,690 (99.04%)
2:39:08.878941 PROGRESS: Decoy precursors: 26 (0.96%)
2:39:08.879000 PROGRESS: 
2:39:08.879049 PROGRESS: Precursor Summary:
2:39:08.880753 PROGRESS: Channel   0:	 0.050 FDR: 2,690; 0.010 FDR: 2,690; 0.001 FDR: 2,253
2:39:08.880847 PROGRESS: 
2:39:08.880905 PROGRESS: Protein Summary:
2:39:08.883375 PROGRESS: Channel   0:	 0.050 FDR: 2,135; 0.010 FDR: 2,135; 0.001 FDR: 1,811
2:39:08.883479 PROGRESS: =========================================================================
2:39:08.883878 INFO: Target number of precursors reached.
2:39:08.910677 INFO: fragments_df: keeping 5000 of 118110 [sum(precursor_idx_mask)=60387 sum(mass_error_mask)=118110 stop_rank=5000
2:39:08.921890 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:09.256873 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:09.942120 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:09.942595 INFO: Using score_cutoff 10.003372669315338 (fac=0.99, q=1)
2:39:09.942914 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:09.943001 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:09.943058 INFO: Updating optimization_manager: score_cutoff        : 10.249605268478392 -> 10.003372669315338
2:39:09.943110 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:09.947059 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:09.954747 INFO: === checking if optimization conditions were reached ===
2:39:09.954870 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:39:09.957929 INFO: Updating optimization_manager: rt_error            : 351.9419811018874 -> 248.23086143380618
2:39:09.958032 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 248.2309.
2:39:09.958095 INFO: ==============================================
2:39:09.958179 INFO: Starting optimization step 7.
2:39:09.958241 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:09.958301 INFO: Using rust extraction backend
2:39:09.958356 PROGRESS: Extracting batch of 5913 precursors
2:39:09.969595 INFO: === Search parameters used ===
2:39:09.969707 INFO: rt_error       : 248.23086143380618
2:39:09.969759 INFO: mobility_error : 0.1
2:39:09.969802 INFO: num_candidates : 3
2:39:09.969844 INFO: ms1_error      : 3
2:39:09.969884 INFO: ms2_error      : 10.0
2:39:09.969923 INFO: fwhm_rt        : 3.0
2:39:09.969962 INFO: quant_window   : 3
2:39:09.970001 INFO: ==============================================
2:39:10.064775 INFO: performing precursor FDR with 40 features
2:39:10.064885 INFO: Decoy channel: -1
2:39:10.064911 INFO: competitive: True
2:39:10.071805 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:10.075802 INFO: Estimating optimal hyperparameters - samples: 14,174, batch_size: 128, learning_rate: 1.77e-04
2:39:10.075927 INFO: Using random state 615304 for train-test-split
2:39:11.491729 INFO: Test AUC: 0.765
2:39:11.491835 INFO: Train AUC: 0.794
2:39:11.491863 INFO: AUC difference: 3.73%
2:39:11.745737 INFO: Resetting torch num_threads to 24
2:39:11.748273 PROGRESS: === Extracted 17718 precursors and 116027 fragments ===
2:39:11.748629 INFO: === FDR correction performed with classifier version 6 ===
2:39:11.749358 PROGRESS: ============================= Precursor FDR =============================
2:39:11.749439 PROGRESS: Total precursors accumulated: 2,730
2:39:11.749494 PROGRESS: Target precursors: 2,703 (99.01%)
2:39:11.749542 PROGRESS: Decoy precursors: 27 (0.99%)
2:39:11.749593 PROGRESS: 
2:39:11.749636 PROGRESS: Precursor Summary:
2:39:11.751293 PROGRESS: Channel   0:	 0.050 FDR: 2,703; 0.010 FDR: 2,703; 0.001 FDR: 2,282
2:39:11.751390 PROGRESS: 
2:39:11.751444 PROGRESS: Protein Summary:
2:39:11.753747 PROGRESS: Channel   0:	 0.050 FDR: 2,139; 0.010 FDR: 2,139; 0.001 FDR: 1,830
2:39:11.753833 PROGRESS: =========================================================================
2:39:11.754184 INFO: Target number of precursors reached.
2:39:11.780685 INFO: fragments_df: keeping 5000 of 116027 [sum(precursor_idx_mask)=59951 sum(mass_error_mask)=116027 stop_rank=5000
2:39:11.792336 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:12.188883 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:12.905133 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:12.905604 INFO: Using score_cutoff 10.176438401985168 (fac=0.99, q=1)
2:39:12.905928 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:12.906003 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:12.906055 INFO: Updating optimization_manager: score_cutoff        : 10.003372669315338 -> 10.176438401985168
2:39:12.906106 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:12.910054 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:12.917468 INFO: === checking if optimization conditions were reached ===
2:39:12.917582 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:39:12.920535 INFO: Updating optimization_manager: rt_error            : 248.23086143380618 -> 260.8705179716472
2:39:12.920636 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 260.8705.
2:39:12.920704 INFO: ==============================================
2:39:12.920772 INFO: Starting optimization step 8.
2:39:12.920825 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:12.920882 INFO: Using rust extraction backend
2:39:12.920936 PROGRESS: Extracting batch of 5913 precursors
2:39:12.932235 INFO: === Search parameters used ===
2:39:12.932347 INFO: rt_error       : 260.8705179716472
2:39:12.932399 INFO: mobility_error : 0.1
2:39:12.932444 INFO: num_candidates : 3
2:39:12.932488 INFO: ms1_error      : 3
2:39:12.932529 INFO: ms2_error      : 10.0
2:39:12.932570 INFO: fwhm_rt        : 3.0
2:39:12.932618 INFO: quant_window   : 3
2:39:12.932658 INFO: ==============================================
2:39:13.026642 INFO: performing precursor FDR with 40 features
2:39:13.026750 INFO: Decoy channel: -1
2:39:13.026774 INFO: competitive: True
2:39:13.031802 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:13.036023 INFO: Estimating optimal hyperparameters - samples: 14,174, batch_size: 128, learning_rate: 1.77e-04
2:39:13.036157 INFO: Using random state 615304 for train-test-split
2:39:14.453540 INFO: Test AUC: 0.787
2:39:14.453651 INFO: Train AUC: 0.789
2:39:14.453682 INFO: AUC difference: 0.29%
2:39:14.706959 INFO: Resetting torch num_threads to 24
2:39:14.709481 PROGRESS: === Extracted 17718 precursors and 116417 fragments ===
2:39:14.709842 INFO: === FDR correction performed with classifier version 6 ===
2:39:14.710572 PROGRESS: ============================= Precursor FDR =============================
2:39:14.710659 PROGRESS: Total precursors accumulated: 2,682
2:39:14.710718 PROGRESS: Target precursors: 2,656 (99.03%)
2:39:14.710769 PROGRESS: Decoy precursors: 26 (0.97%)
2:39:14.710815 PROGRESS: 
2:39:14.710861 PROGRESS: Precursor Summary:
2:39:14.712546 PROGRESS: Channel   0:	 0.050 FDR: 2,656; 0.010 FDR: 2,656; 0.001 FDR: 2,278
2:39:14.712640 PROGRESS: 
2:39:14.712694 PROGRESS: Protein Summary:
2:39:14.715060 PROGRESS: Channel   0:	 0.050 FDR: 2,105; 0.010 FDR: 2,105; 0.001 FDR: 1,831
2:39:14.715159 PROGRESS: =========================================================================
2:39:14.715536 INFO: Target number of precursors reached.
2:39:14.741553 INFO: fragments_df: keeping 5000 of 116417 [sum(precursor_idx_mask)=59266 sum(mass_error_mask)=116417 stop_rank=5000
2:39:14.752711 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:15.143114 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:15.858985 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:15.859442 INFO: Using score_cutoff 10.215952806472778 (fac=0.99, q=1)
2:39:15.859758 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:15.859833 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:15.859887 INFO: Updating optimization_manager: score_cutoff        : 10.176438401985168 -> 10.215952806472778
2:39:15.859939 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:15.863893 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:15.871862 INFO: === checking if optimization conditions were reached ===
2:39:15.871979 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:39:15.874913 INFO: Updating optimization_manager: rt_error            : 260.8705179716472 -> 243.05912249935272
2:39:15.875031 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 243.0591.
2:39:15.875100 INFO: ==============================================
2:39:15.875167 INFO: Starting optimization step 9.
2:39:15.875223 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:15.875284 INFO: Using rust extraction backend
2:39:15.875338 PROGRESS: Extracting batch of 5913 precursors
2:39:15.886780 INFO: === Search parameters used ===
2:39:15.886899 INFO: rt_error       : 243.05912249935272
2:39:15.886951 INFO: mobility_error : 0.1
2:39:15.887011 INFO: num_candidates : 3
2:39:15.887057 INFO: ms1_error      : 3
2:39:15.887099 INFO: ms2_error      : 10.0
2:39:15.887141 INFO: fwhm_rt        : 3.0
2:39:15.887181 INFO: quant_window   : 3
2:39:15.887221 INFO: ==============================================
2:39:15.978077 INFO: performing precursor FDR with 40 features
2:39:15.978185 INFO: Decoy channel: -1
2:39:15.978210 INFO: competitive: True
2:39:15.983189 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:15.987389 INFO: Estimating optimal hyperparameters - samples: 14,172, batch_size: 128, learning_rate: 1.77e-04
2:39:15.987519 INFO: Using random state 615304 for train-test-split
2:39:17.404735 INFO: Test AUC: 0.779
2:39:17.404861 INFO: Train AUC: 0.789
2:39:17.404891 INFO: AUC difference: 1.21%
2:39:17.658862 INFO: Resetting torch num_threads to 24
2:39:17.661400 PROGRESS: === Extracted 17715 precursors and 115888 fragments ===
2:39:17.661774 INFO: === FDR correction performed with classifier version 6 ===
2:39:17.662478 PROGRESS: ============================= Precursor FDR =============================
2:39:17.662561 PROGRESS: Total precursors accumulated: 2,666
2:39:17.662620 PROGRESS: Target precursors: 2,640 (99.02%)
2:39:17.662669 PROGRESS: Decoy precursors: 26 (0.98%)
2:39:17.662719 PROGRESS: 
2:39:17.662763 PROGRESS: Precursor Summary:
2:39:17.664433 PROGRESS: Channel   0:	 0.050 FDR: 2,640; 0.010 FDR: 2,640; 0.001 FDR: 2,256
2:39:17.664526 PROGRESS: 
2:39:17.664578 PROGRESS: Protein Summary:
2:39:17.666852 PROGRESS: Channel   0:	 0.050 FDR: 2,094; 0.010 FDR: 2,094; 0.001 FDR: 1,809
2:39:17.666944 PROGRESS: =========================================================================
2:39:17.667335 INFO: Target number of precursors reached.
2:39:17.693346 INFO: fragments_df: keeping 5000 of 115888 [sum(precursor_idx_mask)=58892 sum(mass_error_mask)=115888 stop_rank=5000
2:39:17.704426 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:18.094089 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:18.810389 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:18.810910 INFO: Using score_cutoff 10.3440104719162 (fac=0.99, q=1)
2:39:18.811255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:18.811336 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:18.811393 INFO: Updating optimization_manager: score_cutoff        : 10.215952806472778 -> 10.3440104719162
2:39:18.811453 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:18.815417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:18.823094 INFO: === checking if optimization conditions were reached ===
2:39:18.823206 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:39:18.826160 INFO: Updating optimization_manager: rt_error            : 243.05912249935272 -> 238.44007450373184
2:39:18.826268 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 238.4401.
2:39:18.826333 INFO: ==============================================
2:39:18.826403 INFO: Starting optimization step 10.
2:39:18.826463 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:18.826525 INFO: Using rust extraction backend
2:39:18.826583 PROGRESS: Extracting batch of 5913 precursors
2:39:18.837906 INFO: === Search parameters used ===
2:39:18.838040 INFO: rt_error       : 238.44007450373184
2:39:18.838093 INFO: mobility_error : 0.1
2:39:18.838140 INFO: num_candidates : 3
2:39:18.838185 INFO: ms1_error      : 3
2:39:18.838229 INFO: ms2_error      : 10.0
2:39:18.838274 INFO: fwhm_rt        : 3.0
2:39:18.838316 INFO: quant_window   : 3
2:39:18.838359 INFO: ==============================================
2:39:18.933956 INFO: performing precursor FDR with 40 features
2:39:18.934063 INFO: Decoy channel: -1
2:39:18.934088 INFO: competitive: True
2:39:18.939076 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:18.943033 INFO: Estimating optimal hyperparameters - samples: 14,170, batch_size: 128, learning_rate: 1.77e-04
2:39:18.943161 INFO: Using random state 615304 for train-test-split
2:39:20.366299 INFO: Test AUC: 0.764
2:39:20.366427 INFO: Train AUC: 0.793
2:39:20.366458 INFO: AUC difference: 3.62%
2:39:20.620651 INFO: Resetting torch num_threads to 24
2:39:20.623159 PROGRESS: === Extracted 17713 precursors and 115756 fragments ===
2:39:20.623532 INFO: === FDR correction performed with classifier version 6 ===
2:39:20.624250 PROGRESS: ============================= Precursor FDR =============================
2:39:20.624335 PROGRESS: Total precursors accumulated: 2,745
2:39:20.624399 PROGRESS: Target precursors: 2,718 (99.02%)
2:39:20.624450 PROGRESS: Decoy precursors: 27 (0.98%)
2:39:20.624504 PROGRESS: 
2:39:20.624547 PROGRESS: Precursor Summary:
2:39:20.626202 PROGRESS: Channel   0:	 0.050 FDR: 2,718; 0.010 FDR: 2,718; 0.001 FDR: 2,254
2:39:20.626289 PROGRESS: 
2:39:20.626342 PROGRESS: Protein Summary:
2:39:20.628690 PROGRESS: Channel   0:	 0.050 FDR: 2,149; 0.010 FDR: 2,149; 0.001 FDR: 1,813
2:39:20.628782 PROGRESS: =========================================================================
2:39:20.629144 INFO: Target number of precursors reached.
2:39:20.654945 INFO: fragments_df: keeping 5000 of 115756 [sum(precursor_idx_mask)=60126 sum(mass_error_mask)=115756 stop_rank=5000
2:39:20.666017 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:21.038951 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:21.687767 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:21.688235 INFO: Using score_cutoff 9.97662632818222 (fac=0.99, q=1)
2:39:21.688555 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:21.688630 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:21.688684 INFO: Updating optimization_manager: score_cutoff        : 10.3440104719162 -> 9.97662632818222
2:39:21.688736 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:21.692671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:21.700603 INFO: === checking if optimization conditions were reached ===
2:39:21.700721 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:39:21.701474 INFO: Updating optimization_manager: rt_error            : 238.44007450373184 -> 238.44007450373184
2:39:21.701598 INFO: Updating optimization_manager: classifier_version  : 6 -> 17
2:39:21.701691 INFO: Updating optimization_manager: score_cutoff        : 9.97662632818222 -> 9.97662632818222
2:39:21.701777 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:21.701858 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:21.701946 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 238.4401 found after 11 searches.
2:39:21.702004 INFO: ==============================================
2:39:21.702069 PROGRESS: Optimization finished for rt_error.
2:39:21.712464 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:21.716232 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:21.723834 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:39:21.723937 PROGRESS: ==============================================
2:39:21.724001 PROGRESS: ms2_error      : 10.0000
2:39:21.724055 PROGRESS: rt_error       : 238.4401
2:39:21.724100 PROGRESS: ==============================================
2:39:21.724847 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:21.860701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:22.208975 INFO: Using rust extraction backend
2:39:22.209295 PROGRESS: Extracting batch of 264177 precursors
2:39:22.626394 INFO: === Search parameters used ===
2:39:22.626670 INFO: rt_error       : 238.44007450373184
2:39:22.626726 INFO: mobility_error : 0.1
2:39:22.626771 INFO: num_candidates : 3
2:39:22.626813 INFO: ms1_error      : 3
2:39:22.626853 INFO: ms2_error      : 10.0
2:39:22.626894 INFO: fwhm_rt        : 3.0
2:39:22.626936 INFO: quant_window   : 3
2:39:22.626987 INFO: ==============================================
2:39:23.312557 INFO: Removed 116492 precursors with score below cutoff 9.97662632818222
2:39:24.011394 INFO: performing precursor FDR with 40 features
2:39:24.011512 INFO: Decoy channel: -1
2:39:24.011538 INFO: competitive: True
2:39:24.073467 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:24.106052 WARNING: FDR calculation for 361803 target and 314236 decoy PSMs
2:39:24.106194 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:39:24.277170 INFO: Estimating optimal hyperparameters - samples: 540,831, batch_size: 2,215, learning_rate: 7.35e-04
2:39:24.277977 INFO: Using random state 880261 for train-test-split
2:39:35.632994 INFO: Test AUC: 0.782
2:39:35.633225 INFO: Train AUC: 0.788
2:39:35.633341 INFO: AUC difference: 0.79%
2:39:36.156187 INFO: Resetting torch num_threads to 24
2:39:36.530465 PROGRESS: ============================= Precursor FDR =============================
2:39:36.530769 PROGRESS: Total precursors accumulated: 123,808
2:39:36.530841 PROGRESS: Target precursors: 122,585 (99.01%)
2:39:36.530894 PROGRESS: Decoy precursors: 1,223 (0.99%)
2:39:36.530942 PROGRESS: 
2:39:36.531001 PROGRESS: Precursor Summary:
2:39:36.569506 PROGRESS: Channel   0:	 0.050 FDR: 122,585; 0.010 FDR: 122,585; 0.001 FDR: 107,141
2:39:36.569763 PROGRESS: 
2:39:36.569827 PROGRESS: Protein Summary:
2:39:36.630857 PROGRESS: Channel   0:	 0.050 FDR: 10,502; 0.010 FDR: 10,502; 0.001 FDR: 10,338
2:39:36.631127 PROGRESS: =========================================================================
2:39:36.633919 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
2:39:36.828055 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
2:39:37.123748 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:39:37.313045 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
2:39:37.313195 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:39:37.313299 INFO: Initializing TimingManager
2:39:37.313937 INFO: Initializing RawFileManager
2:39:50.149765 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.
2:39:50.158365 INFO: Determining DIA cycle
2:39:50.175772 INFO: Found cycle with start 0.00 min and length 300.
2:39:50.345078 INFO: RT (min)            : 0.0 - 26.9
2:39:50.345175 INFO: RT duration (sec)   : 1611.2
2:39:50.345204 INFO: RT duration (min)   : 26.9
2:39:50.345227 INFO: Cycle len (scans)   : 300
2:39:50.345248 INFO: Cycle len (sec)     : 1.65
2:39:50.345269 INFO: Number of cycles    : 978
2:39:50.345289 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:39:50.345320 INFO: Creating DIA data object took: 13.031277894973755
2:39:52.096862 INFO: Creating DIA data NG object took: 1.751404047012329
2:39:52.140267 INFO: Initializing CalibrationManager
2:39:52.140570 INFO: Setting up calibration estimators ..
2:39:52.140637 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:39:52.140726 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'}' ..
2:39:52.140798 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:39:52.140852 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:39:52.140909 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}}' ..
2:39:52.140961 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:39:52.141008 INFO: Done setting up calibration estimators.
2:39:52.141205 INFO: Initializing OptimizationManager
2:39:52.141339 INFO: initial parameter: ms1_error = 3
2:39:52.141393 INFO: initial parameter: ms2_error = 10
2:39:52.141440 INFO: initial parameter: rt_error = 805.6019897460938
2:39:52.141484 INFO: initial parameter: mobility_error = 0.1
2:39:52.141525 INFO: initial parameter: num_candidates = 1
2:39:52.141574 INFO: initial parameter: fwhm_rt = 5
2:39:52.141623 INFO: initial parameter: fwhm_mobility = 0.01
2:39:52.141664 INFO: initial parameter: score_cutoff = 0
2:39:52.141703 INFO: initial parameter: classifier_version = -1
2:39:52.141771 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:39:52.142032 INFO: FDRManager: loading saved state not requested, will be initialized.
2:39:52.142066 INFO: Initializing FDRManager
2:39:52.142099 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:39:52.183367 PROGRESS: Initializing spectral library: 133,585 target precursors potentially observable (0 removed)
2:39:52.209469 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:39:52.209863 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
2:39:52.209960 PROGRESS: Starting initial search for precursors.
2:39:52.210040 INFO: Starting optimization step 0.
2:39:52.210099 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:39:52.210152 INFO: Using rust extraction backend
2:39:52.210203 PROGRESS: Extracting batch of 1974 precursors
2:39:52.215151 INFO: === Search parameters used ===
2:39:52.215261 INFO: rt_error       : 805.6019897460938
2:39:52.215311 INFO: mobility_error : 0.1
2:39:52.215353 INFO: num_candidates : 1
2:39:52.215394 INFO: ms1_error      : 3
2:39:52.215435 INFO: ms2_error      : 10
2:39:52.215474 INFO: fwhm_rt        : 5
2:39:52.215514 INFO: quant_window   : 3
2:39:52.215552 INFO: ==============================================
2:39:52.247480 INFO: performing precursor FDR with 40 features
2:39:52.247549 INFO: Decoy channel: -1
2:39:52.247572 INFO: competitive: True
2:39:52.248789 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:52.250620 INFO: Estimating optimal hyperparameters - samples: 1,577, batch_size: 128, learning_rate: 1.77e-04
2:39:52.251459 INFO: Using random state 377030 for train-test-split
2:39:52.403238 INFO: Test AUC: 0.884
2:39:52.403319 INFO: Train AUC: 0.874
2:39:52.403347 INFO: AUC difference: 1.14%
2:39:52.649257 INFO: Resetting torch num_threads to 24
2:39:52.651016 PROGRESS: === Extracted 1972 precursors and 15226 fragments ===
2:39:52.651395 INFO: === FDR correction performed with classifier version -1 ===
2:39:52.651913 PROGRESS: ============================= Precursor FDR =============================
2:39:52.651996 PROGRESS: Total precursors accumulated: 586
2:39:52.652056 PROGRESS: Target precursors: 581 (99.15%)
2:39:52.652121 PROGRESS: Decoy precursors: 5 (0.85%)
2:39:52.652168 PROGRESS: 
2:39:52.652211 PROGRESS: Precursor Summary:
2:39:52.653358 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   581; 0.001 FDR:   455
2:39:52.653453 PROGRESS: 
2:39:52.653510 PROGRESS: Protein Summary:
2:39:52.654912 PROGRESS: Channel   0:	 0.050 FDR:   540; 0.010 FDR:   540; 0.001 FDR:   424
2:39:52.655008 PROGRESS: =========================================================================
2:39:52.655211 INFO: Target number of precursors not reached yet.
2:39:52.663087 INFO: Starting optimization step 1.
2:39:52.663223 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:39:52.663293 INFO: Using rust extraction backend
2:39:52.663350 PROGRESS: Extracting batch of 3939 precursors
2:39:52.671405 INFO: === Search parameters used ===
2:39:52.671504 INFO: rt_error       : 805.6019897460938
2:39:52.671553 INFO: mobility_error : 0.1
2:39:52.671599 INFO: num_candidates : 1
2:39:52.671641 INFO: ms1_error      : 3
2:39:52.671682 INFO: ms2_error      : 10
2:39:52.671722 INFO: fwhm_rt        : 5
2:39:52.671761 INFO: quant_window   : 3
2:39:52.671802 INFO: ==============================================
2:39:52.737507 INFO: performing precursor FDR with 40 features
2:39:52.737595 INFO: Decoy channel: -1
2:39:52.737618 INFO: competitive: True
2:39:52.741691 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:52.743914 INFO: Estimating optimal hyperparameters - samples: 4,728, batch_size: 128, learning_rate: 1.77e-04
2:39:52.743995 INFO: Using random state 753034 for train-test-split
2:39:53.207681 INFO: Test AUC: 0.901
2:39:53.207767 INFO: Train AUC: 0.898
2:39:53.207794 INFO: AUC difference: 0.32%
2:39:53.451385 INFO: Resetting torch num_threads to 24
2:39:53.454877 PROGRESS: === Extracted 5911 precursors and 45623 fragments ===
2:39:53.455261 INFO: === FDR correction performed with classifier version -1 ===
2:39:53.455930 PROGRESS: ============================= Precursor FDR =============================
2:39:53.456013 PROGRESS: Total precursors accumulated: 2,017
2:39:53.456069 PROGRESS: Target precursors: 1,998 (99.06%)
2:39:53.456117 PROGRESS: Decoy precursors: 19 (0.94%)
2:39:53.456161 PROGRESS: 
2:39:53.456203 PROGRESS: Precursor Summary:
2:39:53.457674 PROGRESS: Channel   0:	 0.050 FDR: 1,998; 0.010 FDR: 1,998; 0.001 FDR: 1,560
2:39:53.457761 PROGRESS: 
2:39:53.457814 PROGRESS: Protein Summary:
2:39:53.459813 PROGRESS: Channel   0:	 0.050 FDR: 1,629; 0.010 FDR: 1,629; 0.001 FDR: 1,295
2:39:53.459907 PROGRESS: =========================================================================
2:39:53.460178 INFO: Target number of precursors reached.
2:39:53.470599 INFO: fragments_df: keeping 5000 of 45623 [sum(precursor_idx_mask)=20176 sum(mass_error_mask)=45623 stop_rank=5000
2:39:53.481284 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:53.774478 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:54.483173 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:39:54.483639 INFO: Using score_cutoff 11.4398972946167 (fac=0.99, q=1)
2:39:54.483963 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:39:54.484037 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:39:54.484089 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.4398972946167
2:39:54.484144 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:54.488071 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:54.496142 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:39:54.496255 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:39:54.496332 INFO: Starting optimization step 2.
2:39:54.496398 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:54.496458 INFO: Using rust extraction backend
2:39:54.496511 PROGRESS: Extracting batch of 5913 precursors
2:39:54.507761 INFO: === Search parameters used ===
2:39:54.507867 INFO: rt_error       : 805.6019897460938
2:39:54.507918 INFO: mobility_error : 0.1
2:39:54.507962 INFO: num_candidates : 3
2:39:54.508004 INFO: ms1_error      : 3
2:39:54.508044 INFO: ms2_error      : 10
2:39:54.508085 INFO: fwhm_rt        : 3.0
2:39:54.508128 INFO: quant_window   : 3
2:39:54.508169 INFO: ==============================================
2:39:56.284357 INFO: performing precursor FDR with 40 features
2:39:56.284478 INFO: Decoy channel: -1
2:39:56.284504 INFO: competitive: True
2:39:56.289532 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:56.293898 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:39:56.294026 INFO: Using random state 996142 for train-test-split
2:39:57.746966 INFO: Test AUC: 0.706
2:39:57.747098 INFO: Train AUC: 0.727
2:39:57.747128 INFO: AUC difference: 2.93%
2:39:58.003945 INFO: Resetting torch num_threads to 24
2:39:58.006533 PROGRESS: === Extracted 17731 precursors and 119038 fragments ===
2:39:58.006902 INFO: === FDR correction performed with classifier version 1 ===
2:39:58.007680 PROGRESS: ============================= Precursor FDR =============================
2:39:58.007772 PROGRESS: Total precursors accumulated: 2,336
2:39:58.007845 PROGRESS: Target precursors: 2,313 (99.02%)
2:39:58.007897 PROGRESS: Decoy precursors: 23 (0.98%)
2:39:58.007943 PROGRESS: 
2:39:58.007987 PROGRESS: Precursor Summary:
2:39:58.009583 PROGRESS: Channel   0:	 0.050 FDR: 2,313; 0.010 FDR: 2,313; 0.001 FDR: 1,524
2:39:58.009676 PROGRESS: 
2:39:58.009742 PROGRESS: Protein Summary:
2:39:58.011976 PROGRESS: Channel   0:	 0.050 FDR: 1,863; 0.010 FDR: 1,863; 0.001 FDR: 1,273
2:39:58.012089 PROGRESS: =========================================================================
2:39:58.012539 INFO: Target number of precursors reached.
2:39:58.037699 INFO: fragments_df: keeping 5000 of 119038 [sum(precursor_idx_mask)=53178 sum(mass_error_mask)=119038 stop_rank=5000
2:39:58.049132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:58.399486 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:59.120312 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:59.120784 INFO: Using score_cutoff 10.905042226409913 (fac=0.99, q=1)
2:39:59.121103 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:39:59.121177 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:39:59.121230 INFO: Updating optimization_manager: score_cutoff        : 11.4398972946167 -> 10.905042226409913
2:39:59.121281 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:59.125242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:59.133118 INFO: === checking if optimization conditions were reached ===
2:39:59.134807 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:39:59.134902 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:39:59.134962 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:39:59.137621 INFO: ==============================================
2:39:59.137700 INFO: Starting optimization step 3.
2:39:59.137762 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:39:59.137820 INFO: Using rust extraction backend
2:39:59.137875 PROGRESS: Extracting batch of 5913 precursors
2:39:59.149765 INFO: === Search parameters used ===
2:39:59.149892 INFO: rt_error       : 805.6019897460938
2:39:59.149943 INFO: mobility_error : 0.1
2:39:59.149987 INFO: num_candidates : 3
2:39:59.150031 INFO: ms1_error      : 3
2:39:59.150073 INFO: ms2_error      : 10.0
2:39:59.150114 INFO: fwhm_rt        : 3.0
2:39:59.150153 INFO: quant_window   : 3
2:39:59.150192 INFO: ==============================================
2:39:59.271349 INFO: performing precursor FDR with 40 features
2:39:59.271455 INFO: Decoy channel: -1
2:39:59.271478 INFO: competitive: True
2:39:59.276720 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:59.280885 INFO: Estimating optimal hyperparameters - samples: 14,187, batch_size: 128, learning_rate: 1.77e-04
2:39:59.281011 INFO: Using random state 478990 for train-test-split
2:40:00.699239 INFO: Test AUC: 0.737
2:40:00.699351 INFO: Train AUC: 0.741
2:40:00.699380 INFO: AUC difference: 0.58%
2:40:00.955654 INFO: Resetting torch num_threads to 24
2:40:00.958217 PROGRESS: === Extracted 17734 precursors and 118903 fragments ===
2:40:00.958590 INFO: === FDR correction performed with classifier version 2 ===
2:40:00.959318 PROGRESS: ============================= Precursor FDR =============================
2:40:00.959409 PROGRESS: Total precursors accumulated: 2,378
2:40:00.959473 PROGRESS: Target precursors: 2,355 (99.03%)
2:40:00.959526 PROGRESS: Decoy precursors: 23 (0.97%)
2:40:00.959574 PROGRESS: 
2:40:00.959621 PROGRESS: Precursor Summary:
2:40:00.961243 PROGRESS: Channel   0:	 0.050 FDR: 2,355; 0.010 FDR: 2,355; 0.001 FDR: 1,738
2:40:00.961338 PROGRESS: 
2:40:00.961393 PROGRESS: Protein Summary:
2:40:00.963594 PROGRESS: Channel   0:	 0.050 FDR: 1,892; 0.010 FDR: 1,892; 0.001 FDR: 1,439
2:40:00.963692 PROGRESS: =========================================================================
2:40:00.964081 INFO: Target number of precursors reached.
2:40:00.989407 INFO: fragments_df: keeping 5000 of 118903 [sum(precursor_idx_mask)=53857 sum(mass_error_mask)=118903 stop_rank=5000
2:40:01.002750 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:01.345283 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:02.062721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:02.063190 INFO: Using score_cutoff 10.78454321308136 (fac=0.99, q=1)
2:40:02.063515 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:02.063593 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:02.063648 INFO: Updating optimization_manager: score_cutoff        : 10.905042226409913 -> 10.78454321308136
2:40:02.063701 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:02.067651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:02.075561 INFO: === checking if optimization conditions were reached ===
2:40:02.077257 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:02.077354 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:40:02.077418 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:02.077484 INFO: ==============================================
2:40:02.077553 INFO: Starting optimization step 4.
2:40:02.077609 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:02.077666 INFO: Using rust extraction backend
2:40:02.077726 PROGRESS: Extracting batch of 5913 precursors
2:40:02.088873 INFO: === Search parameters used ===
2:40:02.088989 INFO: rt_error       : 805.6019897460938
2:40:02.089041 INFO: mobility_error : 0.1
2:40:02.089085 INFO: num_candidates : 3
2:40:02.089129 INFO: ms1_error      : 3
2:40:02.089170 INFO: ms2_error      : 10.0
2:40:02.089211 INFO: fwhm_rt        : 3.0
2:40:02.089252 INFO: quant_window   : 3
2:40:02.089292 INFO: ==============================================
2:40:02.202375 INFO: performing precursor FDR with 40 features
2:40:02.202486 INFO: Decoy channel: -1
2:40:02.202512 INFO: competitive: True
2:40:02.207677 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:02.211764 INFO: Estimating optimal hyperparameters - samples: 14,187, batch_size: 128, learning_rate: 1.77e-04
2:40:02.211895 INFO: Using random state 474729 for train-test-split
2:40:03.651183 INFO: Test AUC: 0.741
2:40:03.651378 INFO: Train AUC: 0.755
2:40:03.651407 INFO: AUC difference: 1.82%
2:40:03.914038 INFO: Resetting torch num_threads to 24
2:40:03.916892 PROGRESS: === Extracted 17734 precursors and 118893 fragments ===
2:40:03.917310 INFO: === FDR correction performed with classifier version 3 ===
2:40:03.918016 PROGRESS: ============================= Precursor FDR =============================
2:40:03.918100 PROGRESS: Total precursors accumulated: 2,464
2:40:03.918155 PROGRESS: Target precursors: 2,440 (99.03%)
2:40:03.918203 PROGRESS: Decoy precursors: 24 (0.97%)
2:40:03.918247 PROGRESS: 
2:40:03.918294 PROGRESS: Precursor Summary:
2:40:03.919935 PROGRESS: Channel   0:	 0.050 FDR: 2,440; 0.010 FDR: 2,440; 0.001 FDR: 2,024
2:40:03.920028 PROGRESS: 
2:40:03.920081 PROGRESS: Protein Summary:
2:40:03.922333 PROGRESS: Channel   0:	 0.050 FDR: 1,951; 0.010 FDR: 1,951; 0.001 FDR: 1,656
2:40:03.922420 PROGRESS: =========================================================================
2:40:03.922949 INFO: Target number of precursors reached.
2:40:03.948835 INFO: fragments_df: keeping 5000 of 118893 [sum(precursor_idx_mask)=55540 sum(mass_error_mask)=118893 stop_rank=5000
2:40:03.961912 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:04.317289 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:05.040024 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:05.040483 INFO: Using score_cutoff 10.356643315887451 (fac=0.99, q=1)
2:40:05.040828 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:05.040903 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:05.040957 INFO: Updating optimization_manager: score_cutoff        : 10.78454321308136 -> 10.356643315887451
2:40:05.041012 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:05.045030 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:05.052941 INFO: === checking if optimization conditions were reached ===
2:40:05.054666 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:05.054773 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:40:05.054845 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:05.054903 INFO: ==============================================
2:40:05.054967 INFO: Starting optimization step 5.
2:40:05.055035 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:05.055092 INFO: Using rust extraction backend
2:40:05.055148 PROGRESS: Extracting batch of 5913 precursors
2:40:05.066252 INFO: === Search parameters used ===
2:40:05.066388 INFO: rt_error       : 805.6019897460938
2:40:05.066438 INFO: mobility_error : 0.1
2:40:05.066483 INFO: num_candidates : 3
2:40:05.066525 INFO: ms1_error      : 3
2:40:05.066566 INFO: ms2_error      : 10.0
2:40:05.066607 INFO: fwhm_rt        : 3.0
2:40:05.066646 INFO: quant_window   : 3
2:40:05.066685 INFO: ==============================================
2:40:05.178002 INFO: performing precursor FDR with 40 features
2:40:05.178109 INFO: Decoy channel: -1
2:40:05.178133 INFO: competitive: True
2:40:05.183316 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:05.187482 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
2:40:05.187607 INFO: Using random state 213139 for train-test-split
2:40:06.612393 INFO: Test AUC: 0.742
2:40:06.612501 INFO: Train AUC: 0.766
2:40:06.612532 INFO: AUC difference: 3.14%
2:40:06.869132 INFO: Resetting torch num_threads to 24
2:40:06.871746 PROGRESS: === Extracted 17733 precursors and 118858 fragments ===
2:40:06.872113 INFO: === FDR correction performed with classifier version 4 ===
2:40:06.872844 PROGRESS: ============================= Precursor FDR =============================
2:40:06.872932 PROGRESS: Total precursors accumulated: 2,541
2:40:06.872993 PROGRESS: Target precursors: 2,516 (99.02%)
2:40:06.873051 PROGRESS: Decoy precursors: 25 (0.98%)
2:40:06.873100 PROGRESS: 
2:40:06.873152 PROGRESS: Precursor Summary:
2:40:06.874744 PROGRESS: Channel   0:	 0.050 FDR: 2,516; 0.010 FDR: 2,516; 0.001 FDR: 1,546
2:40:06.874839 PROGRESS: 
2:40:06.874896 PROGRESS: Protein Summary:
2:40:06.877099 PROGRESS: Channel   0:	 0.050 FDR: 2,004; 0.010 FDR: 2,004; 0.001 FDR: 1,294
2:40:06.877195 PROGRESS: =========================================================================
2:40:06.877587 INFO: Target number of precursors reached.
2:40:06.904012 INFO: fragments_df: keeping 5000 of 118858 [sum(precursor_idx_mask)=56875 sum(mass_error_mask)=118858 stop_rank=5000
2:40:06.915245 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:07.282683 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:08.006103 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:08.006594 INFO: Using score_cutoff 10.277599372386932 (fac=0.99, q=1)
2:40:08.006920 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:08.007009 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:08.007071 INFO: Updating optimization_manager: score_cutoff        : 10.356643315887451 -> 10.277599372386932
2:40:08.007136 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:08.011135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:08.019057 INFO: === checking if optimization conditions were reached ===
2:40:08.020726 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:08.020826 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:40:08.020892 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:08.020951 INFO: ==============================================
2:40:08.021019 INFO: Starting optimization step 6.
2:40:08.021082 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:08.021146 INFO: Using rust extraction backend
2:40:08.021205 PROGRESS: Extracting batch of 5913 precursors
2:40:08.032679 INFO: === Search parameters used ===
2:40:08.032801 INFO: rt_error       : 805.6019897460938
2:40:08.032853 INFO: mobility_error : 0.1
2:40:08.032905 INFO: num_candidates : 3
2:40:08.032964 INFO: ms1_error      : 3
2:40:08.033008 INFO: ms2_error      : 10.0
2:40:08.033052 INFO: fwhm_rt        : 3.0
2:40:08.033094 INFO: quant_window   : 3
2:40:08.033135 INFO: ==============================================
2:40:08.152169 INFO: performing precursor FDR with 40 features
2:40:08.152278 INFO: Decoy channel: -1
2:40:08.152303 INFO: competitive: True
2:40:08.157509 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:08.161723 INFO: Estimating optimal hyperparameters - samples: 14,185, batch_size: 128, learning_rate: 1.77e-04
2:40:08.161859 INFO: Using random state 805520 for train-test-split
2:40:09.580661 INFO: Test AUC: 0.756
2:40:09.580769 INFO: Train AUC: 0.773
2:40:09.580797 INFO: AUC difference: 2.17%
2:40:09.839353 INFO: Resetting torch num_threads to 24
2:40:09.841900 PROGRESS: === Extracted 17732 precursors and 118813 fragments ===
2:40:09.842268 INFO: === FDR correction performed with classifier version 5 ===
2:40:09.842986 PROGRESS: ============================= Precursor FDR =============================
2:40:09.843076 PROGRESS: Total precursors accumulated: 2,508
2:40:09.843148 PROGRESS: Target precursors: 2,484 (99.04%)
2:40:09.843199 PROGRESS: Decoy precursors: 24 (0.96%)
2:40:09.843243 PROGRESS: 
2:40:09.843285 PROGRESS: Precursor Summary:
2:40:09.844862 PROGRESS: Channel   0:	 0.050 FDR: 2,484; 0.010 FDR: 2,484; 0.001 FDR: 1,632
2:40:09.844952 PROGRESS: 
2:40:09.845005 PROGRESS: Protein Summary:
2:40:09.847214 PROGRESS: Channel   0:	 0.050 FDR: 1,979; 0.010 FDR: 1,979; 0.001 FDR: 1,361
2:40:09.847307 PROGRESS: =========================================================================
2:40:09.847708 INFO: Target number of precursors reached.
2:40:09.873663 INFO: fragments_df: keeping 5000 of 118813 [sum(precursor_idx_mask)=56320 sum(mass_error_mask)=118813 stop_rank=5000
2:40:09.887230 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:10.246287 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:10.967026 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:10.967489 INFO: Using score_cutoff 10.404315314483643 (fac=0.99, q=1)
2:40:10.967799 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:10.967872 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:10.967926 INFO: Updating optimization_manager: score_cutoff        : 10.277599372386932 -> 10.404315314483643
2:40:10.967978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:10.971930 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:10.979781 INFO: === checking if optimization conditions were reached ===
2:40:10.981455 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:10.981552 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:40:10.981615 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:40:10.981669 INFO: ==============================================
2:40:10.981732 PROGRESS: Optimization finished for ms2_error.
2:40:10.992325 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:10.996109 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:11.003906 INFO: Starting optimization step 0.
2:40:11.004023 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:11.004093 INFO: Using rust extraction backend
2:40:11.004149 PROGRESS: Extracting batch of 5913 precursors
2:40:11.015254 INFO: === Search parameters used ===
2:40:11.015393 INFO: rt_error       : 805.6019897460938
2:40:11.015443 INFO: mobility_error : 0.1
2:40:11.015488 INFO: num_candidates : 3
2:40:11.015544 INFO: ms1_error      : 3
2:40:11.015585 INFO: ms2_error      : 10.0
2:40:11.015625 INFO: fwhm_rt        : 3.0
2:40:11.015665 INFO: quant_window   : 3
2:40:11.015704 INFO: ==============================================
2:40:11.128148 INFO: performing precursor FDR with 40 features
2:40:11.128255 INFO: Decoy channel: -1
2:40:11.128282 INFO: competitive: True
2:40:11.133405 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:11.137607 INFO: Estimating optimal hyperparameters - samples: 14,185, batch_size: 128, learning_rate: 1.77e-04
2:40:11.137738 INFO: Using random state 509746 for train-test-split
2:40:12.559568 INFO: Test AUC: 0.748
2:40:12.559749 INFO: Train AUC: 0.783
2:40:12.559785 INFO: AUC difference: 4.39%
2:40:12.820431 INFO: Resetting torch num_threads to 24
2:40:12.823009 PROGRESS: === Extracted 17732 precursors and 118827 fragments ===
2:40:12.823405 INFO: === FDR correction performed with classifier version 6 ===
2:40:12.824122 PROGRESS: ============================= Precursor FDR =============================
2:40:12.824210 PROGRESS: Total precursors accumulated: 2,580
2:40:12.824270 PROGRESS: Target precursors: 2,555 (99.03%)
2:40:12.824321 PROGRESS: Decoy precursors: 25 (0.97%)
2:40:12.824368 PROGRESS: 
2:40:12.824414 PROGRESS: Precursor Summary:
2:40:12.826075 PROGRESS: Channel   0:	 0.050 FDR: 2,555; 0.010 FDR: 2,555; 0.001 FDR: 2,225
2:40:12.826164 PROGRESS: 
2:40:12.826222 PROGRESS: Protein Summary:
2:40:12.828556 PROGRESS: Channel   0:	 0.050 FDR: 2,040; 0.010 FDR: 2,040; 0.001 FDR: 1,804
2:40:12.828654 PROGRESS: =========================================================================
2:40:12.829075 INFO: Target number of precursors reached.
2:40:12.855422 INFO: fragments_df: keeping 5000 of 118827 [sum(precursor_idx_mask)=57622 sum(mass_error_mask)=118827 stop_rank=5000
2:40:12.867838 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:13.234216 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:13.955477 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:13.955950 INFO: Using score_cutoff 10.138443662452698 (fac=0.99, q=1)
2:40:13.956278 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:13.956363 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:13.956419 INFO: Updating optimization_manager: score_cutoff        : 10.404315314483643 -> 10.138443662452698
2:40:13.956474 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:13.960422 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:13.968268 INFO: === checking if optimization conditions were reached ===
2:40:13.968390 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:40:13.971141 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 337.25165544674434
2:40:13.971242 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 337.2517.
2:40:13.971305 INFO: ==============================================
2:40:13.971373 INFO: Starting optimization step 1.
2:40:13.971431 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:13.971498 INFO: Using rust extraction backend
2:40:13.971556 PROGRESS: Extracting batch of 5913 precursors
2:40:13.982626 INFO: === Search parameters used ===
2:40:13.982746 INFO: rt_error       : 337.25165544674434
2:40:13.982796 INFO: mobility_error : 0.1
2:40:13.982841 INFO: num_candidates : 3
2:40:13.982883 INFO: ms1_error      : 3
2:40:13.982923 INFO: ms2_error      : 10.0
2:40:13.982962 INFO: fwhm_rt        : 3.0
2:40:13.983018 INFO: quant_window   : 3
2:40:13.983060 INFO: ==============================================
2:40:14.077634 INFO: performing precursor FDR with 40 features
2:40:14.077740 INFO: Decoy channel: -1
2:40:14.077763 INFO: competitive: True
2:40:14.082919 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:14.087020 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:40:14.087156 INFO: Using random state 509746 for train-test-split
2:40:15.519424 INFO: Test AUC: 0.761
2:40:15.519530 INFO: Train AUC: 0.780
2:40:15.519558 INFO: AUC difference: 2.46%
2:40:15.776018 INFO: Resetting torch num_threads to 24
2:40:15.778532 PROGRESS: === Extracted 17726 precursors and 117545 fragments ===
2:40:15.778890 INFO: === FDR correction performed with classifier version 6 ===
2:40:15.779632 PROGRESS: ============================= Precursor FDR =============================
2:40:15.779730 PROGRESS: Total precursors accumulated: 2,671
2:40:15.779788 PROGRESS: Target precursors: 2,645 (99.03%)
2:40:15.779835 PROGRESS: Decoy precursors: 26 (0.97%)
2:40:15.779879 PROGRESS: 
2:40:15.779921 PROGRESS: Precursor Summary:
2:40:15.781514 PROGRESS: Channel   0:	 0.050 FDR: 2,645; 0.010 FDR: 2,645; 0.001 FDR: 1,717
2:40:15.781601 PROGRESS: 
2:40:15.781654 PROGRESS: Protein Summary:
2:40:15.783903 PROGRESS: Channel   0:	 0.050 FDR: 2,096; 0.010 FDR: 2,096; 0.001 FDR: 1,424
2:40:15.784003 PROGRESS: =========================================================================
2:40:15.784381 INFO: Target number of precursors reached.
2:40:15.811082 INFO: fragments_df: keeping 5000 of 117545 [sum(precursor_idx_mask)=59135 sum(mass_error_mask)=117545 stop_rank=5000
2:40:15.822067 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:16.199986 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:16.916873 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:16.917356 INFO: Using score_cutoff 9.945449272155763 (fac=0.99, q=1)
2:40:16.917673 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:16.917750 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:16.917807 INFO: Updating optimization_manager: score_cutoff        : 10.138443662452698 -> 9.945449272155763
2:40:16.917861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:16.921798 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:16.929576 INFO: === checking if optimization conditions were reached ===
2:40:16.929687 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:40:16.932565 INFO: Updating optimization_manager: rt_error            : 337.25165544674434 -> 297.9912170493088
2:40:16.932668 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 297.9912.
2:40:16.932742 INFO: ==============================================
2:40:16.932811 INFO: Starting optimization step 2.
2:40:16.932868 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:16.932930 INFO: Using rust extraction backend
2:40:16.932986 PROGRESS: Extracting batch of 5913 precursors
2:40:16.944100 INFO: === Search parameters used ===
2:40:16.944219 INFO: rt_error       : 297.9912170493088
2:40:16.944270 INFO: mobility_error : 0.1
2:40:16.944315 INFO: num_candidates : 3
2:40:16.944358 INFO: ms1_error      : 3
2:40:16.944398 INFO: ms2_error      : 10.0
2:40:16.944446 INFO: fwhm_rt        : 3.0
2:40:16.944489 INFO: quant_window   : 3
2:40:16.944530 INFO: ==============================================
2:40:17.038807 INFO: performing precursor FDR with 40 features
2:40:17.038914 INFO: Decoy channel: -1
2:40:17.038939 INFO: competitive: True
2:40:17.044039 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:17.048071 INFO: Estimating optimal hyperparameters - samples: 14,181, batch_size: 128, learning_rate: 1.77e-04
2:40:17.048205 INFO: Using random state 509746 for train-test-split
2:40:18.468937 INFO: Test AUC: 0.756
2:40:18.469100 INFO: Train AUC: 0.779
2:40:18.469132 INFO: AUC difference: 2.89%
2:40:18.726372 INFO: Resetting torch num_threads to 24
2:40:18.728902 PROGRESS: === Extracted 17727 precursors and 116943 fragments ===
2:40:18.729293 INFO: === FDR correction performed with classifier version 6 ===
2:40:18.730028 PROGRESS: ============================= Precursor FDR =============================
2:40:18.730115 PROGRESS: Total precursors accumulated: 2,690
2:40:18.730173 PROGRESS: Target precursors: 2,664 (99.03%)
2:40:18.730222 PROGRESS: Decoy precursors: 26 (0.97%)
2:40:18.730267 PROGRESS: 
2:40:18.730310 PROGRESS: Precursor Summary:
2:40:18.731931 PROGRESS: Channel   0:	 0.050 FDR: 2,664; 0.010 FDR: 2,664; 0.001 FDR: 1,650
2:40:18.732029 PROGRESS: 
2:40:18.732084 PROGRESS: Protein Summary:
2:40:18.734317 PROGRESS: Channel   0:	 0.050 FDR: 2,112; 0.010 FDR: 2,112; 0.001 FDR: 1,378
2:40:18.734419 PROGRESS: =========================================================================
2:40:18.734785 INFO: Target number of precursors reached.
2:40:18.762625 INFO: fragments_df: keeping 5000 of 116943 [sum(precursor_idx_mask)=59428 sum(mass_error_mask)=116943 stop_rank=5000
2:40:18.774530 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:19.156853 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:19.874433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:19.874893 INFO: Using score_cutoff 10.145924036121368 (fac=0.99, q=1)
2:40:19.875246 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:19.875325 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:19.875377 INFO: Updating optimization_manager: score_cutoff        : 9.945449272155763 -> 10.145924036121368
2:40:19.875429 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:19.879365 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:19.887143 INFO: === checking if optimization conditions were reached ===
2:40:19.887260 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:40:19.890253 INFO: Updating optimization_manager: rt_error            : 297.9912170493088 -> 288.1637090531103
2:40:19.890348 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 288.1637.
2:40:19.890409 INFO: ==============================================
2:40:19.890474 INFO: Starting optimization step 3.
2:40:19.890529 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:19.890587 INFO: Using rust extraction backend
2:40:19.890640 PROGRESS: Extracting batch of 5913 precursors
2:40:19.901764 INFO: === Search parameters used ===
2:40:19.901897 INFO: rt_error       : 288.1637090531103
2:40:19.901949 INFO: mobility_error : 0.1
2:40:19.901994 INFO: num_candidates : 3
2:40:19.902046 INFO: ms1_error      : 3
2:40:19.902090 INFO: ms2_error      : 10.0
2:40:19.902130 INFO: fwhm_rt        : 3.0
2:40:19.902168 INFO: quant_window   : 3
2:40:19.902208 INFO: ==============================================
2:40:19.994518 INFO: performing precursor FDR with 40 features
2:40:19.994627 INFO: Decoy channel: -1
2:40:19.994651 INFO: competitive: True
2:40:19.999705 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:20.003833 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:40:20.003970 INFO: Using random state 509746 for train-test-split
2:40:21.429596 INFO: Test AUC: 0.766
2:40:21.429709 INFO: Train AUC: 0.776
2:40:21.429739 INFO: AUC difference: 1.31%
2:40:21.685642 INFO: Resetting torch num_threads to 24
2:40:21.688149 PROGRESS: === Extracted 17725 precursors and 116729 fragments ===
2:40:21.688511 INFO: === FDR correction performed with classifier version 6 ===
2:40:21.689221 PROGRESS: ============================= Precursor FDR =============================
2:40:21.689308 PROGRESS: Total precursors accumulated: 2,663
2:40:21.689368 PROGRESS: Target precursors: 2,637 (99.02%)
2:40:21.689420 PROGRESS: Decoy precursors: 26 (0.98%)
2:40:21.689466 PROGRESS: 
2:40:21.689511 PROGRESS: Precursor Summary:
2:40:21.691154 PROGRESS: Channel   0:	 0.050 FDR: 2,637; 0.010 FDR: 2,637; 0.001 FDR: 1,859
2:40:21.691247 PROGRESS: 
2:40:21.691304 PROGRESS: Protein Summary:
2:40:21.693535 PROGRESS: Channel   0:	 0.050 FDR: 2,095; 0.010 FDR: 2,095; 0.001 FDR: 1,531
2:40:21.693627 PROGRESS: =========================================================================
2:40:21.693995 INFO: Target number of precursors reached.
2:40:21.720383 INFO: fragments_df: keeping 5000 of 116729 [sum(precursor_idx_mask)=58836 sum(mass_error_mask)=116729 stop_rank=5000
2:40:21.731340 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:22.110556 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:22.829579 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:22.830039 INFO: Using score_cutoff 10.125415187072754 (fac=0.99, q=1)
2:40:22.830359 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:22.830435 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:22.830497 INFO: Updating optimization_manager: score_cutoff        : 10.145924036121368 -> 10.125415187072754
2:40:22.830548 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:22.834495 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:22.842477 INFO: === checking if optimization conditions were reached ===
2:40:22.842598 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:40:22.845531 INFO: Updating optimization_manager: rt_error            : 288.1637090531103 -> 251.21673202766414
2:40:22.845634 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 251.2167.
2:40:22.845695 INFO: ==============================================
2:40:22.845761 INFO: Starting optimization step 4.
2:40:22.845815 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:22.845872 INFO: Using rust extraction backend
2:40:22.845925 PROGRESS: Extracting batch of 5913 precursors
2:40:22.856941 INFO: === Search parameters used ===
2:40:22.857057 INFO: rt_error       : 251.21673202766414
2:40:22.857118 INFO: mobility_error : 0.1
2:40:22.857164 INFO: num_candidates : 3
2:40:22.857205 INFO: ms1_error      : 3
2:40:22.857245 INFO: ms2_error      : 10.0
2:40:22.857285 INFO: fwhm_rt        : 3.0
2:40:22.857324 INFO: quant_window   : 3
2:40:22.857363 INFO: ==============================================
2:40:22.946930 INFO: performing precursor FDR with 40 features
2:40:22.947048 INFO: Decoy channel: -1
2:40:22.947071 INFO: competitive: True
2:40:22.952063 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:22.956161 INFO: Estimating optimal hyperparameters - samples: 14,179, batch_size: 128, learning_rate: 1.77e-04
2:40:22.956294 INFO: Using random state 509746 for train-test-split
2:40:24.379861 INFO: Test AUC: 0.775
2:40:24.379972 INFO: Train AUC: 0.776
2:40:24.380001 INFO: AUC difference: 0.17%
2:40:24.628789 INFO: Resetting torch num_threads to 24
2:40:24.631301 PROGRESS: === Extracted 17724 precursors and 115662 fragments ===
2:40:24.631663 INFO: === FDR correction performed with classifier version 6 ===
2:40:24.632379 PROGRESS: ============================= Precursor FDR =============================
2:40:24.632461 PROGRESS: Total precursors accumulated: 2,712
2:40:24.632517 PROGRESS: Target precursors: 2,686 (99.04%)
2:40:24.632563 PROGRESS: Decoy precursors: 26 (0.96%)
2:40:24.632606 PROGRESS: 
2:40:24.632648 PROGRESS: Precursor Summary:
2:40:24.634256 PROGRESS: Channel   0:	 0.050 FDR: 2,686; 0.010 FDR: 2,686; 0.001 FDR: 1,686
2:40:24.634341 PROGRESS: 
2:40:24.634394 PROGRESS: Protein Summary:
2:40:24.636647 PROGRESS: Channel   0:	 0.050 FDR: 2,130; 0.010 FDR: 2,130; 0.001 FDR: 1,405
2:40:24.636743 PROGRESS: =========================================================================
2:40:24.637120 INFO: Target number of precursors reached.
2:40:24.663281 INFO: fragments_df: keeping 5000 of 115662 [sum(precursor_idx_mask)=59401 sum(mass_error_mask)=115662 stop_rank=5000
2:40:24.674206 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:25.059410 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:25.778723 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:25.779203 INFO: Using score_cutoff 9.811431776046753 (fac=0.99, q=1)
2:40:25.779524 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:25.779598 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:25.779651 INFO: Updating optimization_manager: score_cutoff        : 10.125415187072754 -> 9.811431776046753
2:40:25.779702 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:25.783670 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:25.791603 INFO: === checking if optimization conditions were reached ===
2:40:25.791724 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:40:25.794709 INFO: Updating optimization_manager: rt_error            : 251.21673202766414 -> 262.72542231109276
2:40:25.794806 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 262.7254.
2:40:25.794869 INFO: ==============================================
2:40:25.794936 INFO: Starting optimization step 5.
2:40:25.795005 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:25.795069 INFO: Using rust extraction backend
2:40:25.795123 PROGRESS: Extracting batch of 5913 precursors
2:40:25.806371 INFO: === Search parameters used ===
2:40:25.806487 INFO: rt_error       : 262.72542231109276
2:40:25.806538 INFO: mobility_error : 0.1
2:40:25.806583 INFO: num_candidates : 3
2:40:25.806626 INFO: ms1_error      : 3
2:40:25.806668 INFO: ms2_error      : 10.0
2:40:25.806710 INFO: fwhm_rt        : 3.0
2:40:25.806751 INFO: quant_window   : 3
2:40:25.806791 INFO: ==============================================
2:40:25.895995 INFO: performing precursor FDR with 40 features
2:40:25.896100 INFO: Decoy channel: -1
2:40:25.896124 INFO: competitive: True
2:40:25.901154 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:25.905118 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:40:25.905245 INFO: Using random state 509746 for train-test-split
2:40:27.308608 INFO: Test AUC: 0.769
2:40:27.308720 INFO: Train AUC: 0.780
2:40:27.308751 INFO: AUC difference: 1.44%
2:40:27.563319 INFO: Resetting torch num_threads to 24
2:40:27.565821 PROGRESS: === Extracted 17728 precursors and 116039 fragments ===
2:40:27.566180 INFO: === FDR correction performed with classifier version 6 ===
2:40:27.566894 PROGRESS: ============================= Precursor FDR =============================
2:40:27.566989 PROGRESS: Total precursors accumulated: 2,673
2:40:27.567054 PROGRESS: Target precursors: 2,647 (99.03%)
2:40:27.567105 PROGRESS: Decoy precursors: 26 (0.97%)
2:40:27.567153 PROGRESS: 
2:40:27.567199 PROGRESS: Precursor Summary:
2:40:27.568794 PROGRESS: Channel   0:	 0.050 FDR: 2,647; 0.010 FDR: 2,647; 0.001 FDR: 1,451
2:40:27.568884 PROGRESS: 
2:40:27.568940 PROGRESS: Protein Summary:
2:40:27.571158 PROGRESS: Channel   0:	 0.050 FDR: 2,100; 0.010 FDR: 2,100; 0.001 FDR: 1,220
2:40:27.571256 PROGRESS: =========================================================================
2:40:27.571641 INFO: Target number of precursors reached.
2:40:27.597560 INFO: fragments_df: keeping 5000 of 116039 [sum(precursor_idx_mask)=58778 sum(mass_error_mask)=116039 stop_rank=5000
2:40:27.608695 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:27.988468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:28.706171 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:28.706642 INFO: Using score_cutoff 9.915055123329163 (fac=0.99, q=1)
2:40:28.706948 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:28.707039 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:28.707094 INFO: Updating optimization_manager: score_cutoff        : 9.811431776046753 -> 9.915055123329163
2:40:28.707146 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:28.711063 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:28.718753 INFO: === checking if optimization conditions were reached ===
2:40:28.718872 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:40:28.719644 INFO: Updating optimization_manager: rt_error            : 262.72542231109276 -> 251.21673202766414
2:40:28.719770 INFO: Updating optimization_manager: classifier_version  : 6 -> 11
2:40:28.719866 INFO: Updating optimization_manager: score_cutoff        : 9.915055123329163 -> 9.811431776046753
2:40:28.719953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:28.720036 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:28.720136 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 251.2167 found after 6 searches.
2:40:28.720194 INFO: ==============================================
2:40:28.720256 PROGRESS: Optimization finished for rt_error.
2:40:28.730650 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:28.734405 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:28.742224 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:40:28.742326 PROGRESS: ==============================================
2:40:28.742390 PROGRESS: ms2_error      : 10.0000
2:40:28.742441 PROGRESS: rt_error       : 251.2167
2:40:28.742485 PROGRESS: ==============================================
2:40:28.743224 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:28.879582 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:29.231620 INFO: Using rust extraction backend
2:40:29.231951 PROGRESS: Extracting batch of 264177 precursors
2:40:29.646532 INFO: === Search parameters used ===
2:40:29.646800 INFO: rt_error       : 251.21673202766414
2:40:29.646854 INFO: mobility_error : 0.1
2:40:29.646901 INFO: num_candidates : 3
2:40:29.646944 INFO: ms1_error      : 3
2:40:29.646995 INFO: ms2_error      : 10.0
2:40:29.647040 INFO: fwhm_rt        : 3.0
2:40:29.647092 INFO: quant_window   : 3
2:40:29.647135 INFO: ==============================================
2:40:30.328778 INFO: Removed 107894 precursors with score below cutoff 9.811431776046753
2:40:31.002733 INFO: performing precursor FDR with 40 features
2:40:31.002846 INFO: Decoy channel: -1
2:40:31.002870 INFO: competitive: True
2:40:31.058018 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:31.091241 WARNING: FDR calculation for 365131 target and 319505 decoy PSMs
2:40:31.091372 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:40:31.264399 INFO: Estimating optimal hyperparameters - samples: 547,708, batch_size: 2,243, learning_rate: 7.40e-04
2:40:31.265298 INFO: Using random state 522008 for train-test-split
2:40:42.708838 INFO: Test AUC: 0.782
2:40:42.709001 INFO: Train AUC: 0.786
2:40:42.709099 INFO: AUC difference: 0.49%
2:40:43.231765 INFO: Resetting torch num_threads to 24
2:40:43.568148 PROGRESS: ============================= Precursor FDR =============================
2:40:43.568426 PROGRESS: Total precursors accumulated: 124,578
2:40:43.568499 PROGRESS: Target precursors: 123,345 (99.01%)
2:40:43.568554 PROGRESS: Decoy precursors: 1,233 (0.99%)
2:40:43.568603 PROGRESS: 
2:40:43.568650 PROGRESS: Precursor Summary:
2:40:43.607603 PROGRESS: Channel   0:	 0.050 FDR: 123,345; 0.010 FDR: 123,345; 0.001 FDR: 108,384
2:40:43.607863 PROGRESS: 
2:40:43.607926 PROGRESS: Protein Summary:
2:40:43.669710 PROGRESS: Channel   0:	 0.050 FDR: 10,513; 0.010 FDR: 10,513; 0.001 FDR: 10,354
2:40:43.669968 PROGRESS: =========================================================================
2:40:43.672848 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
2:40:43.875866 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
2:40:44.172040 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:40:44.368012 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
2:40:44.368159 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:40:44.368255 INFO: Initializing TimingManager
2:40:44.368851 INFO: Initializing RawFileManager
2:40:57.727861 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:40:57.735966 INFO: Determining DIA cycle
2:40:57.752284 INFO: Found cycle with start 0.00 min and length 300.
2:40:57.924665 INFO: RT (min)            : 0.0 - 26.9
2:40:57.924759 INFO: RT duration (sec)   : 1611.2
2:40:57.924788 INFO: RT duration (min)   : 26.9
2:40:57.924810 INFO: Cycle len (scans)   : 300
2:40:57.924831 INFO: Cycle len (sec)     : 1.65
2:40:57.924849 INFO: Number of cycles    : 977
2:40:57.924868 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:40:57.924899 INFO: Creating DIA data object took: 13.555943012237549
2:40:59.654009 INFO: Creating DIA data NG object took: 1.728977918624878
2:40:59.694312 INFO: Initializing CalibrationManager
2:40:59.694613 INFO: Setting up calibration estimators ..
2:40:59.694674 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:40:59.694760 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:40:59.694831 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:40:59.694884 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:40:59.694942 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:40:59.695011 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:40:59.695061 INFO: Done setting up calibration estimators.
2:40:59.695252 INFO: Initializing OptimizationManager
2:40:59.695385 INFO: initial parameter: ms1_error = 3
2:40:59.695437 INFO: initial parameter: ms2_error = 10
2:40:59.695483 INFO: initial parameter: rt_error = 805.6004638671875
2:40:59.695529 INFO: initial parameter: mobility_error = 0.1
2:40:59.695571 INFO: initial parameter: num_candidates = 1
2:40:59.695612 INFO: initial parameter: fwhm_rt = 5
2:40:59.695652 INFO: initial parameter: fwhm_mobility = 0.01
2:40:59.695693 INFO: initial parameter: score_cutoff = 0
2:40:59.695733 INFO: initial parameter: classifier_version = -1
2:40:59.695803 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:40:59.696063 INFO: FDRManager: loading saved state not requested, will be initialized.
2:40:59.696096 INFO: Initializing FDRManager
2:40:59.696127 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:40:59.735481 PROGRESS: Initializing spectral library: 133,585 target precursors potentially observable (0 removed)
2:40:59.761274 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:40:59.761635 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
2:40:59.761728 PROGRESS: Starting initial search for precursors.
2:40:59.761810 INFO: Starting optimization step 0.
2:40:59.761870 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:40:59.761925 INFO: Using rust extraction backend
2:40:59.761978 PROGRESS: Extracting batch of 1974 precursors
2:40:59.766679 INFO: === Search parameters used ===
2:40:59.766781 INFO: rt_error       : 805.6004638671875
2:40:59.766832 INFO: mobility_error : 0.1
2:40:59.766877 INFO: num_candidates : 1
2:40:59.766919 INFO: ms1_error      : 3
2:40:59.766960 INFO: ms2_error      : 10
2:40:59.767013 INFO: fwhm_rt        : 5
2:40:59.767056 INFO: quant_window   : 3
2:40:59.767096 INFO: ==============================================
2:40:59.798263 INFO: performing precursor FDR with 40 features
2:40:59.798329 INFO: Decoy channel: -1
2:40:59.798363 INFO: competitive: True
2:40:59.799655 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:59.801482 INFO: Estimating optimal hyperparameters - samples: 1,579, batch_size: 128, learning_rate: 1.77e-04
2:40:59.802294 INFO: Using random state 5186 for train-test-split
2:40:59.950734 INFO: Test AUC: 0.866
2:40:59.950826 INFO: Train AUC: 0.893
2:40:59.950855 INFO: AUC difference: 3.02%
2:41:00.191946 INFO: Resetting torch num_threads to 24
2:41:00.193635 PROGRESS: === Extracted 1974 precursors and 15329 fragments ===
2:41:00.193995 INFO: === FDR correction performed with classifier version -1 ===
2:41:00.194504 PROGRESS: ============================= Precursor FDR =============================
2:41:00.194586 PROGRESS: Total precursors accumulated: 538
2:41:00.194644 PROGRESS: Target precursors: 533 (99.07%)
2:41:00.194694 PROGRESS: Decoy precursors: 5 (0.93%)
2:41:00.194738 PROGRESS: 
2:41:00.194781 PROGRESS: Precursor Summary:
2:41:00.195878 PROGRESS: Channel   0:	 0.050 FDR:   533; 0.010 FDR:   533; 0.001 FDR:   388
2:41:00.195968 PROGRESS: 
2:41:00.196023 PROGRESS: Protein Summary:
2:41:00.197358 PROGRESS: Channel   0:	 0.050 FDR:   497; 0.010 FDR:   497; 0.001 FDR:   365
2:41:00.197443 PROGRESS: =========================================================================
2:41:00.197656 INFO: Target number of precursors not reached yet.
2:41:00.205327 INFO: Starting optimization step 1.
2:41:00.205434 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:41:00.205506 INFO: Using rust extraction backend
2:41:00.205561 PROGRESS: Extracting batch of 3939 precursors
2:41:00.213388 INFO: === Search parameters used ===
2:41:00.213484 INFO: rt_error       : 805.6004638671875
2:41:00.213533 INFO: mobility_error : 0.1
2:41:00.213578 INFO: num_candidates : 1
2:41:00.213619 INFO: ms1_error      : 3
2:41:00.213659 INFO: ms2_error      : 10
2:41:00.213700 INFO: fwhm_rt        : 5
2:41:00.213738 INFO: quant_window   : 3
2:41:00.213778 INFO: ==============================================
2:41:00.276129 INFO: performing precursor FDR with 40 features
2:41:00.276219 INFO: Decoy channel: -1
2:41:00.276243 INFO: competitive: True
2:41:00.280294 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:00.282606 INFO: Estimating optimal hyperparameters - samples: 4,729, batch_size: 128, learning_rate: 1.77e-04
2:41:00.282687 INFO: Using random state 271617 for train-test-split
2:41:00.732912 INFO: Test AUC: 0.903
2:41:00.733004 INFO: Train AUC: 0.902
2:41:00.733031 INFO: AUC difference: 0.13%
2:41:00.971203 INFO: Resetting torch num_threads to 24
2:41:00.974521 PROGRESS: === Extracted 5912 precursors and 45826 fragments ===
2:41:00.974894 INFO: === FDR correction performed with classifier version -1 ===
2:41:00.975581 PROGRESS: ============================= Precursor FDR =============================
2:41:00.975672 PROGRESS: Total precursors accumulated: 2,211
2:41:00.975729 PROGRESS: Target precursors: 2,190 (99.05%)
2:41:00.975777 PROGRESS: Decoy precursors: 21 (0.95%)
2:41:00.975821 PROGRESS: 
2:41:00.975863 PROGRESS: Precursor Summary:
2:41:00.977391 PROGRESS: Channel   0:	 0.050 FDR: 2,190; 0.010 FDR: 2,190; 0.001 FDR: 1,695
2:41:00.977479 PROGRESS: 
2:41:00.977532 PROGRESS: Protein Summary:
2:41:00.979619 PROGRESS: Channel   0:	 0.050 FDR: 1,765; 0.010 FDR: 1,765; 0.001 FDR: 1,407
2:41:00.979721 PROGRESS: =========================================================================
2:41:00.979990 INFO: Target number of precursors reached.
2:41:00.990408 INFO: fragments_df: keeping 5000 of 45826 [sum(precursor_idx_mask)=21746 sum(mass_error_mask)=45826 stop_rank=5000
2:41:01.001347 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:01.317448 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:02.035389 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:41:02.035849 INFO: Using score_cutoff 10.90244988899231 (fac=0.99, q=1)
2:41:02.036171 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:41:02.036246 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:41:02.036298 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.90244988899231
2:41:02.036353 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:02.040265 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:02.048034 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:41:02.048146 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:41:02.048224 INFO: Starting optimization step 2.
2:41:02.048287 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:02.048347 INFO: Using rust extraction backend
2:41:02.048402 PROGRESS: Extracting batch of 5913 precursors
2:41:02.059420 INFO: === Search parameters used ===
2:41:02.059529 INFO: rt_error       : 805.6004638671875
2:41:02.059579 INFO: mobility_error : 0.1
2:41:02.059623 INFO: num_candidates : 3
2:41:02.059669 INFO: ms1_error      : 3
2:41:02.059712 INFO: ms2_error      : 10
2:41:02.059752 INFO: fwhm_rt        : 3.0
2:41:02.059791 INFO: quant_window   : 3
2:41:02.059830 INFO: ==============================================
2:41:02.190005 INFO: performing precursor FDR with 40 features
2:41:02.190118 INFO: Decoy channel: -1
2:41:02.190141 INFO: competitive: True
2:41:02.195099 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:02.199190 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:41:02.199327 INFO: Using random state 980449 for train-test-split
2:41:03.589399 INFO: Test AUC: 0.709
2:41:03.589508 INFO: Train AUC: 0.725
2:41:03.589537 INFO: AUC difference: 2.22%
2:41:03.839788 INFO: Resetting torch num_threads to 24
2:41:03.842244 PROGRESS: === Extracted 17728 precursors and 119197 fragments ===
2:41:03.842608 INFO: === FDR correction performed with classifier version 1 ===
2:41:03.843303 PROGRESS: ============================= Precursor FDR =============================
2:41:03.843394 PROGRESS: Total precursors accumulated: 2,448
2:41:03.843455 PROGRESS: Target precursors: 2,424 (99.02%)
2:41:03.843508 PROGRESS: Decoy precursors: 24 (0.98%)
2:41:03.843556 PROGRESS: 
2:41:03.843602 PROGRESS: Precursor Summary:
2:41:03.845157 PROGRESS: Channel   0:	 0.050 FDR: 2,424; 0.010 FDR: 2,424; 0.001 FDR: 1,840
2:41:03.845246 PROGRESS: 
2:41:03.845310 PROGRESS: Protein Summary:
2:41:03.847462 PROGRESS: Channel   0:	 0.050 FDR: 1,937; 0.010 FDR: 1,937; 0.001 FDR: 1,517
2:41:03.847562 PROGRESS: =========================================================================
2:41:03.847920 INFO: Target number of precursors reached.
2:41:03.873524 INFO: fragments_df: keeping 5000 of 119197 [sum(precursor_idx_mask)=55453 sum(mass_error_mask)=119197 stop_rank=5000
2:41:03.884520 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:04.231185 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:04.950833 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:04.951327 INFO: Using score_cutoff 10.751456978702546 (fac=0.99, q=1)
2:41:04.951647 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:04.951724 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:04.951778 INFO: Updating optimization_manager: score_cutoff        : 10.90244988899231 -> 10.751456978702546
2:41:04.951832 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:04.955783 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:04.963452 INFO: === checking if optimization conditions were reached ===
2:41:04.965128 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:41:04.965225 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:41:04.965288 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:41:04.965345 INFO: ==============================================
2:41:04.965419 INFO: Starting optimization step 3.
2:41:04.965478 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:04.965538 INFO: Using rust extraction backend
2:41:04.965594 PROGRESS: Extracting batch of 5913 precursors
2:41:04.976642 INFO: === Search parameters used ===
2:41:04.976753 INFO: rt_error       : 805.6004638671875
2:41:04.976804 INFO: mobility_error : 0.1
2:41:04.976851 INFO: num_candidates : 3
2:41:04.976894 INFO: ms1_error      : 3
2:41:04.976937 INFO: ms2_error      : 10.0
2:41:04.976988 INFO: fwhm_rt        : 3.0
2:41:04.977029 INFO: quant_window   : 3
2:41:04.977067 INFO: ==============================================
2:41:05.090875 INFO: performing precursor FDR with 40 features
2:41:05.090997 INFO: Decoy channel: -1
2:41:05.091022 INFO: competitive: True
2:41:05.096102 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:05.100181 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:41:05.100312 INFO: Using random state 173112 for train-test-split
2:41:06.496165 INFO: Test AUC: 0.736
2:41:06.496273 INFO: Train AUC: 0.737
2:41:06.496300 INFO: AUC difference: 0.11%
2:41:06.749678 INFO: Resetting torch num_threads to 24
2:41:06.752154 PROGRESS: === Extracted 17728 precursors and 119226 fragments ===
2:41:06.752512 INFO: === FDR correction performed with classifier version 2 ===
2:41:06.753194 PROGRESS: ============================= Precursor FDR =============================
2:41:06.753276 PROGRESS: Total precursors accumulated: 2,427
2:41:06.753332 PROGRESS: Target precursors: 2,403 (99.01%)
2:41:06.753380 PROGRESS: Decoy precursors: 24 (0.99%)
2:41:06.753423 PROGRESS: 
2:41:06.753467 PROGRESS: Precursor Summary:
2:41:06.755044 PROGRESS: Channel   0:	 0.050 FDR: 2,403; 0.010 FDR: 2,403; 0.001 FDR: 1,782
2:41:06.755144 PROGRESS: 
2:41:06.755199 PROGRESS: Protein Summary:
2:41:06.757345 PROGRESS: Channel   0:	 0.050 FDR: 1,922; 0.010 FDR: 1,922; 0.001 FDR: 1,477
2:41:06.757432 PROGRESS: =========================================================================
2:41:06.757789 INFO: Target number of precursors reached.
2:41:06.783267 INFO: fragments_df: keeping 5000 of 119226 [sum(precursor_idx_mask)=55026 sum(mass_error_mask)=119226 stop_rank=5000
2:41:06.794452 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:07.141531 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:07.858746 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:07.859229 INFO: Using score_cutoff 10.86581266822815 (fac=0.99, q=1)
2:41:07.859540 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:07.859613 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:07.859665 INFO: Updating optimization_manager: score_cutoff        : 10.751456978702546 -> 10.86581266822815
2:41:07.859715 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:07.863636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:07.871314 INFO: === checking if optimization conditions were reached ===
2:41:07.872976 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:41:07.873070 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:41:07.873132 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:41:07.873194 INFO: ==============================================
2:41:07.873258 INFO: Starting optimization step 4.
2:41:07.873313 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:07.873370 INFO: Using rust extraction backend
2:41:07.873424 PROGRESS: Extracting batch of 5913 precursors
2:41:07.884502 INFO: === Search parameters used ===
2:41:07.884628 INFO: rt_error       : 805.6004638671875
2:41:07.884679 INFO: mobility_error : 0.1
2:41:07.884723 INFO: num_candidates : 3
2:41:07.884767 INFO: ms1_error      : 3
2:41:07.884807 INFO: ms2_error      : 10.0
2:41:07.884847 INFO: fwhm_rt        : 3.0
2:41:07.884886 INFO: quant_window   : 3
2:41:07.884924 INFO: ==============================================
2:41:07.996597 INFO: performing precursor FDR with 40 features
2:41:07.996712 INFO: Decoy channel: -1
2:41:07.996737 INFO: competitive: True
2:41:08.001740 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:08.005807 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:41:08.005940 INFO: Using random state 257007 for train-test-split
2:41:09.403639 INFO: Test AUC: 0.739
2:41:09.403748 INFO: Train AUC: 0.751
2:41:09.403779 INFO: AUC difference: 1.58%
2:41:09.660604 INFO: Resetting torch num_threads to 24
2:41:09.663175 PROGRESS: === Extracted 17728 precursors and 119196 fragments ===
2:41:09.663547 INFO: === FDR correction performed with classifier version 3 ===
2:41:09.664263 PROGRESS: ============================= Precursor FDR =============================
2:41:09.664349 PROGRESS: Total precursors accumulated: 2,533
2:41:09.664407 PROGRESS: Target precursors: 2,508 (99.01%)
2:41:09.664466 PROGRESS: Decoy precursors: 25 (0.99%)
2:41:09.664513 PROGRESS: 
2:41:09.664568 PROGRESS: Precursor Summary:
2:41:09.666157 PROGRESS: Channel   0:	 0.050 FDR: 2,508; 0.010 FDR: 2,508; 0.001 FDR: 2,004
2:41:09.666242 PROGRESS: 
2:41:09.666293 PROGRESS: Protein Summary:
2:41:09.668494 PROGRESS: Channel   0:	 0.050 FDR: 1,995; 0.010 FDR: 1,995; 0.001 FDR: 1,632
2:41:09.668587 PROGRESS: =========================================================================
2:41:09.668930 INFO: Target number of precursors reached.
2:41:09.694885 INFO: fragments_df: keeping 5000 of 119196 [sum(precursor_idx_mask)=57039 sum(mass_error_mask)=119196 stop_rank=5000
2:41:09.705940 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:10.073164 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:10.794908 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:10.795518 INFO: Using score_cutoff 10.348304315185546 (fac=0.99, q=1)
2:41:10.795875 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:10.795952 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:10.796004 INFO: Updating optimization_manager: score_cutoff        : 10.86581266822815 -> 10.348304315185546
2:41:10.796063 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:10.800236 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:10.808017 INFO: === checking if optimization conditions were reached ===
2:41:10.809678 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:41:10.809783 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:41:10.809848 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:41:10.809903 INFO: ==============================================
2:41:10.809969 INFO: Starting optimization step 5.
2:41:10.810027 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:10.810092 INFO: Using rust extraction backend
2:41:10.810152 PROGRESS: Extracting batch of 5913 precursors
2:41:10.821234 INFO: === Search parameters used ===
2:41:10.821362 INFO: rt_error       : 805.6004638671875
2:41:10.821413 INFO: mobility_error : 0.1
2:41:10.821456 INFO: num_candidates : 3
2:41:10.821497 INFO: ms1_error      : 3
2:41:10.821538 INFO: ms2_error      : 10.0
2:41:10.821577 INFO: fwhm_rt        : 3.0
2:41:10.821619 INFO: quant_window   : 3
2:41:10.821659 INFO: ==============================================
2:41:10.931311 INFO: performing precursor FDR with 40 features
2:41:10.931420 INFO: Decoy channel: -1
2:41:10.931443 INFO: competitive: True
2:41:10.936579 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:10.940614 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:41:10.940740 INFO: Using random state 521164 for train-test-split
2:41:12.350545 INFO: Test AUC: 0.747
2:41:12.350659 INFO: Train AUC: 0.758
2:41:12.350688 INFO: AUC difference: 1.46%
2:41:12.610615 INFO: Resetting torch num_threads to 24
2:41:12.613964 PROGRESS: === Extracted 17728 precursors and 119172 fragments ===
2:41:12.614341 INFO: === FDR correction performed with classifier version 4 ===
2:41:12.615090 PROGRESS: ============================= Precursor FDR =============================
2:41:12.615185 PROGRESS: Total precursors accumulated: 2,626
2:41:12.615242 PROGRESS: Target precursors: 2,600 (99.01%)
2:41:12.615290 PROGRESS: Decoy precursors: 26 (0.99%)
2:41:12.615339 PROGRESS: 
2:41:12.615384 PROGRESS: Precursor Summary:
2:41:12.617016 PROGRESS: Channel   0:	 0.050 FDR: 2,600; 0.010 FDR: 2,597; 0.001 FDR: 2,043
2:41:12.617108 PROGRESS: 
2:41:12.617163 PROGRESS: Protein Summary:
2:41:12.619433 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,053; 0.001 FDR: 1,663
2:41:12.619528 PROGRESS: =========================================================================
2:41:12.619915 INFO: Target number of precursors reached.
2:41:12.646904 INFO: fragments_df: keeping 5000 of 119172 [sum(precursor_idx_mask)=58754 sum(mass_error_mask)=119172 stop_rank=5000
2:41:12.661392 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:13.040716 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:13.763741 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:13.764224 INFO: Using score_cutoff 10.228013748550415 (fac=0.99, q=1)
2:41:13.764535 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:13.764615 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:13.764671 INFO: Updating optimization_manager: score_cutoff        : 10.348304315185546 -> 10.228013748550415
2:41:13.764731 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:13.768758 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:13.776671 INFO: === checking if optimization conditions were reached ===
2:41:13.778323 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:41:13.778422 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:41:13.778487 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:41:13.778545 INFO: ==============================================
2:41:13.778616 INFO: Starting optimization step 6.
2:41:13.778681 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:13.778742 INFO: Using rust extraction backend
2:41:13.778798 PROGRESS: Extracting batch of 5913 precursors
2:41:13.790304 INFO: === Search parameters used ===
2:41:13.790426 INFO: rt_error       : 805.6004638671875
2:41:13.790482 INFO: mobility_error : 0.1
2:41:13.790531 INFO: num_candidates : 3
2:41:13.790576 INFO: ms1_error      : 3
2:41:13.790619 INFO: ms2_error      : 10.0
2:41:13.790662 INFO: fwhm_rt        : 3.0
2:41:13.790703 INFO: quant_window   : 3
2:41:13.790750 INFO: ==============================================
2:41:13.907954 INFO: performing precursor FDR with 40 features
2:41:13.908061 INFO: Decoy channel: -1
2:41:13.908087 INFO: competitive: True
2:41:13.915015 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:13.919050 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:41:13.919214 INFO: Using random state 770360 for train-test-split
2:41:15.322747 INFO: Test AUC: 0.757
2:41:15.322857 INFO: Train AUC: 0.763
2:41:15.322888 INFO: AUC difference: 0.77%
2:41:15.576226 INFO: Resetting torch num_threads to 24
2:41:15.578731 PROGRESS: === Extracted 17728 precursors and 119159 fragments ===
2:41:15.579128 INFO: === FDR correction performed with classifier version 5 ===
2:41:15.579839 PROGRESS: ============================= Precursor FDR =============================
2:41:15.579926 PROGRESS: Total precursors accumulated: 2,594
2:41:15.579989 PROGRESS: Target precursors: 2,569 (99.04%)
2:41:15.580041 PROGRESS: Decoy precursors: 25 (0.96%)
2:41:15.580086 PROGRESS: 
2:41:15.580129 PROGRESS: Precursor Summary:
2:41:15.581730 PROGRESS: Channel   0:	 0.050 FDR: 2,569; 0.010 FDR: 2,569; 0.001 FDR: 2,019
2:41:15.581817 PROGRESS: 
2:41:15.581872 PROGRESS: Protein Summary:
2:41:15.584103 PROGRESS: Channel   0:	 0.050 FDR: 2,029; 0.010 FDR: 2,029; 0.001 FDR: 1,653
2:41:15.584199 PROGRESS: =========================================================================
2:41:15.584599 INFO: Target number of precursors reached.
2:41:15.610759 INFO: fragments_df: keeping 5000 of 119159 [sum(precursor_idx_mask)=58129 sum(mass_error_mask)=119159 stop_rank=5000
2:41:15.625198 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:16.000984 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:16.719981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:16.720473 INFO: Using score_cutoff 10.03849187736511 (fac=0.99, q=1)
2:41:16.720783 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:16.720856 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:16.720908 INFO: Updating optimization_manager: score_cutoff        : 10.228013748550415 -> 10.03849187736511
2:41:16.720962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:16.724941 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:16.732547 INFO: === checking if optimization conditions were reached ===
2:41:16.734203 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:41:16.734294 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:41:16.734356 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:41:16.734417 INFO: ==============================================
2:41:16.734478 PROGRESS: Optimization finished for ms2_error.
2:41:16.745733 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:16.749500 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:16.757227 INFO: Starting optimization step 0.
2:41:16.757337 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:16.757409 INFO: Using rust extraction backend
2:41:16.757466 PROGRESS: Extracting batch of 5913 precursors
2:41:16.768561 INFO: === Search parameters used ===
2:41:16.768681 INFO: rt_error       : 805.6004638671875
2:41:16.768734 INFO: mobility_error : 0.1
2:41:16.768780 INFO: num_candidates : 3
2:41:16.768823 INFO: ms1_error      : 3
2:41:16.768864 INFO: ms2_error      : 10.0
2:41:16.768908 INFO: fwhm_rt        : 3.0
2:41:16.768954 INFO: quant_window   : 3
2:41:16.768996 INFO: ==============================================
2:41:16.878201 INFO: performing precursor FDR with 40 features
2:41:16.878311 INFO: Decoy channel: -1
2:41:16.878334 INFO: competitive: True
2:41:16.883368 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:16.887402 INFO: Estimating optimal hyperparameters - samples: 14,182, batch_size: 128, learning_rate: 1.77e-04
2:41:16.887537 INFO: Using random state 513152 for train-test-split
2:41:18.299639 INFO: Test AUC: 0.762
2:41:18.299789 INFO: Train AUC: 0.771
2:41:18.299822 INFO: AUC difference: 1.15%
2:41:18.555443 INFO: Resetting torch num_threads to 24
2:41:18.557982 PROGRESS: === Extracted 17728 precursors and 119155 fragments ===
2:41:18.558363 INFO: === FDR correction performed with classifier version 6 ===
2:41:18.559098 PROGRESS: ============================= Precursor FDR =============================
2:41:18.559191 PROGRESS: Total precursors accumulated: 2,641
2:41:18.559251 PROGRESS: Target precursors: 2,615 (99.02%)
2:41:18.559303 PROGRESS: Decoy precursors: 26 (0.98%)
2:41:18.559353 PROGRESS: 
2:41:18.559399 PROGRESS: Precursor Summary:
2:41:18.561041 PROGRESS: Channel   0:	 0.050 FDR: 2,615; 0.010 FDR: 2,615; 0.001 FDR: 2,244
2:41:18.561132 PROGRESS: 
2:41:18.561189 PROGRESS: Protein Summary:
2:41:18.563493 PROGRESS: Channel   0:	 0.050 FDR: 2,066; 0.010 FDR: 2,066; 0.001 FDR: 1,806
2:41:18.563588 PROGRESS: =========================================================================
2:41:18.563979 INFO: Target number of precursors reached.
2:41:18.590130 INFO: fragments_df: keeping 5000 of 119155 [sum(precursor_idx_mask)=59059 sum(mass_error_mask)=119155 stop_rank=5000
2:41:18.601338 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:18.984720 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:19.701085 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:19.701555 INFO: Using score_cutoff 9.988789227676392 (fac=0.99, q=1)
2:41:19.701876 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:19.701960 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:19.702018 INFO: Updating optimization_manager: score_cutoff        : 10.03849187736511 -> 9.988789227676392
2:41:19.702080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:19.706047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:19.713617 INFO: === checking if optimization conditions were reached ===
2:41:19.713741 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:41:19.716527 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 542.8298822691492
2:41:19.716630 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 542.8299.
2:41:19.716694 INFO: ==============================================
2:41:19.716761 INFO: Starting optimization step 1.
2:41:19.716820 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:19.716880 INFO: Using rust extraction backend
2:41:19.716937 PROGRESS: Extracting batch of 5913 precursors
2:41:19.727987 INFO: === Search parameters used ===
2:41:19.728109 INFO: rt_error       : 542.8298822691492
2:41:19.728162 INFO: mobility_error : 0.1
2:41:19.728208 INFO: num_candidates : 3
2:41:19.728252 INFO: ms1_error      : 3
2:41:19.728294 INFO: ms2_error      : 10.0
2:41:19.728335 INFO: fwhm_rt        : 3.0
2:41:19.728388 INFO: quant_window   : 3
2:41:19.728432 INFO: ==============================================
2:41:19.834300 INFO: performing precursor FDR with 40 features
2:41:19.834411 INFO: Decoy channel: -1
2:41:19.834435 INFO: competitive: True
2:41:19.839437 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:19.843376 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:41:19.843503 INFO: Using random state 513152 for train-test-split
2:41:21.239678 INFO: Test AUC: 0.756
2:41:21.239797 INFO: Train AUC: 0.772
2:41:21.239827 INFO: AUC difference: 2.06%
2:41:21.494192 INFO: Resetting torch num_threads to 24
2:41:21.496715 PROGRESS: === Extracted 17725 precursors and 119045 fragments ===
2:41:21.497084 INFO: === FDR correction performed with classifier version 6 ===
2:41:21.497793 PROGRESS: ============================= Precursor FDR =============================
2:41:21.497874 PROGRESS: Total precursors accumulated: 2,661
2:41:21.497931 PROGRESS: Target precursors: 2,635 (99.02%)
2:41:21.497977 PROGRESS: Decoy precursors: 26 (0.98%)
2:41:21.498020 PROGRESS: 
2:41:21.498062 PROGRESS: Precursor Summary:
2:41:21.499703 PROGRESS: Channel   0:	 0.050 FDR: 2,635; 0.010 FDR: 2,635; 0.001 FDR: 2,142
2:41:21.499794 PROGRESS: 
2:41:21.499848 PROGRESS: Protein Summary:
2:41:21.502107 PROGRESS: Channel   0:	 0.050 FDR: 2,080; 0.010 FDR: 2,080; 0.001 FDR: 1,737
2:41:21.502194 PROGRESS: =========================================================================
2:41:21.502559 INFO: Target number of precursors reached.
2:41:21.528948 INFO: fragments_df: keeping 5000 of 119045 [sum(precursor_idx_mask)=59325 sum(mass_error_mask)=119045 stop_rank=5000
2:41:21.539948 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:21.922626 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:22.639217 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:22.639693 INFO: Using score_cutoff 9.968182065582276 (fac=0.99, q=1)
2:41:22.640006 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:22.640082 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:22.640134 INFO: Updating optimization_manager: score_cutoff        : 9.988789227676392 -> 9.968182065582276
2:41:22.640185 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:22.644154 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:22.651726 INFO: === checking if optimization conditions were reached ===
2:41:22.651843 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:41:22.654691 INFO: Updating optimization_manager: rt_error            : 542.8298822691492 -> 497.3755320738918
2:41:22.654794 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 497.3755.
2:41:22.654868 INFO: ==============================================
2:41:22.654937 INFO: Starting optimization step 2.
2:41:22.655010 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:22.655074 INFO: Using rust extraction backend
2:41:22.655128 PROGRESS: Extracting batch of 5913 precursors
2:41:22.666112 INFO: === Search parameters used ===
2:41:22.666226 INFO: rt_error       : 497.3755320738918
2:41:22.666276 INFO: mobility_error : 0.1
2:41:22.666321 INFO: num_candidates : 3
2:41:22.666370 INFO: ms1_error      : 3
2:41:22.666412 INFO: ms2_error      : 10.0
2:41:22.666463 INFO: fwhm_rt        : 3.0
2:41:22.666507 INFO: quant_window   : 3
2:41:22.666548 INFO: ==============================================
2:41:22.776406 INFO: performing precursor FDR with 40 features
2:41:22.776515 INFO: Decoy channel: -1
2:41:22.776538 INFO: competitive: True
2:41:22.781433 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:22.785372 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:41:22.785492 INFO: Using random state 513152 for train-test-split
2:41:24.178103 INFO: Test AUC: 0.750
2:41:24.178211 INFO: Train AUC: 0.770
2:41:24.178241 INFO: AUC difference: 2.65%
2:41:24.431909 INFO: Resetting torch num_threads to 24
2:41:24.434402 PROGRESS: === Extracted 17726 precursors and 118919 fragments ===
2:41:24.434764 INFO: === FDR correction performed with classifier version 6 ===
2:41:24.435485 PROGRESS: ============================= Precursor FDR =============================
2:41:24.435576 PROGRESS: Total precursors accumulated: 2,683
2:41:24.435636 PROGRESS: Target precursors: 2,657 (99.03%)
2:41:24.435688 PROGRESS: Decoy precursors: 26 (0.97%)
2:41:24.435738 PROGRESS: 
2:41:24.435785 PROGRESS: Precursor Summary:
2:41:24.437419 PROGRESS: Channel   0:	 0.050 FDR: 2,657; 0.010 FDR: 2,657; 0.001 FDR: 2,325
2:41:24.437508 PROGRESS: 
2:41:24.437565 PROGRESS: Protein Summary:
2:41:24.439903 PROGRESS: Channel   0:	 0.050 FDR: 2,094; 0.010 FDR: 2,094; 0.001 FDR: 1,863
2:41:24.439998 PROGRESS: =========================================================================
2:41:24.440372 INFO: Target number of precursors reached.
2:41:24.466496 INFO: fragments_df: keeping 5000 of 118919 [sum(precursor_idx_mask)=59704 sum(mass_error_mask)=118919 stop_rank=5000
2:41:24.477537 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:24.863909 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:25.578046 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:25.578513 INFO: Using score_cutoff 9.74620259513855 (fac=0.99, q=1)
2:41:25.578820 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:25.578898 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:25.578953 INFO: Updating optimization_manager: score_cutoff        : 9.968182065582276 -> 9.74620259513855
2:41:25.579041 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:25.582986 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:25.590869 INFO: === checking if optimization conditions were reached ===
2:41:25.590999 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:41:25.593957 INFO: Updating optimization_manager: rt_error            : 497.3755320738918 -> 472.65844594045325
2:41:25.594058 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 472.6584.
2:41:25.594124 INFO: ==============================================
2:41:25.594201 INFO: Starting optimization step 3.
2:41:25.594262 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:25.594324 INFO: Using rust extraction backend
2:41:25.594382 PROGRESS: Extracting batch of 5913 precursors
2:41:25.605391 INFO: === Search parameters used ===
2:41:25.605503 INFO: rt_error       : 472.65844594045325
2:41:25.605556 INFO: mobility_error : 0.1
2:41:25.605602 INFO: num_candidates : 3
2:41:25.605657 INFO: ms1_error      : 3
2:41:25.605709 INFO: ms2_error      : 10.0
2:41:25.605757 INFO: fwhm_rt        : 3.0
2:41:25.605797 INFO: quant_window   : 3
2:41:25.605837 INFO: ==============================================
2:41:25.720409 INFO: performing precursor FDR with 40 features
2:41:25.720519 INFO: Decoy channel: -1
2:41:25.720543 INFO: competitive: True
2:41:25.725312 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:25.729203 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:41:25.729321 INFO: Using random state 513152 for train-test-split
2:41:27.131327 INFO: Test AUC: 0.753
2:41:27.131435 INFO: Train AUC: 0.772
2:41:27.131464 INFO: AUC difference: 2.46%
2:41:27.386822 INFO: Resetting torch num_threads to 24
2:41:27.389317 PROGRESS: === Extracted 17726 precursors and 118879 fragments ===
2:41:27.389676 INFO: === FDR correction performed with classifier version 6 ===
2:41:27.390388 PROGRESS: ============================= Precursor FDR =============================
2:41:27.390470 PROGRESS: Total precursors accumulated: 2,684
2:41:27.390527 PROGRESS: Target precursors: 2,658 (99.03%)
2:41:27.390576 PROGRESS: Decoy precursors: 26 (0.97%)
2:41:27.390623 PROGRESS: 
2:41:27.390666 PROGRESS: Precursor Summary:
2:41:27.392313 PROGRESS: Channel   0:	 0.050 FDR: 2,658; 0.010 FDR: 2,658; 0.001 FDR: 2,230
2:41:27.392402 PROGRESS: 
2:41:27.392455 PROGRESS: Protein Summary:
2:41:27.394723 PROGRESS: Channel   0:	 0.050 FDR: 2,097; 0.010 FDR: 2,097; 0.001 FDR: 1,803
2:41:27.394808 PROGRESS: =========================================================================
2:41:27.395178 INFO: Target number of precursors reached.
2:41:27.421445 INFO: fragments_df: keeping 5000 of 118879 [sum(precursor_idx_mask)=59741 sum(mass_error_mask)=118879 stop_rank=5000
2:41:27.432576 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:27.822026 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:28.535876 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:28.536351 INFO: Using score_cutoff 9.983958245658874 (fac=0.99, q=1)
2:41:28.536666 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:28.536740 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:28.536793 INFO: Updating optimization_manager: score_cutoff        : 9.74620259513855 -> 9.983958245658874
2:41:28.536844 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:28.540813 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:28.548588 INFO: === checking if optimization conditions were reached ===
2:41:28.548697 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:41:28.551627 INFO: Updating optimization_manager: rt_error            : 472.65844594045325 -> 530.5616436586203
2:41:28.551730 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 530.5616.
2:41:28.551793 INFO: ==============================================
2:41:28.551860 INFO: Starting optimization step 4.
2:41:28.551916 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:28.551975 INFO: Using rust extraction backend
2:41:28.552029 PROGRESS: Extracting batch of 5913 precursors
2:41:28.563074 INFO: === Search parameters used ===
2:41:28.563184 INFO: rt_error       : 530.5616436586203
2:41:28.563243 INFO: mobility_error : 0.1
2:41:28.563290 INFO: num_candidates : 3
2:41:28.563334 INFO: ms1_error      : 3
2:41:28.563375 INFO: ms2_error      : 10.0
2:41:28.563416 INFO: fwhm_rt        : 3.0
2:41:28.563454 INFO: quant_window   : 3
2:41:28.563493 INFO: ==============================================
2:41:28.666051 INFO: performing precursor FDR with 40 features
2:41:28.666167 INFO: Decoy channel: -1
2:41:28.666193 INFO: competitive: True
2:41:28.670938 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:28.674860 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:41:28.675002 INFO: Using random state 513152 for train-test-split
2:41:30.075917 INFO: Test AUC: 0.758
2:41:30.076025 INFO: Train AUC: 0.770
2:41:30.076055 INFO: AUC difference: 1.50%
2:41:30.331342 INFO: Resetting torch num_threads to 24
2:41:30.333807 PROGRESS: === Extracted 17725 precursors and 118998 fragments ===
2:41:30.334169 INFO: === FDR correction performed with classifier version 6 ===
2:41:30.334879 PROGRESS: ============================= Precursor FDR =============================
2:41:30.334967 PROGRESS: Total precursors accumulated: 2,661
2:41:30.335041 PROGRESS: Target precursors: 2,635 (99.02%)
2:41:30.335093 PROGRESS: Decoy precursors: 26 (0.98%)
2:41:30.335139 PROGRESS: 
2:41:30.335183 PROGRESS: Precursor Summary:
2:41:30.336816 PROGRESS: Channel   0:	 0.050 FDR: 2,635; 0.010 FDR: 2,635; 0.001 FDR: 2,225
2:41:30.336905 PROGRESS: 
2:41:30.336960 PROGRESS: Protein Summary:
2:41:30.339225 PROGRESS: Channel   0:	 0.050 FDR: 2,077; 0.010 FDR: 2,077; 0.001 FDR: 1,791
2:41:30.339319 PROGRESS: =========================================================================
2:41:30.339680 INFO: Target number of precursors reached.
2:41:30.365800 INFO: fragments_df: keeping 5000 of 118998 [sum(precursor_idx_mask)=59339 sum(mass_error_mask)=118998 stop_rank=5000
2:41:30.376945 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:30.762660 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:31.477968 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:31.478445 INFO: Using score_cutoff 9.854686966896057 (fac=0.99, q=1)
2:41:31.478756 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:31.478832 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:31.478887 INFO: Updating optimization_manager: score_cutoff        : 9.983958245658874 -> 9.854686966896057
2:41:31.478941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:31.482951 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:31.490723 INFO: === checking if optimization conditions were reached ===
2:41:31.490831 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:41:31.493773 INFO: Updating optimization_manager: rt_error            : 530.5616436586203 -> 526.8121171576956
2:41:31.493878 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 526.8121.
2:41:31.493950 INFO: ==============================================
2:41:31.494017 INFO: Starting optimization step 5.
2:41:31.494072 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:31.494129 INFO: Using rust extraction backend
2:41:31.494182 PROGRESS: Extracting batch of 5913 precursors
2:41:31.505271 INFO: === Search parameters used ===
2:41:31.505379 INFO: rt_error       : 526.8121171576956
2:41:31.505429 INFO: mobility_error : 0.1
2:41:31.505472 INFO: num_candidates : 3
2:41:31.505514 INFO: ms1_error      : 3
2:41:31.505555 INFO: ms2_error      : 10.0
2:41:31.505594 INFO: fwhm_rt        : 3.0
2:41:31.505634 INFO: quant_window   : 3
2:41:31.505675 INFO: ==============================================
2:41:31.610087 INFO: performing precursor FDR with 40 features
2:41:31.610196 INFO: Decoy channel: -1
2:41:31.610220 INFO: competitive: True
2:41:31.614984 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:31.618835 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:41:31.618953 INFO: Using random state 513152 for train-test-split
2:41:32.997033 INFO: Test AUC: 0.753
2:41:32.997136 INFO: Train AUC: 0.772
2:41:32.997164 INFO: AUC difference: 2.43%
2:41:33.249803 INFO: Resetting torch num_threads to 24
2:41:33.252303 PROGRESS: === Extracted 17725 precursors and 118993 fragments ===
2:41:33.252661 INFO: === FDR correction performed with classifier version 6 ===
2:41:33.253377 PROGRESS: ============================= Precursor FDR =============================
2:41:33.253460 PROGRESS: Total precursors accumulated: 2,658
2:41:33.253515 PROGRESS: Target precursors: 2,632 (99.02%)
2:41:33.253573 PROGRESS: Decoy precursors: 26 (0.98%)
2:41:33.253617 PROGRESS: 
2:41:33.253658 PROGRESS: Precursor Summary:
2:41:33.255301 PROGRESS: Channel   0:	 0.050 FDR: 2,632; 0.010 FDR: 2,632; 0.001 FDR: 2,228
2:41:33.255392 PROGRESS: 
2:41:33.255450 PROGRESS: Protein Summary:
2:41:33.257741 PROGRESS: Channel   0:	 0.050 FDR: 2,082; 0.010 FDR: 2,082; 0.001 FDR: 1,795
2:41:33.257829 PROGRESS: =========================================================================
2:41:33.258195 INFO: Target number of precursors reached.
2:41:33.284569 INFO: fragments_df: keeping 5000 of 118993 [sum(precursor_idx_mask)=59305 sum(mass_error_mask)=118993 stop_rank=5000
2:41:33.295712 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:33.683120 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:34.398831 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:34.399355 INFO: Using score_cutoff 10.098026341438294 (fac=0.99, q=1)
2:41:34.399707 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:34.399786 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:34.399841 INFO: Updating optimization_manager: score_cutoff        : 9.854686966896057 -> 10.098026341438294
2:41:34.399904 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:34.403909 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:34.411264 INFO: === checking if optimization conditions were reached ===
2:41:34.411381 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:41:34.412182 INFO: Updating optimization_manager: rt_error            : 526.8121171576956 -> 472.65844594045325
2:41:34.412304 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:41:34.412400 INFO: Updating optimization_manager: score_cutoff        : 10.098026341438294 -> 9.983958245658874
2:41:34.412487 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:34.412572 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:34.412663 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 472.6584 found after 6 searches.
2:41:34.412724 INFO: ==============================================
2:41:34.412797 PROGRESS: Optimization finished for rt_error.
2:41:34.424120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:34.427919 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:34.435587 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:41:34.435689 PROGRESS: ==============================================
2:41:34.435755 PROGRESS: ms2_error      : 10.0000
2:41:34.435810 PROGRESS: rt_error       : 472.6584
2:41:34.435857 PROGRESS: ==============================================
2:41:34.436543 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:34.576074 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:34.926372 INFO: Using rust extraction backend
2:41:34.926690 PROGRESS: Extracting batch of 264177 precursors
2:41:35.342466 INFO: === Search parameters used ===
2:41:35.342746 INFO: rt_error       : 472.65844594045325
2:41:35.342805 INFO: mobility_error : 0.1
2:41:35.342855 INFO: num_candidates : 3
2:41:35.342901 INFO: ms1_error      : 3
2:41:35.342944 INFO: ms2_error      : 10.0
2:41:35.342995 INFO: fwhm_rt        : 3.0
2:41:35.343050 INFO: quant_window   : 3
2:41:35.343093 INFO: ==============================================
2:41:36.374777 INFO: Removed 84066 precursors with score below cutoff 9.983958245658874
2:41:37.059628 INFO: performing precursor FDR with 40 features
2:41:37.059739 INFO: Decoy channel: -1
2:41:37.059766 INFO: competitive: True
2:41:37.117794 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:37.331209 INFO: Estimating optimal hyperparameters - samples: 566,772, batch_size: 2,321, learning_rate: 7.53e-04
2:41:37.332061 INFO: Using random state 686559 for train-test-split
2:41:48.516435 INFO: Test AUC: 0.777
2:41:48.516661 INFO: Train AUC: 0.780
2:41:48.516697 INFO: AUC difference: 0.45%
2:41:49.040059 INFO: Resetting torch num_threads to 24
2:41:49.378090 PROGRESS: ============================= Precursor FDR =============================
2:41:49.378398 PROGRESS: Total precursors accumulated: 122,999
2:41:49.378467 PROGRESS: Target precursors: 121,782 (99.01%)
2:41:49.378521 PROGRESS: Decoy precursors: 1,217 (0.99%)
2:41:49.378570 PROGRESS: 
2:41:49.378617 PROGRESS: Precursor Summary:
2:41:49.416238 PROGRESS: Channel   0:	 0.050 FDR: 121,782; 0.010 FDR: 121,782; 0.001 FDR: 108,155
2:41:49.416495 PROGRESS: 
2:41:49.416559 PROGRESS: Protein Summary:
2:41:49.479068 PROGRESS: Channel   0:	 0.050 FDR: 10,515; 0.010 FDR: 10,515; 0.001 FDR: 10,362
2:41:49.479316 PROGRESS: =========================================================================
2:41:49.482091 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
2:41:49.677495 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
2:41:49.936180 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:41:50.192063 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
2:41:50.192215 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:41:50.192312 INFO: Initializing TimingManager
2:41:50.192917 INFO: Initializing RawFileManager
2:42:03.722151 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:42:03.731226 INFO: Determining DIA cycle
2:42:03.748588 INFO: Found cycle with start 0.00 min and length 300.
2:42:03.921856 INFO: RT (min)            : 0.0 - 26.9
2:42:03.921954 INFO: RT duration (sec)   : 1611.2
2:42:03.921987 INFO: RT duration (min)   : 26.9
2:42:03.922011 INFO: Cycle len (scans)   : 300
2:42:03.922032 INFO: Cycle len (sec)     : 1.65
2:42:03.922052 INFO: Number of cycles    : 977
2:42:03.922072 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:42:03.922105 INFO: Creating DIA data object took: 13.729082822799683
2:42:05.759039 INFO: Creating DIA data NG object took: 1.8367834091186523
2:42:05.802368 INFO: Initializing CalibrationManager
2:42:05.802669 INFO: Setting up calibration estimators ..
2:42:05.802731 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:42:05.802816 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:42:05.802889 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:42:05.802944 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:42:05.803045 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:42:05.803098 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:42:05.803144 INFO: Done setting up calibration estimators.
2:42:05.803333 INFO: Initializing OptimizationManager
2:42:05.803458 INFO: initial parameter: ms1_error = 3
2:42:05.803510 INFO: initial parameter: ms2_error = 10
2:42:05.803556 INFO: initial parameter: rt_error = 805.5982666015625
2:42:05.803598 INFO: initial parameter: mobility_error = 0.1
2:42:05.803638 INFO: initial parameter: num_candidates = 1
2:42:05.803678 INFO: initial parameter: fwhm_rt = 5
2:42:05.803718 INFO: initial parameter: fwhm_mobility = 0.01
2:42:05.803757 INFO: initial parameter: score_cutoff = 0
2:42:05.803796 INFO: initial parameter: classifier_version = -1
2:42:05.803874 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:42:05.804116 INFO: FDRManager: loading saved state not requested, will be initialized.
2:42:05.804146 INFO: Initializing FDRManager
2:42:05.804176 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:42:05.843243 PROGRESS: Initializing spectral library: 133,585 target precursors potentially observable (0 removed)
2:42:05.868639 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:42:05.869009 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
2:42:05.869101 PROGRESS: Starting initial search for precursors.
2:42:05.869181 INFO: Starting optimization step 0.
2:42:05.869241 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:42:05.869293 INFO: Using rust extraction backend
2:42:05.869345 PROGRESS: Extracting batch of 1974 precursors
2:42:05.874004 INFO: === Search parameters used ===
2:42:05.874098 INFO: rt_error       : 805.5982666015625
2:42:05.874147 INFO: mobility_error : 0.1
2:42:05.874190 INFO: num_candidates : 1
2:42:05.874231 INFO: ms1_error      : 3
2:42:05.874270 INFO: ms2_error      : 10
2:42:05.874308 INFO: fwhm_rt        : 5
2:42:05.874346 INFO: quant_window   : 3
2:42:05.874384 INFO: ==============================================
2:42:05.907115 INFO: performing precursor FDR with 40 features
2:42:05.907182 INFO: Decoy channel: -1
2:42:05.907206 INFO: competitive: True
2:42:05.908557 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:05.910401 INFO: Estimating optimal hyperparameters - samples: 1,578, batch_size: 128, learning_rate: 1.77e-04
2:42:05.911285 INFO: Using random state 770184 for train-test-split
2:42:06.055489 INFO: Test AUC: 0.862
2:42:06.055569 INFO: Train AUC: 0.897
2:42:06.055597 INFO: AUC difference: 3.85%
2:42:06.291537 INFO: Resetting torch num_threads to 24
2:42:06.293220 PROGRESS: === Extracted 1973 precursors and 15412 fragments ===
2:42:06.293576 INFO: === FDR correction performed with classifier version -1 ===
2:42:06.294080 PROGRESS: ============================= Precursor FDR =============================
2:42:06.294160 PROGRESS: Total precursors accumulated: 567
2:42:06.294217 PROGRESS: Target precursors: 562 (99.12%)
2:42:06.294266 PROGRESS: Decoy precursors: 5 (0.88%)
2:42:06.294310 PROGRESS: 
2:42:06.294353 PROGRESS: Precursor Summary:
2:42:06.295447 PROGRESS: Channel   0:	 0.050 FDR:   562; 0.010 FDR:   562; 0.001 FDR:   368
2:42:06.295535 PROGRESS: 
2:42:06.295588 PROGRESS: Protein Summary:
2:42:06.296915 PROGRESS: Channel   0:	 0.050 FDR:   515; 0.010 FDR:   515; 0.001 FDR:   346
2:42:06.297007 PROGRESS: =========================================================================
2:42:06.297214 INFO: Target number of precursors not reached yet.
2:42:06.304838 INFO: Starting optimization step 1.
2:42:06.304944 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:42:06.305017 INFO: Using rust extraction backend
2:42:06.305076 PROGRESS: Extracting batch of 3939 precursors
2:42:06.312929 INFO: === Search parameters used ===
2:42:06.313025 INFO: rt_error       : 805.5982666015625
2:42:06.313074 INFO: mobility_error : 0.1
2:42:06.313118 INFO: num_candidates : 1
2:42:06.313161 INFO: ms1_error      : 3
2:42:06.313202 INFO: ms2_error      : 10
2:42:06.313242 INFO: fwhm_rt        : 5
2:42:06.313281 INFO: quant_window   : 3
2:42:06.313321 INFO: ==============================================
2:42:06.376028 INFO: performing precursor FDR with 40 features
2:42:06.376115 INFO: Decoy channel: -1
2:42:06.376138 INFO: competitive: True
2:42:06.380160 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:06.382374 INFO: Estimating optimal hyperparameters - samples: 4,729, batch_size: 128, learning_rate: 1.77e-04
2:42:06.382450 INFO: Using random state 384110 for train-test-split
2:42:06.829880 INFO: Test AUC: 0.911
2:42:06.829966 INFO: Train AUC: 0.908
2:42:06.829994 INFO: AUC difference: 0.28%
2:42:07.069842 INFO: Resetting torch num_threads to 24
2:42:07.072988 PROGRESS: === Extracted 5912 precursors and 46181 fragments ===
2:42:07.073356 INFO: === FDR correction performed with classifier version -1 ===
2:42:07.074020 PROGRESS: ============================= Precursor FDR =============================
2:42:07.074101 PROGRESS: Total precursors accumulated: 2,096
2:42:07.074157 PROGRESS: Target precursors: 2,076 (99.05%)
2:42:07.074206 PROGRESS: Decoy precursors: 20 (0.95%)
2:42:07.074250 PROGRESS: 
2:42:07.074293 PROGRESS: Precursor Summary:
2:42:07.075814 PROGRESS: Channel   0:	 0.050 FDR: 2,076; 0.010 FDR: 2,076; 0.001 FDR: 1,703
2:42:07.075906 PROGRESS: 
2:42:07.075961 PROGRESS: Protein Summary:
2:42:07.077985 PROGRESS: Channel   0:	 0.050 FDR: 1,667; 0.010 FDR: 1,667; 0.001 FDR: 1,398
2:42:07.078074 PROGRESS: =========================================================================
2:42:07.078347 INFO: Target number of precursors reached.
2:42:07.088737 INFO: fragments_df: keeping 5000 of 46181 [sum(precursor_idx_mask)=20884 sum(mass_error_mask)=46181 stop_rank=5000
2:42:07.099724 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:07.399985 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:10.010640 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:42:10.011222 INFO: Using score_cutoff 11.516359040737152 (fac=0.99, q=1)
2:42:10.011581 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:42:10.011657 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:42:10.011707 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.516359040737152
2:42:10.011762 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:10.015875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:10.023836 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:42:10.023946 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:42:10.024022 INFO: Starting optimization step 2.
2:42:10.024089 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:10.024158 INFO: Using rust extraction backend
2:42:10.024222 PROGRESS: Extracting batch of 5913 precursors
2:42:10.035631 INFO: === Search parameters used ===
2:42:10.035751 INFO: rt_error       : 805.5982666015625
2:42:10.035803 INFO: mobility_error : 0.1
2:42:10.035849 INFO: num_candidates : 3
2:42:10.035896 INFO: ms1_error      : 3
2:42:10.035937 INFO: ms2_error      : 10
2:42:10.035976 INFO: fwhm_rt        : 3.0
2:42:10.036016 INFO: quant_window   : 3
2:42:10.036054 INFO: ==============================================
2:42:10.174065 INFO: performing precursor FDR with 40 features
2:42:10.174174 INFO: Decoy channel: -1
2:42:10.174197 INFO: competitive: True
2:42:10.179168 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:10.183249 INFO: Estimating optimal hyperparameters - samples: 14,177, batch_size: 128, learning_rate: 1.77e-04
2:42:10.183386 INFO: Using random state 461508 for train-test-split
2:42:11.598709 INFO: Test AUC: 0.724
2:42:11.598821 INFO: Train AUC: 0.726
2:42:11.598853 INFO: AUC difference: 0.20%
2:42:11.854945 INFO: Resetting torch num_threads to 24
2:42:11.857609 PROGRESS: === Extracted 17722 precursors and 119908 fragments ===
2:42:11.857978 INFO: === FDR correction performed with classifier version 1 ===
2:42:11.858730 PROGRESS: ============================= Precursor FDR =============================
2:42:11.858821 PROGRESS: Total precursors accumulated: 2,376
2:42:11.858880 PROGRESS: Target precursors: 2,353 (99.03%)
2:42:11.858931 PROGRESS: Decoy precursors: 23 (0.97%)
2:42:11.858987 PROGRESS: 
2:42:11.859038 PROGRESS: Precursor Summary:
2:42:11.860654 PROGRESS: Channel   0:	 0.050 FDR: 2,353; 0.010 FDR: 2,353; 0.001 FDR: 1,672
2:42:11.860749 PROGRESS: 
2:42:11.860812 PROGRESS: Protein Summary:
2:42:11.863018 PROGRESS: Channel   0:	 0.050 FDR: 1,882; 0.010 FDR: 1,882; 0.001 FDR: 1,388
2:42:11.863120 PROGRESS: =========================================================================
2:42:11.863505 INFO: Target number of precursors reached.
2:42:11.889113 INFO: fragments_df: keeping 5000 of 119908 [sum(precursor_idx_mask)=54293 sum(mass_error_mask)=119908 stop_rank=5000
2:42:11.901586 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:12.245997 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:12.966302 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:12.966779 INFO: Using score_cutoff 11.503086722946167 (fac=0.99, q=1)
2:42:12.967107 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:12.967190 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:12.967245 INFO: Updating optimization_manager: score_cutoff        : 11.516359040737152 -> 11.503086722946167
2:42:12.967299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:12.971276 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:12.979224 INFO: === checking if optimization conditions were reached ===
2:42:12.980953 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:42:12.981053 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:42:12.981118 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:12.981176 INFO: ==============================================
2:42:12.981257 INFO: Starting optimization step 3.
2:42:12.981316 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:12.981373 INFO: Using rust extraction backend
2:42:12.981427 PROGRESS: Extracting batch of 5913 precursors
2:42:12.992655 INFO: === Search parameters used ===
2:42:12.992801 INFO: rt_error       : 805.5982666015625
2:42:12.992853 INFO: mobility_error : 0.1
2:42:12.992898 INFO: num_candidates : 3
2:42:12.992940 INFO: ms1_error      : 3
2:42:12.992982 INFO: ms2_error      : 10.0
2:42:12.993022 INFO: fwhm_rt        : 3.0
2:42:12.993062 INFO: quant_window   : 3
2:42:12.993101 INFO: ==============================================
2:42:13.116449 INFO: performing precursor FDR with 40 features
2:42:13.116559 INFO: Decoy channel: -1
2:42:13.116582 INFO: competitive: True
2:42:13.121492 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:13.125487 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
2:42:13.125619 INFO: Using random state 346228 for train-test-split
2:42:14.579469 INFO: Test AUC: 0.721
2:42:14.579582 INFO: Train AUC: 0.747
2:42:14.579609 INFO: AUC difference: 3.52%
2:42:14.836829 INFO: Resetting torch num_threads to 24
2:42:14.839462 PROGRESS: === Extracted 17723 precursors and 119935 fragments ===
2:42:14.839831 INFO: === FDR correction performed with classifier version 2 ===
2:42:14.840539 PROGRESS: ============================= Precursor FDR =============================
2:42:14.840622 PROGRESS: Total precursors accumulated: 2,488
2:42:14.840679 PROGRESS: Target precursors: 2,464 (99.04%)
2:42:14.840727 PROGRESS: Decoy precursors: 24 (0.96%)
2:42:14.840771 PROGRESS: 
2:42:14.840813 PROGRESS: Precursor Summary:
2:42:14.842469 PROGRESS: Channel   0:	 0.050 FDR: 2,464; 0.010 FDR: 2,464; 0.001 FDR: 2,066
2:42:14.842567 PROGRESS: 
2:42:14.842621 PROGRESS: Protein Summary:
2:42:14.844897 PROGRESS: Channel   0:	 0.050 FDR: 1,963; 0.010 FDR: 1,963; 0.001 FDR: 1,667
2:42:14.844996 PROGRESS: =========================================================================
2:42:14.845363 INFO: Target number of precursors reached.
2:42:14.870957 INFO: fragments_df: keeping 5000 of 119935 [sum(precursor_idx_mask)=56527 sum(mass_error_mask)=119935 stop_rank=5000
2:42:14.882298 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:15.239867 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:15.964868 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:15.965340 INFO: Using score_cutoff 11.023092590618132 (fac=0.99, q=1)
2:42:15.965659 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:15.965734 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:15.965795 INFO: Updating optimization_manager: score_cutoff        : 11.503086722946167 -> 11.023092590618132
2:42:15.965848 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:15.969838 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:15.977675 INFO: === checking if optimization conditions were reached ===
2:42:15.979395 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:15.979505 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:42:15.979568 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:15.979627 INFO: ==============================================
2:42:15.979691 INFO: Starting optimization step 4.
2:42:15.979745 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:15.979801 INFO: Using rust extraction backend
2:42:15.979854 PROGRESS: Extracting batch of 5913 precursors
2:42:15.990958 INFO: === Search parameters used ===
2:42:15.991093 INFO: rt_error       : 805.5982666015625
2:42:15.991144 INFO: mobility_error : 0.1
2:42:15.991188 INFO: num_candidates : 3
2:42:15.991229 INFO: ms1_error      : 3
2:42:15.991268 INFO: ms2_error      : 10.0
2:42:15.991307 INFO: fwhm_rt        : 3.0
2:42:15.991348 INFO: quant_window   : 3
2:42:15.991387 INFO: ==============================================
2:42:16.103527 INFO: performing precursor FDR with 40 features
2:42:16.103635 INFO: Decoy channel: -1
2:42:16.103659 INFO: competitive: True
2:42:16.108598 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:16.112653 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
2:42:16.112783 INFO: Using random state 945652 for train-test-split
2:42:17.553653 INFO: Test AUC: 0.751
2:42:17.553767 INFO: Train AUC: 0.753
2:42:17.553798 INFO: AUC difference: 0.18%
2:42:17.812423 INFO: Resetting torch num_threads to 24
2:42:17.815013 PROGRESS: === Extracted 17723 precursors and 119943 fragments ===
2:42:17.815385 INFO: === FDR correction performed with classifier version 3 ===
2:42:17.816100 PROGRESS: ============================= Precursor FDR =============================
2:42:17.816188 PROGRESS: Total precursors accumulated: 2,542
2:42:17.816248 PROGRESS: Target precursors: 2,517 (99.02%)
2:42:17.816299 PROGRESS: Decoy precursors: 25 (0.98%)
2:42:17.816345 PROGRESS: 
2:42:17.816398 PROGRESS: Precursor Summary:
2:42:17.818072 PROGRESS: Channel   0:	 0.050 FDR: 2,517; 0.010 FDR: 2,517; 0.001 FDR: 2,111
2:42:17.818168 PROGRESS: 
2:42:17.818224 PROGRESS: Protein Summary:
2:42:17.820502 PROGRESS: Channel   0:	 0.050 FDR: 2,002; 0.010 FDR: 2,002; 0.001 FDR: 1,703
2:42:17.820609 PROGRESS: =========================================================================
2:42:17.820989 INFO: Target number of precursors reached.
2:42:17.847113 INFO: fragments_df: keeping 5000 of 119943 [sum(precursor_idx_mask)=57348 sum(mass_error_mask)=119943 stop_rank=5000
2:42:17.858743 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:18.222457 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:18.942350 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:18.942821 INFO: Using score_cutoff 10.634152086639403 (fac=0.99, q=1)
2:42:18.943148 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:18.943230 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:18.943285 INFO: Updating optimization_manager: score_cutoff        : 11.023092590618132 -> 10.634152086639403
2:42:18.943340 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:18.947398 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:18.955420 INFO: === checking if optimization conditions were reached ===
2:42:18.957104 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:18.957209 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:42:18.957275 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:18.957339 INFO: ==============================================
2:42:18.957401 INFO: Starting optimization step 5.
2:42:18.957456 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:18.957513 INFO: Using rust extraction backend
2:42:18.957567 PROGRESS: Extracting batch of 5913 precursors
2:42:18.968661 INFO: === Search parameters used ===
2:42:18.968796 INFO: rt_error       : 805.5982666015625
2:42:18.968863 INFO: mobility_error : 0.1
2:42:18.968917 INFO: num_candidates : 3
2:42:18.968964 INFO: ms1_error      : 3
2:42:18.969010 INFO: ms2_error      : 10.0
2:42:18.969056 INFO: fwhm_rt        : 3.0
2:42:18.969101 INFO: quant_window   : 3
2:42:18.969141 INFO: ==============================================
2:42:19.078360 INFO: performing precursor FDR with 40 features
2:42:19.078471 INFO: Decoy channel: -1
2:42:19.078494 INFO: competitive: True
2:42:19.085722 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:19.089714 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
2:42:19.089849 INFO: Using random state 950559 for train-test-split
2:42:20.491624 INFO: Test AUC: 0.755
2:42:20.491731 INFO: Train AUC: 0.761
2:42:20.491758 INFO: AUC difference: 0.69%
2:42:20.748298 INFO: Resetting torch num_threads to 24
2:42:20.750875 PROGRESS: === Extracted 17723 precursors and 119976 fragments ===
2:42:20.751242 INFO: === FDR correction performed with classifier version 4 ===
2:42:20.751981 PROGRESS: ============================= Precursor FDR =============================
2:42:20.752064 PROGRESS: Total precursors accumulated: 2,577
2:42:20.752120 PROGRESS: Target precursors: 2,552 (99.03%)
2:42:20.752173 PROGRESS: Decoy precursors: 25 (0.97%)
2:42:20.752219 PROGRESS: 
2:42:20.752261 PROGRESS: Precursor Summary:
2:42:20.753922 PROGRESS: Channel   0:	 0.050 FDR: 2,552; 0.010 FDR: 2,552; 0.001 FDR: 2,210
2:42:20.754012 PROGRESS: 
2:42:20.754066 PROGRESS: Protein Summary:
2:42:20.756349 PROGRESS: Channel   0:	 0.050 FDR: 2,027; 0.010 FDR: 2,027; 0.001 FDR: 1,771
2:42:20.756448 PROGRESS: =========================================================================
2:42:20.756834 INFO: Target number of precursors reached.
2:42:20.783745 INFO: fragments_df: keeping 5000 of 119976 [sum(precursor_idx_mask)=58060 sum(mass_error_mask)=119976 stop_rank=5000
2:42:20.794983 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:21.165071 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:21.885744 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:21.886218 INFO: Using score_cutoff 10.542815217018127 (fac=0.99, q=1)
2:42:21.886544 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:21.886623 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:21.886686 INFO: Updating optimization_manager: score_cutoff        : 10.634152086639403 -> 10.542815217018127
2:42:21.886741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:21.890737 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:21.898561 INFO: === checking if optimization conditions were reached ===
2:42:21.900283 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:21.900383 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:42:21.900447 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:21.900504 INFO: ==============================================
2:42:21.900567 INFO: Starting optimization step 6.
2:42:21.900622 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:21.900681 INFO: Using rust extraction backend
2:42:21.900737 PROGRESS: Extracting batch of 5913 precursors
2:42:21.911865 INFO: === Search parameters used ===
2:42:21.911993 INFO: rt_error       : 805.5982666015625
2:42:21.912045 INFO: mobility_error : 0.1
2:42:21.912091 INFO: num_candidates : 3
2:42:21.912135 INFO: ms1_error      : 3
2:42:21.912179 INFO: ms2_error      : 10.0
2:42:21.912221 INFO: fwhm_rt        : 3.0
2:42:21.912262 INFO: quant_window   : 3
2:42:21.912314 INFO: ==============================================
2:42:22.025183 INFO: performing precursor FDR with 40 features
2:42:22.025293 INFO: Decoy channel: -1
2:42:22.025316 INFO: competitive: True
2:42:22.030256 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:22.034223 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
2:42:22.034356 INFO: Using random state 997443 for train-test-split
2:42:23.441642 INFO: Test AUC: 0.753
2:42:23.441750 INFO: Train AUC: 0.771
2:42:23.441779 INFO: AUC difference: 2.35%
2:42:23.697566 INFO: Resetting torch num_threads to 24
2:42:23.700137 PROGRESS: === Extracted 17723 precursors and 119967 fragments ===
2:42:23.700505 INFO: === FDR correction performed with classifier version 5 ===
2:42:23.701224 PROGRESS: ============================= Precursor FDR =============================
2:42:23.701309 PROGRESS: Total precursors accumulated: 2,596
2:42:23.701373 PROGRESS: Target precursors: 2,571 (99.04%)
2:42:23.701424 PROGRESS: Decoy precursors: 25 (0.96%)
2:42:23.701468 PROGRESS: 
2:42:23.701511 PROGRESS: Precursor Summary:
2:42:23.703206 PROGRESS: Channel   0:	 0.050 FDR: 2,571; 0.010 FDR: 2,571; 0.001 FDR: 2,152
2:42:23.703304 PROGRESS: 
2:42:23.703359 PROGRESS: Protein Summary:
2:42:23.705676 PROGRESS: Channel   0:	 0.050 FDR: 2,043; 0.010 FDR: 2,043; 0.001 FDR: 1,735
2:42:23.705766 PROGRESS: =========================================================================
2:42:23.706164 INFO: Target number of precursors reached.
2:42:23.732918 INFO: fragments_df: keeping 5000 of 119967 [sum(precursor_idx_mask)=58296 sum(mass_error_mask)=119967 stop_rank=5000
2:42:23.744286 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:24.123797 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:24.842655 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:24.843132 INFO: Using score_cutoff 10.39471562576294 (fac=0.99, q=1)
2:42:24.843453 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:24.843527 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:24.843579 INFO: Updating optimization_manager: score_cutoff        : 10.542815217018127 -> 10.39471562576294
2:42:24.843630 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:24.847621 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:24.855528 INFO: === checking if optimization conditions were reached ===
2:42:24.857186 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:24.857280 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:42:24.857342 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:42:24.857397 INFO: ==============================================
2:42:24.857459 PROGRESS: Optimization finished for ms2_error.
2:42:24.868024 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:24.871826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:24.879687 INFO: Starting optimization step 0.
2:42:24.879799 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:24.879870 INFO: Using rust extraction backend
2:42:24.879926 PROGRESS: Extracting batch of 5913 precursors
2:42:24.891174 INFO: === Search parameters used ===
2:42:24.891309 INFO: rt_error       : 805.5982666015625
2:42:24.891361 INFO: mobility_error : 0.1
2:42:24.891407 INFO: num_candidates : 3
2:42:24.891450 INFO: ms1_error      : 3
2:42:24.891492 INFO: ms2_error      : 10.0
2:42:24.891532 INFO: fwhm_rt        : 3.0
2:42:24.891571 INFO: quant_window   : 3
2:42:24.891610 INFO: ==============================================
2:42:25.003280 INFO: performing precursor FDR with 40 features
2:42:25.003391 INFO: Decoy channel: -1
2:42:25.003415 INFO: competitive: True
2:42:25.008263 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:25.012303 INFO: Estimating optimal hyperparameters - samples: 14,178, batch_size: 128, learning_rate: 1.77e-04
2:42:25.012440 INFO: Using random state 907047 for train-test-split
2:42:26.402528 INFO: Test AUC: 0.763
2:42:26.402632 INFO: Train AUC: 0.774
2:42:26.402661 INFO: AUC difference: 1.36%
2:42:26.659822 INFO: Resetting torch num_threads to 24
2:42:26.662427 PROGRESS: === Extracted 17723 precursors and 119954 fragments ===
2:42:26.662797 INFO: === FDR correction performed with classifier version 6 ===
2:42:26.663530 PROGRESS: ============================= Precursor FDR =============================
2:42:26.663622 PROGRESS: Total precursors accumulated: 2,645
2:42:26.663682 PROGRESS: Target precursors: 2,619 (99.02%)
2:42:26.663731 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:26.663780 PROGRESS: 
2:42:26.663826 PROGRESS: Precursor Summary:
2:42:26.665495 PROGRESS: Channel   0:	 0.050 FDR: 2,619; 0.010 FDR: 2,619; 0.001 FDR: 2,194
2:42:26.665586 PROGRESS: 
2:42:26.665641 PROGRESS: Protein Summary:
2:42:26.667978 PROGRESS: Channel   0:	 0.050 FDR: 2,070; 0.010 FDR: 2,070; 0.001 FDR: 1,761
2:42:26.668074 PROGRESS: =========================================================================
2:42:26.668458 INFO: Target number of precursors reached.
2:42:26.695630 INFO: fragments_df: keeping 5000 of 119954 [sum(precursor_idx_mask)=59365 sum(mass_error_mask)=119954 stop_rank=5000
2:42:26.706921 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:27.086181 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:27.804513 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:27.804980 INFO: Using score_cutoff 10.313904096221924 (fac=0.99, q=1)
2:42:27.805295 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:27.805380 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:27.805436 INFO: Updating optimization_manager: score_cutoff        : 10.39471562576294 -> 10.313904096221924
2:42:27.805490 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:27.809454 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:27.817347 INFO: === checking if optimization conditions were reached ===
2:42:27.817470 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:42:27.820252 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 428.20868990919564
2:42:27.820356 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 428.2087.
2:42:27.820421 INFO: ==============================================
2:42:27.820491 INFO: Starting optimization step 1.
2:42:27.820550 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:27.820610 INFO: Using rust extraction backend
2:42:27.820666 PROGRESS: Extracting batch of 5913 precursors
2:42:27.831775 INFO: === Search parameters used ===
2:42:27.831917 INFO: rt_error       : 428.20868990919564
2:42:27.831970 INFO: mobility_error : 0.1
2:42:27.832017 INFO: num_candidates : 3
2:42:27.832062 INFO: ms1_error      : 3
2:42:27.832106 INFO: ms2_error      : 10.0
2:42:27.832149 INFO: fwhm_rt        : 3.0
2:42:27.832200 INFO: quant_window   : 3
2:42:27.832243 INFO: ==============================================
2:42:27.934867 INFO: performing precursor FDR with 40 features
2:42:27.934989 INFO: Decoy channel: -1
2:42:27.935017 INFO: competitive: True
2:42:27.939824 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:27.943847 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:42:27.943983 INFO: Using random state 907047 for train-test-split
2:42:29.335991 INFO: Test AUC: 0.754
2:42:29.336101 INFO: Train AUC: 0.777
2:42:29.336131 INFO: AUC difference: 2.97%
2:42:29.591565 INFO: Resetting torch num_threads to 24
2:42:29.594133 PROGRESS: === Extracted 17720 precursors and 119361 fragments ===
2:42:29.594506 INFO: === FDR correction performed with classifier version 6 ===
2:42:29.595245 PROGRESS: ============================= Precursor FDR =============================
2:42:29.595341 PROGRESS: Total precursors accumulated: 2,656
2:42:29.595401 PROGRESS: Target precursors: 2,630 (99.02%)
2:42:29.595462 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:29.595510 PROGRESS: 
2:42:29.595554 PROGRESS: Precursor Summary:
2:42:29.597224 PROGRESS: Channel   0:	 0.050 FDR: 2,630; 0.010 FDR: 2,630; 0.001 FDR: 2,260
2:42:29.597322 PROGRESS: 
2:42:29.597376 PROGRESS: Protein Summary:
2:42:29.599692 PROGRESS: Channel   0:	 0.050 FDR: 2,080; 0.010 FDR: 2,080; 0.001 FDR: 1,810
2:42:29.599791 PROGRESS: =========================================================================
2:42:29.600166 INFO: Target number of precursors reached.
2:42:29.626788 INFO: fragments_df: keeping 5000 of 119361 [sum(precursor_idx_mask)=59484 sum(mass_error_mask)=119361 stop_rank=5000
2:42:29.638027 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:30.020045 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:30.737284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:30.737769 INFO: Using score_cutoff 10.254243721961975 (fac=0.99, q=1)
2:42:30.738094 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:30.738170 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:30.738224 INFO: Updating optimization_manager: score_cutoff        : 10.313904096221924 -> 10.254243721961975
2:42:30.738276 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:30.742260 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:30.750163 INFO: === checking if optimization conditions were reached ===
2:42:30.750278 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:42:30.753178 INFO: Updating optimization_manager: rt_error            : 428.20868990919564 -> 409.44768664845867
2:42:30.753283 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 409.4477.
2:42:30.753348 INFO: ==============================================
2:42:30.753415 INFO: Starting optimization step 2.
2:42:30.753471 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:30.753529 INFO: Using rust extraction backend
2:42:30.753582 PROGRESS: Extracting batch of 5913 precursors
2:42:30.764649 INFO: === Search parameters used ===
2:42:30.764781 INFO: rt_error       : 409.44768664845867
2:42:30.764830 INFO: mobility_error : 0.1
2:42:30.764875 INFO: num_candidates : 3
2:42:30.764916 INFO: ms1_error      : 3
2:42:30.764968 INFO: ms2_error      : 10.0
2:42:30.765009 INFO: fwhm_rt        : 3.0
2:42:30.765049 INFO: quant_window   : 3
2:42:30.765087 INFO: ==============================================
2:42:30.866700 INFO: performing precursor FDR with 40 features
2:42:30.866807 INFO: Decoy channel: -1
2:42:30.866830 INFO: competitive: True
2:42:30.871660 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:30.875583 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:42:30.875713 INFO: Using random state 907047 for train-test-split
2:42:32.253518 INFO: Test AUC: 0.771
2:42:32.253629 INFO: Train AUC: 0.774
2:42:32.253660 INFO: AUC difference: 0.38%
2:42:32.507117 INFO: Resetting torch num_threads to 24
2:42:32.509682 PROGRESS: === Extracted 17720 precursors and 119290 fragments ===
2:42:32.510055 INFO: === FDR correction performed with classifier version 6 ===
2:42:32.510776 PROGRESS: ============================= Precursor FDR =============================
2:42:32.510866 PROGRESS: Total precursors accumulated: 2,642
2:42:32.510936 PROGRESS: Target precursors: 2,616 (99.02%)
2:42:32.511017 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:32.511069 PROGRESS: 
2:42:32.511114 PROGRESS: Precursor Summary:
2:42:32.512759 PROGRESS: Channel   0:	 0.050 FDR: 2,616; 0.010 FDR: 2,616; 0.001 FDR: 2,028
2:42:32.512849 PROGRESS: 
2:42:32.512906 PROGRESS: Protein Summary:
2:42:32.515229 PROGRESS: Channel   0:	 0.050 FDR: 2,074; 0.010 FDR: 2,074; 0.001 FDR: 1,643
2:42:32.515326 PROGRESS: =========================================================================
2:42:32.515703 INFO: Target number of precursors reached.
2:42:32.541936 INFO: fragments_df: keeping 5000 of 119290 [sum(precursor_idx_mask)=59139 sum(mass_error_mask)=119290 stop_rank=5000
2:42:32.553281 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:32.929566 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:33.645611 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:33.646072 INFO: Using score_cutoff 10.251844668388367 (fac=0.99, q=1)
2:42:33.646384 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:33.646458 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:33.646511 INFO: Updating optimization_manager: score_cutoff        : 10.254243721961975 -> 10.251844668388367
2:42:33.646561 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:33.650518 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:33.658378 INFO: === checking if optimization conditions were reached ===
2:42:33.658489 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:42:33.661458 INFO: Updating optimization_manager: rt_error            : 409.44768664845867 -> 418.95528620329736
2:42:33.661561 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 418.9553.
2:42:33.661623 INFO: ==============================================
2:42:33.661690 INFO: Starting optimization step 3.
2:42:33.661745 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:33.661803 INFO: Using rust extraction backend
2:42:33.661856 PROGRESS: Extracting batch of 5913 precursors
2:42:33.672940 INFO: === Search parameters used ===
2:42:33.673053 INFO: rt_error       : 418.95528620329736
2:42:33.673104 INFO: mobility_error : 0.1
2:42:33.673148 INFO: num_candidates : 3
2:42:33.673197 INFO: ms1_error      : 3
2:42:33.673240 INFO: ms2_error      : 10.0
2:42:33.673281 INFO: fwhm_rt        : 3.0
2:42:33.673320 INFO: quant_window   : 3
2:42:33.673359 INFO: ==============================================
2:42:33.781646 INFO: performing precursor FDR with 40 features
2:42:33.781754 INFO: Decoy channel: -1
2:42:33.781778 INFO: competitive: True
2:42:33.786596 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:33.790526 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:42:33.790657 INFO: Using random state 907047 for train-test-split
2:42:35.172828 INFO: Test AUC: 0.755
2:42:35.172935 INFO: Train AUC: 0.777
2:42:35.172963 INFO: AUC difference: 2.81%
2:42:35.427220 INFO: Resetting torch num_threads to 24
2:42:35.429755 PROGRESS: === Extracted 17721 precursors and 119316 fragments ===
2:42:35.430123 INFO: === FDR correction performed with classifier version 6 ===
2:42:35.430830 PROGRESS: ============================= Precursor FDR =============================
2:42:35.430916 PROGRESS: Total precursors accumulated: 2,654
2:42:35.430983 PROGRESS: Target precursors: 2,628 (99.02%)
2:42:35.431038 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:35.431083 PROGRESS: 
2:42:35.431124 PROGRESS: Precursor Summary:
2:42:35.432770 PROGRESS: Channel   0:	 0.050 FDR: 2,628; 0.010 FDR: 2,628; 0.001 FDR: 2,194
2:42:35.432856 PROGRESS: 
2:42:35.432909 PROGRESS: Protein Summary:
2:42:35.435200 PROGRESS: Channel   0:	 0.050 FDR: 2,083; 0.010 FDR: 2,083; 0.001 FDR: 1,764
2:42:35.435296 PROGRESS: =========================================================================
2:42:35.435664 INFO: Target number of precursors reached.
2:42:35.462147 INFO: fragments_df: keeping 5000 of 119316 [sum(precursor_idx_mask)=59402 sum(mass_error_mask)=119316 stop_rank=5000
2:42:35.473337 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:35.852515 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:36.567925 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:36.568389 INFO: Using score_cutoff 10.307780391597749 (fac=0.99, q=1)
2:42:36.568707 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:36.568792 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:36.568846 INFO: Updating optimization_manager: score_cutoff        : 10.251844668388367 -> 10.307780391597749
2:42:36.568897 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:36.572876 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:36.580726 INFO: === checking if optimization conditions were reached ===
2:42:36.580836 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:42:36.583800 INFO: Updating optimization_manager: rt_error            : 418.95528620329736 -> 379.3332281366957
2:42:36.583904 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 379.3332.
2:42:36.583966 INFO: ==============================================
2:42:36.584031 INFO: Starting optimization step 4.
2:42:36.584085 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:36.584141 INFO: Using rust extraction backend
2:42:36.584193 PROGRESS: Extracting batch of 5913 precursors
2:42:36.595315 INFO: === Search parameters used ===
2:42:36.595426 INFO: rt_error       : 379.3332281366957
2:42:36.595483 INFO: mobility_error : 0.1
2:42:36.595530 INFO: num_candidates : 3
2:42:36.595570 INFO: ms1_error      : 3
2:42:36.595610 INFO: ms2_error      : 10.0
2:42:36.595649 INFO: fwhm_rt        : 3.0
2:42:36.595689 INFO: quant_window   : 3
2:42:36.595728 INFO: ==============================================
2:42:36.702784 INFO: performing precursor FDR with 40 features
2:42:36.702895 INFO: Decoy channel: -1
2:42:36.702919 INFO: competitive: True
2:42:36.707753 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:36.711955 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:42:36.712093 INFO: Using random state 907047 for train-test-split
2:42:38.096512 INFO: Test AUC: 0.756
2:42:38.096628 INFO: Train AUC: 0.776
2:42:38.096658 INFO: AUC difference: 2.56%
2:42:38.350215 INFO: Resetting torch num_threads to 24
2:42:38.352729 PROGRESS: === Extracted 17720 precursors and 118988 fragments ===
2:42:38.353097 INFO: === FDR correction performed with classifier version 6 ===
2:42:38.353798 PROGRESS: ============================= Precursor FDR =============================
2:42:38.353885 PROGRESS: Total precursors accumulated: 2,653
2:42:38.353944 PROGRESS: Target precursors: 2,627 (99.02%)
2:42:38.353995 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:38.354042 PROGRESS: 
2:42:38.354086 PROGRESS: Precursor Summary:
2:42:38.355763 PROGRESS: Channel   0:	 0.050 FDR: 2,627; 0.010 FDR: 2,627; 0.001 FDR: 2,190
2:42:38.355858 PROGRESS: 
2:42:38.355915 PROGRESS: Protein Summary:
2:42:38.358226 PROGRESS: Channel   0:	 0.050 FDR: 2,080; 0.010 FDR: 2,080; 0.001 FDR: 1,757
2:42:38.358318 PROGRESS: =========================================================================
2:42:38.358680 INFO: Target number of precursors reached.
2:42:38.384966 INFO: fragments_df: keeping 5000 of 118988 [sum(precursor_idx_mask)=59289 sum(mass_error_mask)=118988 stop_rank=5000
2:42:38.396121 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:38.773495 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:39.488707 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:39.489175 INFO: Using score_cutoff 10.253729639053345 (fac=0.99, q=1)
2:42:39.489484 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:39.489561 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:39.489616 INFO: Updating optimization_manager: score_cutoff        : 10.307780391597749 -> 10.253729639053345
2:42:39.489669 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:39.493662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:39.501683 INFO: === checking if optimization conditions were reached ===
2:42:39.501813 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:42:39.504784 INFO: Updating optimization_manager: rt_error            : 379.3332281366957 -> 403.4628376725763
2:42:39.504888 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 403.4628.
2:42:39.504950 INFO: ==============================================
2:42:39.505018 INFO: Starting optimization step 5.
2:42:39.505075 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:39.505133 INFO: Using rust extraction backend
2:42:39.505185 PROGRESS: Extracting batch of 5913 precursors
2:42:39.516303 INFO: === Search parameters used ===
2:42:39.516412 INFO: rt_error       : 403.4628376725763
2:42:39.516462 INFO: mobility_error : 0.1
2:42:39.516506 INFO: num_candidates : 3
2:42:39.516549 INFO: ms1_error      : 3
2:42:39.516588 INFO: ms2_error      : 10.0
2:42:39.516628 INFO: fwhm_rt        : 3.0
2:42:39.516670 INFO: quant_window   : 3
2:42:39.516708 INFO: ==============================================
2:42:39.617188 INFO: performing precursor FDR with 40 features
2:42:39.617298 INFO: Decoy channel: -1
2:42:39.617322 INFO: competitive: True
2:42:39.622033 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:39.626073 INFO: Estimating optimal hyperparameters - samples: 14,177, batch_size: 128, learning_rate: 1.77e-04
2:42:39.626207 INFO: Using random state 907047 for train-test-split
2:42:41.002308 INFO: Test AUC: 0.758
2:42:41.002415 INFO: Train AUC: 0.776
2:42:41.002443 INFO: AUC difference: 2.34%
2:42:41.254963 INFO: Resetting torch num_threads to 24
2:42:41.257478 PROGRESS: === Extracted 17722 precursors and 119209 fragments ===
2:42:41.257837 INFO: === FDR correction performed with classifier version 6 ===
2:42:41.258533 PROGRESS: ============================= Precursor FDR =============================
2:42:41.258615 PROGRESS: Total precursors accumulated: 2,645
2:42:41.258673 PROGRESS: Target precursors: 2,619 (99.02%)
2:42:41.258720 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:41.258764 PROGRESS: 
2:42:41.258807 PROGRESS: Precursor Summary:
2:42:41.260458 PROGRESS: Channel   0:	 0.050 FDR: 2,619; 0.010 FDR: 2,619; 0.001 FDR: 2,288
2:42:41.260556 PROGRESS: 
2:42:41.260612 PROGRESS: Protein Summary:
2:42:41.262915 PROGRESS: Channel   0:	 0.050 FDR: 2,076; 0.010 FDR: 2,076; 0.001 FDR: 1,834
2:42:41.263016 PROGRESS: =========================================================================
2:42:41.263386 INFO: Target number of precursors reached.
2:42:41.289888 INFO: fragments_df: keeping 5000 of 119209 [sum(precursor_idx_mask)=59169 sum(mass_error_mask)=119209 stop_rank=5000
2:42:41.301139 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:41.677859 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:42.394774 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:42.395250 INFO: Using score_cutoff 10.285612825012208 (fac=0.99, q=1)
2:42:42.395566 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:42.395646 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:42.395704 INFO: Updating optimization_manager: score_cutoff        : 10.253729639053345 -> 10.285612825012208
2:42:42.395760 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:42.399746 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:42.407501 INFO: === checking if optimization conditions were reached ===
2:42:42.407623 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:42:42.410555 INFO: Updating optimization_manager: rt_error            : 403.4628376725763 -> 376.19277241913437
2:42:42.410658 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 376.1928.
2:42:42.410724 INFO: ==============================================
2:42:42.410794 INFO: Starting optimization step 6.
2:42:42.410853 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:42.410923 INFO: Using rust extraction backend
2:42:42.411000 PROGRESS: Extracting batch of 5913 precursors
2:42:42.422178 INFO: === Search parameters used ===
2:42:42.422312 INFO: rt_error       : 376.19277241913437
2:42:42.422365 INFO: mobility_error : 0.1
2:42:42.422411 INFO: num_candidates : 3
2:42:42.422453 INFO: ms1_error      : 3
2:42:42.422494 INFO: ms2_error      : 10.0
2:42:42.422535 INFO: fwhm_rt        : 3.0
2:42:42.422576 INFO: quant_window   : 3
2:42:42.422616 INFO: ==============================================
2:42:42.527656 INFO: performing precursor FDR with 40 features
2:42:42.527766 INFO: Decoy channel: -1
2:42:42.527790 INFO: competitive: True
2:42:42.532518 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:42.536591 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:42:42.536771 INFO: Using random state 907047 for train-test-split
2:42:43.912567 INFO: Test AUC: 0.763
2:42:43.912678 INFO: Train AUC: 0.775
2:42:43.912705 INFO: AUC difference: 1.50%
2:42:44.167882 INFO: Resetting torch num_threads to 24
2:42:44.170392 PROGRESS: === Extracted 17720 precursors and 118948 fragments ===
2:42:44.170752 INFO: === FDR correction performed with classifier version 6 ===
2:42:44.171460 PROGRESS: ============================= Precursor FDR =============================
2:42:44.171551 PROGRESS: Total precursors accumulated: 2,652
2:42:44.171607 PROGRESS: Target precursors: 2,626 (99.02%)
2:42:44.171654 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:44.171696 PROGRESS: 
2:42:44.171737 PROGRESS: Precursor Summary:
2:42:44.173371 PROGRESS: Channel   0:	 0.050 FDR: 2,626; 0.010 FDR: 2,626; 0.001 FDR: 2,290
2:42:44.173454 PROGRESS: 
2:42:44.173507 PROGRESS: Protein Summary:
2:42:44.175827 PROGRESS: Channel   0:	 0.050 FDR: 2,079; 0.010 FDR: 2,079; 0.001 FDR: 1,838
2:42:44.175922 PROGRESS: =========================================================================
2:42:44.176267 INFO: Target number of precursors reached.
2:42:44.202607 INFO: fragments_df: keeping 5000 of 118948 [sum(precursor_idx_mask)=59171 sum(mass_error_mask)=118948 stop_rank=5000
2:42:44.213807 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:44.591512 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:45.309610 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:45.310071 INFO: Using score_cutoff 10.27062262058258 (fac=0.99, q=1)
2:42:45.310385 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:45.310458 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:45.310512 INFO: Updating optimization_manager: score_cutoff        : 10.285612825012208 -> 10.27062262058258
2:42:45.310561 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:45.314526 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:45.322550 INFO: === checking if optimization conditions were reached ===
2:42:45.322660 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:42:45.325600 INFO: Updating optimization_manager: rt_error            : 376.19277241913437 -> 370.30448322528065
2:42:45.325700 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 370.3045.
2:42:45.325761 INFO: ==============================================
2:42:45.325827 INFO: Starting optimization step 7.
2:42:45.325890 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:45.325949 INFO: Using rust extraction backend
2:42:45.326002 PROGRESS: Extracting batch of 5913 precursors
2:42:45.337225 INFO: === Search parameters used ===
2:42:45.337350 INFO: rt_error       : 370.30448322528065
2:42:45.337403 INFO: mobility_error : 0.1
2:42:45.337449 INFO: num_candidates : 3
2:42:45.337493 INFO: ms1_error      : 3
2:42:45.337535 INFO: ms2_error      : 10.0
2:42:45.337575 INFO: fwhm_rt        : 3.0
2:42:45.337615 INFO: quant_window   : 3
2:42:45.337655 INFO: ==============================================
2:42:45.449490 INFO: performing precursor FDR with 40 features
2:42:45.449601 INFO: Decoy channel: -1
2:42:45.449624 INFO: competitive: True
2:42:45.454488 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:45.458643 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:42:45.458783 INFO: Using random state 907047 for train-test-split
2:42:46.845981 INFO: Test AUC: 0.757
2:42:46.846090 INFO: Train AUC: 0.776
2:42:46.846118 INFO: AUC difference: 2.51%
2:42:47.100170 INFO: Resetting torch num_threads to 24
2:42:47.102672 PROGRESS: === Extracted 17721 precursors and 118919 fragments ===
2:42:47.103040 INFO: === FDR correction performed with classifier version 6 ===
2:42:47.103745 PROGRESS: ============================= Precursor FDR =============================
2:42:47.103831 PROGRESS: Total precursors accumulated: 2,644
2:42:47.103886 PROGRESS: Target precursors: 2,618 (99.02%)
2:42:47.103934 PROGRESS: Decoy precursors: 26 (0.98%)
2:42:47.103976 PROGRESS: 
2:42:47.104017 PROGRESS: Precursor Summary:
2:42:47.105642 PROGRESS: Channel   0:	 0.050 FDR: 2,618; 0.010 FDR: 2,618; 0.001 FDR: 2,240
2:42:47.105736 PROGRESS: 
2:42:47.105790 PROGRESS: Protein Summary:
2:42:47.108081 PROGRESS: Channel   0:	 0.050 FDR: 2,074; 0.010 FDR: 2,074; 0.001 FDR: 1,798
2:42:47.108176 PROGRESS: =========================================================================
2:42:47.108532 INFO: Target number of precursors reached.
2:42:47.134695 INFO: fragments_df: keeping 5000 of 118919 [sum(precursor_idx_mask)=59030 sum(mass_error_mask)=118919 stop_rank=5000
2:42:47.145657 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:47.519967 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:48.234151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:48.234634 INFO: Using score_cutoff 10.269274694252015 (fac=0.99, q=1)
2:42:48.234955 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:48.235046 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:48.235103 INFO: Updating optimization_manager: score_cutoff        : 10.27062262058258 -> 10.269274694252015
2:42:48.235158 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:48.239129 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:48.246936 INFO: === checking if optimization conditions were reached ===
2:42:48.247059 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:42:48.247793 INFO: Updating optimization_manager: rt_error            : 370.30448322528065 -> 428.20868990919564
2:42:48.247916 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
2:42:48.248019 INFO: Updating optimization_manager: score_cutoff        : 10.269274694252015 -> 10.254243721961975
2:42:48.248110 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:48.248193 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:48.248277 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 428.2087 found after 8 searches.
2:42:48.248337 INFO: ==============================================
2:42:48.248413 PROGRESS: Optimization finished for rt_error.
2:42:48.258868 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:48.262731 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:48.270531 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:42:48.270637 PROGRESS: ==============================================
2:42:48.270701 PROGRESS: ms2_error      : 10.0000
2:42:48.270755 PROGRESS: rt_error       : 428.2087
2:42:48.270801 PROGRESS: ==============================================
2:42:48.271427 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:48.408015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:48.758661 INFO: Using rust extraction backend
2:42:48.758986 PROGRESS: Extracting batch of 264177 precursors
2:42:49.174860 INFO: === Search parameters used ===
2:42:49.175140 INFO: rt_error       : 428.20868990919564
2:42:49.175200 INFO: mobility_error : 0.1
2:42:49.175270 INFO: num_candidates : 3
2:42:49.175317 INFO: ms1_error      : 3
2:42:49.175359 INFO: ms2_error      : 10.0
2:42:49.175401 INFO: fwhm_rt        : 3.0
2:42:49.175442 INFO: quant_window   : 3
2:42:49.175482 INFO: ==============================================
2:42:50.168704 INFO: Removed 93113 precursors with score below cutoff 10.254243721961975
2:42:50.841660 INFO: performing precursor FDR with 40 features
2:42:50.841776 INFO: Decoy channel: -1
2:42:50.841801 INFO: competitive: True
2:42:50.899243 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:50.932622 WARNING: FDR calculation for 368402 target and 331016 decoy PSMs
2:42:50.932753 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:42:51.110725 INFO: Estimating optimal hyperparameters - samples: 559,534, batch_size: 2,291, learning_rate: 7.48e-04
2:42:51.111734 INFO: Using random state 90428 for train-test-split
2:43:02.144337 INFO: Test AUC: 0.779
2:43:02.144471 INFO: Train AUC: 0.781
2:43:02.144504 INFO: AUC difference: 0.15%
2:43:02.666480 INFO: Resetting torch num_threads to 24
2:43:02.986966 PROGRESS: ============================= Precursor FDR =============================
2:43:02.987251 PROGRESS: Total precursors accumulated: 124,059
2:43:02.987320 PROGRESS: Target precursors: 122,831 (99.01%)
2:43:02.987375 PROGRESS: Decoy precursors: 1,228 (0.99%)
2:43:02.987425 PROGRESS: 
2:43:02.987473 PROGRESS: Precursor Summary:
2:43:03.025172 PROGRESS: Channel   0:	 0.050 FDR: 122,831; 0.010 FDR: 122,831; 0.001 FDR: 109,220
2:43:03.025436 PROGRESS: 
2:43:03.025498 PROGRESS: Protein Summary:
2:43:03.091596 PROGRESS: Channel   0:	 0.050 FDR: 10,524; 0.010 FDR: 10,524; 0.001 FDR: 10,380
2:43:03.091855 PROGRESS: =========================================================================
2:43:03.094602 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
2:43:03.294023 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
2:43:03.593951 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:43:03.746389 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
2:43:03.746540 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:43:03.746623 INFO: Initializing TimingManager
2:43:03.747232 INFO: Initializing RawFileManager
2:43:16.755616 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:43:16.764018 INFO: Determining DIA cycle
2:43:16.781347 INFO: Found cycle with start 0.00 min and length 300.
2:43:16.972489 INFO: RT (min)            : 0.0 - 26.9
2:43:16.972586 INFO: RT duration (sec)   : 1611.2
2:43:16.972614 INFO: RT duration (min)   : 26.9
2:43:16.972637 INFO: Cycle len (scans)   : 300
2:43:16.972657 INFO: Cycle len (sec)     : 1.65
2:43:16.972676 INFO: Number of cycles    : 977
2:43:16.972695 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:43:16.972720 INFO: Creating DIA data object took: 13.225387573242188
2:43:18.835319 INFO: Creating DIA data NG object took: 1.8624675273895264
2:43:18.861460 INFO: Initializing CalibrationManager
2:43:18.861759 INFO: Setting up calibration estimators ..
2:43:18.861820 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:43:18.861891 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'}' ..
2:43:18.861957 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:43:18.862010 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:43:18.862078 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}}' ..
2:43:18.862130 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:43:18.862177 INFO: Done setting up calibration estimators.
2:43:18.862365 INFO: Initializing OptimizationManager
2:43:18.862484 INFO: initial parameter: ms1_error = 3
2:43:18.862544 INFO: initial parameter: ms2_error = 10
2:43:18.862589 INFO: initial parameter: rt_error = 805.6002197265625
2:43:18.862632 INFO: initial parameter: mobility_error = 0.1
2:43:18.862677 INFO: initial parameter: num_candidates = 1
2:43:18.862718 INFO: initial parameter: fwhm_rt = 5
2:43:18.862759 INFO: initial parameter: fwhm_mobility = 0.01
2:43:18.862798 INFO: initial parameter: score_cutoff = 0
2:43:18.862838 INFO: initial parameter: classifier_version = -1
2:43:18.862901 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:43:18.863137 INFO: FDRManager: loading saved state not requested, will be initialized.
2:43:18.863170 INFO: Initializing FDRManager
2:43:18.863201 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:43:18.901192 PROGRESS: Initializing spectral library: 133,585 target precursors potentially observable (0 removed)
2:43:18.926404 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:43:18.926763 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
2:43:18.926851 PROGRESS: Starting initial search for precursors.
2:43:18.926925 INFO: Starting optimization step 0.
2:43:18.926992 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:43:18.927052 INFO: Using rust extraction backend
2:43:18.927107 PROGRESS: Extracting batch of 1974 precursors
2:43:18.931754 INFO: === Search parameters used ===
2:43:18.931856 INFO: rt_error       : 805.6002197265625
2:43:18.931908 INFO: mobility_error : 0.1
2:43:18.931953 INFO: num_candidates : 1
2:43:18.931995 INFO: ms1_error      : 3
2:43:18.932037 INFO: ms2_error      : 10
2:43:18.932080 INFO: fwhm_rt        : 5
2:43:18.932125 INFO: quant_window   : 3
2:43:18.932165 INFO: ==============================================
2:43:18.962843 INFO: performing precursor FDR with 40 features
2:43:18.962909 INFO: Decoy channel: -1
2:43:18.962932 INFO: competitive: True
2:43:18.964121 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:18.965770 INFO: Estimating optimal hyperparameters - samples: 1,579, batch_size: 128, learning_rate: 1.77e-04
2:43:18.966567 INFO: Using random state 462968 for train-test-split
2:43:19.114650 INFO: Test AUC: 0.877
2:43:19.114735 INFO: Train AUC: 0.882
2:43:19.114765 INFO: AUC difference: 0.50%
2:43:19.354599 INFO: Resetting torch num_threads to 24
2:43:19.356304 PROGRESS: === Extracted 1974 precursors and 15271 fragments ===
2:43:19.356673 INFO: === FDR correction performed with classifier version -1 ===
2:43:19.357191 PROGRESS: ============================= Precursor FDR =============================
2:43:19.357279 PROGRESS: Total precursors accumulated: 616
2:43:19.357339 PROGRESS: Target precursors: 610 (99.03%)
2:43:19.357392 PROGRESS: Decoy precursors: 6 (0.97%)
2:43:19.357440 PROGRESS: 
2:43:19.357486 PROGRESS: Precursor Summary:
2:43:19.358593 PROGRESS: Channel   0:	 0.050 FDR:   610; 0.010 FDR:   610; 0.001 FDR:   383
2:43:19.358680 PROGRESS: 
2:43:19.358738 PROGRESS: Protein Summary:
2:43:19.360113 PROGRESS: Channel   0:	 0.050 FDR:   556; 0.010 FDR:   556; 0.001 FDR:   358
2:43:19.360206 PROGRESS: =========================================================================
2:43:19.360418 INFO: Target number of precursors not reached yet.
2:43:19.368089 INFO: Starting optimization step 1.
2:43:19.368198 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:43:19.368272 INFO: Using rust extraction backend
2:43:19.368331 PROGRESS: Extracting batch of 3939 precursors
2:43:19.376195 INFO: === Search parameters used ===
2:43:19.376299 INFO: rt_error       : 805.6002197265625
2:43:19.376353 INFO: mobility_error : 0.1
2:43:19.376408 INFO: num_candidates : 1
2:43:19.376451 INFO: ms1_error      : 3
2:43:19.376492 INFO: ms2_error      : 10
2:43:19.376532 INFO: fwhm_rt        : 5
2:43:19.376571 INFO: quant_window   : 3
2:43:19.376610 INFO: ==============================================
2:43:19.437099 INFO: performing precursor FDR with 40 features
2:43:19.437188 INFO: Decoy channel: -1
2:43:19.437211 INFO: competitive: True
2:43:19.441218 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:19.443460 INFO: Estimating optimal hyperparameters - samples: 4,730, batch_size: 128, learning_rate: 1.77e-04
2:43:19.443543 INFO: Using random state 325745 for train-test-split
2:43:19.890049 INFO: Test AUC: 0.905
2:43:19.890135 INFO: Train AUC: 0.907
2:43:19.890163 INFO: AUC difference: 0.15%
2:43:20.132571 INFO: Resetting torch num_threads to 24
2:43:20.135735 PROGRESS: === Extracted 5913 precursors and 45913 fragments ===
2:43:20.136112 INFO: === FDR correction performed with classifier version -1 ===
2:43:20.136794 PROGRESS: ============================= Precursor FDR =============================
2:43:20.136877 PROGRESS: Total precursors accumulated: 2,193
2:43:20.136936 PROGRESS: Target precursors: 2,172 (99.04%)
2:43:20.136984 PROGRESS: Decoy precursors: 21 (0.96%)
2:43:20.137028 PROGRESS: 
2:43:20.137070 PROGRESS: Precursor Summary:
2:43:20.138592 PROGRESS: Channel   0:	 0.050 FDR: 2,172; 0.010 FDR: 2,172; 0.001 FDR: 1,638
2:43:20.138678 PROGRESS: 
2:43:20.138732 PROGRESS: Protein Summary:
2:43:20.140781 PROGRESS: Channel   0:	 0.050 FDR: 1,739; 0.010 FDR: 1,739; 0.001 FDR: 1,344
2:43:20.140875 PROGRESS: =========================================================================
2:43:20.141140 INFO: Target number of precursors reached.
2:43:20.151481 INFO: fragments_df: keeping 5000 of 45913 [sum(precursor_idx_mask)=21662 sum(mass_error_mask)=45913 stop_rank=5000
2:43:20.162240 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:20.474366 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:21.188016 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:43:21.188484 INFO: Using score_cutoff 10.976970450496674 (fac=0.99, q=1)
2:43:21.188792 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:43:21.188865 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:43:21.188916 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.976970450496674
2:43:21.188967 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:21.192875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:21.200779 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:43:21.200887 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:43:21.200963 INFO: Starting optimization step 2.
2:43:21.201028 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:21.201089 INFO: Using rust extraction backend
2:43:21.201143 PROGRESS: Extracting batch of 5913 precursors
2:43:21.212203 INFO: === Search parameters used ===
2:43:21.212315 INFO: rt_error       : 805.6002197265625
2:43:21.212366 INFO: mobility_error : 0.1
2:43:21.212410 INFO: num_candidates : 3
2:43:21.212451 INFO: ms1_error      : 3
2:43:21.212491 INFO: ms2_error      : 10
2:43:21.212532 INFO: fwhm_rt        : 3.0
2:43:21.212571 INFO: quant_window   : 3
2:43:21.212614 INFO: ==============================================
2:43:21.331832 INFO: performing precursor FDR with 40 features
2:43:21.331939 INFO: Decoy channel: -1
2:43:21.331963 INFO: competitive: True
2:43:21.336988 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:21.340865 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
2:43:21.340993 INFO: Using random state 913084 for train-test-split
2:43:22.720992 INFO: Test AUC: 0.728
2:43:22.721140 INFO: Train AUC: 0.726
2:43:22.721168 INFO: AUC difference: 0.29%
2:43:22.975784 INFO: Resetting torch num_threads to 24
2:43:22.978249 PROGRESS: === Extracted 17733 precursors and 119408 fragments ===
2:43:22.978607 INFO: === FDR correction performed with classifier version 1 ===
2:43:22.979308 PROGRESS: ============================= Precursor FDR =============================
2:43:22.979395 PROGRESS: Total precursors accumulated: 2,544
2:43:22.979451 PROGRESS: Target precursors: 2,519 (99.02%)
2:43:22.979497 PROGRESS: Decoy precursors: 25 (0.98%)
2:43:22.979540 PROGRESS: 
2:43:22.979582 PROGRESS: Precursor Summary:
2:43:22.981176 PROGRESS: Channel   0:	 0.050 FDR: 2,519; 0.010 FDR: 2,519; 0.001 FDR: 2,152
2:43:22.981261 PROGRESS: 
2:43:22.981320 PROGRESS: Protein Summary:
2:43:22.983549 PROGRESS: Channel   0:	 0.050 FDR: 2,004; 0.010 FDR: 2,004; 0.001 FDR: 1,732
2:43:22.983643 PROGRESS: =========================================================================
2:43:22.983992 INFO: Target number of precursors reached.
2:43:23.009773 INFO: fragments_df: keeping 5000 of 119408 [sum(precursor_idx_mask)=57463 sum(mass_error_mask)=119408 stop_rank=5000
2:43:23.020677 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:23.383097 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:24.096036 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:24.096516 INFO: Using score_cutoff 10.773768677330017 (fac=0.99, q=1)
2:43:24.096824 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:24.096902 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:24.096958 INFO: Updating optimization_manager: score_cutoff        : 10.976970450496674 -> 10.773768677330017
2:43:24.097011 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:24.100940 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:24.108789 INFO: === checking if optimization conditions were reached ===
2:43:24.110429 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:43:24.110534 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:43:24.110599 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:43:24.110657 INFO: ==============================================
2:43:24.110732 INFO: Starting optimization step 3.
2:43:24.110793 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:24.110854 INFO: Using rust extraction backend
2:43:24.110912 PROGRESS: Extracting batch of 5913 precursors
2:43:24.122045 INFO: === Search parameters used ===
2:43:24.122189 INFO: rt_error       : 805.6002197265625
2:43:24.122244 INFO: mobility_error : 0.1
2:43:24.122291 INFO: num_candidates : 3
2:43:24.122337 INFO: ms1_error      : 3
2:43:24.122380 INFO: ms2_error      : 10.0
2:43:24.122422 INFO: fwhm_rt        : 3.0
2:43:24.122466 INFO: quant_window   : 3
2:43:24.122526 INFO: ==============================================
2:43:24.235882 INFO: performing precursor FDR with 40 features
2:43:24.235993 INFO: Decoy channel: -1
2:43:24.236017 INFO: competitive: True
2:43:24.240754 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:24.244685 INFO: Estimating optimal hyperparameters - samples: 14,185, batch_size: 128, learning_rate: 1.77e-04
2:43:24.244806 INFO: Using random state 513397 for train-test-split
2:43:25.628496 INFO: Test AUC: 0.735
2:43:25.628607 INFO: Train AUC: 0.742
2:43:25.628636 INFO: AUC difference: 0.96%
2:43:25.880691 INFO: Resetting torch num_threads to 24
2:43:25.883198 PROGRESS: === Extracted 17732 precursors and 119461 fragments ===
2:43:25.883563 INFO: === FDR correction performed with classifier version 2 ===
2:43:25.884260 PROGRESS: ============================= Precursor FDR =============================
2:43:25.884348 PROGRESS: Total precursors accumulated: 2,565
2:43:25.884405 PROGRESS: Target precursors: 2,540 (99.03%)
2:43:25.884455 PROGRESS: Decoy precursors: 25 (0.97%)
2:43:25.884500 PROGRESS: 
2:43:25.884545 PROGRESS: Precursor Summary:
2:43:25.886167 PROGRESS: Channel   0:	 0.050 FDR: 2,540; 0.010 FDR: 2,540; 0.001 FDR: 2,206
2:43:25.886252 PROGRESS: 
2:43:25.886305 PROGRESS: Protein Summary:
2:43:25.888566 PROGRESS: Channel   0:	 0.050 FDR: 2,020; 0.010 FDR: 2,020; 0.001 FDR: 1,771
2:43:25.888661 PROGRESS: =========================================================================
2:43:25.889003 INFO: Target number of precursors reached.
2:43:25.914949 INFO: fragments_df: keeping 5000 of 119461 [sum(precursor_idx_mask)=57785 sum(mass_error_mask)=119461 stop_rank=5000
2:43:25.926095 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:26.289461 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:27.005383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:27.005850 INFO: Using score_cutoff 10.60836092004776 (fac=0.99, q=1)
2:43:27.006160 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:27.006233 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:27.006285 INFO: Updating optimization_manager: score_cutoff        : 10.773768677330017 -> 10.60836092004776
2:43:27.006337 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:27.010267 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:27.018163 INFO: === checking if optimization conditions were reached ===
2:43:27.019814 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:43:27.019913 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:43:27.019981 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:43:27.020036 INFO: ==============================================
2:43:27.020097 INFO: Starting optimization step 4.
2:43:27.020151 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:27.020207 INFO: Using rust extraction backend
2:43:27.020263 PROGRESS: Extracting batch of 5913 precursors
2:43:27.031549 INFO: === Search parameters used ===
2:43:27.031666 INFO: rt_error       : 805.6002197265625
2:43:27.031720 INFO: mobility_error : 0.1
2:43:27.031775 INFO: num_candidates : 3
2:43:27.031817 INFO: ms1_error      : 3
2:43:27.031857 INFO: ms2_error      : 10.0
2:43:27.031895 INFO: fwhm_rt        : 3.0
2:43:27.031934 INFO: quant_window   : 3
2:43:27.031972 INFO: ==============================================
2:43:27.141058 INFO: performing precursor FDR with 40 features
2:43:27.141173 INFO: Decoy channel: -1
2:43:27.141198 INFO: competitive: True
2:43:27.145769 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:27.149653 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
2:43:27.149779 INFO: Using random state 523774 for train-test-split
2:43:28.537461 INFO: Test AUC: 0.742
2:43:28.537562 INFO: Train AUC: 0.751
2:43:28.537590 INFO: AUC difference: 1.17%
2:43:28.790827 INFO: Resetting torch num_threads to 24
2:43:28.793308 PROGRESS: === Extracted 17733 precursors and 119471 fragments ===
2:43:28.793663 INFO: === FDR correction performed with classifier version 3 ===
2:43:28.794369 PROGRESS: ============================= Precursor FDR =============================
2:43:28.794452 PROGRESS: Total precursors accumulated: 2,627
2:43:28.794508 PROGRESS: Target precursors: 2,601 (99.01%)
2:43:28.794554 PROGRESS: Decoy precursors: 26 (0.99%)
2:43:28.794596 PROGRESS: 
2:43:28.794643 PROGRESS: Precursor Summary:
2:43:28.796264 PROGRESS: Channel   0:	 0.050 FDR: 2,601; 0.010 FDR: 2,601; 0.001 FDR: 2,165
2:43:28.796358 PROGRESS: 
2:43:28.796412 PROGRESS: Protein Summary:
2:43:28.798666 PROGRESS: Channel   0:	 0.050 FDR: 2,061; 0.010 FDR: 2,061; 0.001 FDR: 1,738
2:43:28.798753 PROGRESS: =========================================================================
2:43:28.799117 INFO: Target number of precursors reached.
2:43:28.825556 INFO: fragments_df: keeping 5000 of 119471 [sum(precursor_idx_mask)=58944 sum(mass_error_mask)=119471 stop_rank=5000
2:43:28.836515 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:29.215728 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:29.929987 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:29.930457 INFO: Using score_cutoff 10.48110629081726 (fac=0.99, q=1)
2:43:29.930767 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:29.930845 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:29.930901 INFO: Updating optimization_manager: score_cutoff        : 10.60836092004776 -> 10.48110629081726
2:43:29.930955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:29.934890 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:29.942443 INFO: === checking if optimization conditions were reached ===
2:43:29.944087 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:43:29.944195 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:43:29.944261 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:43:29.944319 INFO: ==============================================
2:43:29.944385 INFO: Starting optimization step 5.
2:43:29.944443 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:29.944503 INFO: Using rust extraction backend
2:43:29.944564 PROGRESS: Extracting batch of 5913 precursors
2:43:29.955581 INFO: === Search parameters used ===
2:43:29.955691 INFO: rt_error       : 805.6002197265625
2:43:29.955743 INFO: mobility_error : 0.1
2:43:29.955790 INFO: num_candidates : 3
2:43:29.955833 INFO: ms1_error      : 3
2:43:29.955876 INFO: ms2_error      : 10.0
2:43:29.955918 INFO: fwhm_rt        : 3.0
2:43:29.955959 INFO: quant_window   : 3
2:43:29.955999 INFO: ==============================================
2:43:30.071044 INFO: performing precursor FDR with 40 features
2:43:30.071152 INFO: Decoy channel: -1
2:43:30.071177 INFO: competitive: True
2:43:30.075841 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:30.079782 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
2:43:30.079907 INFO: Using random state 467541 for train-test-split
2:43:31.456920 INFO: Test AUC: 0.741
2:43:31.457025 INFO: Train AUC: 0.763
2:43:31.457056 INFO: AUC difference: 2.88%
2:43:31.711219 INFO: Resetting torch num_threads to 24
2:43:31.713712 PROGRESS: === Extracted 17733 precursors and 119424 fragments ===
2:43:31.714067 INFO: === FDR correction performed with classifier version 4 ===
2:43:31.714776 PROGRESS: ============================= Precursor FDR =============================
2:43:31.714858 PROGRESS: Total precursors accumulated: 2,718
2:43:31.714915 PROGRESS: Target precursors: 2,692 (99.04%)
2:43:31.714978 PROGRESS: Decoy precursors: 26 (0.96%)
2:43:31.715032 PROGRESS: 
2:43:31.715077 PROGRESS: Precursor Summary:
2:43:31.716715 PROGRESS: Channel   0:	 0.050 FDR: 2,692; 0.010 FDR: 2,692; 0.001 FDR: 2,232
2:43:31.716803 PROGRESS: 
2:43:31.716858 PROGRESS: Protein Summary:
2:43:31.719174 PROGRESS: Channel   0:	 0.050 FDR: 2,128; 0.010 FDR: 2,128; 0.001 FDR: 1,791
2:43:31.719270 PROGRESS: =========================================================================
2:43:31.719619 INFO: Target number of precursors reached.
2:43:31.746177 INFO: fragments_df: keeping 5000 of 119424 [sum(precursor_idx_mask)=60632 sum(mass_error_mask)=119424 stop_rank=5000
2:43:31.757383 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:32.148959 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:32.864735 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:32.865196 INFO: Using score_cutoff 10.22503859167099 (fac=0.99, q=1)
2:43:32.865513 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:32.865589 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:32.865643 INFO: Updating optimization_manager: score_cutoff        : 10.48110629081726 -> 10.22503859167099
2:43:32.865696 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:32.869633 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:32.877522 INFO: === checking if optimization conditions were reached ===
2:43:32.879183 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:43:32.879282 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:43:32.879344 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:43:32.879407 INFO: ==============================================
2:43:32.879468 INFO: Starting optimization step 6.
2:43:32.879523 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:32.879579 INFO: Using rust extraction backend
2:43:32.879631 PROGRESS: Extracting batch of 5913 precursors
2:43:32.890656 INFO: === Search parameters used ===
2:43:32.890764 INFO: rt_error       : 805.6002197265625
2:43:32.890813 INFO: mobility_error : 0.1
2:43:32.890857 INFO: num_candidates : 3
2:43:32.890897 INFO: ms1_error      : 3
2:43:32.890938 INFO: ms2_error      : 10.0
2:43:32.890987 INFO: fwhm_rt        : 3.0
2:43:32.891032 INFO: quant_window   : 3
2:43:32.891071 INFO: ==============================================
2:43:32.998605 INFO: performing precursor FDR with 40 features
2:43:32.998713 INFO: Decoy channel: -1
2:43:32.998737 INFO: competitive: True
2:43:33.003448 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:33.007339 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
2:43:33.007461 INFO: Using random state 309482 for train-test-split
2:43:34.387071 INFO: Test AUC: 0.762
2:43:34.387180 INFO: Train AUC: 0.768
2:43:34.387209 INFO: AUC difference: 0.77%
2:43:34.632564 INFO: Resetting torch num_threads to 24
2:43:34.635054 PROGRESS: === Extracted 17733 precursors and 119426 fragments ===
2:43:34.635413 INFO: === FDR correction performed with classifier version 5 ===
2:43:34.636143 PROGRESS: ============================= Precursor FDR =============================
2:43:34.636225 PROGRESS: Total precursors accumulated: 2,741
2:43:34.636286 PROGRESS: Target precursors: 2,714 (99.01%)
2:43:34.636336 PROGRESS: Decoy precursors: 27 (0.99%)
2:43:34.636380 PROGRESS: 
2:43:34.636421 PROGRESS: Precursor Summary:
2:43:34.638063 PROGRESS: Channel   0:	 0.050 FDR: 2,714; 0.010 FDR: 2,714; 0.001 FDR: 2,196
2:43:34.638148 PROGRESS: 
2:43:34.638200 PROGRESS: Protein Summary:
2:43:34.640497 PROGRESS: Channel   0:	 0.050 FDR: 2,145; 0.010 FDR: 2,145; 0.001 FDR: 1,764
2:43:34.640591 PROGRESS: =========================================================================
2:43:34.640942 INFO: Target number of precursors reached.
2:43:34.667234 INFO: fragments_df: keeping 5000 of 119426 [sum(precursor_idx_mask)=61086 sum(mass_error_mask)=119426 stop_rank=5000
2:43:34.678349 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:35.074434 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:35.788777 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:35.789253 INFO: Using score_cutoff 10.224812508487702 (fac=0.99, q=1)
2:43:35.789572 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:35.789650 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:35.789707 INFO: Updating optimization_manager: score_cutoff        : 10.22503859167099 -> 10.224812508487702
2:43:35.789763 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:35.793716 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:35.801634 INFO: === checking if optimization conditions were reached ===
2:43:35.803281 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:43:35.803389 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:43:35.803455 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:43:35.803514 INFO: ==============================================
2:43:35.803579 PROGRESS: Optimization finished for ms2_error.
2:43:35.814070 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:35.817813 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:35.825669 INFO: Starting optimization step 0.
2:43:35.825783 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:35.825853 INFO: Using rust extraction backend
2:43:35.825910 PROGRESS: Extracting batch of 5913 precursors
2:43:35.837008 INFO: === Search parameters used ===
2:43:35.837125 INFO: rt_error       : 805.6002197265625
2:43:35.837176 INFO: mobility_error : 0.1
2:43:35.837219 INFO: num_candidates : 3
2:43:35.837260 INFO: ms1_error      : 3
2:43:35.837301 INFO: ms2_error      : 10.0
2:43:35.837339 INFO: fwhm_rt        : 3.0
2:43:35.837378 INFO: quant_window   : 3
2:43:35.837416 INFO: ==============================================
2:43:35.950866 INFO: performing precursor FDR with 40 features
2:43:35.951003 INFO: Decoy channel: -1
2:43:35.951031 INFO: competitive: True
2:43:35.955684 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:35.959518 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
2:43:35.959639 INFO: Using random state 450756 for train-test-split
2:43:37.384224 INFO: Test AUC: 0.764
2:43:37.384330 INFO: Train AUC: 0.775
2:43:37.384358 INFO: AUC difference: 1.49%
2:43:37.638093 INFO: Resetting torch num_threads to 24
2:43:37.640586 PROGRESS: === Extracted 17733 precursors and 119429 fragments ===
2:43:37.640947 INFO: === FDR correction performed with classifier version 6 ===
2:43:37.641656 PROGRESS: ============================= Precursor FDR =============================
2:43:37.641738 PROGRESS: Total precursors accumulated: 2,769
2:43:37.641793 PROGRESS: Target precursors: 2,742 (99.02%)
2:43:37.641841 PROGRESS: Decoy precursors: 27 (0.98%)
2:43:37.641886 PROGRESS: 
2:43:37.641928 PROGRESS: Precursor Summary:
2:43:37.643595 PROGRESS: Channel   0:	 0.050 FDR: 2,742; 0.010 FDR: 2,742; 0.001 FDR: 2,240
2:43:37.643685 PROGRESS: 
2:43:37.643740 PROGRESS: Protein Summary:
2:43:37.646041 PROGRESS: Channel   0:	 0.050 FDR: 2,165; 0.010 FDR: 2,165; 0.001 FDR: 1,797
2:43:37.646128 PROGRESS: =========================================================================
2:43:37.646470 INFO: Target number of precursors reached.
2:43:37.673073 INFO: fragments_df: keeping 5000 of 119429 [sum(precursor_idx_mask)=61564 sum(mass_error_mask)=119429 stop_rank=5000
2:43:37.684141 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:38.078235 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:38.790564 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:38.791037 INFO: Using score_cutoff 10.140389614963532 (fac=0.99, q=1)
2:43:38.791360 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:38.791440 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:38.791499 INFO: Updating optimization_manager: score_cutoff        : 10.224812508487702 -> 10.140389614963532
2:43:38.791551 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:38.795496 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:38.803218 INFO: === checking if optimization conditions were reached ===
2:43:38.803335 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:43:38.806141 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 363.72671412567155
2:43:38.806238 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 363.7267.
2:43:38.806299 INFO: ==============================================
2:43:38.806366 INFO: Starting optimization step 1.
2:43:38.806424 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:38.806485 INFO: Using rust extraction backend
2:43:38.806540 PROGRESS: Extracting batch of 5913 precursors
2:43:38.817603 INFO: === Search parameters used ===
2:43:38.817716 INFO: rt_error       : 363.72671412567155
2:43:38.817768 INFO: mobility_error : 0.1
2:43:38.817812 INFO: num_candidates : 3
2:43:38.817853 INFO: ms1_error      : 3
2:43:38.817893 INFO: ms2_error      : 10.0
2:43:38.817933 INFO: fwhm_rt        : 3.0
2:43:38.817982 INFO: quant_window   : 3
2:43:38.818032 INFO: ==============================================
2:43:38.914101 INFO: performing precursor FDR with 40 features
2:43:38.914210 INFO: Decoy channel: -1
2:43:38.914233 INFO: competitive: True
2:43:38.920537 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:38.924401 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:43:38.924525 INFO: Using random state 450756 for train-test-split
2:43:40.328204 INFO: Test AUC: 0.762
2:43:40.328315 INFO: Train AUC: 0.777
2:43:40.328349 INFO: AUC difference: 1.93%
2:43:40.573659 INFO: Resetting torch num_threads to 24
2:43:40.576194 PROGRESS: === Extracted 17731 precursors and 118474 fragments ===
2:43:40.576566 INFO: === FDR correction performed with classifier version 6 ===
2:43:40.577296 PROGRESS: ============================= Precursor FDR =============================
2:43:40.577384 PROGRESS: Total precursors accumulated: 2,815
2:43:40.577444 PROGRESS: Target precursors: 2,788 (99.04%)
2:43:40.577494 PROGRESS: Decoy precursors: 27 (0.96%)
2:43:40.577542 PROGRESS: 
2:43:40.577588 PROGRESS: Precursor Summary:
2:43:40.579270 PROGRESS: Channel   0:	 0.050 FDR: 2,788; 0.010 FDR: 2,788; 0.001 FDR: 2,136
2:43:40.579363 PROGRESS: 
2:43:40.579419 PROGRESS: Protein Summary:
2:43:40.581775 PROGRESS: Channel   0:	 0.050 FDR: 2,198; 0.010 FDR: 2,198; 0.001 FDR: 1,718
2:43:40.581869 PROGRESS: =========================================================================
2:43:40.582214 INFO: Target number of precursors reached.
2:43:40.608781 INFO: fragments_df: keeping 5000 of 118474 [sum(precursor_idx_mask)=62289 sum(mass_error_mask)=118474 stop_rank=5000
2:43:40.619736 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:41.023361 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:41.741233 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:41.741704 INFO: Using score_cutoff 10.135473773860932 (fac=0.99, q=1)
2:43:41.742033 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:41.742109 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:41.742164 INFO: Updating optimization_manager: score_cutoff        : 10.140389614963532 -> 10.135473773860932
2:43:41.742215 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:41.746146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:41.753941 INFO: === checking if optimization conditions were reached ===
2:43:41.754052 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:43:41.756984 INFO: Updating optimization_manager: rt_error            : 363.72671412567155 -> 322.5427197294885
2:43:41.757085 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 322.5427.
2:43:41.757149 INFO: ==============================================
2:43:41.757216 INFO: Starting optimization step 2.
2:43:41.757273 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:41.757334 INFO: Using rust extraction backend
2:43:41.757390 PROGRESS: Extracting batch of 5913 precursors
2:43:41.768342 INFO: === Search parameters used ===
2:43:41.768451 INFO: rt_error       : 322.5427197294885
2:43:41.768503 INFO: mobility_error : 0.1
2:43:41.768548 INFO: num_candidates : 3
2:43:41.768592 INFO: ms1_error      : 3
2:43:41.768635 INFO: ms2_error      : 10.0
2:43:41.768685 INFO: fwhm_rt        : 3.0
2:43:41.768729 INFO: quant_window   : 3
2:43:41.768770 INFO: ==============================================
2:43:41.866735 INFO: performing precursor FDR with 40 features
2:43:41.866847 INFO: Decoy channel: -1
2:43:41.866873 INFO: competitive: True
2:43:41.871440 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:41.875344 INFO: Estimating optimal hyperparameters - samples: 14,184, batch_size: 128, learning_rate: 1.77e-04
2:43:41.875465 INFO: Using random state 450756 for train-test-split
2:43:43.296327 INFO: Test AUC: 0.765
2:43:43.296434 INFO: Train AUC: 0.773
2:43:43.296477 INFO: AUC difference: 1.03%
2:43:43.541234 INFO: Resetting torch num_threads to 24
2:43:43.543723 PROGRESS: === Extracted 17730 precursors and 117926 fragments ===
2:43:43.544081 INFO: === FDR correction performed with classifier version 6 ===
2:43:43.544807 PROGRESS: ============================= Precursor FDR =============================
2:43:43.544887 PROGRESS: Total precursors accumulated: 2,824
2:43:43.544943 PROGRESS: Target precursors: 2,797 (99.04%)
2:43:43.544991 PROGRESS: Decoy precursors: 27 (0.96%)
2:43:43.545035 PROGRESS: 
2:43:43.545078 PROGRESS: Precursor Summary:
2:43:43.546734 PROGRESS: Channel   0:	 0.050 FDR: 2,797; 0.010 FDR: 2,797; 0.001 FDR: 2,286
2:43:43.546819 PROGRESS: 
2:43:43.546873 PROGRESS: Protein Summary:
2:43:43.549237 PROGRESS: Channel   0:	 0.050 FDR: 2,205; 0.010 FDR: 2,205; 0.001 FDR: 1,830
2:43:43.549329 PROGRESS: =========================================================================
2:43:43.549677 INFO: Target number of precursors reached.
2:43:43.576360 INFO: fragments_df: keeping 5000 of 117926 [sum(precursor_idx_mask)=62252 sum(mass_error_mask)=117926 stop_rank=5000
2:43:43.587335 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:43.929499 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:44.578230 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:44.578688 INFO: Using score_cutoff 10.137860053253174 (fac=0.99, q=1)
2:43:44.579000 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:44.579079 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:44.579132 INFO: Updating optimization_manager: score_cutoff        : 10.135473773860932 -> 10.137860053253174
2:43:44.579183 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:44.583120 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:44.590911 INFO: === checking if optimization conditions were reached ===
2:43:44.591034 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:43:44.594066 INFO: Updating optimization_manager: rt_error            : 322.5427197294885 -> 351.2007552754461
2:43:44.594161 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 351.2008.
2:43:44.594221 INFO: ==============================================
2:43:44.594286 INFO: Starting optimization step 3.
2:43:44.594339 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:44.594395 INFO: Using rust extraction backend
2:43:44.594448 PROGRESS: Extracting batch of 5913 precursors
2:43:44.605429 INFO: === Search parameters used ===
2:43:44.605550 INFO: rt_error       : 351.2007552754461
2:43:44.605599 INFO: mobility_error : 0.1
2:43:44.605642 INFO: num_candidates : 3
2:43:44.605692 INFO: ms1_error      : 3
2:43:44.605734 INFO: ms2_error      : 10.0
2:43:44.605774 INFO: fwhm_rt        : 3.0
2:43:44.605813 INFO: quant_window   : 3
2:43:44.605851 INFO: ==============================================
2:43:44.710186 INFO: performing precursor FDR with 40 features
2:43:44.710290 INFO: Decoy channel: -1
2:43:44.710314 INFO: competitive: True
2:43:44.714854 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:44.718692 INFO: Estimating optimal hyperparameters - samples: 14,185, batch_size: 128, learning_rate: 1.77e-04
2:43:44.718808 INFO: Using random state 450756 for train-test-split
2:43:46.122361 INFO: Test AUC: 0.757
2:43:46.122474 INFO: Train AUC: 0.779
2:43:46.122504 INFO: AUC difference: 2.84%
2:43:46.366172 INFO: Resetting torch num_threads to 24
2:43:46.368677 PROGRESS: === Extracted 17732 precursors and 118306 fragments ===
2:43:46.369042 INFO: === FDR correction performed with classifier version 6 ===
2:43:46.369768 PROGRESS: ============================= Precursor FDR =============================
2:43:46.369855 PROGRESS: Total precursors accumulated: 2,795
2:43:46.369916 PROGRESS: Target precursors: 2,768 (99.03%)
2:43:46.369967 PROGRESS: Decoy precursors: 27 (0.97%)
2:43:46.370015 PROGRESS: 
2:43:46.370073 PROGRESS: Precursor Summary:
2:43:46.371715 PROGRESS: Channel   0:	 0.050 FDR: 2,768; 0.010 FDR: 2,768; 0.001 FDR: 2,229
2:43:46.371812 PROGRESS: 
2:43:46.371866 PROGRESS: Protein Summary:
2:43:46.374185 PROGRESS: Channel   0:	 0.050 FDR: 2,182; 0.010 FDR: 2,182; 0.001 FDR: 1,790
2:43:46.374274 PROGRESS: =========================================================================
2:43:46.374624 INFO: Target number of precursors reached.
2:43:46.401102 INFO: fragments_df: keeping 5000 of 118306 [sum(precursor_idx_mask)=61909 sum(mass_error_mask)=118306 stop_rank=5000
2:43:46.412225 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:46.749909 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:47.396250 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:47.396711 INFO: Using score_cutoff 10.168029733371734 (fac=0.99, q=1)
2:43:47.397021 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:47.397096 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:47.397148 INFO: Updating optimization_manager: score_cutoff        : 10.137860053253174 -> 10.168029733371734
2:43:47.397198 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:47.401149 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:47.409150 INFO: === checking if optimization conditions were reached ===
2:43:47.409259 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:43:47.412283 INFO: Updating optimization_manager: rt_error            : 351.2007552754461 -> 295.7320074526856
2:43:47.412385 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 295.7320.
2:43:47.412446 INFO: ==============================================
2:43:47.412512 INFO: Starting optimization step 4.
2:43:47.412566 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:47.412623 INFO: Using rust extraction backend
2:43:47.412674 PROGRESS: Extracting batch of 5913 precursors
2:43:47.423691 INFO: === Search parameters used ===
2:43:47.423806 INFO: rt_error       : 295.7320074526856
2:43:47.423866 INFO: mobility_error : 0.1
2:43:47.423912 INFO: num_candidates : 3
2:43:47.423953 INFO: ms1_error      : 3
2:43:47.423993 INFO: ms2_error      : 10.0
2:43:47.424034 INFO: fwhm_rt        : 3.0
2:43:47.424073 INFO: quant_window   : 3
2:43:47.424112 INFO: ==============================================
2:43:47.521735 INFO: performing precursor FDR with 40 features
2:43:47.521846 INFO: Decoy channel: -1
2:43:47.521869 INFO: competitive: True
2:43:47.526416 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:47.530318 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:43:47.530445 INFO: Using random state 450756 for train-test-split
2:43:48.944767 INFO: Test AUC: 0.769
2:43:48.944875 INFO: Train AUC: 0.778
2:43:48.944902 INFO: AUC difference: 1.25%
2:43:49.191033 INFO: Resetting torch num_threads to 24
2:43:49.193522 PROGRESS: === Extracted 17726 precursors and 117504 fragments ===
2:43:49.193885 INFO: === FDR correction performed with classifier version 6 ===
2:43:49.194599 PROGRESS: ============================= Precursor FDR =============================
2:43:49.194684 PROGRESS: Total precursors accumulated: 2,802
2:43:49.194748 PROGRESS: Target precursors: 2,775 (99.04%)
2:43:49.194796 PROGRESS: Decoy precursors: 27 (0.96%)
2:43:49.194839 PROGRESS: 
2:43:49.194880 PROGRESS: Precursor Summary:
2:43:49.196548 PROGRESS: Channel   0:	 0.050 FDR: 2,775; 0.010 FDR: 2,775; 0.001 FDR: 2,365
2:43:49.196640 PROGRESS: 
2:43:49.196693 PROGRESS: Protein Summary:
2:43:49.199068 PROGRESS: Channel   0:	 0.050 FDR: 2,188; 0.010 FDR: 2,188; 0.001 FDR: 1,889
2:43:49.199161 PROGRESS: =========================================================================
2:43:49.199506 INFO: Target number of precursors reached.
2:43:49.225980 INFO: fragments_df: keeping 5000 of 117504 [sum(precursor_idx_mask)=61931 sum(mass_error_mask)=117504 stop_rank=5000
2:43:49.236996 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:49.573004 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:50.226134 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:50.226589 INFO: Using score_cutoff 10.210517595291137 (fac=0.99, q=1)
2:43:50.226896 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:50.226983 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:50.227044 INFO: Updating optimization_manager: score_cutoff        : 10.168029733371734 -> 10.210517595291137
2:43:50.227100 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:50.231050 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:50.238783 INFO: === checking if optimization conditions were reached ===
2:43:50.238895 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:43:50.241916 INFO: Updating optimization_manager: rt_error            : 295.7320074526856 -> 291.3954003998161
2:43:50.242023 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 291.3954.
2:43:50.242090 INFO: ==============================================
2:43:50.242167 INFO: Starting optimization step 5.
2:43:50.242228 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:50.242291 INFO: Using rust extraction backend
2:43:50.242350 PROGRESS: Extracting batch of 5913 precursors
2:43:50.253577 INFO: === Search parameters used ===
2:43:50.253689 INFO: rt_error       : 291.3954003998161
2:43:50.253744 INFO: mobility_error : 0.1
2:43:50.253792 INFO: num_candidates : 3
2:43:50.253837 INFO: ms1_error      : 3
2:43:50.253881 INFO: ms2_error      : 10.0
2:43:50.253927 INFO: fwhm_rt        : 3.0
2:43:50.253972 INFO: quant_window   : 3
2:43:50.254014 INFO: ==============================================
2:43:50.354937 INFO: performing precursor FDR with 40 features
2:43:50.355059 INFO: Decoy channel: -1
2:43:50.355086 INFO: competitive: True
2:43:50.359814 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:50.363659 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:43:50.363783 INFO: Using random state 450756 for train-test-split
2:43:51.784327 INFO: Test AUC: 0.760
2:43:51.784432 INFO: Train AUC: 0.779
2:43:51.784462 INFO: AUC difference: 2.47%
2:43:52.030216 INFO: Resetting torch num_threads to 24
2:43:52.032708 PROGRESS: === Extracted 17726 precursors and 117388 fragments ===
2:43:52.033081 INFO: === FDR correction performed with classifier version 6 ===
2:43:52.033805 PROGRESS: ============================= Precursor FDR =============================
2:43:52.033890 PROGRESS: Total precursors accumulated: 2,828
2:43:52.033948 PROGRESS: Target precursors: 2,800 (99.01%)
2:43:52.033997 PROGRESS: Decoy precursors: 28 (0.99%)
2:43:52.034042 PROGRESS: 
2:43:52.034086 PROGRESS: Precursor Summary:
2:43:52.035764 PROGRESS: Channel   0:	 0.050 FDR: 2,800; 0.010 FDR: 2,800; 0.001 FDR: 2,326
2:43:52.035857 PROGRESS: 
2:43:52.035911 PROGRESS: Protein Summary:
2:43:52.038257 PROGRESS: Channel   0:	 0.050 FDR: 2,213; 0.010 FDR: 2,213; 0.001 FDR: 1,862
2:43:52.038344 PROGRESS: =========================================================================
2:43:52.038697 INFO: Target number of precursors reached.
2:43:52.064959 INFO: fragments_df: keeping 5000 of 117388 [sum(precursor_idx_mask)=62160 sum(mass_error_mask)=117388 stop_rank=5000
2:43:52.076083 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:52.416232 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:53.061285 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:53.061757 INFO: Using score_cutoff 9.85472676229477 (fac=0.99, q=1)
2:43:53.062072 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:53.062155 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:53.062214 INFO: Updating optimization_manager: score_cutoff        : 10.210517595291137 -> 9.85472676229477
2:43:53.062281 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:53.066224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:53.073928 INFO: === checking if optimization conditions were reached ===
2:43:53.074044 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:43:53.074752 INFO: Updating optimization_manager: rt_error            : 291.3954003998161 -> 291.3954003998161
2:43:53.074868 INFO: Updating optimization_manager: classifier_version  : 6 -> 12
2:43:53.074959 INFO: Updating optimization_manager: score_cutoff        : 9.85472676229477 -> 9.85472676229477
2:43:53.075061 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:53.075144 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:53.075235 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 291.3954 found after 6 searches.
2:43:53.075293 INFO: ==============================================
2:43:53.075356 PROGRESS: Optimization finished for rt_error.
2:43:53.085758 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:53.089531 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:53.097240 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:43:53.097345 PROGRESS: ==============================================
2:43:53.097405 PROGRESS: ms2_error      : 10.0000
2:43:53.097456 PROGRESS: rt_error       : 291.3954
2:43:53.097502 PROGRESS: ==============================================
2:43:53.098104 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:53.234754 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:53.588929 INFO: Using rust extraction backend
2:43:53.589227 PROGRESS: Extracting batch of 264177 precursors
2:43:54.003019 INFO: === Search parameters used ===
2:43:54.003290 INFO: rt_error       : 291.3954003998161
2:43:54.003345 INFO: mobility_error : 0.1
2:43:54.003392 INFO: num_candidates : 3
2:43:54.003436 INFO: ms1_error      : 3
2:43:54.003477 INFO: ms2_error      : 10.0
2:43:54.003517 INFO: fwhm_rt        : 3.0
2:43:54.003572 INFO: quant_window   : 3
2:43:54.003622 INFO: ==============================================
2:43:54.758759 INFO: Removed 96319 precursors with score below cutoff 9.85472676229477
2:43:55.411304 INFO: performing precursor FDR with 40 features
2:43:55.411426 INFO: Decoy channel: -1
2:43:55.411453 INFO: competitive: True
2:43:55.467940 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:55.500528 WARNING: FDR calculation for 368764 target and 327448 decoy PSMs
2:43:55.500661 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:43:55.677550 INFO: Estimating optimal hyperparameters - samples: 556,969, batch_size: 2,281, learning_rate: 7.46e-04
2:43:55.678373 INFO: Using random state 309512 for train-test-split
2:44:07.297527 INFO: Test AUC: 0.782
2:44:07.297658 INFO: Train AUC: 0.786
2:44:07.297694 INFO: AUC difference: 0.47%
2:44:07.822626 INFO: Resetting torch num_threads to 24
2:44:08.147997 PROGRESS: ============================= Precursor FDR =============================
2:44:08.148268 PROGRESS: Total precursors accumulated: 125,442
2:44:08.148340 PROGRESS: Target precursors: 124,200 (99.01%)
2:44:08.148394 PROGRESS: Decoy precursors: 1,242 (0.99%)
2:44:08.148445 PROGRESS: 
2:44:08.148492 PROGRESS: Precursor Summary:
2:44:08.187185 PROGRESS: Channel   0:	 0.050 FDR: 124,200; 0.010 FDR: 124,200; 0.001 FDR: 109,868
2:44:08.187421 PROGRESS: 
2:44:08.187483 PROGRESS: Protein Summary:
2:44:08.255309 PROGRESS: Channel   0:	 0.050 FDR: 10,523; 0.010 FDR: 10,523; 0.001 FDR: 10,390
2:44:08.255553 PROGRESS: =========================================================================
2:44:08.258442 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
2:44:08.457173 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
2:44:08.760746 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:44:08.928792 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:44:08.928934 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:44:08.929017 INFO: Initializing TimingManager
2:44:08.929557 INFO: Initializing RawFileManager
2:44:22.607673 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:44:22.616092 INFO: Determining DIA cycle
2:44:22.633444 INFO: Found cycle with start 0.00 min and length 300.
2:44:22.803911 INFO: RT (min)            : 0.0 - 26.9
2:44:22.804100 INFO: RT duration (sec)   : 1611.2
2:44:22.804131 INFO: RT duration (min)   : 26.9
2:44:22.804154 INFO: Cycle len (scans)   : 300
2:44:22.804174 INFO: Cycle len (sec)     : 1.65
2:44:22.804193 INFO: Number of cycles    : 978
2:44:22.804213 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:44:22.804238 INFO: Creating DIA data object took: 13.874583959579468
2:44:24.623643 INFO: Creating DIA data NG object took: 1.8192758560180664
2:44:24.648851 INFO: Initializing CalibrationManager
2:44:24.649143 INFO: Setting up calibration estimators ..
2:44:24.649205 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:44:24.649272 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:44:24.649334 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:44:24.649385 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:44:24.649436 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:44:24.649486 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:44:24.649531 INFO: Done setting up calibration estimators.
2:44:24.649748 INFO: Initializing OptimizationManager
2:44:24.649878 INFO: initial parameter: ms1_error = 3
2:44:24.649932 INFO: initial parameter: ms2_error = 10
2:44:24.649982 INFO: initial parameter: rt_error = 805.611083984375
2:44:24.650027 INFO: initial parameter: mobility_error = 0.1
2:44:24.650069 INFO: initial parameter: num_candidates = 1
2:44:24.650110 INFO: initial parameter: fwhm_rt = 5
2:44:24.650151 INFO: initial parameter: fwhm_mobility = 0.01
2:44:24.650192 INFO: initial parameter: score_cutoff = 0
2:44:24.650232 INFO: initial parameter: classifier_version = -1
2:44:24.650299 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:44:24.650530 INFO: FDRManager: loading saved state not requested, will be initialized.
2:44:24.650563 INFO: Initializing FDRManager
2:44:24.650593 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:44:24.688643 PROGRESS: Initializing spectral library: 133,585 target precursors potentially observable (0 removed)
2:44:24.713878 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:44:24.714234 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:44:24.714324 PROGRESS: Starting initial search for precursors.
2:44:24.714401 INFO: Starting optimization step 0.
2:44:24.714460 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:44:24.714515 INFO: Using rust extraction backend
2:44:24.714574 PROGRESS: Extracting batch of 1974 precursors
2:44:24.719032 INFO: === Search parameters used ===
2:44:24.719132 INFO: rt_error       : 805.611083984375
2:44:24.719182 INFO: mobility_error : 0.1
2:44:24.719226 INFO: num_candidates : 1
2:44:24.719267 INFO: ms1_error      : 3
2:44:24.719308 INFO: ms2_error      : 10
2:44:24.719348 INFO: fwhm_rt        : 5
2:44:24.719387 INFO: quant_window   : 3
2:44:24.719426 INFO: ==============================================
2:44:24.750516 INFO: performing precursor FDR with 40 features
2:44:24.750585 INFO: Decoy channel: -1
2:44:24.750608 INFO: competitive: True
2:44:24.751804 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:24.753480 INFO: Estimating optimal hyperparameters - samples: 1,579, batch_size: 128, learning_rate: 1.77e-04
2:44:24.754278 INFO: Using random state 831687 for train-test-split
2:44:24.902026 INFO: Test AUC: 0.879
2:44:24.902106 INFO: Train AUC: 0.887
2:44:24.902133 INFO: AUC difference: 0.98%
2:44:25.141840 INFO: Resetting torch num_threads to 24
2:44:25.143545 PROGRESS: === Extracted 1974 precursors and 15369 fragments ===
2:44:25.143908 INFO: === FDR correction performed with classifier version -1 ===
2:44:25.144417 PROGRESS: ============================= Precursor FDR =============================
2:44:25.144497 PROGRESS: Total precursors accumulated: 617
2:44:25.144553 PROGRESS: Target precursors: 611 (99.03%)
2:44:25.144601 PROGRESS: Decoy precursors: 6 (0.97%)
2:44:25.144644 PROGRESS: 
2:44:25.144685 PROGRESS: Precursor Summary:
2:44:25.145796 PROGRESS: Channel   0:	 0.050 FDR:   611; 0.010 FDR:   611; 0.001 FDR:   378
2:44:25.145877 PROGRESS: 
2:44:25.145930 PROGRESS: Protein Summary:
2:44:25.147300 PROGRESS: Channel   0:	 0.050 FDR:   563; 0.010 FDR:   563; 0.001 FDR:   355
2:44:25.147389 PROGRESS: =========================================================================
2:44:25.147589 INFO: Target number of precursors not reached yet.
2:44:25.155237 INFO: Starting optimization step 1.
2:44:25.155341 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:44:25.155411 INFO: Using rust extraction backend
2:44:25.155468 PROGRESS: Extracting batch of 3939 precursors
2:44:25.163291 INFO: === Search parameters used ===
2:44:25.163398 INFO: rt_error       : 805.611083984375
2:44:25.163447 INFO: mobility_error : 0.1
2:44:25.163493 INFO: num_candidates : 1
2:44:25.163535 INFO: ms1_error      : 3
2:44:25.163575 INFO: ms2_error      : 10
2:44:25.163615 INFO: fwhm_rt        : 5
2:44:25.163654 INFO: quant_window   : 3
2:44:25.163692 INFO: ==============================================
2:44:25.228713 INFO: performing precursor FDR with 40 features
2:44:25.228799 INFO: Decoy channel: -1
2:44:25.228823 INFO: competitive: True
2:44:25.232867 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:25.235082 INFO: Estimating optimal hyperparameters - samples: 4,730, batch_size: 128, learning_rate: 1.77e-04
2:44:25.235164 INFO: Using random state 37487 for train-test-split
2:44:25.696897 INFO: Test AUC: 0.909
2:44:25.696988 INFO: Train AUC: 0.905
2:44:25.697016 INFO: AUC difference: 0.42%
2:44:25.934597 INFO: Resetting torch num_threads to 24
2:44:25.937735 PROGRESS: === Extracted 5913 precursors and 45986 fragments ===
2:44:25.938112 INFO: === FDR correction performed with classifier version -1 ===
2:44:25.938775 PROGRESS: ============================= Precursor FDR =============================
2:44:25.938859 PROGRESS: Total precursors accumulated: 2,198
2:44:25.938915 PROGRESS: Target precursors: 2,177 (99.04%)
2:44:25.938964 PROGRESS: Decoy precursors: 21 (0.96%)
2:44:25.939029 PROGRESS: 
2:44:25.939072 PROGRESS: Precursor Summary:
2:44:25.940602 PROGRESS: Channel   0:	 0.050 FDR: 2,177; 0.010 FDR: 2,177; 0.001 FDR: 1,766
2:44:25.940689 PROGRESS: 
2:44:25.940742 PROGRESS: Protein Summary:
2:44:25.942800 PROGRESS: Channel   0:	 0.050 FDR: 1,743; 0.010 FDR: 1,743; 0.001 FDR: 1,436
2:44:25.942890 PROGRESS: =========================================================================
2:44:25.943153 INFO: Target number of precursors reached.
2:44:25.953578 INFO: fragments_df: keeping 5000 of 45986 [sum(precursor_idx_mask)=21664 sum(mass_error_mask)=45986 stop_rank=5000
2:44:25.964357 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:26.231544 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:26.878647 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:44:26.879121 INFO: Using score_cutoff 11.131384367752075 (fac=0.99, q=1)
2:44:26.879445 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:44:26.879519 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:44:26.879570 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.131384367752075
2:44:26.879621 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:26.883558 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:26.891451 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:44:26.891554 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:44:26.891629 INFO: Starting optimization step 2.
2:44:26.891691 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:26.891753 INFO: Using rust extraction backend
2:44:26.891806 PROGRESS: Extracting batch of 5913 precursors
2:44:26.902820 INFO: === Search parameters used ===
2:44:26.902932 INFO: rt_error       : 805.611083984375
2:44:26.902990 INFO: mobility_error : 0.1
2:44:26.903039 INFO: num_candidates : 3
2:44:26.903081 INFO: ms1_error      : 3
2:44:26.903122 INFO: ms2_error      : 10
2:44:26.903161 INFO: fwhm_rt        : 3.0
2:44:26.903201 INFO: quant_window   : 3
2:44:26.903240 INFO: ==============================================
2:44:27.034802 INFO: performing precursor FDR with 40 features
2:44:27.034912 INFO: Decoy channel: -1
2:44:27.034936 INFO: competitive: True
2:44:27.039616 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:27.043486 INFO: Estimating optimal hyperparameters - samples: 14,188, batch_size: 128, learning_rate: 1.77e-04
2:44:27.043608 INFO: Using random state 963781 for train-test-split
2:44:28.453897 INFO: Test AUC: 0.730
2:44:28.454008 INFO: Train AUC: 0.730
2:44:28.454037 INFO: AUC difference: 0.00%
2:44:28.704916 INFO: Resetting torch num_threads to 24
2:44:28.707389 PROGRESS: === Extracted 17736 precursors and 119364 fragments ===
2:44:28.707761 INFO: === FDR correction performed with classifier version 1 ===
2:44:28.708454 PROGRESS: ============================= Precursor FDR =============================
2:44:28.708542 PROGRESS: Total precursors accumulated: 2,493
2:44:28.708603 PROGRESS: Target precursors: 2,469 (99.04%)
2:44:28.708653 PROGRESS: Decoy precursors: 24 (0.96%)
2:44:28.708701 PROGRESS: 
2:44:28.708746 PROGRESS: Precursor Summary:
2:44:28.710323 PROGRESS: Channel   0:	 0.050 FDR: 2,469; 0.010 FDR: 2,469; 0.001 FDR: 1,853
2:44:28.710414 PROGRESS: 
2:44:28.710485 PROGRESS: Protein Summary:
2:44:28.712707 PROGRESS: Channel   0:	 0.050 FDR: 1,969; 0.010 FDR: 1,969; 0.001 FDR: 1,516
2:44:28.712806 PROGRESS: =========================================================================
2:44:28.713162 INFO: Target number of precursors reached.
2:44:28.738831 INFO: fragments_df: keeping 5000 of 119364 [sum(precursor_idx_mask)=56091 sum(mass_error_mask)=119364 stop_rank=5000
2:44:28.749964 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:29.048933 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:29.694345 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:29.694811 INFO: Using score_cutoff 10.74130161781311 (fac=0.99, q=1)
2:44:29.695155 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:29.695237 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:29.695291 INFO: Updating optimization_manager: score_cutoff        : 11.131384367752075 -> 10.74130161781311
2:44:29.695342 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:29.699290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:29.706817 INFO: === checking if optimization conditions were reached ===
2:44:29.708489 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:44:29.708592 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:44:29.708656 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:29.708714 INFO: ==============================================
2:44:29.708787 INFO: Starting optimization step 3.
2:44:29.708844 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:29.708903 INFO: Using rust extraction backend
2:44:29.708958 PROGRESS: Extracting batch of 5913 precursors
2:44:29.720008 INFO: === Search parameters used ===
2:44:29.720136 INFO: rt_error       : 805.611083984375
2:44:29.720188 INFO: mobility_error : 0.1
2:44:29.720232 INFO: num_candidates : 3
2:44:29.720273 INFO: ms1_error      : 3
2:44:29.720314 INFO: ms2_error      : 10.0
2:44:29.720355 INFO: fwhm_rt        : 3.0
2:44:29.720394 INFO: quant_window   : 3
2:44:29.720433 INFO: ==============================================
2:44:29.834693 INFO: performing precursor FDR with 40 features
2:44:29.834801 INFO: Decoy channel: -1
2:44:29.834824 INFO: competitive: True
2:44:29.839377 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:29.843270 INFO: Estimating optimal hyperparameters - samples: 14,188, batch_size: 128, learning_rate: 1.77e-04
2:44:29.843391 INFO: Using random state 744422 for train-test-split
2:44:31.263209 INFO: Test AUC: 0.739
2:44:31.263315 INFO: Train AUC: 0.742
2:44:31.263342 INFO: AUC difference: 0.37%
2:44:31.514092 INFO: Resetting torch num_threads to 24
2:44:31.516559 PROGRESS: === Extracted 17736 precursors and 119394 fragments ===
2:44:31.516914 INFO: === FDR correction performed with classifier version 2 ===
2:44:31.517598 PROGRESS: ============================= Precursor FDR =============================
2:44:31.517678 PROGRESS: Total precursors accumulated: 2,573
2:44:31.517732 PROGRESS: Target precursors: 2,548 (99.03%)
2:44:31.517780 PROGRESS: Decoy precursors: 25 (0.97%)
2:44:31.517822 PROGRESS: 
2:44:31.517863 PROGRESS: Precursor Summary:
2:44:31.519432 PROGRESS: Channel   0:	 0.050 FDR: 2,548; 0.010 FDR: 2,548; 0.001 FDR: 1,900
2:44:31.519527 PROGRESS: 
2:44:31.519581 PROGRESS: Protein Summary:
2:44:31.521757 PROGRESS: Channel   0:	 0.050 FDR: 2,018; 0.010 FDR: 2,018; 0.001 FDR: 1,551
2:44:31.521843 PROGRESS: =========================================================================
2:44:31.522190 INFO: Target number of precursors reached.
2:44:31.547673 INFO: fragments_df: keeping 5000 of 119394 [sum(precursor_idx_mask)=57580 sum(mass_error_mask)=119394 stop_rank=5000
2:44:31.558774 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:31.875082 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:32.560921 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:32.561394 INFO: Using score_cutoff 10.313276216411591 (fac=0.99, q=1)
2:44:32.561706 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:32.561779 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:32.561830 INFO: Updating optimization_manager: score_cutoff        : 10.74130161781311 -> 10.313276216411591
2:44:32.561882 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:32.565852 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:32.573525 INFO: === checking if optimization conditions were reached ===
2:44:32.575188 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:32.575294 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:44:32.575357 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:32.575421 INFO: ==============================================
2:44:32.575489 INFO: Starting optimization step 4.
2:44:32.575545 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:32.575602 INFO: Using rust extraction backend
2:44:32.575656 PROGRESS: Extracting batch of 5913 precursors
2:44:32.586672 INFO: === Search parameters used ===
2:44:32.586787 INFO: rt_error       : 805.611083984375
2:44:32.586856 INFO: mobility_error : 0.1
2:44:32.586901 INFO: num_candidates : 3
2:44:32.586943 INFO: ms1_error      : 3
2:44:32.586992 INFO: ms2_error      : 10.0
2:44:32.587037 INFO: fwhm_rt        : 3.0
2:44:32.587076 INFO: quant_window   : 3
2:44:32.587115 INFO: ==============================================
2:44:32.703599 INFO: performing precursor FDR with 40 features
2:44:32.703702 INFO: Decoy channel: -1
2:44:32.703728 INFO: competitive: True
2:44:32.708341 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:32.712238 INFO: Estimating optimal hyperparameters - samples: 14,189, batch_size: 128, learning_rate: 1.77e-04
2:44:32.712355 INFO: Using random state 481822 for train-test-split
2:44:34.126724 INFO: Test AUC: 0.747
2:44:34.126828 INFO: Train AUC: 0.752
2:44:34.126858 INFO: AUC difference: 0.66%
2:44:34.380140 INFO: Resetting torch num_threads to 24
2:44:34.382598 PROGRESS: === Extracted 17737 precursors and 119388 fragments ===
2:44:34.382962 INFO: === FDR correction performed with classifier version 3 ===
2:44:34.383679 PROGRESS: ============================= Precursor FDR =============================
2:44:34.383767 PROGRESS: Total precursors accumulated: 2,626
2:44:34.383827 PROGRESS: Target precursors: 2,600 (99.01%)
2:44:34.383878 PROGRESS: Decoy precursors: 26 (0.99%)
2:44:34.383924 PROGRESS: 
2:44:34.383975 PROGRESS: Precursor Summary:
2:44:34.385587 PROGRESS: Channel   0:	 0.050 FDR: 2,600; 0.010 FDR: 2,593; 0.001 FDR: 2,051
2:44:34.385674 PROGRESS: 
2:44:34.385731 PROGRESS: Protein Summary:
2:44:34.387981 PROGRESS: Channel   0:	 0.050 FDR: 2,050; 0.010 FDR: 2,045; 0.001 FDR: 1,655
2:44:34.388075 PROGRESS: =========================================================================
2:44:34.388427 INFO: Target number of precursors reached.
2:44:34.414365 INFO: fragments_df: keeping 5000 of 119388 [sum(precursor_idx_mask)=58463 sum(mass_error_mask)=119388 stop_rank=5000
2:44:34.425565 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:36.875411 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:37.594968 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:37.595452 INFO: Using score_cutoff 10.162361631774903 (fac=0.99, q=1)
2:44:37.595770 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:37.595849 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:37.595905 INFO: Updating optimization_manager: score_cutoff        : 10.313276216411591 -> 10.162361631774903
2:44:37.595957 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:37.600025 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:37.607713 INFO: === checking if optimization conditions were reached ===
2:44:37.609442 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:37.609545 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:44:37.609612 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:37.609668 INFO: ==============================================
2:44:37.609731 INFO: Starting optimization step 5.
2:44:37.609788 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:37.609846 INFO: Using rust extraction backend
2:44:37.609900 PROGRESS: Extracting batch of 5913 precursors
2:44:37.621238 INFO: === Search parameters used ===
2:44:37.621372 INFO: rt_error       : 805.611083984375
2:44:37.621424 INFO: mobility_error : 0.1
2:44:37.621470 INFO: num_candidates : 3
2:44:37.621512 INFO: ms1_error      : 3
2:44:37.621554 INFO: ms2_error      : 10.0
2:44:37.621596 INFO: fwhm_rt        : 3.0
2:44:37.621637 INFO: quant_window   : 3
2:44:37.621678 INFO: ==============================================
2:44:37.735105 INFO: performing precursor FDR with 40 features
2:44:37.735213 INFO: Decoy channel: -1
2:44:37.735238 INFO: competitive: True
2:44:37.740337 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:37.744531 INFO: Estimating optimal hyperparameters - samples: 14,189, batch_size: 128, learning_rate: 1.77e-04
2:44:37.744684 INFO: Using random state 541292 for train-test-split
2:44:39.185761 INFO: Test AUC: 0.753
2:44:39.185874 INFO: Train AUC: 0.762
2:44:39.185904 INFO: AUC difference: 1.21%
2:44:39.442089 INFO: Resetting torch num_threads to 24
2:44:39.444708 PROGRESS: === Extracted 17737 precursors and 119354 fragments ===
2:44:39.445080 INFO: === FDR correction performed with classifier version 4 ===
2:44:39.445811 PROGRESS: ============================= Precursor FDR =============================
2:44:39.445901 PROGRESS: Total precursors accumulated: 2,687
2:44:39.445961 PROGRESS: Target precursors: 2,661 (99.03%)
2:44:39.446012 PROGRESS: Decoy precursors: 26 (0.97%)
2:44:39.446066 PROGRESS: 
2:44:39.446114 PROGRESS: Precursor Summary:
2:44:39.447842 PROGRESS: Channel   0:	 0.050 FDR: 2,661; 0.010 FDR: 2,661; 0.001 FDR: 2,256
2:44:39.447942 PROGRESS: 
2:44:39.448000 PROGRESS: Protein Summary:
2:44:39.450403 PROGRESS: Channel   0:	 0.050 FDR: 2,096; 0.010 FDR: 2,096; 0.001 FDR: 1,807
2:44:39.450503 PROGRESS: =========================================================================
2:44:39.450881 INFO: Target number of precursors reached.
2:44:39.477125 INFO: fragments_df: keeping 5000 of 119354 [sum(precursor_idx_mask)=59642 sum(mass_error_mask)=119354 stop_rank=5000
2:44:39.488170 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:39.874009 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:40.592328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:40.592781 INFO: Using score_cutoff 9.61905864715576 (fac=0.99, q=1)
2:44:40.593096 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:40.593174 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:40.593229 INFO: Updating optimization_manager: score_cutoff        : 10.162361631774903 -> 9.61905864715576
2:44:40.593282 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:40.597255 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:40.604814 INFO: === checking if optimization conditions were reached ===
2:44:40.606505 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:40.606605 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:44:40.606669 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:40.606728 INFO: ==============================================
2:44:40.606791 INFO: Starting optimization step 6.
2:44:40.606848 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:40.606907 INFO: Using rust extraction backend
2:44:40.606963 PROGRESS: Extracting batch of 5913 precursors
2:44:40.618138 INFO: === Search parameters used ===
2:44:40.618270 INFO: rt_error       : 805.611083984375
2:44:40.618323 INFO: mobility_error : 0.1
2:44:40.618370 INFO: num_candidates : 3
2:44:40.618414 INFO: ms1_error      : 3
2:44:40.618457 INFO: ms2_error      : 10.0
2:44:40.618498 INFO: fwhm_rt        : 3.0
2:44:40.618540 INFO: quant_window   : 3
2:44:40.618581 INFO: ==============================================
2:44:40.734301 INFO: performing precursor FDR with 40 features
2:44:40.734411 INFO: Decoy channel: -1
2:44:40.734437 INFO: competitive: True
2:44:40.739748 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:40.743924 INFO: Estimating optimal hyperparameters - samples: 14,189, batch_size: 128, learning_rate: 1.77e-04
2:44:40.744061 INFO: Using random state 503805 for train-test-split
2:44:42.185655 INFO: Test AUC: 0.775
2:44:42.185762 INFO: Train AUC: 0.766
2:44:42.185791 INFO: AUC difference: 1.21%
2:44:42.440738 INFO: Resetting torch num_threads to 24
2:44:42.443379 PROGRESS: === Extracted 17737 precursors and 119347 fragments ===
2:44:42.443744 INFO: === FDR correction performed with classifier version 5 ===
2:44:42.444473 PROGRESS: ============================= Precursor FDR =============================
2:44:42.444561 PROGRESS: Total precursors accumulated: 2,723
2:44:42.444626 PROGRESS: Target precursors: 2,697 (99.05%)
2:44:42.444687 PROGRESS: Decoy precursors: 26 (0.95%)
2:44:42.444733 PROGRESS: 
2:44:42.444776 PROGRESS: Precursor Summary:
2:44:42.446481 PROGRESS: Channel   0:	 0.050 FDR: 2,697; 0.010 FDR: 2,697; 0.001 FDR: 2,272
2:44:42.446571 PROGRESS: 
2:44:42.446627 PROGRESS: Protein Summary:
2:44:42.449020 PROGRESS: Channel   0:	 0.050 FDR: 2,127; 0.010 FDR: 2,127; 0.001 FDR: 1,817
2:44:42.449123 PROGRESS: =========================================================================
2:44:42.449492 INFO: Target number of precursors reached.
2:44:42.475965 INFO: fragments_df: keeping 5000 of 119347 [sum(precursor_idx_mask)=60393 sum(mass_error_mask)=119347 stop_rank=5000
2:44:42.487073 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:42.876861 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:43.593413 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:43.593886 INFO: Using score_cutoff 9.976747432708741 (fac=0.99, q=1)
2:44:43.594204 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:43.594284 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:43.594340 INFO: Updating optimization_manager: score_cutoff        : 9.61905864715576 -> 9.976747432708741
2:44:43.594395 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:43.598355 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:43.605933 INFO: === checking if optimization conditions were reached ===
2:44:43.607621 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:43.607724 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:44:43.607789 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:44:43.607846 INFO: ==============================================
2:44:43.607911 PROGRESS: Optimization finished for ms2_error.
2:44:43.618506 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:43.622298 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:43.629920 INFO: Starting optimization step 0.
2:44:43.630031 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:43.630105 INFO: Using rust extraction backend
2:44:43.630166 PROGRESS: Extracting batch of 5913 precursors
2:44:43.641287 INFO: === Search parameters used ===
2:44:43.641425 INFO: rt_error       : 805.611083984375
2:44:43.641478 INFO: mobility_error : 0.1
2:44:43.641526 INFO: num_candidates : 3
2:44:43.641585 INFO: ms1_error      : 3
2:44:43.641628 INFO: ms2_error      : 10.0
2:44:43.641670 INFO: fwhm_rt        : 3.0
2:44:43.641711 INFO: quant_window   : 3
2:44:43.641753 INFO: ==============================================
2:44:43.757245 INFO: performing precursor FDR with 40 features
2:44:43.757351 INFO: Decoy channel: -1
2:44:43.757376 INFO: competitive: True
2:44:43.762513 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:43.766569 INFO: Estimating optimal hyperparameters - samples: 14,189, batch_size: 128, learning_rate: 1.77e-04
2:44:43.766704 INFO: Using random state 351453 for train-test-split
2:44:45.182866 INFO: Test AUC: 0.764
2:44:45.183019 INFO: Train AUC: 0.777
2:44:45.183050 INFO: AUC difference: 1.70%
2:44:45.438264 INFO: Resetting torch num_threads to 24
2:44:45.440848 PROGRESS: === Extracted 17737 precursors and 119363 fragments ===
2:44:45.441223 INFO: === FDR correction performed with classifier version 6 ===
2:44:45.441947 PROGRESS: ============================= Precursor FDR =============================
2:44:45.442031 PROGRESS: Total precursors accumulated: 2,760
2:44:45.442089 PROGRESS: Target precursors: 2,733 (99.02%)
2:44:45.442139 PROGRESS: Decoy precursors: 27 (0.98%)
2:44:45.442184 PROGRESS: 
2:44:45.442227 PROGRESS: Precursor Summary:
2:44:45.443916 PROGRESS: Channel   0:	 0.050 FDR: 2,733; 0.010 FDR: 2,733; 0.001 FDR: 2,403
2:44:45.444010 PROGRESS: 
2:44:45.444064 PROGRESS: Protein Summary:
2:44:45.446445 PROGRESS: Channel   0:	 0.050 FDR: 2,148; 0.010 FDR: 2,148; 0.001 FDR: 1,914
2:44:45.446535 PROGRESS: =========================================================================
2:44:45.446911 INFO: Target number of precursors reached.
2:44:45.473400 INFO: fragments_df: keeping 5000 of 119363 [sum(precursor_idx_mask)=60962 sum(mass_error_mask)=119363 stop_rank=5000
2:44:45.484448 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:45.881227 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:46.599420 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:46.599890 INFO: Using score_cutoff 9.762457131958007 (fac=0.99, q=1)
2:44:46.600211 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:46.600292 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:46.600346 INFO: Updating optimization_manager: score_cutoff        : 9.976747432708741 -> 9.762457131958007
2:44:46.600397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:46.604374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:46.612124 INFO: === checking if optimization conditions were reached ===
2:44:46.612232 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:44:46.615063 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 418.2844705579299
2:44:46.615169 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 418.2845.
2:44:46.615230 INFO: ==============================================
2:44:46.615296 INFO: Starting optimization step 1.
2:44:46.615350 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:46.615416 INFO: Using rust extraction backend
2:44:46.615470 PROGRESS: Extracting batch of 5913 precursors
2:44:46.626559 INFO: === Search parameters used ===
2:44:46.626677 INFO: rt_error       : 418.2844705579299
2:44:46.626728 INFO: mobility_error : 0.1
2:44:46.626773 INFO: num_candidates : 3
2:44:46.626816 INFO: ms1_error      : 3
2:44:46.626857 INFO: ms2_error      : 10.0
2:44:46.626899 INFO: fwhm_rt        : 3.0
2:44:46.626940 INFO: quant_window   : 3
2:44:46.627012 INFO: ==============================================
2:44:46.729759 INFO: performing precursor FDR with 40 features
2:44:46.729867 INFO: Decoy channel: -1
2:44:46.729891 INFO: competitive: True
2:44:46.734919 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:46.739028 INFO: Estimating optimal hyperparameters - samples: 14,189, batch_size: 128, learning_rate: 1.77e-04
2:44:46.739163 INFO: Using random state 351453 for train-test-split
2:44:48.160281 INFO: Test AUC: 0.767
2:44:48.160403 INFO: Train AUC: 0.776
2:44:48.160432 INFO: AUC difference: 1.18%
2:44:48.417437 INFO: Resetting torch num_threads to 24
2:44:48.420035 PROGRESS: === Extracted 17737 precursors and 118761 fragments ===
2:44:48.420406 INFO: === FDR correction performed with classifier version 6 ===
2:44:48.421131 PROGRESS: ============================= Precursor FDR =============================
2:44:48.421214 PROGRESS: Total precursors accumulated: 2,776
2:44:48.421271 PROGRESS: Target precursors: 2,749 (99.03%)
2:44:48.421319 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:48.421362 PROGRESS: 
2:44:48.421403 PROGRESS: Precursor Summary:
2:44:48.423121 PROGRESS: Channel   0:	 0.050 FDR: 2,749; 0.010 FDR: 2,749; 0.001 FDR: 2,398
2:44:48.423214 PROGRESS: 
2:44:48.423268 PROGRESS: Protein Summary:
2:44:48.425694 PROGRESS: Channel   0:	 0.050 FDR: 2,158; 0.010 FDR: 2,158; 0.001 FDR: 1,910
2:44:48.425790 PROGRESS: =========================================================================
2:44:48.426167 INFO: Target number of precursors reached.
2:44:48.452633 INFO: fragments_df: keeping 5000 of 118761 [sum(precursor_idx_mask)=61129 sum(mass_error_mask)=118761 stop_rank=5000
2:44:48.463978 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:48.861822 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:49.585387 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:49.585852 INFO: Using score_cutoff 9.616308940887452 (fac=0.99, q=1)
2:44:49.586178 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:49.586263 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:49.586318 INFO: Updating optimization_manager: score_cutoff        : 9.762457131958007 -> 9.616308940887452
2:44:49.586370 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:49.590341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:49.597906 INFO: === checking if optimization conditions were reached ===
2:44:49.598020 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:44:49.600989 INFO: Updating optimization_manager: rt_error            : 418.2844705579299 -> 393.0385619036664
2:44:49.601097 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 393.0386.
2:44:49.601172 INFO: ==============================================
2:44:49.601241 INFO: Starting optimization step 2.
2:44:49.601297 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:49.601355 INFO: Using rust extraction backend
2:44:49.601408 PROGRESS: Extracting batch of 5913 precursors
2:44:49.612523 INFO: === Search parameters used ===
2:44:49.612663 INFO: rt_error       : 393.0385619036664
2:44:49.612715 INFO: mobility_error : 0.1
2:44:49.612760 INFO: num_candidates : 3
2:44:49.612802 INFO: ms1_error      : 3
2:44:49.612842 INFO: ms2_error      : 10.0
2:44:49.612892 INFO: fwhm_rt        : 3.0
2:44:49.612939 INFO: quant_window   : 3
2:44:49.612982 INFO: ==============================================
2:44:49.721564 INFO: performing precursor FDR with 40 features
2:44:49.721675 INFO: Decoy channel: -1
2:44:49.721699 INFO: competitive: True
2:44:49.726947 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:49.731070 INFO: Estimating optimal hyperparameters - samples: 14,189, batch_size: 128, learning_rate: 1.77e-04
2:44:49.731207 INFO: Using random state 351453 for train-test-split
2:44:51.157694 INFO: Test AUC: 0.753
2:44:51.157804 INFO: Train AUC: 0.780
2:44:51.157832 INFO: AUC difference: 3.41%
2:44:51.405452 INFO: Resetting torch num_threads to 24
2:44:51.408015 PROGRESS: === Extracted 17737 precursors and 118605 fragments ===
2:44:51.408381 INFO: === FDR correction performed with classifier version 6 ===
2:44:51.409107 PROGRESS: ============================= Precursor FDR =============================
2:44:51.409191 PROGRESS: Total precursors accumulated: 2,807
2:44:51.409249 PROGRESS: Target precursors: 2,780 (99.04%)
2:44:51.409297 PROGRESS: Decoy precursors: 27 (0.96%)
2:44:51.409341 PROGRESS: 
2:44:51.409384 PROGRESS: Precursor Summary:
2:44:51.411104 PROGRESS: Channel   0:	 0.050 FDR: 2,780; 0.010 FDR: 2,780; 0.001 FDR: 2,385
2:44:51.411200 PROGRESS: 
2:44:51.411255 PROGRESS: Protein Summary:
2:44:51.413665 PROGRESS: Channel   0:	 0.050 FDR: 2,182; 0.010 FDR: 2,182; 0.001 FDR: 1,905
2:44:51.413756 PROGRESS: =========================================================================
2:44:51.414116 INFO: Target number of precursors reached.
2:44:51.440534 INFO: fragments_df: keeping 5000 of 118605 [sum(precursor_idx_mask)=61657 sum(mass_error_mask)=118605 stop_rank=5000
2:44:51.451900 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:51.854712 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:52.571975 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:52.572442 INFO: Using score_cutoff 9.554872964859008 (fac=0.99, q=1)
2:44:52.572756 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:52.572830 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:52.572881 INFO: Updating optimization_manager: score_cutoff        : 9.616308940887452 -> 9.554872964859008
2:44:52.572931 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:52.576916 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:52.584282 INFO: === checking if optimization conditions were reached ===
2:44:52.584385 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:44:52.587482 INFO: Updating optimization_manager: rt_error            : 393.0385619036664 -> 365.2959354216314
2:44:52.587585 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 365.2959.
2:44:52.587647 INFO: ==============================================
2:44:52.587713 INFO: Starting optimization step 3.
2:44:52.587769 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:52.587827 INFO: Using rust extraction backend
2:44:52.587880 PROGRESS: Extracting batch of 5913 precursors
2:44:52.598960 INFO: === Search parameters used ===
2:44:52.599102 INFO: rt_error       : 365.2959354216314
2:44:52.599154 INFO: mobility_error : 0.1
2:44:52.599198 INFO: num_candidates : 3
2:44:52.599247 INFO: ms1_error      : 3
2:44:52.599290 INFO: ms2_error      : 10.0
2:44:52.599330 INFO: fwhm_rt        : 3.0
2:44:52.599369 INFO: quant_window   : 3
2:44:52.599408 INFO: ==============================================
2:44:52.705309 INFO: performing precursor FDR with 40 features
2:44:52.705417 INFO: Decoy channel: -1
2:44:52.705441 INFO: competitive: True
2:44:52.710723 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:52.714804 INFO: Estimating optimal hyperparameters - samples: 14,188, batch_size: 128, learning_rate: 1.77e-04
2:44:52.714940 INFO: Using random state 351453 for train-test-split
2:44:54.118758 INFO: Test AUC: 0.760
2:44:54.118876 INFO: Train AUC: 0.777
2:44:54.118908 INFO: AUC difference: 2.26%
2:44:54.369202 INFO: Resetting torch num_threads to 24
2:44:54.371820 PROGRESS: === Extracted 17736 precursors and 118373 fragments ===
2:44:54.372203 INFO: === FDR correction performed with classifier version 6 ===
2:44:54.372940 PROGRESS: ============================= Precursor FDR =============================
2:44:54.373029 PROGRESS: Total precursors accumulated: 2,773
2:44:54.373091 PROGRESS: Target precursors: 2,746 (99.03%)
2:44:54.373147 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:54.373197 PROGRESS: 
2:44:54.373247 PROGRESS: Precursor Summary:
2:44:54.374986 PROGRESS: Channel   0:	 0.050 FDR: 2,746; 0.010 FDR: 2,746; 0.001 FDR: 2,364
2:44:54.375087 PROGRESS: 
2:44:54.375147 PROGRESS: Protein Summary:
2:44:54.377545 PROGRESS: Channel   0:	 0.050 FDR: 2,156; 0.010 FDR: 2,156; 0.001 FDR: 1,889
2:44:54.377642 PROGRESS: =========================================================================
2:44:54.378017 INFO: Target number of precursors reached.
2:44:54.404473 INFO: fragments_df: keeping 5000 of 118373 [sum(precursor_idx_mask)=61033 sum(mass_error_mask)=118373 stop_rank=5000
2:44:54.415755 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:54.808173 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:55.529350 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:55.529811 INFO: Using score_cutoff 9.702618598937988 (fac=0.99, q=1)
2:44:55.530130 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:55.530209 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:55.530273 INFO: Updating optimization_manager: score_cutoff        : 9.554872964859008 -> 9.702618598937988
2:44:55.530326 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:55.534284 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:55.541916 INFO: === checking if optimization conditions were reached ===
2:44:55.542030 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:44:55.545121 INFO: Updating optimization_manager: rt_error            : 365.2959354216314 -> 245.11836690390538
2:44:55.545231 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 245.1184.
2:44:55.545294 INFO: ==============================================
2:44:55.545362 INFO: Starting optimization step 4.
2:44:55.545419 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:55.545478 INFO: Using rust extraction backend
2:44:55.545534 PROGRESS: Extracting batch of 5913 precursors
2:44:55.556767 INFO: === Search parameters used ===
2:44:55.556926 INFO: rt_error       : 245.11836690390538
2:44:55.556989 INFO: mobility_error : 0.1
2:44:55.557036 INFO: num_candidates : 3
2:44:55.557078 INFO: ms1_error      : 3
2:44:55.557118 INFO: ms2_error      : 10.0
2:44:55.557160 INFO: fwhm_rt        : 3.0
2:44:55.557199 INFO: quant_window   : 3
2:44:55.557237 INFO: ==============================================
2:44:55.652452 INFO: performing precursor FDR with 40 features
2:44:55.652562 INFO: Decoy channel: -1
2:44:55.652586 INFO: competitive: True
2:44:55.657486 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:55.661572 INFO: Estimating optimal hyperparameters - samples: 14,180, batch_size: 128, learning_rate: 1.77e-04
2:44:55.661711 INFO: Using random state 351453 for train-test-split
2:44:57.085967 INFO: Test AUC: 0.756
2:44:57.086074 INFO: Train AUC: 0.775
2:44:57.086101 INFO: AUC difference: 2.42%
2:44:57.335137 INFO: Resetting torch num_threads to 24
2:44:57.337709 PROGRESS: === Extracted 17725 precursors and 116346 fragments ===
2:44:57.338071 INFO: === FDR correction performed with classifier version 6 ===
2:44:57.338801 PROGRESS: ============================= Precursor FDR =============================
2:44:57.338884 PROGRESS: Total precursors accumulated: 2,795
2:44:57.338941 PROGRESS: Target precursors: 2,768 (99.03%)
2:44:57.339001 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:57.339050 PROGRESS: 
2:44:57.339093 PROGRESS: Precursor Summary:
2:44:57.340796 PROGRESS: Channel   0:	 0.050 FDR: 2,768; 0.010 FDR: 2,768; 0.001 FDR: 2,260
2:44:57.340883 PROGRESS: 
2:44:57.340938 PROGRESS: Protein Summary:
2:44:57.343318 PROGRESS: Channel   0:	 0.050 FDR: 2,173; 0.010 FDR: 2,173; 0.001 FDR: 1,810
2:44:57.343413 PROGRESS: =========================================================================
2:44:57.343799 INFO: Target number of precursors reached.
2:44:57.370147 INFO: fragments_df: keeping 5000 of 116346 [sum(precursor_idx_mask)=60903 sum(mass_error_mask)=116346 stop_rank=5000
2:44:57.381376 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:57.783917 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:58.498798 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:58.499284 INFO: Using score_cutoff 9.60519217414856 (fac=0.99, q=1)
2:44:58.499609 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:58.499684 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:58.499740 INFO: Updating optimization_manager: score_cutoff        : 9.702618598937988 -> 9.60519217414856
2:44:58.499792 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:58.503774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:58.511196 INFO: === checking if optimization conditions were reached ===
2:44:58.511305 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:44:58.514342 INFO: Updating optimization_manager: rt_error            : 245.11836690390538 -> 216.405787702293
2:44:58.514439 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 216.4058.
2:44:58.514500 INFO: ==============================================
2:44:58.514565 INFO: Starting optimization step 5.
2:44:58.514619 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:58.514678 INFO: Using rust extraction backend
2:44:58.514730 PROGRESS: Extracting batch of 5913 precursors
2:44:58.525779 INFO: === Search parameters used ===
2:44:58.525903 INFO: rt_error       : 216.405787702293
2:44:58.525954 INFO: mobility_error : 0.1
2:44:58.525999 INFO: num_candidates : 3
2:44:58.526042 INFO: ms1_error      : 3
2:44:58.526083 INFO: ms2_error      : 10.0
2:44:58.526123 INFO: fwhm_rt        : 3.0
2:44:58.526161 INFO: quant_window   : 3
2:44:58.526199 INFO: ==============================================
2:44:58.625061 INFO: performing precursor FDR with 40 features
2:44:58.625173 INFO: Decoy channel: -1
2:44:58.625216 INFO: competitive: True
2:44:58.629989 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:58.634024 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:44:58.634161 INFO: Using random state 351453 for train-test-split
2:45:00.040315 INFO: Test AUC: 0.756
2:45:00.040424 INFO: Train AUC: 0.779
2:45:00.040454 INFO: AUC difference: 2.84%
2:45:00.296568 INFO: Resetting torch num_threads to 24
2:45:00.299107 PROGRESS: === Extracted 17720 precursors and 115215 fragments ===
2:45:00.299467 INFO: === FDR correction performed with classifier version 6 ===
2:45:00.300198 PROGRESS: ============================= Precursor FDR =============================
2:45:00.300282 PROGRESS: Total precursors accumulated: 2,800
2:45:00.300343 PROGRESS: Target precursors: 2,773 (99.04%)
2:45:00.300394 PROGRESS: Decoy precursors: 27 (0.96%)
2:45:00.300441 PROGRESS: 
2:45:00.300487 PROGRESS: Precursor Summary:
2:45:00.302167 PROGRESS: Channel   0:	 0.050 FDR: 2,773; 0.010 FDR: 2,773; 0.001 FDR: 2,362
2:45:00.302257 PROGRESS: 
2:45:00.302313 PROGRESS: Protein Summary:
2:45:00.304682 PROGRESS: Channel   0:	 0.050 FDR: 2,179; 0.010 FDR: 2,179; 0.001 FDR: 1,886
2:45:00.304779 PROGRESS: =========================================================================
2:45:00.305159 INFO: Target number of precursors reached.
2:45:00.331272 INFO: fragments_df: keeping 5000 of 115215 [sum(precursor_idx_mask)=60610 sum(mass_error_mask)=115215 stop_rank=5000
2:45:00.342515 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:00.745312 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:01.427850 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:01.428337 INFO: Using score_cutoff 9.329285680389404 (fac=0.99, q=1)
2:45:01.428648 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:01.428725 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:01.428778 INFO: Updating optimization_manager: score_cutoff        : 9.60519217414856 -> 9.329285680389404
2:45:01.428831 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:01.432802 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:01.440553 INFO: === checking if optimization conditions were reached ===
2:45:01.440667 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:45:01.443733 INFO: Updating optimization_manager: rt_error            : 216.405787702293 -> 213.02307175993406
2:45:01.443835 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 213.0231.
2:45:01.443900 INFO: ==============================================
2:45:01.443969 INFO: Starting optimization step 6.
2:45:01.444027 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:45:01.444088 INFO: Using rust extraction backend
2:45:01.444151 PROGRESS: Extracting batch of 5913 precursors
2:45:01.455206 INFO: === Search parameters used ===
2:45:01.455329 INFO: rt_error       : 213.02307175993406
2:45:01.455381 INFO: mobility_error : 0.1
2:45:01.455426 INFO: num_candidates : 3
2:45:01.455471 INFO: ms1_error      : 3
2:45:01.455516 INFO: ms2_error      : 10.0
2:45:01.455557 INFO: fwhm_rt        : 3.0
2:45:01.455598 INFO: quant_window   : 3
2:45:01.455637 INFO: ==============================================
2:45:01.549748 INFO: performing precursor FDR with 40 features
2:45:01.549854 INFO: Decoy channel: -1
2:45:01.549879 INFO: competitive: True
2:45:01.554758 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:01.558877 INFO: Estimating optimal hyperparameters - samples: 14,176, batch_size: 128, learning_rate: 1.77e-04
2:45:01.559035 INFO: Using random state 351453 for train-test-split
2:45:02.966843 INFO: Test AUC: 0.756
2:45:02.966949 INFO: Train AUC: 0.775
2:45:02.966988 INFO: AUC difference: 2.46%
2:45:03.216139 INFO: Resetting torch num_threads to 24
2:45:03.218687 PROGRESS: === Extracted 17720 precursors and 115140 fragments ===
2:45:03.219064 INFO: === FDR correction performed with classifier version 6 ===
2:45:03.219794 PROGRESS: ============================= Precursor FDR =============================
2:45:03.219877 PROGRESS: Total precursors accumulated: 2,783
2:45:03.219934 PROGRESS: Target precursors: 2,756 (99.03%)
2:45:03.219982 PROGRESS: Decoy precursors: 27 (0.97%)
2:45:03.220024 PROGRESS: 
2:45:03.220065 PROGRESS: Precursor Summary:
2:45:03.221781 PROGRESS: Channel   0:	 0.050 FDR: 2,756; 0.010 FDR: 2,756; 0.001 FDR: 2,565
2:45:03.221874 PROGRESS: 
2:45:03.221927 PROGRESS: Protein Summary:
2:45:03.224321 PROGRESS: Channel   0:	 0.050 FDR: 2,165; 0.010 FDR: 2,165; 0.001 FDR: 2,031
2:45:03.224422 PROGRESS: =========================================================================
2:45:03.224804 INFO: Target number of precursors reached.
2:45:03.251345 INFO: fragments_df: keeping 5000 of 115140 [sum(precursor_idx_mask)=60352 sum(mass_error_mask)=115140 stop_rank=5000
2:45:03.262494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:03.597190 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:04.246915 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:04.247376 INFO: Using score_cutoff 9.596816843032837 (fac=0.99, q=1)
2:45:04.247694 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:04.247772 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:04.247828 INFO: Updating optimization_manager: score_cutoff        : 9.329285680389404 -> 9.596816843032837
2:45:04.247885 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:04.251862 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:04.259319 INFO: === checking if optimization conditions were reached ===
2:45:04.259433 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:45:04.260161 INFO: Updating optimization_manager: rt_error            : 213.02307175993406 -> 393.0385619036664
2:45:04.260285 INFO: Updating optimization_manager: classifier_version  : 6 -> 9
2:45:04.260382 INFO: Updating optimization_manager: score_cutoff        : 9.596816843032837 -> 9.554872964859008
2:45:04.260473 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:04.260568 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:04.260655 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 393.0386 found after 7 searches.
2:45:04.260715 INFO: ==============================================
2:45:04.260782 PROGRESS: Optimization finished for rt_error.
2:45:04.271209 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:04.274980 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:04.282616 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:45:04.282746 PROGRESS: ==============================================
2:45:04.282814 PROGRESS: ms2_error      : 10.0000
2:45:04.282871 PROGRESS: rt_error       : 393.0386
2:45:04.282918 PROGRESS: ==============================================
2:45:04.283582 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:04.419120 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:04.765074 INFO: Using rust extraction backend
2:45:04.765393 PROGRESS: Extracting batch of 264177 precursors
2:45:05.180838 INFO: === Search parameters used ===
2:45:05.181127 INFO: rt_error       : 393.0385619036664
2:45:05.181188 INFO: mobility_error : 0.1
2:45:05.181237 INFO: num_candidates : 3
2:45:05.181282 INFO: ms1_error      : 3
2:45:05.181340 INFO: ms2_error      : 10.0
2:45:05.181386 INFO: fwhm_rt        : 3.0
2:45:05.181429 INFO: quant_window   : 3
2:45:05.181474 INFO: ==============================================
2:45:06.123402 INFO: Removed 72638 precursors with score below cutoff 9.554872964859008
2:45:06.792378 INFO: performing precursor FDR with 40 features
2:45:06.792500 INFO: Decoy channel: -1
2:45:06.792527 INFO: competitive: True
2:45:06.851766 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:07.077207 INFO: Estimating optimal hyperparameters - samples: 575,914, batch_size: 2,358, learning_rate: 7.59e-04
2:45:07.078182 INFO: Using random state 703905 for train-test-split
2:45:18.954756 INFO: Test AUC: 0.776
2:45:18.954898 INFO: Train AUC: 0.779
2:45:18.954932 INFO: AUC difference: 0.41%
2:45:19.470421 INFO: Resetting torch num_threads to 24
2:45:19.783454 PROGRESS: ============================= Precursor FDR =============================
2:45:19.783719 PROGRESS: Total precursors accumulated: 125,039
2:45:19.783791 PROGRESS: Target precursors: 123,801 (99.01%)
2:45:19.783846 PROGRESS: Decoy precursors: 1,238 (0.99%)
2:45:19.783895 PROGRESS: 
2:45:19.783943 PROGRESS: Precursor Summary:
2:45:19.822855 PROGRESS: Channel   0:	 0.050 FDR: 123,801; 0.010 FDR: 123,801; 0.001 FDR: 110,305
2:45:19.823114 PROGRESS: 
2:45:19.823180 PROGRESS: Protein Summary:
2:45:19.890027 PROGRESS: Channel   0:	 0.050 FDR: 10,527; 0.010 FDR: 10,527; 0.001 FDR: 10,389
2:45:19.890281 PROGRESS: =========================================================================
2:45:19.893016 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
2:45:20.081968 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
2:45:20.384217 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:45:21.112052 PROGRESS: Processing search outputs
2:45:21.112176 PROGRESS: === Performing protein grouping and FDR ===
2:45:21.112213 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:45:21.205605 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:45:21.289658 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:45:21.378079 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:45:21.467849 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:45:21.563488 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:45:21.679559 INFO: Performing protein inference
2:45:22.744763 INFO: Inference strategy: library. Using library grouping for protein inference
2:45:22.749340 INFO: Performing protein FDR
2:45:26.708002 INFO: Normalizing q-values using 10,534 targets and 3,684 decoys
2:45:26.711446 INFO: Test AUC: 1.000
2:45:26.711504 INFO: Train AUC: 1.000
2:45:26.711540 INFO: AUC difference: 0.00%
2:45:27.595834 INFO: ================ Protein FDR =================
2:45:27.595987 INFO: Unique protein groups in output
2:45:27.596019 INFO:   1% protein FDR: 10,534
2:45:27.596042 INFO: 
2:45:27.596061 INFO: Unique precursor in output
2:45:27.596080 INFO:   1% protein FDR: 133,287
2:45:27.596098 INFO: ================================================
2:45:27.694047 PROGRESS: Building search statistics
2:45:27.830625 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:45:27.830827 INFO: Initializing OptimizationManager
2:45:27.831235 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:45:27.831314 INFO: Initializing CalibrationManager
2:45:27.831553 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:45:27.831645 INFO: Initializing RawFileManager
2:45:27.875767 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:45:27.875967 INFO: Initializing OptimizationManager
2:45:27.876181 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:45:27.876261 INFO: Initializing CalibrationManager
2:45:27.876479 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:45:27.876558 INFO: Initializing RawFileManager
2:45:27.920367 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:45:27.920559 INFO: Initializing OptimizationManager
2:45:27.920765 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:45:27.920834 INFO: Initializing CalibrationManager
2:45:27.921049 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:45:27.921117 INFO: Initializing RawFileManager
2:45:27.964957 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:45:27.965142 INFO: Initializing OptimizationManager
2:45:27.965362 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:45:27.965440 INFO: Initializing CalibrationManager
2:45:27.965663 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:45:27.965737 INFO: Initializing RawFileManager
2:45:28.010237 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:45:28.010447 INFO: Initializing OptimizationManager
2:45:28.010670 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:45:28.010742 INFO: Initializing CalibrationManager
2:45:28.010965 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:45:28.011055 INFO: Initializing RawFileManager
2:45:28.055821 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:45:28.056014 INFO: Initializing OptimizationManager
2:45:28.056254 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:45:28.056328 INFO: Initializing CalibrationManager
2:45:28.056557 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:45:28.056632 INFO: Initializing RawFileManager
2:45:28.060912 INFO: Writing stat output to disk
2:45:28.060981 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
2:45:28.074038 PROGRESS: Building internal statistics
2:45:28.074413 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:45:28.074459 INFO: Initializing TimingManager
2:45:28.074876 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:45:28.074917 INFO: Initializing TimingManager
2:45:28.075168 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:45:28.075215 INFO: Initializing TimingManager
2:45:28.075420 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:45:28.075456 INFO: Initializing TimingManager
2:45:28.075652 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:45:28.075685 INFO: Initializing TimingManager
2:45:28.075878 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:45:28.075919 INFO: Initializing TimingManager
2:45:28.076389 INFO: Writing internal output to disk
2:45:28.076437 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
2:45:28.172979 INFO: Performing label free quantification
2:45:28.173130 INFO: Accumulating fragment data
2:45:28.173185 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:45:28.254506 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:45:29.881721 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:45:31.493585 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:45:33.171886 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:45:34.869932 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:45:36.851889 INFO: Performing label free quantification on the precursor level
2:45:36.852039 INFO: Filtering fragments by quality
2:45:37.260684 INFO: Performing label-free quantification with directlfq normalization
2:45:37.884221 INFO: 133287 lfq-groups total
2:46:15.444625 INFO: using 24 processes
2:46:16.060083 INFO: lfq-object 0
2:46:16.932724 INFO: lfq-object 100
2:46:17.058865 INFO: lfq-object 200
2:46:17.178218 INFO: lfq-object 1400
2:46:17.186811 INFO: lfq-object 300
2:46:17.308574 INFO: lfq-object 1500
2:46:17.315526 INFO: lfq-object 400
2:46:17.438768 INFO: lfq-object 1600
2:46:17.448242 INFO: lfq-object 500
2:46:17.569196 INFO: lfq-object 1700
2:46:17.570916 INFO: lfq-object 2800
2:46:17.578462 INFO: lfq-object 600
2:46:17.696525 INFO: lfq-object 1800
2:46:17.699544 INFO: lfq-object 2900
2:46:17.710209 INFO: lfq-object 700
2:46:17.822162 INFO: lfq-object 1900
2:46:17.829797 INFO: lfq-object 3000
2:46:17.839406 INFO: lfq-object 800
2:46:17.949885 INFO: lfq-object 2000
2:46:17.956294 INFO: lfq-object 3100
2:46:17.973135 INFO: lfq-object 900
2:46:18.054979 INFO: lfq-object 4200
2:46:18.082376 INFO: lfq-object 2100
2:46:18.083645 INFO: lfq-object 3200
2:46:18.100309 INFO: lfq-object 1000
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2:46:18.967664 INFO: lfq-object 6000
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2:46:19.075006 INFO: lfq-object 7200
2:46:19.100329 INFO: lfq-object 6100
2:46:19.110628 INFO: lfq-object 5000
2:46:19.117644 INFO: lfq-object 4000
2:46:19.204137 INFO: lfq-object 7300
2:46:19.227727 INFO: lfq-object 8400
2:46:19.230020 INFO: lfq-object 6200
2:46:19.240067 INFO: lfq-object 5100
2:46:19.247670 INFO: lfq-object 4100
2:46:19.334282 INFO: lfq-object 7400
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2:46:19.359012 INFO: lfq-object 6300
2:46:19.370593 INFO: lfq-object 5200
2:46:19.461959 INFO: lfq-object 7500
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2:47:58.368982 INFO: Performing label free quantification on the peptide level
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2:50:09.395090 INFO: Performing label free quantification on the pg level
2:50:09.395262 INFO: Filtering fragments by quality
2:50:09.803884 INFO: Performing label-free quantification with directlfq normalization
2:50:10.017387 INFO: 10534 lfq-groups total
2:50:17.964762 INFO: using 24 processes
2:50:18.124394 INFO: lfq-object 0
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2:50:19.972288 INFO: lfq-object 2800
2:50:20.012796 INFO: lfq-object 1800
2:50:20.027661 INFO: lfq-object 1700
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2:50:20.085514 INFO: lfq-object 3100
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2:50:20.666432 INFO: lfq-object 4000
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2:50:22.473921 INFO: lfq-object 7600
2:50:22.513598 INFO: lfq-object 7700
2:50:22.655071 INFO: lfq-object 6800
2:50:22.684602 INFO: lfq-object 6900
2:50:22.833626 INFO: lfq-object 8000
2:50:22.855600 INFO: lfq-object 7900
2:50:22.858143 INFO: lfq-object 8100
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2:50:22.884559 INFO: lfq-object 7000
2:50:22.929630 INFO: lfq-object 7800
2:50:22.949343 INFO: lfq-object 8400
2:50:22.983441 INFO: lfq-object 8600
2:50:23.023619 INFO: lfq-object 8800
2:50:23.026144 INFO: lfq-object 8700
2:50:23.184111 INFO: lfq-object 8500
2:50:23.412086 INFO: lfq-object 8900
2:50:23.415569 INFO: lfq-object 9600
2:50:23.424515 INFO: lfq-object 9100
2:50:23.434117 INFO: lfq-object 9500
2:50:23.435933 INFO: lfq-object 9300
2:50:23.451738 INFO: lfq-object 9400
2:50:23.476135 INFO: lfq-object 9700
2:50:23.523397 INFO: lfq-object 9900
2:50:23.523733 INFO: lfq-object 9800
2:50:23.550692 INFO: lfq-object 9200
2:50:23.838093 INFO: lfq-object 9000
2:50:23.861039 INFO: lfq-object 10000
2:50:23.912858 INFO: lfq-object 10100
2:50:23.965741 INFO: lfq-object 10500
2:50:23.991256 INFO: lfq-object 10200
2:50:24.004688 INFO: lfq-object 10400
2:50:24.153448 INFO: lfq-object 10300
2:50:26.383826 INFO: Writing psm output to disk
2:50:26.515795 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
2:50:27.601173 INFO: Writing precursor output to disk
2:50:27.607192 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
2:50:27.746853 INFO: Writing peptide output to disk
2:50:27.751954 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
2:50:27.858152 INFO: Writing pg output to disk
2:50:27.860929 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
2:50:27.948405 PROGRESS: Building MBR spectral library
2:50:27.948605 INFO: Running MbrLibraryBuilder
2:50:28.372421 INFO: MBR spectral library contains 133,287 precursors, 10,534 proteins
2:50:28.372563 INFO: Writing MBR spectral library to disk
2:50:29.302463 PROGRESS: =================== Search step 'mbr' finished ===================
2:50:29.354876 INFO: =================== Search Finished ===================
