0:00:00.000144 INFO: Output directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output/work/88/22a70f5f0ae3769684d496ade2ae84.
0:00:00.000523 INFO: User provided config file: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.018806 PROGRESS:           _      _         ___ ___   _   
0:00:00.019180 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.019219 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.019245 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.019270 PROGRESS:            |_|                           
0:00:00.019297 PROGRESS: 
0:00:00.019329 PROGRESS: version: 2.1.1
0:00:00.019351 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.019410 INFO: hostname: thestral
0:00:00.019486 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.019546 PROGRESS: python: 3.11.11 (CPython)
0:00:00.019685 INFO: date: 2026-07-08 19:54:36
0:00:00.019706 INFO: ================ AlphaX Environment ===============
0:00:00.019737 INFO: alphabase       : 1.8.1
0:00:00.019762 INFO: alpharaw        : 0.5.0
0:00:00.019786 INFO: alphatims       : 1.0.9
0:00:00.019810 INFO: alphapeptdeep   : 1.4.2
0:00:00.019834 INFO: directlfq       : 0.3.3
0:00:00.019852 INFO: ===================================================
0:00:00.019871 INFO: ================= Pip Environment =================
0:00:00.112801 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
0:00:00.113188 INFO: ===================================================
0:00:00.113282 INFO: =================== Running step 'library' ===================
0:00:00.113792 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
0:00:00.129235 INFO: loading additional config provided via CLI
0:00:00.129730 INFO: loading additional config provided via CLI parameters
0:00:00.130431 INFO: Updating config with 'user defined'
0:00:00.130627 INFO: Updating config with 'user defined (cli)'
0:00:00.130835 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}}, {'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'}]
0:00:00.131110 INFO: Updating config with 'user defined'
0:00:00.131170 INFO: Updating config with 'user defined (cli)'
0:00:00.131196 INFO: Updating config with 'multistep search'
0:00:00.131300 INFO: ├──version: None
0:00:00.131336 INFO: ├──workflow_name: None
0:00:00.131361 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library [multistep search, default: None][0m
0:00:00.131389 INFO: ├──library_path: None
0:00:00.131409 INFO: ├──raw_paths:
0:00:00.131431 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.131470 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.131504 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.131528 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.131547 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.131566 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.131632 INFO: ├──fasta_paths:
0:00:00.131656 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.131688 INFO: ├──quant_directory: None
0:00:00.131705 INFO: ├──general
0:00:00.131733 INFO: │   [32;20m├──thread_count: 24 [user defined, default: 10][0m
0:00:00.131754 INFO: │   ├──transfer_step_enabled: False
0:00:00.131777 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.131799 INFO: │   ├──reuse_calibration: False
0:00:00.131817 INFO: │   ├──reuse_quant: False
0:00:00.131837 INFO: │   ├──log_level: INFO
0:00:00.131857 INFO: │   ├──use_gpu: True
0:00:00.131878 INFO: │   ├──save_figures: True
0:00:00.131903 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.131924 INFO: │   ├──save_flat_library: False
0:00:00.131943 INFO: │   ├──input_library_type: base
0:00:00.131963 INFO: │   ├──save_mbr_library: True
0:00:00.131983 INFO: │   ├──random_state: None
0:00:00.132000 INFO: │   └──fail_fast: False
0:00:00.132019 INFO: ├──library_loading
0:00:00.132041 INFO: │   └──drop_decoys: False
0:00:00.132061 INFO: ├──library_prediction
0:00:00.132082 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.132100 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.132121 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.132143 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.132164 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.132182 INFO: │   ├──missed_cleavages: 1
0:00:00.132202 INFO: │   ├──precursor_len:
0:00:00.132223 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.132241 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.132258 INFO: │   ├──precursor_charge:
0:00:00.132278 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.132295 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.132313 INFO: │   ├──precursor_mz:
0:00:00.132336 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
0:00:00.132355 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
0:00:00.132372 INFO: │   ├──fragment_mz:
0:00:00.132390 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
0:00:00.132407 INFO: │   │   - 2000.0
0:00:00.132426 INFO: │   ├──nce: 25.0
0:00:00.132442 INFO: │   ├──fragment_types:
0:00:00.132460 INFO: │   │   - b
0:00:00.132477 INFO: │   │   - y
0:00:00.132494 INFO: │   ├──max_fragment_charge: 2
0:00:00.132512 INFO: │   ├──instrument: Lumos
0:00:00.132531 INFO: │   ├──peptdeep_model_path: None
0:00:00.132548 INFO: │   ├──peptdeep_model_type: generic
0:00:00.132565 INFO: │   ├──predict_charge: False
0:00:00.132586 INFO: │   └──min_charge_probability: 0.1
0:00:00.132602 INFO: ├──custom_modifications:
0:00:00.132624 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.132645 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.132665 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.132682 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.132702 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.132719 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.132737 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.132754 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.132772 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.132790 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.132808 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.132825 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.132851 INFO: │   ├──name: Label:13C(12)@K
0:00:00.132868 INFO: │   └──composition: C(12)
0:00:00.132890 INFO: ├──search
0:00:00.132909 INFO: │   ├──extraction_backend: rust
0:00:00.132926 INFO: │   [32;20m├──target_ms1_tolerance: 3 [user defined, default: 5][0m
0:00:00.132944 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.132962 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.132982 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.133000 INFO: │   ├──quant_window: 3
0:00:00.133017 INFO: │   ├──target_num_candidates: 3
0:00:00.133034 INFO: │   ├──channel_filter: 
0:00:00.133052 INFO: │   ├──compete_for_fragments: True
0:00:00.133069 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.133087 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.133104 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.133121 INFO: │   ├──optimized_peak_group_score: False
0:00:00.133139 INFO: │   ├──exclude_shared_ions: True
0:00:00.133156 INFO: │   ├──quant_all: True
0:00:00.133175 INFO: │   └──experimental_xic: True
0:00:00.133194 INFO: ├──calibration
0:00:00.133214 INFO: │   ├──batch_size: 1000
0:00:00.133234 INFO: │   ├──optimization_lock_target: 1000
0:00:00.133251 INFO: │   ├──max_steps: 20
0:00:00.133270 INFO: │   ├──min_steps: 5
0:00:00.133287 INFO: │   ├──max_skips: 1
0:00:00.133306 INFO: │   ├──max_fragments: 5000
0:00:00.133324 INFO: │   └──min_correlation: 0.7
0:00:00.133341 INFO: ├──search_initial
0:00:00.133361 INFO: │   ├──num_candidates: 1
0:00:00.133381 INFO: │   ├──ms1_tolerance: 30
0:00:00.133400 INFO: │   ├──ms2_tolerance: 30
0:00:00.133420 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.133438 INFO: │   └──rt_tolerance: 0.5
0:00:00.133456 INFO: ├──library_multiplexing
0:00:00.133480 INFO: │   ├──enabled: False
0:00:00.133499 INFO: │   ├──input_channel: 0
0:00:00.133518 INFO: │   └──multiplex_mapping:
0:00:00.133536 INFO: ├──multiplexing
0:00:00.133558 INFO: │   ├──enabled: False
0:00:00.133579 INFO: │   ├──target_channels: 4,8
0:00:00.133597 INFO: │   ├──decoy_channel: 12
0:00:00.133615 INFO: │   ├──reference_channel: 0
0:00:00.133632 INFO: │   └──competitive_scoring: True
0:00:00.133650 INFO: ├──fdr
0:00:00.133669 INFO: │   ├──fdr: 0.01
0:00:00.133688 INFO: │   ├──group_level: proteins
0:00:00.133707 INFO: │   ├──inference_strategy: heuristic
0:00:00.133723 INFO: │   ├──competitive_scoring: True
0:00:00.133742 INFO: │   ├──keep_decoys: False
0:00:00.133760 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.133779 INFO: │   ├──channel_wise_fdr: False
0:00:00.133797 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.133813 INFO: ├──search_output
0:00:00.133832 INFO: │   ├──file_format: parquet
0:00:00.133848 INFO: │   ├──precursor_level_lfq: True
0:00:00.133867 INFO: │   ├──peptide_level_lfq: True
0:00:00.133885 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.133905 INFO: │   ├──min_k_fragments: 12
0:00:00.133922 INFO: │   ├──min_correlation: 0.9
0:00:00.133941 INFO: │   ├──num_samples_quadratic: 50
0:00:00.133959 INFO: │   ├──min_nonnan: 3
0:00:00.133978 INFO: │   ├──normalization_method: directlfq
0:00:00.133996 INFO: │   [32;20m└──normalize_directlfq: False [user defined, default: True][0m
0:00:00.134014 INFO: ├──optimization
0:00:00.134034 INFO: │   ├──order_of_optimization: None
0:00:00.134052 INFO: │   ├──ms2_error
0:00:00.134073 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.134093 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.134111 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.134162 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.134180 INFO: │   │   ├──try_narrower_values: True
0:00:00.134203 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.134222 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.134242 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.134261 INFO: │   ├──ms1_error
0:00:00.134280 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.134299 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.134316 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.134333 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.134351 INFO: │   │   ├──try_narrower_values: False
0:00:00.134368 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.134386 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.134406 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.134422 INFO: │   ├──mobility_error
0:00:00.134440 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.134458 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.134477 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.134497 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.134517 INFO: │   │   ├──try_narrower_values: False
0:00:00.134537 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.134554 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.134573 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.134591 INFO: │   └──rt_error
0:00:00.134610 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.134629 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.134649 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.134667 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.134688 INFO: │       ├──try_narrower_values: True
0:00:00.134708 INFO: │       ├──maximal_decrease: 0.1
0:00:00.134726 INFO: │       ├──favour_narrower_optimum: False
0:00:00.134745 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.134767 INFO: ├──optimization_manager
0:00:00.134787 INFO: │   ├──fwhm_rt: 5
0:00:00.134806 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.134824 INFO: │   └──score_cutoff: 0
0:00:00.134843 INFO: ├──transfer_library
0:00:00.134863 INFO: │   ├──enabled: False
0:00:00.134882 INFO: │   ├──fragment_types:
0:00:00.134900 INFO: │   │   - b
0:00:00.134916 INFO: │   │   - y
0:00:00.134935 INFO: │   ├──max_charge: 2
0:00:00.134954 INFO: │   ├──top_k_samples: 3
0:00:00.134973 INFO: │   ├──norm_delta_max: True
0:00:00.134993 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.135011 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.135028 INFO: └──transfer_learning
0:00:00.135047 INFO:     ├──enabled: False
0:00:00.135067 INFO:     ├──batch_size: 2000
0:00:00.135087 INFO:     ├──max_lr: 0.0001
0:00:00.135104 INFO:     ├──train_fraction: 0.7
0:00:00.135122 INFO:     ├──validation_fraction: 0.2
0:00:00.135141 INFO:     ├──test_fraction: 0.1
0:00:00.135158 INFO:     ├──test_interval: 1
0:00:00.135176 INFO:     ├──lr_patience: 3
0:00:00.135194 INFO:     ├──epochs: 51
0:00:00.135213 INFO:     ├──warmup_epochs: 5
0:00:00.135230 INFO:     ├──nce: 25
0:00:00.135249 INFO:     └──instrument: Lumos
0:00:00.144064 INFO: Registering 7 custom modifications
0:00:00.213449 INFO: Searching 6 files:
0:00:00.213769 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.213794 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.213813 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.213832 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.213852 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.213870 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.213931 INFO: Using 1 fasta files:
0:00:00.213951 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.213985 INFO: Using library: None
0:00:00.214007 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library
0:00:00.214058 PROGRESS: Loading spectral library
0:00:00.214108 PROGRESS: No library provided. Building library from fasta files.
0:00:00.214182 INFO: Running FastaDigest
0:00:00.218002 INFO: Digesting fasta file
0:00:17.756546 INFO: Adding modifications
0:08:17.869000 INFO: Removing non-canonical amino acids
0:08:56.627137 INFO: Fasta library contains 6,091,314 precursors
0:08:56.639565 PROGRESS: Predicting library properties.
0:08:56.639796 INFO: Running PeptDeepPrediction
0:08:56.641819 INFO: Device set to cpu
0:09:05.607676 INFO: Loading PeptDeep models of type generic
0:09:13.012293 INFO: Predicting RT, MS2 and mobility
0:09:13.012625 INFO: Using multiprocessing with 24 processes ...
0:09:19.197210 INFO: Predicting rt,ms2,mobility ...
0:40:04.608165 INFO: Adding fragment mz information
0:40:04.948230 INFO: Adding fragment intensity information
0:40:05.254256 INFO: Adding precursor information
0:40:05.609284 INFO: Running PrecursorInitializer
0:40:05.631004 INFO: Running AnnotateFasta
0:40:40.795037 INFO: Running IsotopeGenerator
0:40:40.796647 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:45:26.788489 INFO: Running RTNormalization
0:45:26.789145 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:45:26.789300 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.hdf
0:46:02.336545 INFO: Running DecoyGenerator
0:49:33.601553 INFO: Running FlattenLibrary
0:50:51.851693 INFO: Running InitFlatColumns
0:50:52.270844 INFO: Running LogFlatLibraryStats
0:50:52.270991 INFO: ============ Library Stats ============
0:50:52.271037 INFO: Number of precursors: 12,150,378
0:50:55.191246 INFO: 	thereof targets:6,091,314
0:50:55.191492 INFO: 	thereof decoys: 6,059,064
0:50:55.275874 INFO: Number of elution groups: 6,091,314
0:50:55.276021 INFO: 	average size: 1.99
0:50:55.674451 INFO: Number of proteins: 117,993
0:50:55.707313 INFO: Number of channels: 1 ([0])
0:50:55.707546 INFO: Isotopes Distribution for 4 isotopes
0:50:55.707580 INFO: =======================================
0:50:55.730438 PROGRESS: =================== Starting Search Workflows for step library ===================
0:50:55.730665 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:50:55.730744 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
0:50:55.730847 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:50:55.731146 INFO: Initializing TimingManager
0:50:55.731708 INFO: Initializing RawFileManager
0:51:13.939083 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.
0:51:13.952407 INFO: Determining DIA cycle
0:51:14.396958 INFO: Found cycle with start 0.00 min and length 300.
0:51:15.450686 INFO: RT (min)            : 0.0 - 26.9
0:51:15.450803 INFO: RT duration (sec)   : 1611.2
0:51:15.450845 INFO: RT duration (min)   : 26.9
0:51:15.450877 INFO: Cycle len (scans)   : 300
0:51:15.450906 INFO: Cycle len (sec)     : 1.65
0:51:15.450934 INFO: Number of cycles    : 977
0:51:15.450962 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:51:15.451015 INFO: Creating DIA data object took: 19.71919870376587
0:51:18.666743 INFO: Creating DIA data NG object took: 3.215517282485962
0:51:28.019831 INFO: Initializing CalibrationManager
0:51:28.020434 INFO: Setting up calibration estimators ..
0:51:28.020509 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:51:28.020604 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'}' ..
0:51:28.020737 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:51:28.020802 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:51:28.020863 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}}' ..
0:51:28.020919 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:51:28.020967 INFO: Done setting up calibration estimators.
0:51:28.021505 INFO: Initializing OptimizationManager
0:51:28.021668 INFO: initial parameter: ms1_error = 30
0:51:28.021730 INFO: initial parameter: ms2_error = 30
0:51:28.021784 INFO: initial parameter: rt_error = 805.5992431640625
0:51:28.021834 INFO: initial parameter: mobility_error = 0.1
0:51:28.021879 INFO: initial parameter: num_candidates = 1
0:51:28.021923 INFO: initial parameter: fwhm_rt = 5
0:51:28.021968 INFO: initial parameter: fwhm_mobility = 0.01
0:51:28.022011 INFO: initial parameter: score_cutoff = 0
0:51:28.022053 INFO: initial parameter: classifier_version = -1
0:51:28.022131 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:51:28.022545 INFO: FDRManager: loading saved state not requested, will be initialized.
0:51:28.022582 INFO: Initializing FDRManager
0:51:28.022635 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:51:31.345363 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:51:33.280971 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:51:33.281739 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:51:33.281934 PROGRESS: Starting initial search for precursors.
0:51:33.282053 INFO: Starting optimization step 0.
0:51:33.282131 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:51:33.282206 INFO: Using rust extraction backend
0:51:33.282314 PROGRESS: Extracting batch of 1972 precursors
0:51:33.289657 INFO: === Search parameters used ===
0:51:33.289783 INFO: rt_error       : 805.5992431640625
0:51:33.289839 INFO: mobility_error : 0.1
0:51:33.289886 INFO: num_candidates : 1
0:51:33.289929 INFO: ms1_error      : 30
0:51:33.289970 INFO: ms2_error      : 30
0:51:33.290012 INFO: fwhm_rt        : 5
0:51:33.290057 INFO: quant_window   : 3
0:51:33.290099 INFO: ==============================================
0:51:33.347193 INFO: performing precursor FDR with 40 features
0:51:33.347316 INFO: Decoy channel: -1
0:51:33.347350 INFO: competitive: True
0:51:33.349313 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:33.352517 INFO: Estimating optimal hyperparameters - samples: 1,569, batch_size: 128, learning_rate: 1.77e-04
0:51:33.353911 INFO: Using random state 766969 for train-test-split
0:51:33.582955 INFO: Test AUC: 0.479
0:51:33.583071 INFO: Train AUC: 0.587
0:51:33.583112 INFO: AUC difference: 18.48%
0:51:33.583144 WARNING: AUC difference > 5%. This may indicate overfitting.
0:51:33.903131 INFO: Resetting torch num_threads to 24
0:51:33.904806 PROGRESS: === Extracted 1962 precursors and 9371 fragments ===
0:51:33.905203 INFO: === FDR correction performed with classifier version -1 ===
0:51:33.905694 PROGRESS: ============================= Precursor FDR =============================
0:51:33.905777 PROGRESS: Total precursors accumulated: 7
0:51:33.905836 PROGRESS: Target precursors: 7 (100.00%)
0:51:33.905886 PROGRESS: Decoy precursors: 0 (0.00%)
0:51:33.905932 PROGRESS: 
0:51:33.905976 PROGRESS: Precursor Summary:
0:51:33.907065 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:51:33.907148 PROGRESS: 
0:51:33.907201 PROGRESS: Protein Summary:
0:51:33.908394 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:51:33.908493 PROGRESS: =========================================================================
0:51:33.908709 INFO: Target number of precursors not reached yet.
0:51:33.996320 INFO: Starting optimization step 1.
0:51:33.996569 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:51:33.996656 INFO: Using rust extraction backend
0:51:33.996720 PROGRESS: Extracting batch of 3939 precursors
0:51:34.006676 INFO: === Search parameters used ===
0:51:34.006868 INFO: rt_error       : 805.5992431640625
0:51:34.006920 INFO: mobility_error : 0.1
0:51:34.006967 INFO: num_candidates : 1
0:51:34.007009 INFO: ms1_error      : 30
0:51:34.007048 INFO: ms2_error      : 30
0:51:34.007089 INFO: fwhm_rt        : 5
0:51:34.007128 INFO: quant_window   : 3
0:51:34.007166 INFO: ==============================================
0:51:34.086001 INFO: performing precursor FDR with 40 features
0:51:34.086123 INFO: Decoy channel: -1
0:51:34.086147 INFO: competitive: True
0:51:34.091696 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:34.095132 INFO: Estimating optimal hyperparameters - samples: 4,700, batch_size: 128, learning_rate: 1.77e-04
0:51:34.095229 INFO: Using random state 645386 for train-test-split
0:51:34.595202 INFO: Test AUC: 0.518
0:51:34.595301 INFO: Train AUC: 0.577
0:51:34.595331 INFO: AUC difference: 10.29%
0:51:34.595353 WARNING: AUC difference > 5%. This may indicate overfitting.
0:51:34.853544 INFO: Resetting torch num_threads to 24
0:51:34.857006 PROGRESS: === Extracted 5875 precursors and 27894 fragments ===
0:51:34.857500 INFO: === FDR correction performed with classifier version -1 ===
0:51:34.858019 PROGRESS: ============================= Precursor FDR =============================
0:51:34.858102 PROGRESS: Total precursors accumulated: 13
0:51:34.858159 PROGRESS: Target precursors: 13 (100.00%)
0:51:34.858205 PROGRESS: Decoy precursors: 0 (0.00%)
0:51:34.858249 PROGRESS: 
0:51:34.858293 PROGRESS: Precursor Summary:
0:51:34.859361 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
0:51:34.859447 PROGRESS: 
0:51:34.859524 PROGRESS: Protein Summary:
0:51:34.860698 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
0:51:34.860780 PROGRESS: =========================================================================
0:51:34.861047 INFO: Target number of precursors not reached yet.
0:51:34.956941 INFO: Starting optimization step 2.
0:51:34.957170 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:51:34.957263 INFO: Using rust extraction backend
0:51:34.957332 PROGRESS: Extracting batch of 7870 precursors
0:51:34.973984 INFO: === Search parameters used ===
0:51:34.974202 INFO: rt_error       : 805.5992431640625
0:51:34.974255 INFO: mobility_error : 0.1
0:51:34.974301 INFO: num_candidates : 1
0:51:34.974344 INFO: ms1_error      : 30
0:51:34.974386 INFO: ms2_error      : 30
0:51:34.974429 INFO: fwhm_rt        : 5
0:51:34.974470 INFO: quant_window   : 3
0:51:34.974509 INFO: ==============================================
0:51:35.094524 INFO: performing precursor FDR with 40 features
0:51:35.094647 INFO: Decoy channel: -1
0:51:35.094672 INFO: competitive: True
0:51:35.104018 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:35.109629 INFO: Estimating optimal hyperparameters - samples: 10,935, batch_size: 128, learning_rate: 1.77e-04
0:51:35.109804 INFO: Using random state 574123 for train-test-split
0:51:36.296635 INFO: Test AUC: 0.558
0:51:36.296749 INFO: Train AUC: 0.595
0:51:36.296778 INFO: AUC difference: 6.24%
0:51:36.296801 WARNING: AUC difference > 5%. This may indicate overfitting.
0:51:36.554247 INFO: Resetting torch num_threads to 24
0:51:36.560303 PROGRESS: === Extracted 13669 precursors and 65007 fragments ===
0:51:36.560870 INFO: === FDR correction performed with classifier version -1 ===
0:51:36.561461 PROGRESS: ============================= Precursor FDR =============================
0:51:36.561548 PROGRESS: Total precursors accumulated: 44
0:51:36.561615 PROGRESS: Target precursors: 44 (100.00%)
0:51:36.561664 PROGRESS: Decoy precursors: 0 (0.00%)
0:51:36.561708 PROGRESS: 
0:51:36.561753 PROGRESS: Precursor Summary:
0:51:36.562840 PROGRESS: Channel   0:	 0.050 FDR:    44; 0.010 FDR:    44; 0.001 FDR:    44
0:51:36.562924 PROGRESS: 
0:51:36.562978 PROGRESS: Protein Summary:
0:51:36.564176 PROGRESS: Channel   0:	 0.050 FDR:    44; 0.010 FDR:    44; 0.001 FDR:    44
0:51:36.564265 PROGRESS: =========================================================================
0:51:36.564649 INFO: Target number of precursors not reached yet.
0:51:36.675557 INFO: Starting optimization step 3.
0:51:36.675815 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:51:36.675899 INFO: Using rust extraction backend
0:51:36.675963 PROGRESS: Extracting batch of 15774 precursors
0:51:36.708046 INFO: === Search parameters used ===
0:51:36.708283 INFO: rt_error       : 805.5992431640625
0:51:36.708336 INFO: mobility_error : 0.1
0:51:36.708383 INFO: num_candidates : 1
0:51:36.708427 INFO: ms1_error      : 30
0:51:36.708469 INFO: ms2_error      : 30
0:51:36.708524 INFO: fwhm_rt        : 5
0:51:36.708567 INFO: quant_window   : 3
0:51:36.708607 INFO: ==============================================
0:51:36.955213 INFO: performing precursor FDR with 40 features
0:51:36.955360 INFO: Decoy channel: -1
0:51:36.955385 INFO: competitive: True
0:51:36.970912 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:36.980639 INFO: Estimating optimal hyperparameters - samples: 23,431, batch_size: 128, learning_rate: 1.77e-04
0:51:36.981039 INFO: Using random state 669011 for train-test-split
0:51:40.223581 INFO: Test AUC: 0.568
0:51:40.223733 INFO: Train AUC: 0.604
0:51:40.223766 INFO: AUC difference: 5.92%
0:51:40.223792 WARNING: AUC difference > 5%. This may indicate overfitting.
0:51:40.513993 INFO: Resetting torch num_threads to 24
0:51:40.542377 PROGRESS: === Extracted 29289 precursors and 139482 fragments ===
0:51:40.543259 INFO: === FDR correction performed with classifier version -1 ===
0:51:40.544048 PROGRESS: ============================= Precursor FDR =============================
0:51:40.544149 PROGRESS: Total precursors accumulated: 62
0:51:40.544214 PROGRESS: Target precursors: 62 (100.00%)
0:51:40.544268 PROGRESS: Decoy precursors: 0 (0.00%)
0:51:40.544322 PROGRESS: 
0:51:40.544371 PROGRESS: Precursor Summary:
0:51:40.545484 PROGRESS: Channel   0:	 0.050 FDR:    62; 0.010 FDR:    62; 0.001 FDR:    62
0:51:40.545573 PROGRESS: 
0:51:40.545632 PROGRESS: Protein Summary:
0:51:40.546889 PROGRESS: Channel   0:	 0.050 FDR:    61; 0.010 FDR:    61; 0.001 FDR:    61
0:51:40.546981 PROGRESS: =========================================================================
0:51:40.548564 INFO: Target number of precursors not reached yet.
0:51:40.708076 INFO: Starting optimization step 4.
0:51:40.708406 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:51:40.708514 INFO: Using rust extraction backend
0:51:40.708592 PROGRESS: Extracting batch of 31503 precursors
0:51:40.774930 INFO: === Search parameters used ===
0:51:40.775267 INFO: rt_error       : 805.5992431640625
0:51:40.775328 INFO: mobility_error : 0.1
0:51:40.775379 INFO: num_candidates : 1
0:51:40.775427 INFO: ms1_error      : 30
0:51:40.775485 INFO: ms2_error      : 30
0:51:40.775530 INFO: fwhm_rt        : 5
0:51:40.775571 INFO: quant_window   : 3
0:51:40.775613 INFO: ==============================================
0:51:41.288279 INFO: performing precursor FDR with 40 features
0:51:41.288465 INFO: Decoy channel: -1
0:51:41.288504 INFO: competitive: True
0:51:41.330934 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:41.352987 INFO: Estimating optimal hyperparameters - samples: 48,403, batch_size: 198, learning_rate: 2.20e-04
0:51:41.353281 INFO: Using random state 681121 for train-test-split
0:51:46.549301 INFO: Test AUC: 0.575
0:51:46.549456 INFO: Train AUC: 0.612
0:51:46.549493 INFO: AUC difference: 6.12%
0:51:46.549520 WARNING: AUC difference > 5%. This may indicate overfitting.
0:51:47.599540 INFO: Resetting torch num_threads to 24
0:51:47.622303 PROGRESS: === Extracted 60504 precursors and 288227 fragments ===
0:51:47.623131 INFO: === FDR correction performed with classifier version -1 ===
0:51:47.623818 PROGRESS: ============================= Precursor FDR =============================
0:51:47.623917 PROGRESS: Total precursors accumulated: 140
0:51:47.623981 PROGRESS: Target precursors: 139 (99.29%)
0:51:47.624034 PROGRESS: Decoy precursors: 1 (0.71%)
0:51:47.624081 PROGRESS: 
0:51:47.624129 PROGRESS: Precursor Summary:
0:51:47.625183 PROGRESS: Channel   0:	 0.050 FDR:   139; 0.010 FDR:   139; 0.001 FDR:   122
0:51:47.625278 PROGRESS: 
0:51:47.625333 PROGRESS: Protein Summary:
0:51:47.626486 PROGRESS: Channel   0:	 0.050 FDR:   134; 0.010 FDR:   134; 0.001 FDR:   119
0:51:47.626573 PROGRESS: =========================================================================
0:51:47.628403 INFO: Target number of precursors not reached yet.
0:51:47.937428 INFO: Starting optimization step 5.
0:51:47.937742 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:51:47.937845 INFO: Using rust extraction backend
0:51:47.937922 PROGRESS: Extracting batch of 63125 precursors
0:51:48.054403 INFO: === Search parameters used ===
0:51:48.054712 INFO: rt_error       : 805.5992431640625
0:51:48.054781 INFO: mobility_error : 0.1
0:51:48.054833 INFO: num_candidates : 1
0:51:48.054878 INFO: ms1_error      : 30
0:51:48.054924 INFO: ms2_error      : 30
0:51:48.054967 INFO: fwhm_rt        : 5
0:51:48.055011 INFO: quant_window   : 3
0:51:48.055052 INFO: ==============================================
0:51:48.995796 INFO: performing precursor FDR with 40 features
0:51:48.995944 INFO: Decoy channel: -1
0:51:48.995972 INFO: competitive: True
0:51:49.084102 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:49.129404 INFO: Estimating optimal hyperparameters - samples: 98,428, batch_size: 403, learning_rate: 3.14e-04
0:51:49.129739 INFO: Using random state 991000 for train-test-split
0:51:55.657330 INFO: Test AUC: 0.591
0:51:55.657475 INFO: Train AUC: 0.608
0:51:55.657508 INFO: AUC difference: 2.86%
0:51:55.955833 INFO: Resetting torch num_threads to 24
0:51:56.004766 PROGRESS: === Extracted 123036 precursors and 586164 fragments ===
0:51:56.005648 INFO: === FDR correction performed with classifier version -1 ===
0:51:56.006671 PROGRESS: ============================= Precursor FDR =============================
0:51:56.006798 PROGRESS: Total precursors accumulated: 481
0:51:56.006864 PROGRESS: Target precursors: 477 (99.17%)
0:51:56.006917 PROGRESS: Decoy precursors: 4 (0.83%)
0:51:56.006965 PROGRESS: 
0:51:56.007030 PROGRESS: Precursor Summary:
0:51:56.008269 PROGRESS: Channel   0:	 0.050 FDR:   477; 0.010 FDR:   477; 0.001 FDR:   253
0:51:56.008363 PROGRESS: 
0:51:56.008419 PROGRESS: Protein Summary:
0:51:56.009785 PROGRESS: Channel   0:	 0.050 FDR:   439; 0.010 FDR:   439; 0.001 FDR:   239
0:51:56.009874 PROGRESS: =========================================================================
0:51:56.013623 INFO: Target number of precursors not reached yet.
0:51:57.791041 INFO: Starting optimization step 6.
0:51:57.791407 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:51:57.791544 INFO: Using rust extraction backend
0:51:57.791635 PROGRESS: Extracting batch of 126147 precursors
0:51:58.027410 INFO: === Search parameters used ===
0:51:58.027802 INFO: rt_error       : 805.5992431640625
0:51:58.027870 INFO: mobility_error : 0.1
0:51:58.027920 INFO: num_candidates : 1
0:51:58.027981 INFO: ms1_error      : 30
0:51:58.028027 INFO: ms2_error      : 30
0:51:58.028086 INFO: fwhm_rt        : 5
0:51:58.028130 INFO: quant_window   : 3
0:51:58.028174 INFO: ==============================================
0:52:00.089526 INFO: performing precursor FDR with 40 features
0:52:00.089674 INFO: Decoy channel: -1
0:52:00.089702 INFO: competitive: True
0:52:00.232172 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:00.326771 INFO: Estimating optimal hyperparameters - samples: 198,315, batch_size: 812, learning_rate: 4.45e-04
0:52:00.327345 INFO: Using random state 115693 for train-test-split
0:52:09.466401 INFO: Test AUC: 0.591
0:52:09.466570 INFO: Train AUC: 0.608
0:52:09.466606 INFO: AUC difference: 2.73%
0:52:09.829105 INFO: Resetting torch num_threads to 24
0:52:09.896359 PROGRESS: === Extracted 247894 precursors and 1179500 fragments ===
0:52:09.897331 INFO: === FDR correction performed with classifier version -1 ===
0:52:09.898210 PROGRESS: ============================= Precursor FDR =============================
0:52:09.898305 PROGRESS: Total precursors accumulated: 841
0:52:09.898367 PROGRESS: Target precursors: 833 (99.05%)
0:52:09.898419 PROGRESS: Decoy precursors: 8 (0.95%)
0:52:09.898466 PROGRESS: 
0:52:09.898510 PROGRESS: Precursor Summary:
0:52:09.899704 PROGRESS: Channel   0:	 0.050 FDR:   833; 0.010 FDR:   833; 0.001 FDR:     0
0:52:09.899799 PROGRESS: 
0:52:09.899861 PROGRESS: Protein Summary:
0:52:09.901312 PROGRESS: Channel   0:	 0.050 FDR:   730; 0.010 FDR:   730; 0.001 FDR:     0
0:52:09.901414 PROGRESS: =========================================================================
0:52:09.906884 INFO: Target number of precursors not reached yet.
0:52:10.614410 INFO: Starting optimization step 7.
0:52:10.614816 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:52:10.614928 INFO: Using rust extraction backend
0:52:10.615020 PROGRESS: Extracting batch of 252313 precursors
0:52:11.058920 INFO: === Search parameters used ===
0:52:11.059232 INFO: rt_error       : 805.5992431640625
0:52:11.059297 INFO: mobility_error : 0.1
0:52:11.059349 INFO: num_candidates : 1
0:52:11.059393 INFO: ms1_error      : 30
0:52:11.059446 INFO: ms2_error      : 30
0:52:11.059512 INFO: fwhm_rt        : 5
0:52:11.059563 INFO: quant_window   : 3
0:52:11.059609 INFO: ==============================================
0:52:14.013805 INFO: performing precursor FDR with 40 features
0:52:14.013961 INFO: Decoy channel: -1
0:52:14.013991 INFO: competitive: True
0:52:14.399162 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:14.635535 INFO: Estimating optimal hyperparameters - samples: 398,149, batch_size: 1,630, learning_rate: 6.31e-04
0:52:14.636352 INFO: Using random state 261289 for train-test-split
0:52:29.661155 INFO: Test AUC: 0.588
0:52:29.661323 INFO: Train AUC: 0.609
0:52:29.661363 INFO: AUC difference: 3.31%
0:52:30.120857 INFO: Resetting torch num_threads to 24
0:52:30.268102 PROGRESS: === Extracted 497687 precursors and 2367300 fragments ===
0:52:30.269064 INFO: === FDR correction performed with classifier version -1 ===
0:52:30.270271 PROGRESS: ============================= Precursor FDR =============================
0:52:30.270371 PROGRESS: Total precursors accumulated: 2,076
0:52:30.270438 PROGRESS: Target precursors: 2,056 (99.04%)
0:52:30.270495 PROGRESS: Decoy precursors: 20 (0.96%)
0:52:30.270548 PROGRESS: 
0:52:30.270599 PROGRESS: Precursor Summary:
0:52:30.272330 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,056; 0.001 FDR: 1,295
0:52:30.272432 PROGRESS: 
0:52:30.272492 PROGRESS: Protein Summary:
0:52:30.274624 PROGRESS: Channel   0:	 0.050 FDR: 1,600; 0.010 FDR: 1,600; 0.001 FDR: 1,045
0:52:30.274723 PROGRESS: =========================================================================
0:52:30.284786 INFO: Target number of precursors reached.
0:52:30.586278 INFO: fragments_df: keeping 5000 of 2367300 [sum(precursor_idx_mask)=21842 sum(mass_error_mask)=2367300 stop_rank=5000
0:52:31.111399 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:31.476132 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:32.304481 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:52:32.305068 INFO: Using score_cutoff 12.193334193706512 (fac=0.99, q=1)
0:52:32.305490 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:52:32.305571 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:52:32.305627 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.193334193706512
0:52:32.305698 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:32.464358 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:32.821584 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:52:32.821913 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:52:32.822041 INFO: Starting optimization step 8.
0:52:32.822118 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:52:32.822205 INFO: Using rust extraction backend
0:52:32.822285 PROGRESS: Extracting batch of 250330 precursors
0:52:33.421815 INFO: === Search parameters used ===
0:52:33.422124 INFO: rt_error       : 805.5992431640625
0:52:33.422188 INFO: mobility_error : 0.1
0:52:33.422235 INFO: num_candidates : 3
0:52:33.422278 INFO: ms1_error      : 30
0:52:33.422318 INFO: ms2_error      : 30
0:52:33.422358 INFO: fwhm_rt        : 3.0
0:52:33.422395 INFO: quant_window   : 3
0:52:33.422441 INFO: ==============================================
0:52:39.042681 INFO: performing precursor FDR with 40 features
0:52:39.042889 INFO: Decoy channel: -1
0:52:39.042924 INFO: competitive: True
0:52:39.367987 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:39.881168 INFO: Estimating optimal hyperparameters - samples: 595,076, batch_size: 2,437, learning_rate: 7.71e-04
0:52:39.883017 INFO: Using random state 538223 for train-test-split
0:52:58.010919 INFO: Test AUC: 0.597
0:52:58.011062 INFO: Train AUC: 0.608
0:52:58.011097 INFO: AUC difference: 1.79%
0:52:58.512798 INFO: Resetting torch num_threads to 24
0:52:58.544445 PROGRESS: === Extracted 743845 precursors and 3456805 fragments ===
0:52:58.545003 INFO: === FDR correction performed with classifier version 7 ===
0:52:58.545642 PROGRESS: ============================= Precursor FDR =============================
0:52:58.545734 PROGRESS: Total precursors accumulated: 1,141
0:52:58.545797 PROGRESS: Target precursors: 1,130 (99.04%)
0:52:58.545850 PROGRESS: Decoy precursors: 11 (0.96%)
0:52:58.545897 PROGRESS: 
0:52:58.545946 PROGRESS: Precursor Summary:
0:52:58.547127 PROGRESS: Channel   0:	 0.050 FDR: 1,130; 0.010 FDR: 1,130; 0.001 FDR:     6
0:52:58.547215 PROGRESS: 
0:52:58.547273 PROGRESS: Protein Summary:
0:52:58.548769 PROGRESS: Channel   0:	 0.050 FDR:   997; 0.010 FDR:   997; 0.001 FDR:     6
0:52:58.548863 PROGRESS: =========================================================================
0:52:58.566182 INFO: Target number of precursors reached.
0:52:58.935421 INFO: fragments_df: keeping 5000 of 3456805 [sum(precursor_idx_mask)=23723 sum(mass_error_mask)=3456805 stop_rank=5000
0:52:59.442073 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:59.651141 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:00.380655 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:00.381225 INFO: Using score_cutoff 8.170495115947723 (fac=0.99, q=1)
0:53:00.381602 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:00.381681 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:00.381736 INFO: Updating optimization_manager: score_cutoff        : 12.193334193706512 -> 8.170495115947723
0:53:00.381802 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:00.533781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:00.881070 INFO: === checking if optimization conditions were reached ===
0:53:00.884043 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:53:00.884175 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:53:00.884254 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:53:00.884327 INFO: ==============================================
0:53:00.884409 INFO: Starting optimization step 9.
0:53:00.884480 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:53:00.884558 INFO: Using rust extraction backend
0:53:00.884636 PROGRESS: Extracting batch of 250330 precursors
0:53:01.329658 INFO: === Search parameters used ===
0:53:01.329957 INFO: rt_error       : 805.5992431640625
0:53:01.330043 INFO: mobility_error : 0.1
0:53:01.330095 INFO: num_candidates : 3
0:53:01.330137 INFO: ms1_error      : 30
0:53:01.330178 INFO: ms2_error      : 10.0
0:53:01.330221 INFO: fwhm_rt        : 3.0
0:53:01.330262 INFO: quant_window   : 3
0:53:01.330301 INFO: ==============================================
0:53:05.200633 INFO: performing precursor FDR with 40 features
0:53:05.200790 INFO: Decoy channel: -1
0:53:05.200816 INFO: competitive: True
0:53:05.412179 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:05.771707 INFO: Estimating optimal hyperparameters - samples: 599,375, batch_size: 2,455, learning_rate: 7.74e-04
0:53:05.773016 INFO: Using random state 827710 for train-test-split
0:53:26.070888 INFO: Test AUC: 0.607
0:53:26.071031 INFO: Train AUC: 0.614
0:53:26.071067 INFO: AUC difference: 1.16%
0:53:26.566986 INFO: Resetting torch num_threads to 24
0:53:26.601400 PROGRESS: === Extracted 749219 precursors and 4032912 fragments ===
0:53:26.601947 INFO: === FDR correction performed with classifier version 8 ===
0:53:26.602668 PROGRESS: ============================= Precursor FDR =============================
0:53:26.602761 PROGRESS: Total precursors accumulated: 1,479
0:53:26.602824 PROGRESS: Target precursors: 1,465 (99.05%)
0:53:26.602878 PROGRESS: Decoy precursors: 14 (0.95%)
0:53:26.602926 PROGRESS: 
0:53:26.602972 PROGRESS: Precursor Summary:
0:53:26.604258 PROGRESS: Channel   0:	 0.050 FDR: 1,465; 0.010 FDR: 1,465; 0.001 FDR:     2
0:53:26.604354 PROGRESS: 
0:53:26.604411 PROGRESS: Protein Summary:
0:53:26.606000 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR: 1,240; 0.001 FDR:     2
0:53:26.606091 PROGRESS: =========================================================================
0:53:26.625036 INFO: Target number of precursors reached.
0:53:27.059597 INFO: fragments_df: keeping 5000 of 4032912 [sum(precursor_idx_mask)=35099 sum(mass_error_mask)=4032912 stop_rank=5000
0:53:27.511239 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:53:27.752296 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:28.483320 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:28.483825 INFO: Using score_cutoff 11.697189134216309 (fac=0.99, q=1)
0:53:28.484152 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:28.484230 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:28.484295 INFO: Updating optimization_manager: score_cutoff        : 8.170495115947723 -> 11.697189134216309
0:53:28.484353 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:28.637882 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:29.002456 INFO: === checking if optimization conditions were reached ===
0:53:29.005139 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:53:29.005264 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:53:29.005342 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:53:29.005413 INFO: ==============================================
0:53:29.005494 INFO: Starting optimization step 10.
0:53:29.005565 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:53:29.005640 INFO: Using rust extraction backend
0:53:29.005711 PROGRESS: Extracting batch of 250330 precursors
0:53:29.456131 INFO: === Search parameters used ===
0:53:29.456419 INFO: rt_error       : 805.5992431640625
0:53:29.456479 INFO: mobility_error : 0.1
0:53:29.456529 INFO: num_candidates : 3
0:53:29.456573 INFO: ms1_error      : 30
0:53:29.456627 INFO: ms2_error      : 10.0
0:53:29.456671 INFO: fwhm_rt        : 3.0
0:53:29.456713 INFO: quant_window   : 3
0:53:29.456756 INFO: ==============================================
0:53:33.773610 INFO: performing precursor FDR with 40 features
0:53:33.773749 INFO: Decoy channel: -1
0:53:33.773777 INFO: competitive: True
0:53:34.030165 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:34.383356 INFO: Estimating optimal hyperparameters - samples: 599,372, batch_size: 2,455, learning_rate: 7.74e-04
0:53:34.385171 INFO: Using random state 989703 for train-test-split
0:53:51.830642 INFO: Test AUC: 0.608
0:53:51.830925 INFO: Train AUC: 0.618
0:53:51.830964 INFO: AUC difference: 1.67%
0:53:52.354173 INFO: Resetting torch num_threads to 24
0:53:52.399699 PROGRESS: === Extracted 749216 precursors and 4033065 fragments ===
0:53:52.400406 INFO: === FDR correction performed with classifier version 9 ===
0:53:52.401251 PROGRESS: ============================= Precursor FDR =============================
0:53:52.401345 PROGRESS: Total precursors accumulated: 1,762
0:53:52.401408 PROGRESS: Target precursors: 1,745 (99.04%)
0:53:52.401460 PROGRESS: Decoy precursors: 17 (0.96%)
0:53:52.401509 PROGRESS: 
0:53:52.401556 PROGRESS: Precursor Summary:
0:53:52.402926 PROGRESS: Channel   0:	 0.050 FDR: 1,745; 0.010 FDR: 1,745; 0.001 FDR:   240
0:53:52.403016 PROGRESS: 
0:53:52.403074 PROGRESS: Protein Summary:
0:53:52.404815 PROGRESS: Channel   0:	 0.050 FDR: 1,476; 0.010 FDR: 1,476; 0.001 FDR:   222
0:53:52.404910 PROGRESS: =========================================================================
0:53:52.441735 INFO: Target number of precursors reached.
0:53:53.029752 INFO: fragments_df: keeping 5000 of 4033065 [sum(precursor_idx_mask)=40458 sum(mass_error_mask)=4033065 stop_rank=5000
0:53:53.555942 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:53:53.846698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:54.613749 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:54.614265 INFO: Using score_cutoff 8.49385761795044 (fac=0.99, q=1)
0:53:54.614715 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:54.614796 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:54.614854 INFO: Updating optimization_manager: score_cutoff        : 11.697189134216309 -> 8.49385761795044
0:53:54.614916 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:54.770329 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:55.117658 INFO: === checking if optimization conditions were reached ===
0:53:55.120664 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:53:55.120879 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:53:55.120965 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:53:55.121049 INFO: ==============================================
0:53:55.121134 INFO: Starting optimization step 11.
0:53:55.121208 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:53:55.121307 INFO: Using rust extraction backend
0:53:55.121402 PROGRESS: Extracting batch of 250330 precursors
0:53:55.560449 INFO: === Search parameters used ===
0:53:55.560744 INFO: rt_error       : 805.5992431640625
0:53:55.560815 INFO: mobility_error : 0.1
0:53:55.560877 INFO: num_candidates : 3
0:53:55.560925 INFO: ms1_error      : 30
0:53:55.560969 INFO: ms2_error      : 10.0
0:53:55.561010 INFO: fwhm_rt        : 3.0
0:53:55.561051 INFO: quant_window   : 3
0:53:55.561097 INFO: ==============================================
0:53:59.591640 INFO: performing precursor FDR with 40 features
0:53:59.591781 INFO: Decoy channel: -1
0:53:59.591809 INFO: competitive: True
0:53:59.812296 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:00.153837 INFO: Estimating optimal hyperparameters - samples: 599,367, batch_size: 2,455, learning_rate: 7.74e-04
0:54:00.155117 INFO: Using random state 822080 for train-test-split
0:54:19.185136 INFO: Test AUC: 0.613
0:54:19.185501 INFO: Train AUC: 0.621
0:54:19.185564 INFO: AUC difference: 1.41%
0:54:19.781899 INFO: Resetting torch num_threads to 24
0:54:19.815675 PROGRESS: === Extracted 749209 precursors and 4033057 fragments ===
0:54:19.816347 INFO: === FDR correction performed with classifier version 10 ===
0:54:19.817211 PROGRESS: ============================= Precursor FDR =============================
0:54:19.817314 PROGRESS: Total precursors accumulated: 1,796
0:54:19.817387 PROGRESS: Target precursors: 1,779 (99.05%)
0:54:19.817455 PROGRESS: Decoy precursors: 17 (0.95%)
0:54:19.817503 PROGRESS: 
0:54:19.817549 PROGRESS: Precursor Summary:
0:54:19.818933 PROGRESS: Channel   0:	 0.050 FDR: 1,779; 0.010 FDR: 1,779; 0.001 FDR:     2
0:54:19.819022 PROGRESS: 
0:54:19.819077 PROGRESS: Protein Summary:
0:54:19.820790 PROGRESS: Channel   0:	 0.050 FDR: 1,510; 0.010 FDR: 1,510; 0.001 FDR:     2
0:54:19.820897 PROGRESS: =========================================================================
0:54:19.847373 INFO: Target number of precursors reached.
0:54:20.287414 INFO: fragments_df: keeping 5000 of 4033057 [sum(precursor_idx_mask)=40895 sum(mass_error_mask)=4033057 stop_rank=5000
0:54:20.816304 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:54:21.283439 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:54:22.103388 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:54:22.104082 INFO: Using score_cutoff 7.582014818000794 (fac=0.99, q=1)
0:54:22.104737 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:54:22.104868 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:54:22.104934 INFO: Updating optimization_manager: score_cutoff        : 8.49385761795044 -> 7.582014818000794
0:54:22.105029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:22.262824 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:22.614704 INFO: === checking if optimization conditions were reached ===
0:54:22.617942 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:54:22.618179 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:54:22.618279 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:54:22.618358 INFO: ==============================================
0:54:22.618469 INFO: Starting optimization step 12.
0:54:22.618553 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:54:22.618700 INFO: Using rust extraction backend
0:54:22.618833 PROGRESS: Extracting batch of 250330 precursors
0:54:23.080340 INFO: === Search parameters used ===
0:54:23.080641 INFO: rt_error       : 805.5992431640625
0:54:23.080723 INFO: mobility_error : 0.1
0:54:23.080774 INFO: num_candidates : 3
0:54:23.080816 INFO: ms1_error      : 30
0:54:23.080857 INFO: ms2_error      : 10.0
0:54:23.080897 INFO: fwhm_rt        : 3.0
0:54:23.080936 INFO: quant_window   : 3
0:54:23.080975 INFO: ==============================================
0:54:27.299526 INFO: performing precursor FDR with 40 features
0:54:27.299707 INFO: Decoy channel: -1
0:54:27.299734 INFO: competitive: True
0:54:27.529377 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:27.891650 INFO: Estimating optimal hyperparameters - samples: 599,378, batch_size: 2,455, learning_rate: 7.74e-04
0:54:27.892836 INFO: Using random state 33158 for train-test-split
0:54:45.101331 INFO: Test AUC: 0.612
0:54:45.101523 INFO: Train AUC: 0.622
0:54:45.101564 INFO: AUC difference: 1.65%
0:54:46.355376 INFO: Resetting torch num_threads to 24
0:54:46.387035 PROGRESS: === Extracted 749223 precursors and 4032949 fragments ===
0:54:46.387619 INFO: === FDR correction performed with classifier version 11 ===
0:54:46.388545 PROGRESS: ============================= Precursor FDR =============================
0:54:46.388642 PROGRESS: Total precursors accumulated: 1,903
0:54:46.388705 PROGRESS: Target precursors: 1,885 (99.05%)
0:54:46.388762 PROGRESS: Decoy precursors: 18 (0.95%)
0:54:46.388810 PROGRESS: 
0:54:46.388858 PROGRESS: Precursor Summary:
0:54:46.390334 PROGRESS: Channel   0:	 0.050 FDR: 1,885; 0.010 FDR: 1,885; 0.001 FDR: 1,077
0:54:46.390432 PROGRESS: 
0:54:46.390489 PROGRESS: Protein Summary:
0:54:46.392469 PROGRESS: Channel   0:	 0.050 FDR: 1,588; 0.010 FDR: 1,588; 0.001 FDR:   927
0:54:46.392571 PROGRESS: =========================================================================
0:54:46.412482 INFO: Target number of precursors reached.
0:54:46.870562 INFO: fragments_df: keeping 5000 of 4032949 [sum(precursor_idx_mask)=43573 sum(mass_error_mask)=4032949 stop_rank=5000
0:54:47.340422 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:54:47.646651 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:54:48.413078 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:54:48.413578 INFO: Using score_cutoff 8.826518336105346 (fac=0.99, q=1)
0:54:48.413906 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:54:48.413982 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:54:48.414036 INFO: Updating optimization_manager: score_cutoff        : 7.582014818000794 -> 8.826518336105346
0:54:48.414092 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:48.570079 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:48.922164 INFO: === checking if optimization conditions were reached ===
0:54:48.925169 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:54:48.925371 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
0:54:48.925452 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:54:48.925523 INFO: ==============================================
0:54:48.925611 PROGRESS: Optimization finished for ms2_error.
0:54:49.375288 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:49.533134 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:49.880745 INFO: Starting optimization step 0.
0:54:49.881053 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:54:49.881154 INFO: Using rust extraction backend
0:54:49.881230 PROGRESS: Extracting batch of 250330 precursors
0:54:50.327807 INFO: === Search parameters used ===
0:54:50.328127 INFO: rt_error       : 805.5992431640625
0:54:50.328199 INFO: mobility_error : 0.1
0:54:50.328250 INFO: num_candidates : 3
0:54:50.328296 INFO: ms1_error      : 30
0:54:50.328340 INFO: ms2_error      : 10.0
0:54:50.328384 INFO: fwhm_rt        : 3.0
0:54:50.328427 INFO: quant_window   : 3
0:54:50.328469 INFO: ==============================================
0:54:54.483902 INFO: performing precursor FDR with 40 features
0:54:54.484036 INFO: Decoy channel: -1
0:54:54.484063 INFO: competitive: True
0:54:54.704185 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:55.048401 INFO: Estimating optimal hyperparameters - samples: 599,364, batch_size: 2,454, learning_rate: 7.74e-04
0:54:55.049488 INFO: Using random state 839597 for train-test-split
0:55:08.735196 INFO: Test AUC: 0.614
0:55:08.735359 INFO: Train AUC: 0.626
0:55:08.735393 INFO: AUC difference: 1.87%
0:55:09.248751 INFO: Resetting torch num_threads to 24
0:55:09.284005 PROGRESS: === Extracted 749205 precursors and 4033271 fragments ===
0:55:09.284581 INFO: === FDR correction performed with classifier version 12 ===
0:55:09.285410 PROGRESS: ============================= Precursor FDR =============================
0:55:09.285502 PROGRESS: Total precursors accumulated: 1,961
0:55:09.285564 PROGRESS: Target precursors: 1,942 (99.03%)
0:55:09.285618 PROGRESS: Decoy precursors: 19 (0.97%)
0:55:09.285665 PROGRESS: 
0:55:09.285721 PROGRESS: Precursor Summary:
0:55:09.287243 PROGRESS: Channel   0:	 0.050 FDR: 1,942; 0.010 FDR: 1,942; 0.001 FDR: 1,504
0:55:09.287332 PROGRESS: 
0:55:09.287395 PROGRESS: Protein Summary:
0:55:09.289408 PROGRESS: Channel   0:	 0.050 FDR: 1,635; 0.010 FDR: 1,635; 0.001 FDR: 1,268
0:55:09.289505 PROGRESS: =========================================================================
0:55:09.308117 INFO: Target number of precursors reached.
0:55:09.730850 INFO: fragments_df: keeping 5000 of 4033271 [sum(precursor_idx_mask)=43587 sum(mass_error_mask)=4033271 stop_rank=5000
0:55:10.323106 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:10.704096 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:11.530939 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:11.531506 INFO: Using score_cutoff 7.357187026119233 (fac=0.99, q=1)
0:55:11.531873 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:11.531960 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:11.532017 INFO: Updating optimization_manager: score_cutoff        : 8.826518336105346 -> 7.357187026119233
0:55:11.532082 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:11.689828 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:12.049497 INFO: === checking if optimization conditions were reached ===
0:55:12.049816 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:55:12.053577 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 982.1054930224011
0:55:12.053700 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 982.1055.
0:55:12.053813 INFO: ==============================================
0:55:12.053906 INFO: Starting optimization step 1.
0:55:12.053980 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:55:12.054060 INFO: Using rust extraction backend
0:55:12.054137 PROGRESS: Extracting batch of 250330 precursors
0:55:12.527047 INFO: === Search parameters used ===
0:55:12.527369 INFO: rt_error       : 982.1054930224011
0:55:12.527441 INFO: mobility_error : 0.1
0:55:12.527514 INFO: num_candidates : 3
0:55:12.527564 INFO: ms1_error      : 30
0:55:12.527608 INFO: ms2_error      : 10.0
0:55:12.527651 INFO: fwhm_rt        : 3.0
0:55:12.527695 INFO: quant_window   : 3
0:55:12.527738 INFO: ==============================================
0:55:17.104406 INFO: performing precursor FDR with 40 features
0:55:17.104551 INFO: Decoy channel: -1
0:55:17.104577 INFO: competitive: True
0:55:17.314459 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:17.658492 INFO: Estimating optimal hyperparameters - samples: 599,336, batch_size: 2,454, learning_rate: 7.74e-04
0:55:17.659513 INFO: Using random state 839597 for train-test-split
0:55:30.606355 INFO: Test AUC: 0.612
0:55:30.606485 INFO: Train AUC: 0.624
0:55:30.606531 INFO: AUC difference: 2.00%
0:55:31.097124 INFO: Resetting torch num_threads to 24
0:55:31.131906 PROGRESS: === Extracted 749170 precursors and 4032164 fragments ===
0:55:31.132463 INFO: === FDR correction performed with classifier version 12 ===
0:55:31.133169 PROGRESS: ============================= Precursor FDR =============================
0:55:31.133275 PROGRESS: Total precursors accumulated: 1,525
0:55:31.133338 PROGRESS: Target precursors: 1,510 (99.02%)
0:55:31.133390 PROGRESS: Decoy precursors: 15 (0.98%)
0:55:31.133438 PROGRESS: 
0:55:31.133484 PROGRESS: Precursor Summary:
0:55:31.134765 PROGRESS: Channel   0:	 0.050 FDR: 1,510; 0.010 FDR: 1,510; 0.001 FDR:     2
0:55:31.134851 PROGRESS: 
0:55:31.134907 PROGRESS: Protein Summary:
0:55:31.136537 PROGRESS: Channel   0:	 0.050 FDR: 1,272; 0.010 FDR: 1,272; 0.001 FDR:     2
0:55:31.136633 PROGRESS: =========================================================================
0:55:31.154666 INFO: Target number of precursors reached.
0:55:31.606637 INFO: fragments_df: keeping 5000 of 4032164 [sum(precursor_idx_mask)=35981 sum(mass_error_mask)=4032164 stop_rank=5000
0:55:32.077206 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:32.326277 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:33.044037 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:33.044523 INFO: Using score_cutoff 11.222979657268523 (fac=0.99, q=1)
0:55:33.044859 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:33.044938 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:33.044993 INFO: Updating optimization_manager: score_cutoff        : 7.357187026119233 -> 11.222979657268523
0:55:33.045054 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:33.197014 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:33.543826 INFO: === checking if optimization conditions were reached ===
0:55:33.544178 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:55:33.547956 INFO: Updating optimization_manager: rt_error            : 982.1054930224011 -> 715.3690751582799
0:55:33.548156 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 715.3691.
0:55:33.548243 INFO: ==============================================
0:55:33.548336 INFO: Starting optimization step 2.
0:55:33.548412 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:55:33.548506 INFO: Using rust extraction backend
0:55:33.548587 PROGRESS: Extracting batch of 250330 precursors
0:55:33.988134 INFO: === Search parameters used ===
0:55:33.988426 INFO: rt_error       : 715.3690751582799
0:55:33.988500 INFO: mobility_error : 0.1
0:55:33.988552 INFO: num_candidates : 3
0:55:33.988598 INFO: ms1_error      : 30
0:55:33.988639 INFO: ms2_error      : 10.0
0:55:33.988681 INFO: fwhm_rt        : 3.0
0:55:33.988721 INFO: quant_window   : 3
0:55:33.988762 INFO: ==============================================
0:55:38.173899 INFO: performing precursor FDR with 40 features
0:55:38.174046 INFO: Decoy channel: -1
0:55:38.174073 INFO: competitive: True
0:55:38.420236 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:38.769008 INFO: Estimating optimal hyperparameters - samples: 599,330, batch_size: 2,454, learning_rate: 7.74e-04
0:55:38.770080 INFO: Using random state 839597 for train-test-split
0:55:52.076848 INFO: Test AUC: 0.613
0:55:52.076995 INFO: Train AUC: 0.626
0:55:52.077030 INFO: AUC difference: 2.14%
0:55:52.569262 INFO: Resetting torch num_threads to 24
0:55:52.600346 PROGRESS: === Extracted 749163 precursors and 4029509 fragments ===
0:55:52.600885 INFO: === FDR correction performed with classifier version 12 ===
0:55:52.601774 PROGRESS: ============================= Precursor FDR =============================
0:55:52.601866 PROGRESS: Total precursors accumulated: 2,048
0:55:52.601928 PROGRESS: Target precursors: 2,028 (99.02%)
0:55:52.601981 PROGRESS: Decoy precursors: 20 (0.98%)
0:55:52.602038 PROGRESS: 
0:55:52.602084 PROGRESS: Precursor Summary:
0:55:52.603593 PROGRESS: Channel   0:	 0.050 FDR: 2,028; 0.010 FDR: 2,028; 0.001 FDR: 1,280
0:55:52.603686 PROGRESS: 
0:55:52.603740 PROGRESS: Protein Summary:
0:55:52.605734 PROGRESS: Channel   0:	 0.050 FDR: 1,731; 0.010 FDR: 1,731; 0.001 FDR: 1,093
0:55:52.605823 PROGRESS: =========================================================================
0:55:52.624356 INFO: Target number of precursors reached.
0:55:53.069985 INFO: fragments_df: keeping 5000 of 4029509 [sum(precursor_idx_mask)=44427 sum(mass_error_mask)=4029509 stop_rank=5000
0:55:53.347674 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:53.732452 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:54.594924 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:54.595430 INFO: Using score_cutoff 7.207247249364853 (fac=0.99, q=1)
0:55:54.595778 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:54.595858 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:54.595916 INFO: Updating optimization_manager: score_cutoff        : 11.222979657268523 -> 7.207247249364853
0:55:54.595974 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:54.675069 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:54.867937 INFO: === checking if optimization conditions were reached ===
0:55:54.868306 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:55:54.872805 INFO: Updating optimization_manager: rt_error            : 715.3690751582799 -> 921.2697173783774
0:55:54.872949 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 921.2697.
0:55:54.873038 INFO: ==============================================
0:55:54.873136 INFO: Starting optimization step 3.
0:55:54.873218 PROGRESS: === Extracting elution groups 0 to 63000 ===
0:55:54.873302 INFO: Using rust extraction backend
0:55:54.873397 PROGRESS: Extracting batch of 124183 precursors
0:55:55.124032 INFO: === Search parameters used ===
0:55:55.124404 INFO: rt_error       : 921.2697173783774
0:55:55.124489 INFO: mobility_error : 0.1
0:55:55.124555 INFO: num_candidates : 3
0:55:55.124622 INFO: ms1_error      : 30
0:55:55.124682 INFO: ms2_error      : 10.0
0:55:55.124741 INFO: fwhm_rt        : 3.0
0:55:55.124805 INFO: quant_window   : 3
0:55:55.124866 INFO: ==============================================
0:55:57.320819 INFO: performing precursor FDR with 40 features
0:55:57.320953 INFO: Decoy channel: -1
0:55:57.320978 INFO: competitive: True
0:55:57.424012 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:57.563631 INFO: Estimating optimal hyperparameters - samples: 297,344, batch_size: 1,217, learning_rate: 5.45e-04
0:55:57.564329 INFO: Using random state 839597 for train-test-split
0:56:06.199761 INFO: Test AUC: 0.612
0:56:06.199889 INFO: Train AUC: 0.630
0:56:06.199924 INFO: AUC difference: 2.89%
0:56:06.573294 INFO: Resetting torch num_threads to 24
0:56:06.588550 PROGRESS: === Extracted 371680 precursors and 2003284 fragments ===
0:56:06.589049 INFO: === FDR correction performed with classifier version 12 ===
0:56:06.589648 PROGRESS: ============================= Precursor FDR =============================
0:56:06.589740 PROGRESS: Total precursors accumulated: 950
0:56:06.589812 PROGRESS: Target precursors: 941 (99.05%)
0:56:06.589866 PROGRESS: Decoy precursors: 9 (0.95%)
0:56:06.589913 PROGRESS: 
0:56:06.589959 PROGRESS: Precursor Summary:
0:56:06.591175 PROGRESS: Channel   0:	 0.050 FDR:   941; 0.010 FDR:   941; 0.001 FDR:   808
0:56:06.591264 PROGRESS: 
0:56:06.591318 PROGRESS: Protein Summary:
0:56:06.592847 PROGRESS: Channel   0:	 0.050 FDR:   857; 0.010 FDR:   857; 0.001 FDR:   733
0:56:06.592939 PROGRESS: =========================================================================
0:56:06.602069 INFO: Target number of precursors not reached yet.
0:56:06.862430 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:06.938515 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:07.135838 INFO: === skipping optimization until target number of precursors are found ===
0:56:07.136177 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:56:07.136335 INFO: Starting optimization step 4.
0:56:07.136433 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:56:07.136534 INFO: Using rust extraction backend
0:56:07.136622 PROGRESS: Extracting batch of 126147 precursors
0:56:07.370024 INFO: === Search parameters used ===
0:56:07.370313 INFO: rt_error       : 921.2697173783774
0:56:07.370376 INFO: mobility_error : 0.1
0:56:07.370446 INFO: num_candidates : 3
0:56:07.370501 INFO: ms1_error      : 30
0:56:07.370545 INFO: ms2_error      : 10.0
0:56:07.370595 INFO: fwhm_rt        : 3.0
0:56:07.370636 INFO: quant_window   : 3
0:56:07.370675 INFO: ==============================================
0:56:09.654339 INFO: performing precursor FDR with 40 features
0:56:09.654471 INFO: Decoy channel: -1
0:56:09.654497 INFO: competitive: True
0:56:09.982578 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:10.322562 INFO: Estimating optimal hyperparameters - samples: 599,330, batch_size: 2,454, learning_rate: 7.74e-04
0:56:10.323633 INFO: Using random state 839597 for train-test-split
0:56:23.103729 INFO: Test AUC: 0.615
0:56:23.103861 INFO: Train AUC: 0.625
0:56:23.103898 INFO: AUC difference: 1.68%
0:56:23.593923 INFO: Resetting torch num_threads to 24
0:56:23.708357 PROGRESS: === Extracted 749163 precursors and 4032734 fragments ===
0:56:23.709138 INFO: === FDR correction performed with classifier version 12 ===
0:56:23.710136 PROGRESS: ============================= Precursor FDR =============================
0:56:23.710240 PROGRESS: Total precursors accumulated: 1,853
0:56:23.710301 PROGRESS: Target precursors: 1,835 (99.03%)
0:56:23.710352 PROGRESS: Decoy precursors: 18 (0.97%)
0:56:23.710398 PROGRESS: 
0:56:23.710445 PROGRESS: Precursor Summary:
0:56:23.711953 PROGRESS: Channel   0:	 0.050 FDR: 1,835; 0.010 FDR: 1,835; 0.001 FDR: 1,216
0:56:23.712055 PROGRESS: 
0:56:23.712113 PROGRESS: Protein Summary:
0:56:23.714029 PROGRESS: Channel   0:	 0.050 FDR: 1,543; 0.010 FDR: 1,543; 0.001 FDR: 1,035
0:56:23.714119 PROGRESS: =========================================================================
0:56:23.724635 INFO: Target number of precursors reached.
0:56:24.180431 INFO: fragments_df: keeping 5000 of 4032734 [sum(precursor_idx_mask)=42800 sum(mass_error_mask)=4032734 stop_rank=5000
0:56:24.626982 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:24.952573 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:25.731176 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:25.731712 INFO: Using score_cutoff 10.164391149902345 (fac=0.99, q=1)
0:56:25.732042 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:25.732114 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:25.732166 INFO: Updating optimization_manager: score_cutoff        : 7.207247249364853 -> 10.164391149902345
0:56:25.732217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:25.886588 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:26.233410 INFO: === checking if optimization conditions were reached ===
0:56:26.233741 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:56:26.237874 INFO: Updating optimization_manager: rt_error            : 921.2697173783774 -> 960.0630311781616
0:56:26.238074 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 960.0630.
0:56:26.238160 INFO: ==============================================
0:56:26.238255 INFO: Starting optimization step 5.
0:56:26.238331 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:56:26.238417 INFO: Using rust extraction backend
0:56:26.238493 PROGRESS: Extracting batch of 250330 precursors
0:56:26.681251 INFO: === Search parameters used ===
0:56:26.681583 INFO: rt_error       : 960.0630311781616
0:56:26.681652 INFO: mobility_error : 0.1
0:56:26.681701 INFO: num_candidates : 3
0:56:26.681746 INFO: ms1_error      : 30
0:56:26.681789 INFO: ms2_error      : 10.0
0:56:26.681832 INFO: fwhm_rt        : 3.0
0:56:26.681874 INFO: quant_window   : 3
0:56:26.681915 INFO: ==============================================
0:56:30.918901 INFO: performing precursor FDR with 40 features
0:56:30.919046 INFO: Decoy channel: -1
0:56:30.919072 INFO: competitive: True
0:56:31.142510 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:31.494627 INFO: Estimating optimal hyperparameters - samples: 599,335, batch_size: 2,454, learning_rate: 7.74e-04
0:56:31.495935 INFO: Using random state 839597 for train-test-split
0:56:41.352179 INFO: Test AUC: 0.612
0:56:41.352316 INFO: Train AUC: 0.627
0:56:41.352365 INFO: AUC difference: 2.36%
0:56:41.834943 INFO: Resetting torch num_threads to 24
0:56:41.862943 PROGRESS: === Extracted 749169 precursors and 4033047 fragments ===
0:56:41.863473 INFO: === FDR correction performed with classifier version 12 ===
0:56:41.864163 PROGRESS: ============================= Precursor FDR =============================
0:56:41.864252 PROGRESS: Total precursors accumulated: 1,859
0:56:41.864314 PROGRESS: Target precursors: 1,841 (99.03%)
0:56:41.864367 PROGRESS: Decoy precursors: 18 (0.97%)
0:56:41.864414 PROGRESS: 
0:56:41.864460 PROGRESS: Precursor Summary:
0:56:41.865846 PROGRESS: Channel   0:	 0.050 FDR: 1,841; 0.010 FDR: 1,841; 0.001 FDR:   845
0:56:41.865936 PROGRESS: 
0:56:41.865991 PROGRESS: Protein Summary:
0:56:41.867823 PROGRESS: Channel   0:	 0.050 FDR: 1,558; 0.010 FDR: 1,558; 0.001 FDR:   739
0:56:41.867917 PROGRESS: =========================================================================
0:56:41.882484 INFO: Target number of precursors reached.
0:56:42.300554 INFO: fragments_df: keeping 5000 of 4033047 [sum(precursor_idx_mask)=41873 sum(mass_error_mask)=4033047 stop_rank=5000
0:56:42.775900 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:43.100703 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:43.853929 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:43.854440 INFO: Using score_cutoff 8.004918754577636 (fac=0.99, q=1)
0:56:43.854764 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:43.854841 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:43.854896 INFO: Updating optimization_manager: score_cutoff        : 10.164391149902345 -> 8.004918754577636
0:56:43.854949 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:44.008441 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:44.364324 INFO: === checking if optimization conditions were reached ===
0:56:44.364673 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:56:44.366099 INFO: Updating optimization_manager: rt_error            : 960.0630311781616 -> 715.3690751582799
0:56:44.366254 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
0:56:44.366374 INFO: Updating optimization_manager: score_cutoff        : 8.004918754577636 -> 7.207247249364853
0:56:44.366495 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:44.366608 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:44.366719 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 715.3691 found after 5 searches.
0:56:44.366811 INFO: ==============================================
0:56:44.366909 PROGRESS: Optimization finished for rt_error.
0:56:44.647386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:44.724896 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:44.908044 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:56:44.908341 PROGRESS: ==============================================
0:56:44.908451 PROGRESS: ms2_error      : 10.0000
0:56:44.908528 PROGRESS: rt_error       : 715.3691
0:56:44.908593 PROGRESS: ==============================================
0:56:44.909693 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:52.766730 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:10.557019 INFO: Using rust extraction backend
0:57:10.557389 PROGRESS: Extracting batch of 11997144 precursors
0:57:27.661097 INFO: === Search parameters used ===
0:57:27.661819 INFO: rt_error       : 715.3690751582799
0:57:27.661963 INFO: mobility_error : 0.1
0:57:27.662055 INFO: num_candidates : 3
0:57:27.662146 INFO: ms1_error      : 30
0:57:27.662215 INFO: ms2_error      : 10.0
0:57:27.662289 INFO: fwhm_rt        : 3.0
0:57:27.662357 INFO: quant_window   : 3
0:57:27.662431 INFO: ==============================================
0:58:53.151424 INFO: Removed 2316788 precursors with score below cutoff 7.207247249364853
0:59:32.915097 INFO: performing precursor FDR with 40 features
0:59:32.915269 INFO: Decoy channel: -1
0:59:32.915303 INFO: competitive: True
0:59:36.822609 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:52.634611 INFO: Estimating optimal hyperparameters - samples: 26,939,415, batch_size: 4,096, learning_rate: 1.00e-03
0:59:52.722294 INFO: Using random state 589334 for train-test-split
1:18:09.533970 INFO: Test AUC: 0.621
1:18:09.534484 INFO: Train AUC: 0.621
1:18:09.534566 INFO: AUC difference: 0.10%
1:18:17.076121 INFO: Resetting torch num_threads to 24
1:18:19.564233 PROGRESS: ============================= Precursor FDR =============================
1:18:19.564600 PROGRESS: Total precursors accumulated: 92,297
1:18:19.564680 PROGRESS: Target precursors: 91,384 (99.01%)
1:18:19.564739 PROGRESS: Decoy precursors: 913 (0.99%)
1:18:19.564790 PROGRESS: 
1:18:19.564837 PROGRESS: Precursor Summary:
1:18:19.595662 PROGRESS: Channel   0:	 0.050 FDR: 91,384; 0.010 FDR: 91,384; 0.001 FDR: 58,701
1:18:19.595916 PROGRESS: 
1:18:19.595982 PROGRESS: Protein Summary:
1:18:19.635250 PROGRESS: Channel   0:	 0.050 FDR: 14,541; 0.010 FDR: 14,541; 0.001 FDR: 9,500
1:18:19.635511 PROGRESS: =========================================================================
1:18:19.873227 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
1:18:20.046170 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
1:18:20.286800 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:18:21.074476 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
1:18:21.074660 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:18:21.074763 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
1:18:21.075002 INFO: Initializing TimingManager
1:18:21.075591 INFO: Initializing RawFileManager
1:18:35.897073 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:18:35.905385 INFO: Determining DIA cycle
1:18:35.922878 INFO: Found cycle with start 0.00 min and length 300.
1:18:36.099107 INFO: RT (min)            : 0.0 - 26.9
1:18:36.099222 INFO: RT duration (sec)   : 1611.2
1:18:36.099251 INFO: RT duration (min)   : 26.9
1:18:36.099276 INFO: Cycle len (scans)   : 300
1:18:36.099296 INFO: Cycle len (sec)     : 1.65
1:18:36.099315 INFO: Number of cycles    : 978
1:18:36.099335 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:18:36.099365 INFO: Creating DIA data object took: 15.023675918579102
1:18:37.988086 INFO: Creating DIA data NG object took: 1.888566493988037
1:18:39.886575 INFO: Initializing CalibrationManager
1:18:39.886909 INFO: Setting up calibration estimators ..
1:18:39.886987 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:18:39.887115 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1:18:39.887295 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:18:39.887363 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:18:39.887438 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1:18:39.887513 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:18:39.887562 INFO: Done setting up calibration estimators.
1:18:39.887844 INFO: Initializing OptimizationManager
1:18:39.888031 INFO: initial parameter: ms1_error = 30
1:18:39.888088 INFO: initial parameter: ms2_error = 30
1:18:39.888138 INFO: initial parameter: rt_error = 805.6019897460938
1:18:39.888181 INFO: initial parameter: mobility_error = 0.1
1:18:39.888223 INFO: initial parameter: num_candidates = 1
1:18:39.888266 INFO: initial parameter: fwhm_rt = 5
1:18:39.888319 INFO: initial parameter: fwhm_mobility = 0.01
1:18:39.888362 INFO: initial parameter: score_cutoff = 0
1:18:39.888403 INFO: initial parameter: classifier_version = -1
1:18:39.888472 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:18:39.888873 INFO: FDRManager: loading saved state not requested, will be initialized.
1:18:39.888911 INFO: Initializing FDRManager
1:18:39.888959 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:18:41.836004 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:18:42.798550 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:18:42.799004 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
1:18:42.799121 PROGRESS: Starting initial search for precursors.
1:18:42.799219 INFO: Starting optimization step 0.
1:18:42.799286 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:18:42.799356 INFO: Using rust extraction backend
1:18:42.799428 PROGRESS: Extracting batch of 1972 precursors
1:18:42.811832 INFO: === Search parameters used ===
1:18:42.811962 INFO: rt_error       : 805.6019897460938
1:18:42.812013 INFO: mobility_error : 0.1
1:18:42.812063 INFO: num_candidates : 1
1:18:42.812105 INFO: ms1_error      : 30
1:18:42.812145 INFO: ms2_error      : 30
1:18:42.812185 INFO: fwhm_rt        : 5
1:18:42.812223 INFO: quant_window   : 3
1:18:42.812262 INFO: ==============================================
1:18:42.850824 INFO: performing precursor FDR with 40 features
1:18:42.850922 INFO: Decoy channel: -1
1:18:42.850945 INFO: competitive: True
1:18:42.852291 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:42.854692 INFO: Estimating optimal hyperparameters - samples: 1,563, batch_size: 128, learning_rate: 1.77e-04
1:18:42.855676 INFO: Using random state 72883 for train-test-split
1:18:43.014977 INFO: Test AUC: 0.484
1:18:43.015068 INFO: Train AUC: 0.574
1:18:43.015096 INFO: AUC difference: 15.73%
1:18:43.015116 WARNING: AUC difference > 5%. This may indicate overfitting.
1:18:43.265157 INFO: Resetting torch num_threads to 24
1:18:43.266821 PROGRESS: === Extracted 1954 precursors and 9234 fragments ===
1:18:43.267184 INFO: === FDR correction performed with classifier version -1 ===
1:18:43.267674 PROGRESS: ============================= Precursor FDR =============================
1:18:43.267762 PROGRESS: Total precursors accumulated: 3
1:18:43.267825 PROGRESS: Target precursors: 3 (100.00%)
1:18:43.267875 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:43.267920 PROGRESS: 
1:18:43.267963 PROGRESS: Precursor Summary:
1:18:43.269008 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1:18:43.269089 PROGRESS: 
1:18:43.269142 PROGRESS: Protein Summary:
1:18:43.270287 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1:18:43.270369 PROGRESS: =========================================================================
1:18:43.270599 INFO: Target number of precursors not reached yet.
1:18:43.357716 INFO: Starting optimization step 1.
1:18:43.357934 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:18:43.358015 INFO: Using rust extraction backend
1:18:43.358073 PROGRESS: Extracting batch of 3939 precursors
1:18:43.366565 INFO: === Search parameters used ===
1:18:43.366696 INFO: rt_error       : 805.6019897460938
1:18:43.366747 INFO: mobility_error : 0.1
1:18:43.366791 INFO: num_candidates : 1
1:18:43.366833 INFO: ms1_error      : 30
1:18:43.366876 INFO: ms2_error      : 30
1:18:43.366915 INFO: fwhm_rt        : 5
1:18:43.366955 INFO: quant_window   : 3
1:18:43.366994 INFO: ==============================================
1:18:43.429292 INFO: performing precursor FDR with 40 features
1:18:43.429402 INFO: Decoy channel: -1
1:18:43.429425 INFO: competitive: True
1:18:43.435418 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:43.437750 INFO: Estimating optimal hyperparameters - samples: 4,680, batch_size: 128, learning_rate: 1.77e-04
1:18:43.437833 INFO: Using random state 498756 for train-test-split
1:18:43.904365 INFO: Test AUC: 0.534
1:18:43.904470 INFO: Train AUC: 0.594
1:18:43.904501 INFO: AUC difference: 10.03%
1:18:43.904522 WARNING: AUC difference > 5%. This may indicate overfitting.
1:18:44.153236 INFO: Resetting torch num_threads to 24
1:18:44.156482 PROGRESS: === Extracted 5850 precursors and 27549 fragments ===
1:18:44.156868 INFO: === FDR correction performed with classifier version -1 ===
1:18:44.157409 PROGRESS: ============================= Precursor FDR =============================
1:18:44.157498 PROGRESS: Total precursors accumulated: 11
1:18:44.157557 PROGRESS: Target precursors: 11 (100.00%)
1:18:44.157616 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:44.157664 PROGRESS: 
1:18:44.157708 PROGRESS: Precursor Summary:
1:18:44.158773 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1:18:44.158858 PROGRESS: 
1:18:44.158913 PROGRESS: Protein Summary:
1:18:44.160113 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1:18:44.160203 PROGRESS: =========================================================================
1:18:44.160488 INFO: Target number of precursors not reached yet.
1:18:44.254554 INFO: Starting optimization step 2.
1:18:44.254800 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:18:44.254883 INFO: Using rust extraction backend
1:18:44.254942 PROGRESS: Extracting batch of 7870 precursors
1:18:44.270370 INFO: === Search parameters used ===
1:18:44.270553 INFO: rt_error       : 805.6019897460938
1:18:44.270605 INFO: mobility_error : 0.1
1:18:44.270650 INFO: num_candidates : 1
1:18:44.270693 INFO: ms1_error      : 30
1:18:44.270733 INFO: ms2_error      : 30
1:18:44.270774 INFO: fwhm_rt        : 5
1:18:44.270814 INFO: quant_window   : 3
1:18:44.270853 INFO: ==============================================
1:18:44.383056 INFO: performing precursor FDR with 40 features
1:18:44.383170 INFO: Decoy channel: -1
1:18:44.383193 INFO: competitive: True
1:18:44.389708 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:44.393675 INFO: Estimating optimal hyperparameters - samples: 10,906, batch_size: 128, learning_rate: 1.77e-04
1:18:44.393799 INFO: Using random state 625271 for train-test-split
1:18:45.567911 INFO: Test AUC: 0.562
1:18:45.568023 INFO: Train AUC: 0.595
1:18:45.568052 INFO: AUC difference: 5.64%
1:18:45.568073 WARNING: AUC difference > 5%. This may indicate overfitting.
1:18:46.507468 INFO: Resetting torch num_threads to 24
1:18:46.522428 PROGRESS: === Extracted 13633 precursors and 64139 fragments ===
1:18:46.522890 INFO: === FDR correction performed with classifier version -1 ===
1:18:46.523431 PROGRESS: ============================= Precursor FDR =============================
1:18:46.523530 PROGRESS: Total precursors accumulated: 43
1:18:46.523588 PROGRESS: Target precursors: 43 (100.00%)
1:18:46.523637 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:46.523679 PROGRESS: 
1:18:46.523721 PROGRESS: Precursor Summary:
1:18:46.524776 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:    43; 0.001 FDR:    43
1:18:46.524858 PROGRESS: 
1:18:46.524910 PROGRESS: Protein Summary:
1:18:46.526066 PROGRESS: Channel   0:	 0.050 FDR:    43; 0.010 FDR:    43; 0.001 FDR:    43
1:18:46.526149 PROGRESS: =========================================================================
1:18:46.526526 INFO: Target number of precursors not reached yet.
1:18:46.648023 INFO: Starting optimization step 3.
1:18:46.648278 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:18:46.648362 INFO: Using rust extraction backend
1:18:46.648424 PROGRESS: Extracting batch of 15774 precursors
1:18:46.678519 INFO: === Search parameters used ===
1:18:46.678742 INFO: rt_error       : 805.6019897460938
1:18:46.678798 INFO: mobility_error : 0.1
1:18:46.678843 INFO: num_candidates : 1
1:18:46.678884 INFO: ms1_error      : 30
1:18:46.678925 INFO: ms2_error      : 30
1:18:46.678975 INFO: fwhm_rt        : 5
1:18:46.679017 INFO: quant_window   : 3
1:18:46.679066 INFO: ==============================================
1:18:46.872540 INFO: performing precursor FDR with 40 features
1:18:46.872663 INFO: Decoy channel: -1
1:18:46.872687 INFO: competitive: True
1:18:46.884003 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:46.890866 INFO: Estimating optimal hyperparameters - samples: 23,409, batch_size: 128, learning_rate: 1.77e-04
1:18:46.891051 INFO: Using random state 77625 for train-test-split
1:18:49.393470 INFO: Test AUC: 0.579
1:18:49.393607 INFO: Train AUC: 0.609
1:18:49.393639 INFO: AUC difference: 4.91%
1:18:49.657737 INFO: Resetting torch num_threads to 24
1:18:49.664798 PROGRESS: === Extracted 29262 precursors and 137918 fragments ===
1:18:49.665339 INFO: === FDR correction performed with classifier version -1 ===
1:18:49.665915 PROGRESS: ============================= Precursor FDR =============================
1:18:49.666009 PROGRESS: Total precursors accumulated: 88
1:18:49.666071 PROGRESS: Target precursors: 88 (100.00%)
1:18:49.666126 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:49.666175 PROGRESS: 
1:18:49.666220 PROGRESS: Precursor Summary:
1:18:49.667290 PROGRESS: Channel   0:	 0.050 FDR:    88; 0.010 FDR:    88; 0.001 FDR:    88
1:18:49.667379 PROGRESS: 
1:18:49.667437 PROGRESS: Protein Summary:
1:18:49.668645 PROGRESS: Channel   0:	 0.050 FDR:    87; 0.010 FDR:    87; 0.001 FDR:    87
1:18:49.668734 PROGRESS: =========================================================================
1:18:49.669261 INFO: Target number of precursors not reached yet.
1:18:49.801538 INFO: Starting optimization step 4.
1:18:49.801821 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:18:49.801929 INFO: Using rust extraction backend
1:18:49.801995 PROGRESS: Extracting batch of 31503 precursors
1:18:49.857847 INFO: === Search parameters used ===
1:18:49.858143 INFO: rt_error       : 805.6019897460938
1:18:49.858198 INFO: mobility_error : 0.1
1:18:49.858244 INFO: num_candidates : 1
1:18:49.858287 INFO: ms1_error      : 30
1:18:49.858326 INFO: ms2_error      : 30
1:18:49.858367 INFO: fwhm_rt        : 5
1:18:49.858405 INFO: quant_window   : 3
1:18:49.858443 INFO: ==============================================
1:18:50.223869 INFO: performing precursor FDR with 40 features
1:18:50.223991 INFO: Decoy channel: -1
1:18:50.224015 INFO: competitive: True
1:18:50.247194 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:50.262001 INFO: Estimating optimal hyperparameters - samples: 48,340, batch_size: 198, learning_rate: 2.20e-04
1:18:50.262221 INFO: Using random state 610789 for train-test-split
1:18:53.067467 INFO: Test AUC: 0.582
1:18:53.067593 INFO: Train AUC: 0.617
1:18:53.067625 INFO: AUC difference: 5.65%
1:18:53.067649 WARNING: AUC difference > 5%. This may indicate overfitting.
1:18:53.343766 INFO: Resetting torch num_threads to 24
1:18:53.357893 PROGRESS: === Extracted 60425 precursors and 284757 fragments ===
1:18:53.358563 INFO: === FDR correction performed with classifier version -1 ===
1:18:53.359196 PROGRESS: ============================= Precursor FDR =============================
1:18:53.359292 PROGRESS: Total precursors accumulated: 214
1:18:53.359355 PROGRESS: Target precursors: 212 (99.07%)
1:18:53.359408 PROGRESS: Decoy precursors: 2 (0.93%)
1:18:53.359468 PROGRESS: 
1:18:53.359523 PROGRESS: Precursor Summary:
1:18:53.360563 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:   212; 0.001 FDR:    92
1:18:53.360652 PROGRESS: 
1:18:53.360709 PROGRESS: Protein Summary:
1:18:53.361853 PROGRESS: Channel   0:	 0.050 FDR:   204; 0.010 FDR:   204; 0.001 FDR:    90
1:18:53.361942 PROGRESS: =========================================================================
1:18:53.363260 INFO: Target number of precursors not reached yet.
1:18:53.552902 INFO: Starting optimization step 5.
1:18:53.553202 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:18:53.553290 INFO: Using rust extraction backend
1:18:53.553355 PROGRESS: Extracting batch of 63125 precursors
1:18:53.664002 INFO: === Search parameters used ===
1:18:53.664290 INFO: rt_error       : 805.6019897460938
1:18:53.664351 INFO: mobility_error : 0.1
1:18:53.664400 INFO: num_candidates : 1
1:18:53.664446 INFO: ms1_error      : 30
1:18:53.664492 INFO: ms2_error      : 30
1:18:53.664537 INFO: fwhm_rt        : 5
1:18:53.664581 INFO: quant_window   : 3
1:18:53.664623 INFO: ==============================================
1:18:54.307190 INFO: performing precursor FDR with 40 features
1:18:54.307333 INFO: Decoy channel: -1
1:18:54.307359 INFO: competitive: True
1:18:54.356229 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:54.389268 INFO: Estimating optimal hyperparameters - samples: 98,384, batch_size: 402, learning_rate: 3.13e-04
1:18:54.389570 INFO: Using random state 517524 for train-test-split
1:18:57.713414 INFO: Test AUC: 0.589
1:18:57.713541 INFO: Train AUC: 0.613
1:18:57.713573 INFO: AUC difference: 3.82%
1:18:57.995176 INFO: Resetting torch num_threads to 24
1:18:58.017475 PROGRESS: === Extracted 122980 precursors and 579692 fragments ===
1:18:58.018154 INFO: === FDR correction performed with classifier version -1 ===
1:18:58.018790 PROGRESS: ============================= Precursor FDR =============================
1:18:58.018882 PROGRESS: Total precursors accumulated: 453
1:18:58.018944 PROGRESS: Target precursors: 449 (99.12%)
1:18:58.018995 PROGRESS: Decoy precursors: 4 (0.88%)
1:18:58.019043 PROGRESS: 
1:18:58.019101 PROGRESS: Precursor Summary:
1:18:58.020226 PROGRESS: Channel   0:	 0.050 FDR:   449; 0.010 FDR:   449; 0.001 FDR:   330
1:18:58.020318 PROGRESS: 
1:18:58.020374 PROGRESS: Protein Summary:
1:18:58.021652 PROGRESS: Channel   0:	 0.050 FDR:   419; 0.010 FDR:   419; 0.001 FDR:   314
1:18:58.021739 PROGRESS: =========================================================================
1:18:58.023923 INFO: Target number of precursors not reached yet.
1:18:58.369845 INFO: Starting optimization step 6.
1:18:58.370123 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:18:58.370211 INFO: Using rust extraction backend
1:18:58.370276 PROGRESS: Extracting batch of 126147 precursors
1:18:58.587003 INFO: === Search parameters used ===
1:18:58.587271 INFO: rt_error       : 805.6019897460938
1:18:58.587327 INFO: mobility_error : 0.1
1:18:58.587376 INFO: num_candidates : 1
1:18:58.587422 INFO: ms1_error      : 30
1:18:58.587476 INFO: ms2_error      : 30
1:18:58.587526 INFO: fwhm_rt        : 5
1:18:58.587569 INFO: quant_window   : 3
1:18:58.587610 INFO: ==============================================
1:18:59.844247 INFO: performing precursor FDR with 40 features
1:18:59.844378 INFO: Decoy channel: -1
1:18:59.844404 INFO: competitive: True
1:18:59.951286 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:00.043149 INFO: Estimating optimal hyperparameters - samples: 198,258, batch_size: 812, learning_rate: 4.45e-04
1:19:00.043704 INFO: Using random state 394832 for train-test-split
1:19:06.421121 INFO: Test AUC: 0.590
1:19:06.421247 INFO: Train AUC: 0.610
1:19:06.421280 INFO: AUC difference: 3.35%
1:19:06.755007 INFO: Resetting torch num_threads to 24
1:19:06.840889 PROGRESS: === Extracted 247823 precursors and 1166515 fragments ===
1:19:06.841580 INFO: === FDR correction performed with classifier version -1 ===
1:19:06.842375 PROGRESS: ============================= Precursor FDR =============================
1:19:06.842479 PROGRESS: Total precursors accumulated: 877
1:19:06.842540 PROGRESS: Target precursors: 869 (99.09%)
1:19:06.842591 PROGRESS: Decoy precursors: 8 (0.91%)
1:19:06.842637 PROGRESS: 
1:19:06.842680 PROGRESS: Precursor Summary:
1:19:06.843918 PROGRESS: Channel   0:	 0.050 FDR:   869; 0.010 FDR:   869; 0.001 FDR:   478
1:19:06.844011 PROGRESS: 
1:19:06.844066 PROGRESS: Protein Summary:
1:19:06.845522 PROGRESS: Channel   0:	 0.050 FDR:   762; 0.010 FDR:   762; 0.001 FDR:   435
1:19:06.845609 PROGRESS: =========================================================================
1:19:06.850280 INFO: Target number of precursors not reached yet.
1:19:07.289848 INFO: Starting optimization step 7.
1:19:07.290141 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:19:07.290239 INFO: Using rust extraction backend
1:19:07.290310 PROGRESS: Extracting batch of 252313 precursors
1:19:07.725553 INFO: === Search parameters used ===
1:19:07.725861 INFO: rt_error       : 805.6019897460938
1:19:07.725939 INFO: mobility_error : 0.1
1:19:07.726003 INFO: num_candidates : 1
1:19:07.726060 INFO: ms1_error      : 30
1:19:07.726116 INFO: ms2_error      : 30
1:19:07.726160 INFO: fwhm_rt        : 5
1:19:07.726202 INFO: quant_window   : 3
1:19:07.726244 INFO: ==============================================
1:19:10.094573 INFO: performing precursor FDR with 40 features
1:19:10.094709 INFO: Decoy channel: -1
1:19:10.094737 INFO: competitive: True
1:19:10.317165 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:10.506830 INFO: Estimating optimal hyperparameters - samples: 397,994, batch_size: 1,630, learning_rate: 6.31e-04
1:19:10.507627 INFO: Using random state 812462 for train-test-split
1:19:17.752034 INFO: Test AUC: 0.593
1:19:17.752179 INFO: Train AUC: 0.607
1:19:17.752214 INFO: AUC difference: 2.39%
1:19:18.177432 INFO: Resetting torch num_threads to 24
1:19:18.261827 PROGRESS: === Extracted 497493 precursors and 2340396 fragments ===
1:19:18.262559 INFO: === FDR correction performed with classifier version -1 ===
1:19:18.263561 PROGRESS: ============================= Precursor FDR =============================
1:19:18.263655 PROGRESS: Total precursors accumulated: 1,959
1:19:18.263716 PROGRESS: Target precursors: 1,940 (99.03%)
1:19:18.263767 PROGRESS: Decoy precursors: 19 (0.97%)
1:19:18.263814 PROGRESS: 
1:19:18.263860 PROGRESS: Precursor Summary:
1:19:18.265330 PROGRESS: Channel   0:	 0.050 FDR: 1,940; 0.010 FDR: 1,940; 0.001 FDR: 1,268
1:19:18.265419 PROGRESS: 
1:19:18.265477 PROGRESS: Protein Summary:
1:19:18.267409 PROGRESS: Channel   0:	 0.050 FDR: 1,527; 0.010 FDR: 1,527; 0.001 FDR: 1,024
1:19:18.267516 PROGRESS: =========================================================================
1:19:18.275325 INFO: Target number of precursors reached.
1:19:18.552067 INFO: fragments_df: keeping 5000 of 2340396 [sum(precursor_idx_mask)=20726 sum(mass_error_mask)=2340396 stop_rank=5000
1:19:19.257719 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:19:19.533839 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:19:20.232522 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:19:20.232995 INFO: Using score_cutoff 12.818945619106293 (fac=0.99, q=1)
1:19:20.233331 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:19:20.233412 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:19:20.233469 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.818945619106293
1:19:20.233529 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:19:20.546575 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:19:21.239664 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:19:21.239922 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:19:21.240034 INFO: Starting optimization step 8.
1:19:21.240101 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:19:21.240171 INFO: Using rust extraction backend
1:19:21.240232 PROGRESS: Extracting batch of 502643 precursors
1:19:22.099354 INFO: === Search parameters used ===
1:19:22.099632 INFO: rt_error       : 805.6019897460938
1:19:22.099695 INFO: mobility_error : 0.1
1:19:22.099746 INFO: num_candidates : 3
1:19:22.099792 INFO: ms1_error      : 30
1:19:22.099833 INFO: ms2_error      : 30
1:19:22.099874 INFO: fwhm_rt        : 3.0
1:19:22.099922 INFO: quant_window   : 3
1:19:22.099965 INFO: ==============================================
1:19:30.414986 INFO: performing precursor FDR with 40 features
1:19:30.415116 INFO: Decoy channel: -1
1:19:30.415142 INFO: competitive: True
1:19:30.877776 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:31.529899 INFO: Estimating optimal hyperparameters - samples: 1,194,328, batch_size: 4,096, learning_rate: 1.00e-03
1:19:31.532422 INFO: Using random state 876483 for train-test-split
1:19:53.607828 INFO: Test AUC: 0.599
1:19:53.607998 INFO: Train AUC: 0.606
1:19:53.608035 INFO: AUC difference: 1.15%
1:19:54.348016 INFO: Resetting torch num_threads to 24
1:19:54.410297 PROGRESS: === Extracted 1492911 precursors and 6883455 fragments ===
1:19:54.410853 INFO: === FDR correction performed with classifier version 7 ===
1:19:54.411827 PROGRESS: ============================= Precursor FDR =============================
1:19:54.411924 PROGRESS: Total precursors accumulated: 2,789
1:19:54.411985 PROGRESS: Target precursors: 2,762 (99.03%)
1:19:54.412037 PROGRESS: Decoy precursors: 27 (0.97%)
1:19:54.412097 PROGRESS: 
1:19:54.412144 PROGRESS: Precursor Summary:
1:19:54.413922 PROGRESS: Channel   0:	 0.050 FDR: 2,762; 0.010 FDR: 2,762; 0.001 FDR: 1,814
1:19:54.414019 PROGRESS: 
1:19:54.414076 PROGRESS: Protein Summary:
1:19:54.416439 PROGRESS: Channel   0:	 0.050 FDR: 2,102; 0.010 FDR: 2,102; 0.001 FDR: 1,431
1:19:54.416538 PROGRESS: =========================================================================
1:19:54.447618 INFO: Target number of precursors reached.
1:19:55.192497 INFO: fragments_df: keeping 5000 of 6883455 [sum(precursor_idx_mask)=60100 sum(mass_error_mask)=6883455 stop_rank=5000
1:19:55.750912 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:19:56.248510 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:19:57.109334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:19:57.109821 INFO: Using score_cutoff 11.706331341075897 (fac=0.99, q=1)
1:19:57.110217 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:19:57.110305 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:19:57.110358 INFO: Updating optimization_manager: score_cutoff        : 12.818945619106293 -> 11.706331341075897
1:19:57.110412 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:19:57.262095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:19:57.612917 INFO: === checking if optimization conditions were reached ===
1:19:57.615675 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
1:19:57.615799 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:19:57.615880 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:19:57.615952 INFO: ==============================================
1:19:57.616032 INFO: Starting optimization step 9.
1:19:57.616100 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:19:57.616178 INFO: Using rust extraction backend
1:19:57.616255 PROGRESS: Extracting batch of 250330 precursors
1:19:58.050804 INFO: === Search parameters used ===
1:19:58.051062 INFO: rt_error       : 805.6019897460938
1:19:58.051131 INFO: mobility_error : 0.1
1:19:58.051178 INFO: num_candidates : 3
1:19:58.051220 INFO: ms1_error      : 30
1:19:58.051260 INFO: ms2_error      : 10.0
1:19:58.051311 INFO: fwhm_rt        : 3.0
1:19:58.051352 INFO: quant_window   : 3
1:19:58.051391 INFO: ==============================================
1:20:02.039466 INFO: performing precursor FDR with 40 features
1:20:02.039598 INFO: Decoy channel: -1
1:20:02.039625 INFO: competitive: True
1:20:02.242450 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:02.566642 INFO: Estimating optimal hyperparameters - samples: 599,401, batch_size: 2,455, learning_rate: 7.74e-04
1:20:02.567783 INFO: Using random state 723990 for train-test-split
1:20:15.621655 INFO: Test AUC: 0.606
1:20:15.621825 INFO: Train AUC: 0.614
1:20:15.621862 INFO: AUC difference: 1.32%
1:20:16.103839 INFO: Resetting torch num_threads to 24
1:20:16.134058 PROGRESS: === Extracted 749252 precursors and 4010553 fragments ===
1:20:16.134569 INFO: === FDR correction performed with classifier version 8 ===
1:20:16.135295 PROGRESS: ============================= Precursor FDR =============================
1:20:16.135387 PROGRESS: Total precursors accumulated: 1,816
1:20:16.135451 PROGRESS: Target precursors: 1,799 (99.06%)
1:20:16.135518 PROGRESS: Decoy precursors: 17 (0.94%)
1:20:16.135570 PROGRESS: 
1:20:16.135618 PROGRESS: Precursor Summary:
1:20:16.137051 PROGRESS: Channel   0:	 0.050 FDR: 1,799; 0.010 FDR: 1,799; 0.001 FDR: 1,339
1:20:16.137138 PROGRESS: 
1:20:16.137195 PROGRESS: Protein Summary:
1:20:16.139055 PROGRESS: Channel   0:	 0.050 FDR: 1,512; 0.010 FDR: 1,512; 0.001 FDR: 1,141
1:20:16.139153 PROGRESS: =========================================================================
1:20:16.155510 INFO: Target number of precursors reached.
1:20:16.591195 INFO: fragments_df: keeping 5000 of 4010553 [sum(precursor_idx_mask)=42448 sum(mass_error_mask)=4010553 stop_rank=5000
1:20:17.056642 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:17.334383 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:18.056670 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:18.057133 INFO: Using score_cutoff 10.536489023208619 (fac=0.99, q=1)
1:20:18.057451 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:18.057525 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:18.057580 INFO: Updating optimization_manager: score_cutoff        : 11.706331341075897 -> 10.536489023208619
1:20:18.057638 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:18.209782 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:18.553400 INFO: === checking if optimization conditions were reached ===
1:20:18.555607 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:20:18.555715 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:20:18.555783 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:20:18.555841 INFO: ==============================================
1:20:18.555914 INFO: Starting optimization step 10.
1:20:18.555973 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:18.556049 INFO: Using rust extraction backend
1:20:18.556118 PROGRESS: Extracting batch of 250330 precursors
1:20:18.988745 INFO: === Search parameters used ===
1:20:18.989021 INFO: rt_error       : 805.6019897460938
1:20:18.989080 INFO: mobility_error : 0.1
1:20:18.989126 INFO: num_candidates : 3
1:20:18.989176 INFO: ms1_error      : 30
1:20:18.989217 INFO: ms2_error      : 10.0
1:20:18.989256 INFO: fwhm_rt        : 3.0
1:20:18.989294 INFO: quant_window   : 3
1:20:18.989331 INFO: ==============================================
1:20:22.763427 INFO: performing precursor FDR with 40 features
1:20:22.763557 INFO: Decoy channel: -1
1:20:22.763584 INFO: competitive: True
1:20:22.962293 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:23.271590 INFO: Estimating optimal hyperparameters - samples: 599,407, batch_size: 2,455, learning_rate: 7.74e-04
1:20:23.272883 INFO: Using random state 137640 for train-test-split
1:20:37.171756 INFO: Test AUC: 0.607
1:20:37.171897 INFO: Train AUC: 0.618
1:20:37.171934 INFO: AUC difference: 1.87%
1:20:37.674586 INFO: Resetting torch num_threads to 24
1:20:37.705108 PROGRESS: === Extracted 749259 precursors and 4010385 fragments ===
1:20:37.705617 INFO: === FDR correction performed with classifier version 9 ===
1:20:37.706362 PROGRESS: ============================= Precursor FDR =============================
1:20:37.706455 PROGRESS: Total precursors accumulated: 1,869
1:20:37.706519 PROGRESS: Target precursors: 1,851 (99.04%)
1:20:37.706573 PROGRESS: Decoy precursors: 18 (0.96%)
1:20:37.706621 PROGRESS: 
1:20:37.706668 PROGRESS: Precursor Summary:
1:20:37.708118 PROGRESS: Channel   0:	 0.050 FDR: 1,851; 0.010 FDR: 1,851; 0.001 FDR: 1,289
1:20:37.708213 PROGRESS: 
1:20:37.708274 PROGRESS: Protein Summary:
1:20:37.710171 PROGRESS: Channel   0:	 0.050 FDR: 1,543; 0.010 FDR: 1,543; 0.001 FDR: 1,102
1:20:37.710278 PROGRESS: =========================================================================
1:20:37.727571 INFO: Target number of precursors reached.
1:20:38.168899 INFO: fragments_df: keeping 5000 of 4010385 [sum(precursor_idx_mask)=43315 sum(mass_error_mask)=4010385 stop_rank=5000
1:20:38.608453 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:38.906808 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:39.637313 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:39.637798 INFO: Using score_cutoff 10.447697982788085 (fac=0.99, q=1)
1:20:39.638114 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:39.638191 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:39.638245 INFO: Updating optimization_manager: score_cutoff        : 10.536489023208619 -> 10.447697982788085
1:20:39.638302 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:39.789521 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:40.141759 INFO: === checking if optimization conditions were reached ===
1:20:40.144688 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:20:40.144898 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:20:40.144984 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:20:40.145057 INFO: ==============================================
1:20:40.145147 INFO: Starting optimization step 11.
1:20:40.145229 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:40.145322 INFO: Using rust extraction backend
1:20:40.145406 PROGRESS: Extracting batch of 250330 precursors
1:20:40.581383 INFO: === Search parameters used ===
1:20:40.581691 INFO: rt_error       : 805.6019897460938
1:20:40.581771 INFO: mobility_error : 0.1
1:20:40.581850 INFO: num_candidates : 3
1:20:40.581908 INFO: ms1_error      : 30
1:20:40.581960 INFO: ms2_error      : 10.0
1:20:40.582013 INFO: fwhm_rt        : 3.0
1:20:40.582069 INFO: quant_window   : 3
1:20:40.582120 INFO: ==============================================
1:20:44.397583 INFO: performing precursor FDR with 40 features
1:20:44.397704 INFO: Decoy channel: -1
1:20:44.397731 INFO: competitive: True
1:20:44.594626 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:44.897666 INFO: Estimating optimal hyperparameters - samples: 599,392, batch_size: 2,455, learning_rate: 7.74e-04
1:20:44.898800 INFO: Using random state 178339 for train-test-split
1:20:57.294278 INFO: Test AUC: 0.610
1:20:57.294416 INFO: Train AUC: 0.624
1:20:57.294451 INFO: AUC difference: 2.12%
1:20:57.779970 INFO: Resetting torch num_threads to 24
1:20:57.809050 PROGRESS: === Extracted 749240 precursors and 4009829 fragments ===
1:20:57.809531 INFO: === FDR correction performed with classifier version 10 ===
1:20:57.810306 PROGRESS: ============================= Precursor FDR =============================
1:20:57.810395 PROGRESS: Total precursors accumulated: 2,061
1:20:57.810457 PROGRESS: Target precursors: 2,041 (99.03%)
1:20:57.810508 PROGRESS: Decoy precursors: 20 (0.97%)
1:20:57.810555 PROGRESS: 
1:20:57.810600 PROGRESS: Precursor Summary:
1:20:57.812077 PROGRESS: Channel   0:	 0.050 FDR: 2,041; 0.010 FDR: 2,041; 0.001 FDR: 1,400
1:20:57.812180 PROGRESS: 
1:20:57.812237 PROGRESS: Protein Summary:
1:20:57.814216 PROGRESS: Channel   0:	 0.050 FDR: 1,701; 0.010 FDR: 1,701; 0.001 FDR: 1,195
1:20:57.814306 PROGRESS: =========================================================================
1:20:57.830989 INFO: Target number of precursors reached.
1:20:58.276599 INFO: fragments_df: keeping 5000 of 4009829 [sum(precursor_idx_mask)=47630 sum(mass_error_mask)=4009829 stop_rank=5000
1:20:58.543681 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:58.845938 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:59.568342 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:59.568812 INFO: Using score_cutoff 10.503704223632813 (fac=0.99, q=1)
1:20:59.569130 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:59.569211 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:59.569266 INFO: Updating optimization_manager: score_cutoff        : 10.447697982788085 -> 10.503704223632813
1:20:59.569321 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:59.645281 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:59.812213 INFO: === checking if optimization conditions were reached ===
1:20:59.814806 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:20:59.814928 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:20:59.815008 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:20:59.815079 INFO: ==============================================
1:20:59.815166 INFO: Starting optimization step 12.
1:20:59.815239 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:20:59.815341 INFO: Using rust extraction backend
1:20:59.815422 PROGRESS: Extracting batch of 124183 precursors
1:21:00.031219 INFO: === Search parameters used ===
1:21:00.031501 INFO: rt_error       : 805.6019897460938
1:21:00.031564 INFO: mobility_error : 0.1
1:21:00.031612 INFO: num_candidates : 3
1:21:00.031655 INFO: ms1_error      : 30
1:21:00.031697 INFO: ms2_error      : 10.0
1:21:00.031740 INFO: fwhm_rt        : 3.0
1:21:00.031782 INFO: quant_window   : 3
1:21:00.031822 INFO: ==============================================
1:21:01.822316 INFO: performing precursor FDR with 40 features
1:21:01.822453 INFO: Decoy channel: -1
1:21:01.822478 INFO: competitive: True
1:21:01.930645 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:02.131056 INFO: Estimating optimal hyperparameters - samples: 297,356, batch_size: 1,217, learning_rate: 5.45e-04
1:21:02.131827 INFO: Using random state 722653 for train-test-split
1:21:09.974056 INFO: Test AUC: 0.611
1:21:09.974227 INFO: Train AUC: 0.632
1:21:09.974269 INFO: AUC difference: 3.18%
1:21:10.349755 INFO: Resetting torch num_threads to 24
1:21:10.375392 PROGRESS: === Extracted 371696 precursors and 1993027 fragments ===
1:21:10.376023 INFO: === FDR correction performed with classifier version 11 ===
1:21:10.376908 PROGRESS: ============================= Precursor FDR =============================
1:21:10.377018 PROGRESS: Total precursors accumulated: 1,016
1:21:10.377098 PROGRESS: Target precursors: 1,006 (99.02%)
1:21:10.377184 PROGRESS: Decoy precursors: 10 (0.98%)
1:21:10.377236 PROGRESS: 
1:21:10.377283 PROGRESS: Precursor Summary:
1:21:10.378555 PROGRESS: Channel   0:	 0.050 FDR: 1,006; 0.010 FDR: 1,006; 0.001 FDR:   165
1:21:10.378655 PROGRESS: 
1:21:10.378712 PROGRESS: Protein Summary:
1:21:10.380224 PROGRESS: Channel   0:	 0.050 FDR:   911; 0.010 FDR:   911; 0.001 FDR:   158
1:21:10.380319 PROGRESS: =========================================================================
1:21:10.389761 INFO: Target number of precursors reached.
1:21:10.609868 INFO: fragments_df: keeping 5000 of 1993027 [sum(precursor_idx_mask)=23338 sum(mass_error_mask)=1993027 stop_rank=5000
1:21:10.881222 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:11.206359 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:12.020482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:12.020936 INFO: Using score_cutoff 9.653693578720095 (fac=0.99, q=1)
1:21:12.021245 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:12.021321 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:12.021375 INFO: Updating optimization_manager: score_cutoff        : 10.503704223632813 -> 9.653693578720095
1:21:12.021430 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:12.098929 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:12.322315 INFO: === checking if optimization conditions were reached ===
1:21:12.325532 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:21:12.325741 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:21:12.325851 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:21:12.325933 INFO: ==============================================
1:21:12.326032 PROGRESS: Optimization finished for ms2_error.
1:21:12.683655 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:12.767674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:12.971617 INFO: Starting optimization step 0.
1:21:12.971959 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:21:12.972098 INFO: Using rust extraction backend
1:21:12.972199 PROGRESS: Extracting batch of 124183 precursors
1:21:13.226688 INFO: === Search parameters used ===
1:21:13.227037 INFO: rt_error       : 805.6019897460938
1:21:13.227123 INFO: mobility_error : 0.1
1:21:13.227193 INFO: num_candidates : 3
1:21:13.227252 INFO: ms1_error      : 30
1:21:13.227313 INFO: ms2_error      : 10.0
1:21:13.227374 INFO: fwhm_rt        : 3.0
1:21:13.227446 INFO: quant_window   : 3
1:21:13.227525 INFO: ==============================================
1:21:15.489816 INFO: performing precursor FDR with 40 features
1:21:15.489975 INFO: Decoy channel: -1
1:21:15.490008 INFO: competitive: True
1:21:15.632723 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:15.796187 INFO: Estimating optimal hyperparameters - samples: 297,362, batch_size: 1,217, learning_rate: 5.45e-04
1:21:15.797014 INFO: Using random state 530785 for train-test-split
1:21:21.646785 INFO: Test AUC: 0.616
1:21:21.646953 INFO: Train AUC: 0.636
1:21:21.646999 INFO: AUC difference: 3.06%
1:21:22.156359 INFO: Resetting torch num_threads to 24
1:21:22.172423 PROGRESS: === Extracted 371703 precursors and 1992886 fragments ===
1:21:22.172935 INFO: === FDR correction performed with classifier version 12 ===
1:21:22.173552 PROGRESS: ============================= Precursor FDR =============================
1:21:22.173639 PROGRESS: Total precursors accumulated: 1,059
1:21:22.173700 PROGRESS: Target precursors: 1,049 (99.06%)
1:21:22.173751 PROGRESS: Decoy precursors: 10 (0.94%)
1:21:22.173799 PROGRESS: 
1:21:22.173846 PROGRESS: Precursor Summary:
1:21:22.175030 PROGRESS: Channel   0:	 0.050 FDR: 1,049; 0.010 FDR: 1,049; 0.001 FDR:   144
1:21:22.175131 PROGRESS: 
1:21:22.175187 PROGRESS: Protein Summary:
1:21:22.176744 PROGRESS: Channel   0:	 0.050 FDR:   953; 0.010 FDR:   953; 0.001 FDR:   139
1:21:22.176841 PROGRESS: =========================================================================
1:21:22.185898 INFO: Target number of precursors reached.
1:21:22.410792 INFO: fragments_df: keeping 5000 of 1992886 [sum(precursor_idx_mask)=23991 sum(mass_error_mask)=1992886 stop_rank=5000
1:21:22.676657 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:22.932020 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:23.736238 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:23.736796 INFO: Using score_cutoff 9.100005194091796 (fac=0.99, q=1)
1:21:23.737176 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:23.737255 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:23.737311 INFO: Updating optimization_manager: score_cutoff        : 9.653693578720095 -> 9.100005194091796
1:21:23.737368 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:23.823214 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:24.013652 INFO: === checking if optimization conditions were reached ===
1:21:24.013970 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:21:24.016908 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 782.7707799244936
1:21:24.017034 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 782.7708.
1:21:24.017129 INFO: ==============================================
1:21:24.017216 INFO: Starting optimization step 1.
1:21:24.017288 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:21:24.017364 INFO: Using rust extraction backend
1:21:24.017437 PROGRESS: Extracting batch of 124183 precursors
1:21:24.312467 INFO: === Search parameters used ===
1:21:24.312783 INFO: rt_error       : 782.7707799244936
1:21:24.312841 INFO: mobility_error : 0.1
1:21:24.312891 INFO: num_candidates : 3
1:21:24.312938 INFO: ms1_error      : 30
1:21:24.312982 INFO: ms2_error      : 10.0
1:21:24.313023 INFO: fwhm_rt        : 3.0
1:21:24.313065 INFO: quant_window   : 3
1:21:24.313105 INFO: ==============================================
1:21:26.074667 INFO: performing precursor FDR with 40 features
1:21:26.074784 INFO: Decoy channel: -1
1:21:26.074810 INFO: competitive: True
1:21:26.165894 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:26.353120 INFO: Estimating optimal hyperparameters - samples: 297,359, batch_size: 1,217, learning_rate: 5.45e-04
1:21:26.353816 INFO: Using random state 530785 for train-test-split
1:21:31.879248 INFO: Test AUC: 0.614
1:21:31.879370 INFO: Train AUC: 0.637
1:21:31.879402 INFO: AUC difference: 3.60%
1:21:32.897457 INFO: Resetting torch num_threads to 24
1:21:32.912195 PROGRESS: === Extracted 371699 precursors and 1993037 fragments ===
1:21:32.912663 INFO: === FDR correction performed with classifier version 12 ===
1:21:32.913232 PROGRESS: ============================= Precursor FDR =============================
1:21:32.913322 PROGRESS: Total precursors accumulated: 952
1:21:32.913382 PROGRESS: Target precursors: 943 (99.05%)
1:21:32.913432 PROGRESS: Decoy precursors: 9 (0.95%)
1:21:32.913479 PROGRESS: 
1:21:32.913524 PROGRESS: Precursor Summary:
1:21:32.914681 PROGRESS: Channel   0:	 0.050 FDR:   943; 0.010 FDR:   943; 0.001 FDR:    63
1:21:32.914768 PROGRESS: 
1:21:32.914824 PROGRESS: Protein Summary:
1:21:32.916236 PROGRESS: Channel   0:	 0.050 FDR:   857; 0.010 FDR:   857; 0.001 FDR:    62
1:21:32.916327 PROGRESS: =========================================================================
1:21:32.922923 INFO: Target number of precursors not reached yet.
1:21:33.171380 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:33.247800 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:33.430201 INFO: === skipping optimization until target number of precursors are found ===
1:21:33.430511 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:21:33.430632 INFO: Starting optimization step 2.
1:21:33.430711 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:21:33.430791 INFO: Using rust extraction backend
1:21:33.430864 PROGRESS: Extracting batch of 126147 precursors
1:21:33.653575 INFO: === Search parameters used ===
1:21:33.653851 INFO: rt_error       : 782.7707799244936
1:21:33.653912 INFO: mobility_error : 0.1
1:21:33.653960 INFO: num_candidates : 3
1:21:33.654004 INFO: ms1_error      : 30
1:21:33.654047 INFO: ms2_error      : 10.0
1:21:33.654099 INFO: fwhm_rt        : 3.0
1:21:33.654143 INFO: quant_window   : 3
1:21:33.654184 INFO: ==============================================
1:21:35.617529 INFO: performing precursor FDR with 40 features
1:21:35.617664 INFO: Decoy channel: -1
1:21:35.617691 INFO: competitive: True
1:21:35.896993 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:36.212846 INFO: Estimating optimal hyperparameters - samples: 599,384, batch_size: 2,455, learning_rate: 7.74e-04
1:21:36.213798 INFO: Using random state 530785 for train-test-split
1:21:49.488799 INFO: Test AUC: 0.616
1:21:49.488955 INFO: Train AUC: 0.625
1:21:49.488991 INFO: AUC difference: 1.45%
1:21:50.075967 INFO: Resetting torch num_threads to 24
1:21:50.233822 PROGRESS: === Extracted 749230 precursors and 4010300 fragments ===
1:21:50.234584 INFO: === FDR correction performed with classifier version 12 ===
1:21:50.235711 PROGRESS: ============================= Precursor FDR =============================
1:21:50.235825 PROGRESS: Total precursors accumulated: 2,062
1:21:50.235902 PROGRESS: Target precursors: 2,042 (99.03%)
1:21:50.235954 PROGRESS: Decoy precursors: 20 (0.97%)
1:21:50.236002 PROGRESS: 
1:21:50.236047 PROGRESS: Precursor Summary:
1:21:50.237618 PROGRESS: Channel   0:	 0.050 FDR: 2,042; 0.010 FDR: 2,042; 0.001 FDR: 1,456
1:21:50.237718 PROGRESS: 
1:21:50.237775 PROGRESS: Protein Summary:
1:21:50.239835 PROGRESS: Channel   0:	 0.050 FDR: 1,708; 0.010 FDR: 1,708; 0.001 FDR: 1,238
1:21:50.239936 PROGRESS: =========================================================================
1:21:50.253739 INFO: Target number of precursors reached.
1:21:50.721274 INFO: fragments_df: keeping 5000 of 4010300 [sum(precursor_idx_mask)=46571 sum(mass_error_mask)=4010300 stop_rank=5000
1:21:51.064633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:51.415273 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:52.208939 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:52.209587 INFO: Using score_cutoff 9.059546066665648 (fac=0.99, q=1)
1:21:52.210027 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:52.210136 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:52.210211 INFO: Updating optimization_manager: score_cutoff        : 9.100005194091796 -> 9.059546066665648
1:21:52.210284 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:52.293457 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:52.481802 INFO: === checking if optimization conditions were reached ===
1:21:52.482161 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:21:52.486022 INFO: Updating optimization_manager: rt_error            : 782.7707799244936 -> 978.9922647367499
1:21:52.486223 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 978.9923.
1:21:52.486303 INFO: ==============================================
1:21:52.486384 INFO: Starting optimization step 3.
1:21:52.486447 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:21:52.486517 INFO: Using rust extraction backend
1:21:52.486580 PROGRESS: Extracting batch of 124183 precursors
1:21:52.713509 INFO: === Search parameters used ===
1:21:52.713817 INFO: rt_error       : 978.9922647367499
1:21:52.713875 INFO: mobility_error : 0.1
1:21:52.713924 INFO: num_candidates : 3
1:21:52.713979 INFO: ms1_error      : 30
1:21:52.714022 INFO: ms2_error      : 10.0
1:21:52.714064 INFO: fwhm_rt        : 3.0
1:21:52.714105 INFO: quant_window   : 3
1:21:52.714144 INFO: ==============================================
1:21:54.787374 INFO: performing precursor FDR with 40 features
1:21:54.787508 INFO: Decoy channel: -1
1:21:54.787532 INFO: competitive: True
1:21:54.899241 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:55.053628 INFO: Estimating optimal hyperparameters - samples: 297,350, batch_size: 1,217, learning_rate: 5.45e-04
1:21:55.054188 INFO: Using random state 530785 for train-test-split
1:22:03.333644 INFO: Test AUC: 0.614
1:22:03.333819 INFO: Train AUC: 0.636
1:22:03.333867 INFO: AUC difference: 3.44%
1:22:03.750386 INFO: Resetting torch num_threads to 24
1:22:03.764928 PROGRESS: === Extracted 371688 precursors and 1992779 fragments ===
1:22:03.765397 INFO: === FDR correction performed with classifier version 12 ===
1:22:03.766003 PROGRESS: ============================= Precursor FDR =============================
1:22:03.766095 PROGRESS: Total precursors accumulated: 913
1:22:03.766157 PROGRESS: Target precursors: 904 (99.01%)
1:22:03.766210 PROGRESS: Decoy precursors: 9 (0.99%)
1:22:03.766257 PROGRESS: 
1:22:03.766302 PROGRESS: Precursor Summary:
1:22:03.767463 PROGRESS: Channel   0:	 0.050 FDR:   904; 0.010 FDR:   904; 0.001 FDR:   243
1:22:03.767556 PROGRESS: 
1:22:03.767613 PROGRESS: Protein Summary:
1:22:03.769027 PROGRESS: Channel   0:	 0.050 FDR:   825; 0.010 FDR:   825; 0.001 FDR:   229
1:22:03.769119 PROGRESS: =========================================================================
1:22:03.775611 INFO: Target number of precursors not reached yet.
1:22:04.062853 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:04.142961 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:04.326163 INFO: === skipping optimization until target number of precursors are found ===
1:22:04.326453 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:22:04.326556 INFO: Starting optimization step 4.
1:22:04.326626 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:22:04.326705 INFO: Using rust extraction backend
1:22:04.326775 PROGRESS: Extracting batch of 126147 precursors
1:22:04.546144 INFO: === Search parameters used ===
1:22:04.546433 INFO: rt_error       : 978.9922647367499
1:22:04.546495 INFO: mobility_error : 0.1
1:22:04.546544 INFO: num_candidates : 3
1:22:04.546587 INFO: ms1_error      : 30
1:22:04.546630 INFO: ms2_error      : 10.0
1:22:04.546673 INFO: fwhm_rt        : 3.0
1:22:04.546714 INFO: quant_window   : 3
1:22:04.546754 INFO: ==============================================
1:22:06.712250 INFO: performing precursor FDR with 40 features
1:22:06.712369 INFO: Decoy channel: -1
1:22:06.712396 INFO: competitive: True
1:22:07.006108 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:07.318453 INFO: Estimating optimal hyperparameters - samples: 599,360, batch_size: 2,454, learning_rate: 7.74e-04
1:22:07.319351 INFO: Using random state 530785 for train-test-split
1:22:20.688411 INFO: Test AUC: 0.615
1:22:20.688549 INFO: Train AUC: 0.626
1:22:20.688590 INFO: AUC difference: 1.73%
1:22:21.173435 INFO: Resetting torch num_threads to 24
1:22:21.320720 PROGRESS: === Extracted 749201 precursors and 4009577 fragments ===
1:22:21.321460 INFO: === FDR correction performed with classifier version 12 ===
1:22:21.322482 PROGRESS: ============================= Precursor FDR =============================
1:22:21.322574 PROGRESS: Total precursors accumulated: 1,978
1:22:21.322635 PROGRESS: Target precursors: 1,959 (99.04%)
1:22:21.322686 PROGRESS: Decoy precursors: 19 (0.96%)
1:22:21.322743 PROGRESS: 
1:22:21.322789 PROGRESS: Precursor Summary:
1:22:21.324330 PROGRESS: Channel   0:	 0.050 FDR: 1,959; 0.010 FDR: 1,959; 0.001 FDR: 1,521
1:22:21.324431 PROGRESS: 
1:22:21.324488 PROGRESS: Protein Summary:
1:22:21.326474 PROGRESS: Channel   0:	 0.050 FDR: 1,632; 0.010 FDR: 1,632; 0.001 FDR: 1,292
1:22:21.326564 PROGRESS: =========================================================================
1:22:21.337073 INFO: Target number of precursors reached.
1:22:21.805238 INFO: fragments_df: keeping 5000 of 4009577 [sum(precursor_idx_mask)=46032 sum(mass_error_mask)=4009577 stop_rank=5000
1:22:22.251129 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:22.573234 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:23.313433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:23.313895 INFO: Using score_cutoff 10.976638482284546 (fac=0.99, q=1)
1:22:23.314207 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:23.314286 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:23.314342 INFO: Updating optimization_manager: score_cutoff        : 9.059546066665648 -> 10.976638482284546
1:22:23.314397 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:23.465268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:23.805210 INFO: === checking if optimization conditions were reached ===
1:22:23.805532 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:22:23.809413 INFO: Updating optimization_manager: rt_error            : 978.9922647367499 -> 373.28910685302253
1:22:23.809583 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 373.2891.
1:22:23.809668 INFO: ==============================================
1:22:23.809753 INFO: Starting optimization step 5.
1:22:23.809825 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:23.809901 INFO: Using rust extraction backend
1:22:23.809972 PROGRESS: Extracting batch of 250330 precursors
1:22:24.241498 INFO: === Search parameters used ===
1:22:24.241802 INFO: rt_error       : 373.28910685302253
1:22:24.241863 INFO: mobility_error : 0.1
1:22:24.241914 INFO: num_candidates : 3
1:22:24.241961 INFO: ms1_error      : 30
1:22:24.242004 INFO: ms2_error      : 10.0
1:22:24.242046 INFO: fwhm_rt        : 3.0
1:22:24.242088 INFO: quant_window   : 3
1:22:24.242134 INFO: ==============================================
1:22:27.574053 INFO: performing precursor FDR with 40 features
1:22:27.574178 INFO: Decoy channel: -1
1:22:27.574208 INFO: competitive: True
1:22:27.774855 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:28.088077 INFO: Estimating optimal hyperparameters - samples: 597,571, batch_size: 2,447, learning_rate: 7.73e-04
1:22:28.089083 INFO: Using random state 530785 for train-test-split
1:22:40.936530 INFO: Test AUC: 0.609
1:22:40.936698 INFO: Train AUC: 0.621
1:22:40.936732 INFO: AUC difference: 1.97%
1:22:41.425726 INFO: Resetting torch num_threads to 24
1:22:41.454352 PROGRESS: === Extracted 746964 precursors and 3821997 fragments ===
1:22:41.454876 INFO: === FDR correction performed with classifier version 12 ===
1:22:41.455615 PROGRESS: ============================= Precursor FDR =============================
1:22:41.455708 PROGRESS: Total precursors accumulated: 2,026
1:22:41.455784 PROGRESS: Target precursors: 2,006 (99.01%)
1:22:41.455834 PROGRESS: Decoy precursors: 20 (0.99%)
1:22:41.455878 PROGRESS: 
1:22:41.455920 PROGRESS: Precursor Summary:
1:22:41.457402 PROGRESS: Channel   0:	 0.050 FDR: 2,006; 0.010 FDR: 2,006; 0.001 FDR: 1,483
1:22:41.457487 PROGRESS: 
1:22:41.457539 PROGRESS: Protein Summary:
1:22:41.459543 PROGRESS: Channel   0:	 0.050 FDR: 1,673; 0.010 FDR: 1,673; 0.001 FDR: 1,258
1:22:41.459636 PROGRESS: =========================================================================
1:22:41.474009 INFO: Target number of precursors reached.
1:22:41.891193 INFO: fragments_df: keeping 5000 of 3821997 [sum(precursor_idx_mask)=46481 sum(mass_error_mask)=3821997 stop_rank=5000
1:22:42.333322 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:42.645505 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:43.402468 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:43.402933 INFO: Using score_cutoff 10.709296789169311 (fac=0.99, q=1)
1:22:43.403251 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:43.403327 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:43.403380 INFO: Updating optimization_manager: score_cutoff        : 10.976638482284546 -> 10.709296789169311
1:22:43.403431 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:43.557729 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:43.907560 INFO: === checking if optimization conditions were reached ===
1:22:43.907865 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:22:43.911400 INFO: Updating optimization_manager: rt_error            : 373.28910685302253 -> 349.33738242326336
1:22:43.911548 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 349.3374.
1:22:43.911625 INFO: ==============================================
1:22:43.911706 INFO: Starting optimization step 6.
1:22:43.911780 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:43.911851 INFO: Using rust extraction backend
1:22:43.911921 PROGRESS: Extracting batch of 250330 precursors
1:22:44.339873 INFO: === Search parameters used ===
1:22:44.340139 INFO: rt_error       : 349.33738242326336
1:22:44.340198 INFO: mobility_error : 0.1
1:22:44.340249 INFO: num_candidates : 3
1:22:44.340295 INFO: ms1_error      : 30
1:22:44.340337 INFO: ms2_error      : 10.0
1:22:44.340379 INFO: fwhm_rt        : 3.0
1:22:44.340418 INFO: quant_window   : 3
1:22:44.340461 INFO: ==============================================
1:22:47.488569 INFO: performing precursor FDR with 40 features
1:22:47.488691 INFO: Decoy channel: -1
1:22:47.488719 INFO: competitive: True
1:22:47.689736 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:47.998592 INFO: Estimating optimal hyperparameters - samples: 597,100, batch_size: 2,445, learning_rate: 7.73e-04
1:22:47.999698 INFO: Using random state 530785 for train-test-split
1:22:59.917229 INFO: Test AUC: 0.610
1:22:59.917392 INFO: Train AUC: 0.620
1:22:59.917429 INFO: AUC difference: 1.62%
1:23:00.403343 INFO: Resetting torch num_threads to 24
1:23:00.432187 PROGRESS: === Extracted 746376 precursors and 3773713 fragments ===
1:23:00.432692 INFO: === FDR correction performed with classifier version 12 ===
1:23:00.433433 PROGRESS: ============================= Precursor FDR =============================
1:23:00.433534 PROGRESS: Total precursors accumulated: 1,960
1:23:00.433601 PROGRESS: Target precursors: 1,941 (99.03%)
1:23:00.433654 PROGRESS: Decoy precursors: 19 (0.97%)
1:23:00.433702 PROGRESS: 
1:23:00.433748 PROGRESS: Precursor Summary:
1:23:00.435220 PROGRESS: Channel   0:	 0.050 FDR: 1,941; 0.010 FDR: 1,941; 0.001 FDR: 1,410
1:23:00.435304 PROGRESS: 
1:23:00.435359 PROGRESS: Protein Summary:
1:23:00.437295 PROGRESS: Channel   0:	 0.050 FDR: 1,614; 0.010 FDR: 1,614; 0.001 FDR: 1,198
1:23:00.437391 PROGRESS: =========================================================================
1:23:00.452981 INFO: Target number of precursors reached.
1:23:00.859188 INFO: fragments_df: keeping 5000 of 3773713 [sum(precursor_idx_mask)=45133 sum(mass_error_mask)=3773713 stop_rank=5000
1:23:01.308988 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:01.571549 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:02.219880 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:02.220342 INFO: Using score_cutoff 10.653789808273316 (fac=0.99, q=1)
1:23:02.220650 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:02.220726 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:02.220778 INFO: Updating optimization_manager: score_cutoff        : 10.709296789169311 -> 10.653789808273316
1:23:02.220833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:02.368983 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:02.690170 INFO: === checking if optimization conditions were reached ===
1:23:02.690525 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:23:02.694346 INFO: Updating optimization_manager: rt_error            : 349.33738242326336 -> 438.28181906177974
1:23:02.694509 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 438.2818.
1:23:02.694585 INFO: ==============================================
1:23:02.694682 INFO: Starting optimization step 7.
1:23:02.694755 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:02.694847 INFO: Using rust extraction backend
1:23:02.694927 PROGRESS: Extracting batch of 250330 precursors
1:23:03.123261 INFO: === Search parameters used ===
1:23:03.123555 INFO: rt_error       : 438.28181906177974
1:23:03.123620 INFO: mobility_error : 0.1
1:23:03.123665 INFO: num_candidates : 3
1:23:03.123706 INFO: ms1_error      : 30
1:23:03.123745 INFO: ms2_error      : 10.0
1:23:03.123784 INFO: fwhm_rt        : 3.0
1:23:03.123823 INFO: quant_window   : 3
1:23:03.123863 INFO: ==============================================
1:23:06.378221 INFO: performing precursor FDR with 40 features
1:23:06.378338 INFO: Decoy channel: -1
1:23:06.378365 INFO: competitive: True
1:23:06.579795 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:06.894753 INFO: Estimating optimal hyperparameters - samples: 598,244, batch_size: 2,450, learning_rate: 7.73e-04
1:23:06.895742 INFO: Using random state 530785 for train-test-split
1:23:19.497890 INFO: Test AUC: 0.611
1:23:19.498023 INFO: Train AUC: 0.623
1:23:19.498055 INFO: AUC difference: 1.93%
1:23:19.984418 INFO: Resetting torch num_threads to 24
1:23:20.012946 PROGRESS: === Extracted 747806 precursors and 3903153 fragments ===
1:23:20.013444 INFO: === FDR correction performed with classifier version 12 ===
1:23:20.014230 PROGRESS: ============================= Precursor FDR =============================
1:23:20.014322 PROGRESS: Total precursors accumulated: 1,974
1:23:20.014384 PROGRESS: Target precursors: 1,955 (99.04%)
1:23:20.014436 PROGRESS: Decoy precursors: 19 (0.96%)
1:23:20.014484 PROGRESS: 
1:23:20.014530 PROGRESS: Precursor Summary:
1:23:20.016008 PROGRESS: Channel   0:	 0.050 FDR: 1,955; 0.010 FDR: 1,955; 0.001 FDR: 1,488
1:23:20.016106 PROGRESS: 
1:23:20.016162 PROGRESS: Protein Summary:
1:23:20.018122 PROGRESS: Channel   0:	 0.050 FDR: 1,630; 0.010 FDR: 1,630; 0.001 FDR: 1,265
1:23:20.018214 PROGRESS: =========================================================================
1:23:20.034757 INFO: Target number of precursors reached.
1:23:20.472558 INFO: fragments_df: keeping 5000 of 3903153 [sum(precursor_idx_mask)=45387 sum(mass_error_mask)=3903153 stop_rank=5000
1:23:20.900467 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:21.185072 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:21.904204 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:21.904665 INFO: Using score_cutoff 10.109974005889892 (fac=0.99, q=1)
1:23:21.904975 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:21.905052 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:21.905113 INFO: Updating optimization_manager: score_cutoff        : 10.653789808273316 -> 10.109974005889892
1:23:21.905168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:22.053908 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:22.389307 INFO: === checking if optimization conditions were reached ===
1:23:22.389608 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:23:22.393473 INFO: Updating optimization_manager: rt_error            : 438.28181906177974 -> 383.80946713233493
1:23:22.393651 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 383.8095.
1:23:22.393733 INFO: ==============================================
1:23:22.393821 INFO: Starting optimization step 8.
1:23:22.393892 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:22.393972 INFO: Using rust extraction backend
1:23:22.394046 PROGRESS: Extracting batch of 250330 precursors
1:23:22.826679 INFO: === Search parameters used ===
1:23:22.826953 INFO: rt_error       : 383.80946713233493
1:23:22.827015 INFO: mobility_error : 0.1
1:23:22.827063 INFO: num_candidates : 3
1:23:22.827108 INFO: ms1_error      : 30
1:23:22.827151 INFO: ms2_error      : 10.0
1:23:22.827193 INFO: fwhm_rt        : 3.0
1:23:22.827235 INFO: quant_window   : 3
1:23:22.827276 INFO: ==============================================
1:23:25.992129 INFO: performing precursor FDR with 40 features
1:23:25.992254 INFO: Decoy channel: -1
1:23:25.992282 INFO: competitive: True
1:23:26.184038 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:26.479579 INFO: Estimating optimal hyperparameters - samples: 597,773, batch_size: 2,448, learning_rate: 7.73e-04
1:23:26.480681 INFO: Using random state 530785 for train-test-split
1:23:38.798280 INFO: Test AUC: 0.608
1:23:38.798404 INFO: Train AUC: 0.621
1:23:38.798437 INFO: AUC difference: 2.04%
1:23:39.302975 INFO: Resetting torch num_threads to 24
1:23:39.332587 PROGRESS: === Extracted 747217 precursors and 3841012 fragments ===
1:23:39.333067 INFO: === FDR correction performed with classifier version 12 ===
1:23:39.333793 PROGRESS: ============================= Precursor FDR =============================
1:23:39.333884 PROGRESS: Total precursors accumulated: 2,029
1:23:39.333945 PROGRESS: Target precursors: 2,009 (99.01%)
1:23:39.333996 PROGRESS: Decoy precursors: 20 (0.99%)
1:23:39.334044 PROGRESS: 
1:23:39.334090 PROGRESS: Precursor Summary:
1:23:39.335573 PROGRESS: Channel   0:	 0.050 FDR: 2,009; 0.010 FDR: 2,009; 0.001 FDR: 1,491
1:23:39.335670 PROGRESS: 
1:23:39.335727 PROGRESS: Protein Summary:
1:23:39.337708 PROGRESS: Channel   0:	 0.050 FDR: 1,676; 0.010 FDR: 1,676; 0.001 FDR: 1,266
1:23:39.337800 PROGRESS: =========================================================================
1:23:39.353159 INFO: Target number of precursors reached.
1:23:39.780185 INFO: fragments_df: keeping 5000 of 3841012 [sum(precursor_idx_mask)=46447 sum(mass_error_mask)=3841012 stop_rank=5000
1:23:40.204669 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:40.454944 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:41.124977 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:41.125442 INFO: Using score_cutoff 10.157764361572266 (fac=0.99, q=1)
1:23:41.125753 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:41.125838 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:41.125896 INFO: Updating optimization_manager: score_cutoff        : 10.109974005889892 -> 10.157764361572266
1:23:41.125958 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:41.277634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:41.620327 INFO: === checking if optimization conditions were reached ===
1:23:41.620598 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:23:41.623881 INFO: Updating optimization_manager: rt_error            : 383.80946713233493 -> 486.59746296321515
1:23:41.624025 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 486.5975.
1:23:41.624094 INFO: ==============================================
1:23:41.624167 INFO: Starting optimization step 9.
1:23:41.624230 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:41.624295 INFO: Using rust extraction backend
1:23:41.624353 PROGRESS: Extracting batch of 250330 precursors
1:23:42.060043 INFO: === Search parameters used ===
1:23:42.060317 INFO: rt_error       : 486.59746296321515
1:23:42.060381 INFO: mobility_error : 0.1
1:23:42.060431 INFO: num_candidates : 3
1:23:42.060476 INFO: ms1_error      : 30
1:23:42.060519 INFO: ms2_error      : 10.0
1:23:42.060561 INFO: fwhm_rt        : 3.0
1:23:42.060612 INFO: quant_window   : 3
1:23:42.060657 INFO: ==============================================
1:23:45.328244 INFO: performing precursor FDR with 40 features
1:23:45.328370 INFO: Decoy channel: -1
1:23:45.328397 INFO: competitive: True
1:23:45.521163 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:45.829766 INFO: Estimating optimal hyperparameters - samples: 598,636, batch_size: 2,452, learning_rate: 7.74e-04
1:23:45.830909 INFO: Using random state 530785 for train-test-split
1:23:54.461394 INFO: Test AUC: 0.611
1:23:54.461528 INFO: Train AUC: 0.624
1:23:54.461562 INFO: AUC difference: 2.08%
1:23:54.933244 INFO: Resetting torch num_threads to 24
1:23:54.961695 PROGRESS: === Extracted 748295 precursors and 3942764 fragments ===
1:23:54.962172 INFO: === FDR correction performed with classifier version 12 ===
1:23:54.962873 PROGRESS: ============================= Precursor FDR =============================
1:23:54.962962 PROGRESS: Total precursors accumulated: 1,950
1:23:54.963025 PROGRESS: Target precursors: 1,931 (99.03%)
1:23:54.963076 PROGRESS: Decoy precursors: 19 (0.97%)
1:23:54.963124 PROGRESS: 
1:23:54.963170 PROGRESS: Precursor Summary:
1:23:54.964639 PROGRESS: Channel   0:	 0.050 FDR: 1,931; 0.010 FDR: 1,931; 0.001 FDR: 1,536
1:23:54.964731 PROGRESS: 
1:23:54.964786 PROGRESS: Protein Summary:
1:23:54.966735 PROGRESS: Channel   0:	 0.050 FDR: 1,613; 0.010 FDR: 1,613; 0.001 FDR: 1,307
1:23:54.966828 PROGRESS: =========================================================================
1:23:54.982732 INFO: Target number of precursors reached.
1:23:55.392867 INFO: fragments_df: keeping 5000 of 3942764 [sum(precursor_idx_mask)=45067 sum(mass_error_mask)=3942764 stop_rank=5000
1:23:55.815560 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:56.127308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:56.878915 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:56.879389 INFO: Using score_cutoff 10.49805167198181 (fac=0.99, q=1)
1:23:56.879707 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:56.879787 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:56.879844 INFO: Updating optimization_manager: score_cutoff        : 10.157764361572266 -> 10.49805167198181
1:23:56.879897 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:57.033984 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:57.385157 INFO: === checking if optimization conditions were reached ===
1:23:57.385473 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:23:57.389231 INFO: Updating optimization_manager: rt_error            : 486.59746296321515 -> 484.63194171317446
1:23:57.389425 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 484.6319.
1:23:57.389508 INFO: ==============================================
1:23:57.389593 INFO: Starting optimization step 10.
1:23:57.389665 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:57.389744 INFO: Using rust extraction backend
1:23:57.389816 PROGRESS: Extracting batch of 250330 precursors
1:23:57.817778 INFO: === Search parameters used ===
1:23:57.818059 INFO: rt_error       : 484.63194171317446
1:23:57.818118 INFO: mobility_error : 0.1
1:23:57.818168 INFO: num_candidates : 3
1:23:57.818214 INFO: ms1_error      : 30
1:23:57.818274 INFO: ms2_error      : 10.0
1:23:57.818320 INFO: fwhm_rt        : 3.0
1:23:57.818371 INFO: quant_window   : 3
1:23:57.818417 INFO: ==============================================
1:24:01.074730 INFO: performing precursor FDR with 40 features
1:24:01.074856 INFO: Decoy channel: -1
1:24:01.074880 INFO: competitive: True
1:24:01.270149 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:01.579702 INFO: Estimating optimal hyperparameters - samples: 598,656, batch_size: 2,452, learning_rate: 7.74e-04
1:24:01.580718 INFO: Using random state 530785 for train-test-split
1:24:10.506932 INFO: Test AUC: 0.611
1:24:10.507058 INFO: Train AUC: 0.624
1:24:10.507092 INFO: AUC difference: 2.10%
1:24:11.006693 INFO: Resetting torch num_threads to 24
1:24:11.036546 PROGRESS: === Extracted 748320 precursors and 3943644 fragments ===
1:24:11.037035 INFO: === FDR correction performed with classifier version 12 ===
1:24:11.037851 PROGRESS: ============================= Precursor FDR =============================
1:24:11.037941 PROGRESS: Total precursors accumulated: 2,029
1:24:11.038002 PROGRESS: Target precursors: 2,009 (99.01%)
1:24:11.038057 PROGRESS: Decoy precursors: 20 (0.99%)
1:24:11.038121 PROGRESS: 
1:24:11.038168 PROGRESS: Precursor Summary:
1:24:11.039663 PROGRESS: Channel   0:	 0.050 FDR: 2,009; 0.010 FDR: 2,009; 0.001 FDR: 1,486
1:24:11.039757 PROGRESS: 
1:24:11.039815 PROGRESS: Protein Summary:
1:24:11.041819 PROGRESS: Channel   0:	 0.050 FDR: 1,676; 0.010 FDR: 1,676; 0.001 FDR: 1,259
1:24:11.041914 PROGRESS: =========================================================================
1:24:11.059666 INFO: Target number of precursors reached.
1:24:11.487351 INFO: fragments_df: keeping 5000 of 3943644 [sum(precursor_idx_mask)=46732 sum(mass_error_mask)=3943644 stop_rank=5000
1:24:11.913812 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:12.205674 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:12.926506 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:24:12.926962 INFO: Using score_cutoff 10.178458799743654 (fac=0.99, q=1)
1:24:12.927265 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:12.927344 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:12.927401 INFO: Updating optimization_manager: score_cutoff        : 10.49805167198181 -> 10.178458799743654
1:24:12.927464 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:13.077581 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:13.413960 INFO: === checking if optimization conditions were reached ===
1:24:13.414259 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
1:24:13.415464 INFO: Updating optimization_manager: rt_error            : 484.63194171317446 -> 805.6019897460938
1:24:13.415667 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1:24:13.415791 INFO: Updating optimization_manager: score_cutoff        : 10.178458799743654 -> 9.100005194091796
1:24:13.415901 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:13.416006 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:13.416117 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 805.6020 found after 9 searches.
1:24:13.416209 INFO: ==============================================
1:24:13.416310 PROGRESS: Optimization finished for rt_error.
1:24:13.674104 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:13.749915 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:13.925187 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:24:13.925473 PROGRESS: ==============================================
1:24:13.925570 PROGRESS: ms2_error      : 10.0000
1:24:13.925638 PROGRESS: rt_error       : 805.6020
1:24:13.925694 PROGRESS: ==============================================
1:24:13.926698 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:21.556052 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:39.040038 INFO: Using rust extraction backend
1:24:39.040322 PROGRESS: Extracting batch of 11997144 precursors
1:24:55.361295 INFO: === Search parameters used ===
1:24:55.361555 INFO: rt_error       : 805.6019897460938
1:24:55.361616 INFO: mobility_error : 0.1
1:24:55.361666 INFO: num_candidates : 3
1:24:55.361713 INFO: ms1_error      : 30
1:24:55.361755 INFO: ms2_error      : 10.0
1:24:55.361799 INFO: fwhm_rt        : 3.0
1:24:55.361841 INFO: quant_window   : 3
1:24:55.361883 INFO: ==============================================
1:26:01.490911 INFO: Removed 5305429 precursors with score below cutoff 9.100005194091796
1:26:35.183608 INFO: performing precursor FDR with 40 features
1:26:35.183733 INFO: Decoy channel: -1
1:26:35.183759 INFO: competitive: True
1:26:38.531537 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:51.308085 INFO: Estimating optimal hyperparameters - samples: 24,548,473, batch_size: 4,096, learning_rate: 1.00e-03
1:26:51.385684 INFO: Using random state 204079 for train-test-split
1:34:26.210377 INFO: Test AUC: 0.622
1:34:26.210673 INFO: Train AUC: 0.623
1:34:26.210725 INFO: AUC difference: 0.06%
1:34:33.493760 INFO: Resetting torch num_threads to 24
1:34:35.679515 PROGRESS: ============================= Precursor FDR =============================
1:34:35.679998 PROGRESS: Total precursors accumulated: 93,402
1:34:35.680080 PROGRESS: Target precursors: 92,478 (99.01%)
1:34:35.680140 PROGRESS: Decoy precursors: 924 (0.99%)
1:34:35.680192 PROGRESS: 
1:34:35.680238 PROGRESS: Precursor Summary:
1:34:35.704614 PROGRESS: Channel   0:	 0.050 FDR: 92,478; 0.010 FDR: 92,478; 0.001 FDR: 56,568
1:34:35.704861 PROGRESS: 
1:34:35.704924 PROGRESS: Protein Summary:
1:34:35.738435 PROGRESS: Channel   0:	 0.050 FDR: 13,588; 0.010 FDR: 13,588; 0.001 FDR: 9,180
1:34:35.738680 PROGRESS: =========================================================================
1:34:35.941343 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
1:34:36.105358 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
1:34:36.346859 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:34:36.854226 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
1:34:36.854383 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:34:36.854471 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
1:34:36.854639 INFO: Initializing TimingManager
1:34:36.855090 INFO: Initializing RawFileManager
1:34:50.350973 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.
1:34:50.359588 INFO: Determining DIA cycle
1:34:50.376967 INFO: Found cycle with start 0.00 min and length 300.
1:34:50.545378 INFO: RT (min)            : 0.0 - 26.9
1:34:50.545475 INFO: RT duration (sec)   : 1611.2
1:34:50.545515 INFO: RT duration (min)   : 26.9
1:34:50.545537 INFO: Cycle len (scans)   : 300
1:34:50.545557 INFO: Cycle len (sec)     : 1.65
1:34:50.545575 INFO: Number of cycles    : 977
1:34:50.545594 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:34:50.545622 INFO: Creating DIA data object took: 13.690440893173218
1:34:52.313741 INFO: Creating DIA data NG object took: 1.7679827213287354
1:34:53.691627 INFO: Initializing CalibrationManager
1:34:53.691919 INFO: Setting up calibration estimators ..
1:34:53.691981 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:34:53.692064 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'}' ..
1:34:53.692170 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:34:53.692233 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:34:53.692289 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}}' ..
1:34:53.692351 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:34:53.692398 INFO: Done setting up calibration estimators.
1:34:53.692608 INFO: Initializing OptimizationManager
1:34:53.692754 INFO: initial parameter: ms1_error = 30
1:34:53.692809 INFO: initial parameter: ms2_error = 30
1:34:53.692857 INFO: initial parameter: rt_error = 805.6004638671875
1:34:53.692901 INFO: initial parameter: mobility_error = 0.1
1:34:53.692944 INFO: initial parameter: num_candidates = 1
1:34:53.692985 INFO: initial parameter: fwhm_rt = 5
1:34:53.693027 INFO: initial parameter: fwhm_mobility = 0.01
1:34:53.693067 INFO: initial parameter: score_cutoff = 0
1:34:53.693107 INFO: initial parameter: classifier_version = -1
1:34:53.693182 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:34:53.693488 INFO: FDRManager: loading saved state not requested, will be initialized.
1:34:53.693521 INFO: Initializing FDRManager
1:34:53.693560 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:34:55.281779 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:34:56.217223 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:34:56.217799 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
1:34:56.217922 PROGRESS: Starting initial search for precursors.
1:34:56.218021 INFO: Starting optimization step 0.
1:34:56.218088 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:34:56.218155 INFO: Using rust extraction backend
1:34:56.218230 PROGRESS: Extracting batch of 1972 precursors
1:34:56.223899 INFO: === Search parameters used ===
1:34:56.224016 INFO: rt_error       : 805.6004638671875
1:34:56.224072 INFO: mobility_error : 0.1
1:34:56.224122 INFO: num_candidates : 1
1:34:56.224168 INFO: ms1_error      : 30
1:34:56.224210 INFO: ms2_error      : 30
1:34:56.224252 INFO: fwhm_rt        : 5
1:34:56.224293 INFO: quant_window   : 3
1:34:56.224334 INFO: ==============================================
1:34:56.257248 INFO: performing precursor FDR with 40 features
1:34:56.257325 INFO: Decoy channel: -1
1:34:56.257350 INFO: competitive: True
1:34:56.258708 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:56.260726 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
1:34:56.261825 INFO: Using random state 261857 for train-test-split
1:34:56.411188 INFO: Test AUC: 0.473
1:34:56.411266 INFO: Train AUC: 0.557
1:34:56.411298 INFO: AUC difference: 15.21%
1:34:56.411320 WARNING: AUC difference > 5%. This may indicate overfitting.
1:34:56.652886 INFO: Resetting torch num_threads to 24
1:34:56.654481 PROGRESS: === Extracted 1957 precursors and 9337 fragments ===
1:34:56.654874 INFO: === FDR correction performed with classifier version -1 ===
1:34:56.655360 PROGRESS: ============================= Precursor FDR =============================
1:34:56.655441 PROGRESS: Total precursors accumulated: 6
1:34:56.655513 PROGRESS: Target precursors: 6 (100.00%)
1:34:56.655563 PROGRESS: Decoy precursors: 0 (0.00%)
1:34:56.655608 PROGRESS: 
1:34:56.655651 PROGRESS: Precursor Summary:
1:34:56.656703 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:34:56.656786 PROGRESS: 
1:34:56.656840 PROGRESS: Protein Summary:
1:34:56.657979 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:34:56.658064 PROGRESS: =========================================================================
1:34:56.658279 INFO: Target number of precursors not reached yet.
1:34:56.742162 INFO: Starting optimization step 1.
1:34:56.742386 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:34:56.742465 INFO: Using rust extraction backend
1:34:56.742523 PROGRESS: Extracting batch of 3939 precursors
1:34:56.750880 INFO: === Search parameters used ===
1:34:56.751005 INFO: rt_error       : 805.6004638671875
1:34:56.751055 INFO: mobility_error : 0.1
1:34:56.751099 INFO: num_candidates : 1
1:34:56.751141 INFO: ms1_error      : 30
1:34:56.751181 INFO: ms2_error      : 30
1:34:56.751222 INFO: fwhm_rt        : 5
1:34:56.751260 INFO: quant_window   : 3
1:34:56.751300 INFO: ==============================================
1:34:56.811472 INFO: performing precursor FDR with 40 features
1:34:56.811565 INFO: Decoy channel: -1
1:34:56.811589 INFO: competitive: True
1:34:56.816100 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:56.818783 INFO: Estimating optimal hyperparameters - samples: 4,684, batch_size: 128, learning_rate: 1.77e-04
1:34:56.818864 INFO: Using random state 674562 for train-test-split
1:34:57.270510 INFO: Test AUC: 0.538
1:34:57.270602 INFO: Train AUC: 0.550
1:34:57.270630 INFO: AUC difference: 2.29%
1:34:57.513512 INFO: Resetting torch num_threads to 24
1:34:57.516508 PROGRESS: === Extracted 5856 precursors and 27913 fragments ===
1:34:57.516872 INFO: === FDR correction performed with classifier version -1 ===
1:34:57.517382 PROGRESS: ============================= Precursor FDR =============================
1:34:57.517465 PROGRESS: Total precursors accumulated: 19
1:34:57.517520 PROGRESS: Target precursors: 19 (100.00%)
1:34:57.517566 PROGRESS: Decoy precursors: 0 (0.00%)
1:34:57.517609 PROGRESS: 
1:34:57.517650 PROGRESS: Precursor Summary:
1:34:57.518693 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:34:57.518775 PROGRESS: 
1:34:57.518827 PROGRESS: Protein Summary:
1:34:57.519995 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:34:57.520082 PROGRESS: =========================================================================
1:34:57.520350 INFO: Target number of precursors not reached yet.
1:34:57.609559 INFO: Starting optimization step 2.
1:34:57.609801 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:34:57.609879 INFO: Using rust extraction backend
1:34:57.609936 PROGRESS: Extracting batch of 7870 precursors
1:34:57.624881 INFO: === Search parameters used ===
1:34:57.625027 INFO: rt_error       : 805.6004638671875
1:34:57.625077 INFO: mobility_error : 0.1
1:34:57.625121 INFO: num_candidates : 1
1:34:57.625162 INFO: ms1_error      : 30
1:34:57.625201 INFO: ms2_error      : 30
1:34:57.625241 INFO: fwhm_rt        : 5
1:34:57.625280 INFO: quant_window   : 3
1:34:57.625320 INFO: ==============================================
1:34:57.737717 INFO: performing precursor FDR with 40 features
1:34:57.737826 INFO: Decoy channel: -1
1:34:57.737849 INFO: competitive: True
1:34:57.743943 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:57.747766 INFO: Estimating optimal hyperparameters - samples: 10,923, batch_size: 128, learning_rate: 1.77e-04
1:34:57.747876 INFO: Using random state 342575 for train-test-split
1:34:58.841094 INFO: Test AUC: 0.547
1:34:58.841212 INFO: Train AUC: 0.585
1:34:58.841240 INFO: AUC difference: 6.45%
1:34:58.841261 WARNING: AUC difference > 5%. This may indicate overfitting.
1:34:59.868085 INFO: Resetting torch num_threads to 24
1:34:59.872410 PROGRESS: === Extracted 13654 precursors and 64748 fragments ===
1:34:59.872858 INFO: === FDR correction performed with classifier version -1 ===
1:34:59.873373 PROGRESS: ============================= Precursor FDR =============================
1:34:59.873455 PROGRESS: Total precursors accumulated: 1
1:34:59.873512 PROGRESS: Target precursors: 1 (100.00%)
1:34:59.873560 PROGRESS: Decoy precursors: 0 (0.00%)
1:34:59.873602 PROGRESS: 
1:34:59.873644 PROGRESS: Precursor Summary:
1:34:59.874674 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:34:59.874754 PROGRESS: 
1:34:59.874806 PROGRESS: Protein Summary:
1:34:59.875970 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:34:59.876056 PROGRESS: =========================================================================
1:34:59.876394 INFO: Target number of precursors not reached yet.
1:34:59.975853 INFO: Starting optimization step 3.
1:34:59.976102 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:34:59.976184 INFO: Using rust extraction backend
1:34:59.976244 PROGRESS: Extracting batch of 15774 precursors
1:35:00.006596 INFO: === Search parameters used ===
1:35:00.006806 INFO: rt_error       : 805.6004638671875
1:35:00.006859 INFO: mobility_error : 0.1
1:35:00.006903 INFO: num_candidates : 1
1:35:00.006944 INFO: ms1_error      : 30
1:35:00.006983 INFO: ms2_error      : 30
1:35:00.007034 INFO: fwhm_rt        : 5
1:35:00.007073 INFO: quant_window   : 3
1:35:00.007118 INFO: ==============================================
1:35:00.179679 INFO: performing precursor FDR with 40 features
1:35:00.179795 INFO: Decoy channel: -1
1:35:00.179819 INFO: competitive: True
1:35:00.190947 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:00.197921 INFO: Estimating optimal hyperparameters - samples: 23,428, batch_size: 128, learning_rate: 1.77e-04
1:35:00.198098 INFO: Using random state 494718 for train-test-split
1:35:02.552169 INFO: Test AUC: 0.563
1:35:02.552278 INFO: Train AUC: 0.602
1:35:02.552306 INFO: AUC difference: 6.43%
1:35:02.552327 WARNING: AUC difference > 5%. This may indicate overfitting.
1:35:02.803184 INFO: Resetting torch num_threads to 24
1:35:02.811159 PROGRESS: === Extracted 29286 precursors and 138452 fragments ===
1:35:02.811679 INFO: === FDR correction performed with classifier version -1 ===
1:35:02.812233 PROGRESS: ============================= Precursor FDR =============================
1:35:02.812321 PROGRESS: Total precursors accumulated: 1
1:35:02.812379 PROGRESS: Target precursors: 1 (100.00%)
1:35:02.812428 PROGRESS: Decoy precursors: 0 (0.00%)
1:35:02.812484 PROGRESS: 
1:35:02.812527 PROGRESS: Precursor Summary:
1:35:02.813562 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:35:02.813642 PROGRESS: 
1:35:02.813695 PROGRESS: Protein Summary:
1:35:02.814825 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:35:02.814906 PROGRESS: =========================================================================
1:35:02.815429 INFO: Target number of precursors not reached yet.
1:35:02.934872 INFO: Starting optimization step 4.
1:35:02.935140 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:35:02.935221 INFO: Using rust extraction backend
1:35:02.935285 PROGRESS: Extracting batch of 31503 precursors
1:35:02.990410 INFO: === Search parameters used ===
1:35:02.990657 INFO: rt_error       : 805.6004638671875
1:35:02.990710 INFO: mobility_error : 0.1
1:35:02.990755 INFO: num_candidates : 1
1:35:02.990798 INFO: ms1_error      : 30
1:35:02.990838 INFO: ms2_error      : 30
1:35:02.990876 INFO: fwhm_rt        : 5
1:35:02.990914 INFO: quant_window   : 3
1:35:02.990955 INFO: ==============================================
1:35:03.283194 INFO: performing precursor FDR with 40 features
1:35:03.283326 INFO: Decoy channel: -1
1:35:03.283351 INFO: competitive: True
1:35:03.305452 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:03.320174 INFO: Estimating optimal hyperparameters - samples: 48,353, batch_size: 198, learning_rate: 2.20e-04
1:35:03.320413 INFO: Using random state 256495 for train-test-split
1:35:06.888397 INFO: Test AUC: 0.582
1:35:06.888508 INFO: Train AUC: 0.610
1:35:06.888539 INFO: AUC difference: 4.50%
1:35:07.144430 INFO: Resetting torch num_threads to 24
1:35:07.155115 PROGRESS: === Extracted 60442 precursors and 286294 fragments ===
1:35:07.155826 INFO: === FDR correction performed with classifier version -1 ===
1:35:07.156450 PROGRESS: ============================= Precursor FDR =============================
1:35:07.156540 PROGRESS: Total precursors accumulated: 1
1:35:07.156600 PROGRESS: Target precursors: 1 (100.00%)
1:35:07.156651 PROGRESS: Decoy precursors: 0 (0.00%)
1:35:07.156697 PROGRESS: 
1:35:07.156742 PROGRESS: Precursor Summary:
1:35:07.157798 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:35:07.157882 PROGRESS: 
1:35:07.157937 PROGRESS: Protein Summary:
1:35:07.159112 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:35:07.159215 PROGRESS: =========================================================================
1:35:07.160252 INFO: Target number of precursors not reached yet.
1:35:07.321992 INFO: Starting optimization step 5.
1:35:07.322268 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:35:07.322352 INFO: Using rust extraction backend
1:35:07.322417 PROGRESS: Extracting batch of 63125 precursors
1:35:07.432007 INFO: === Search parameters used ===
1:35:07.432300 INFO: rt_error       : 805.6004638671875
1:35:07.432357 INFO: mobility_error : 0.1
1:35:07.432405 INFO: num_candidates : 1
1:35:07.432448 INFO: ms1_error      : 30
1:35:07.432508 INFO: ms2_error      : 30
1:35:07.432552 INFO: fwhm_rt        : 5
1:35:07.432593 INFO: quant_window   : 3
1:35:07.432634 INFO: ==============================================
1:35:07.986349 INFO: performing precursor FDR with 40 features
1:35:07.986467 INFO: Decoy channel: -1
1:35:07.986491 INFO: competitive: True
1:35:08.031394 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:08.064552 INFO: Estimating optimal hyperparameters - samples: 98,368, batch_size: 402, learning_rate: 3.13e-04
1:35:08.064874 INFO: Using random state 838965 for train-test-split
1:35:12.684639 INFO: Test AUC: 0.587
1:35:12.684755 INFO: Train AUC: 0.609
1:35:12.684788 INFO: AUC difference: 3.62%
1:35:12.970934 INFO: Resetting torch num_threads to 24
1:35:12.994667 PROGRESS: === Extracted 122961 precursors and 582938 fragments ===
1:35:12.995345 INFO: === FDR correction performed with classifier version -1 ===
1:35:12.995993 PROGRESS: ============================= Precursor FDR =============================
1:35:12.996088 PROGRESS: Total precursors accumulated: 326
1:35:12.996150 PROGRESS: Target precursors: 323 (99.08%)
1:35:12.996203 PROGRESS: Decoy precursors: 3 (0.92%)
1:35:12.996258 PROGRESS: 
1:35:12.996315 PROGRESS: Precursor Summary:
1:35:12.997339 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:     1
1:35:12.997427 PROGRESS: 
1:35:12.997483 PROGRESS: Protein Summary:
1:35:12.998648 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:     1
1:35:12.998736 PROGRESS: =========================================================================
1:35:13.001014 INFO: Target number of precursors not reached yet.
1:35:13.289433 INFO: Starting optimization step 6.
1:35:13.289707 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:35:13.289796 INFO: Using rust extraction backend
1:35:13.289860 PROGRESS: Extracting batch of 126147 precursors
1:35:13.507218 INFO: === Search parameters used ===
1:35:13.507505 INFO: rt_error       : 805.6004638671875
1:35:13.507569 INFO: mobility_error : 0.1
1:35:13.507619 INFO: num_candidates : 1
1:35:13.507665 INFO: ms1_error      : 30
1:35:13.507714 INFO: ms2_error      : 30
1:35:13.507773 INFO: fwhm_rt        : 5
1:35:13.507818 INFO: quant_window   : 3
1:35:13.507860 INFO: ==============================================
1:35:14.619812 INFO: performing precursor FDR with 40 features
1:35:14.619938 INFO: Decoy channel: -1
1:35:14.619964 INFO: competitive: True
1:35:14.717180 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:14.802763 INFO: Estimating optimal hyperparameters - samples: 198,220, batch_size: 811, learning_rate: 4.45e-04
1:35:14.803175 INFO: Using random state 726699 for train-test-split
1:35:21.033184 INFO: Test AUC: 0.588
1:35:21.033306 INFO: Train AUC: 0.606
1:35:21.033337 INFO: AUC difference: 3.01%
1:35:21.358865 INFO: Resetting torch num_threads to 24
1:35:21.401246 PROGRESS: === Extracted 247775 precursors and 1172804 fragments ===
1:35:21.401954 INFO: === FDR correction performed with classifier version -1 ===
1:35:21.402721 PROGRESS: ============================= Precursor FDR =============================
1:35:21.402809 PROGRESS: Total precursors accumulated: 872
1:35:21.402869 PROGRESS: Target precursors: 864 (99.08%)
1:35:21.402920 PROGRESS: Decoy precursors: 8 (0.92%)
1:35:21.402966 PROGRESS: 
1:35:21.403009 PROGRESS: Precursor Summary:
1:35:21.404164 PROGRESS: Channel   0:	 0.050 FDR:   864; 0.010 FDR:   864; 0.001 FDR:     3
1:35:21.404255 PROGRESS: 
1:35:21.404310 PROGRESS: Protein Summary:
1:35:21.405682 PROGRESS: Channel   0:	 0.050 FDR:   763; 0.010 FDR:   763; 0.001 FDR:     3
1:35:21.405771 PROGRESS: =========================================================================
1:35:21.409979 INFO: Target number of precursors not reached yet.
1:35:21.825618 INFO: Starting optimization step 7.
1:35:21.825905 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:35:21.825990 INFO: Using rust extraction backend
1:35:21.826054 PROGRESS: Extracting batch of 252313 precursors
1:35:22.255893 INFO: === Search parameters used ===
1:35:22.256170 INFO: rt_error       : 805.6004638671875
1:35:22.256227 INFO: mobility_error : 0.1
1:35:22.256277 INFO: num_candidates : 1
1:35:22.256321 INFO: ms1_error      : 30
1:35:22.256374 INFO: ms2_error      : 30
1:35:22.256418 INFO: fwhm_rt        : 5
1:35:22.256459 INFO: quant_window   : 3
1:35:22.256498 INFO: ==============================================
1:35:24.360298 INFO: performing precursor FDR with 40 features
1:35:24.360431 INFO: Decoy channel: -1
1:35:24.360462 INFO: competitive: True
1:35:24.558051 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:24.746643 INFO: Estimating optimal hyperparameters - samples: 398,041, batch_size: 1,630, learning_rate: 6.31e-04
1:35:24.747286 INFO: Using random state 753356 for train-test-split
1:35:34.683771 INFO: Test AUC: 0.594
1:35:34.683926 INFO: Train AUC: 0.606
1:35:34.683961 INFO: AUC difference: 1.89%
1:35:35.090065 INFO: Resetting torch num_threads to 24
1:35:35.176616 PROGRESS: === Extracted 497552 precursors and 2354608 fragments ===
1:35:35.177363 INFO: === FDR correction performed with classifier version -1 ===
1:35:35.178345 PROGRESS: ============================= Precursor FDR =============================
1:35:35.178437 PROGRESS: Total precursors accumulated: 1,922
1:35:35.178498 PROGRESS: Target precursors: 1,903 (99.01%)
1:35:35.178550 PROGRESS: Decoy precursors: 19 (0.99%)
1:35:35.178598 PROGRESS: 
1:35:35.178645 PROGRESS: Precursor Summary:
1:35:35.180170 PROGRESS: Channel   0:	 0.050 FDR: 1,903; 0.010 FDR: 1,903; 0.001 FDR: 1,519
1:35:35.180277 PROGRESS: 
1:35:35.180335 PROGRESS: Protein Summary:
1:35:35.182315 PROGRESS: Channel   0:	 0.050 FDR: 1,502; 0.010 FDR: 1,502; 0.001 FDR: 1,210
1:35:35.182411 PROGRESS: =========================================================================
1:35:35.189761 INFO: Target number of precursors reached.
1:35:35.442514 INFO: fragments_df: keeping 5000 of 2354608 [sum(precursor_idx_mask)=20008 sum(mass_error_mask)=2354608 stop_rank=5000
1:35:36.130404 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:36.416375 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:37.130456 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:35:37.130926 INFO: Using score_cutoff 12.535589266204834 (fac=0.99, q=1)
1:35:37.131236 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:35:37.131311 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:35:37.131363 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.535589266204834
1:35:37.131415 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:37.440547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:38.116562 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:35:38.116803 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:35:38.116909 INFO: Starting optimization step 8.
1:35:38.116970 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:35:38.117037 INFO: Using rust extraction backend
1:35:38.117096 PROGRESS: Extracting batch of 502643 precursors
1:35:38.973050 INFO: === Search parameters used ===
1:35:38.973343 INFO: rt_error       : 805.6004638671875
1:35:38.973406 INFO: mobility_error : 0.1
1:35:38.973453 INFO: num_candidates : 3
1:35:38.973495 INFO: ms1_error      : 30
1:35:38.973536 INFO: ms2_error      : 30
1:35:38.973576 INFO: fwhm_rt        : 3.0
1:35:38.973633 INFO: quant_window   : 3
1:35:38.973674 INFO: ==============================================
1:35:46.428595 INFO: performing precursor FDR with 40 features
1:35:46.428727 INFO: Decoy channel: -1
1:35:46.428753 INFO: competitive: True
1:35:46.826160 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:47.468321 INFO: Estimating optimal hyperparameters - samples: 1,194,556, batch_size: 4,096, learning_rate: 1.00e-03
1:35:47.470666 INFO: Using random state 602197 for train-test-split
1:36:09.626063 INFO: Test AUC: 0.600
1:36:09.626214 INFO: Train AUC: 0.606
1:36:09.626248 INFO: AUC difference: 0.89%
1:36:10.355290 INFO: Resetting torch num_threads to 24
1:36:10.421660 PROGRESS: === Extracted 1493196 precursors and 6912230 fragments ===
1:36:10.422198 INFO: === FDR correction performed with classifier version 7 ===
1:36:10.423155 PROGRESS: ============================= Precursor FDR =============================
1:36:10.423261 PROGRESS: Total precursors accumulated: 2,334
1:36:10.423325 PROGRESS: Target precursors: 2,311 (99.01%)
1:36:10.423379 PROGRESS: Decoy precursors: 23 (0.99%)
1:36:10.423429 PROGRESS: 
1:36:10.423499 PROGRESS: Precursor Summary:
1:36:10.425196 PROGRESS: Channel   0:	 0.050 FDR: 2,311; 0.010 FDR: 2,311; 0.001 FDR: 1,335
1:36:10.425304 PROGRESS: 
1:36:10.425361 PROGRESS: Protein Summary:
1:36:10.427446 PROGRESS: Channel   0:	 0.050 FDR: 1,781; 0.010 FDR: 1,781; 0.001 FDR: 1,060
1:36:10.427556 PROGRESS: =========================================================================
1:36:10.459283 INFO: Target number of precursors reached.
1:36:11.213392 INFO: fragments_df: keeping 5000 of 6912230 [sum(precursor_idx_mask)=50564 sum(mass_error_mask)=6912230 stop_rank=5000
1:36:11.791598 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:12.130654 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:12.844800 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:12.845273 INFO: Using score_cutoff 12.673598047256469 (fac=0.99, q=1)
1:36:12.845594 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:12.845677 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:12.845734 INFO: Updating optimization_manager: score_cutoff        : 12.535589266204834 -> 12.673598047256469
1:36:12.845793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:13.007058 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:13.377388 INFO: === checking if optimization conditions were reached ===
1:36:13.380092 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
1:36:13.380265 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:36:13.380347 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:36:13.380445 INFO: ==============================================
1:36:13.380519 INFO: Starting optimization step 9.
1:36:13.380585 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:13.380652 INFO: Using rust extraction backend
1:36:13.380716 PROGRESS: Extracting batch of 250330 precursors
1:36:13.806649 INFO: === Search parameters used ===
1:36:13.806928 INFO: rt_error       : 805.6004638671875
1:36:13.806984 INFO: mobility_error : 0.1
1:36:13.807032 INFO: num_candidates : 3
1:36:13.807076 INFO: ms1_error      : 30
1:36:13.807119 INFO: ms2_error      : 10.0
1:36:13.807179 INFO: fwhm_rt        : 3.0
1:36:13.807225 INFO: quant_window   : 3
1:36:13.807266 INFO: ==============================================
1:36:17.215279 INFO: performing precursor FDR with 40 features
1:36:17.215401 INFO: Decoy channel: -1
1:36:17.215428 INFO: competitive: True
1:36:17.405203 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:17.709802 INFO: Estimating optimal hyperparameters - samples: 599,391, batch_size: 2,455, learning_rate: 7.74e-04
1:36:17.710837 INFO: Using random state 278833 for train-test-split
1:36:30.374617 INFO: Test AUC: 0.606
1:36:30.374775 INFO: Train AUC: 0.614
1:36:30.374811 INFO: AUC difference: 1.28%
1:36:30.854126 INFO: Resetting torch num_threads to 24
1:36:30.880610 PROGRESS: === Extracted 749239 precursors and 4025260 fragments ===
1:36:30.881118 INFO: === FDR correction performed with classifier version 8 ===
1:36:30.881826 PROGRESS: ============================= Precursor FDR =============================
1:36:30.881919 PROGRESS: Total precursors accumulated: 1,781
1:36:30.881982 PROGRESS: Target precursors: 1,764 (99.05%)
1:36:30.882035 PROGRESS: Decoy precursors: 17 (0.95%)
1:36:30.882094 PROGRESS: 
1:36:30.882139 PROGRESS: Precursor Summary:
1:36:30.883567 PROGRESS: Channel   0:	 0.050 FDR: 1,764; 0.010 FDR: 1,764; 0.001 FDR: 1,245
1:36:30.883662 PROGRESS: 
1:36:30.883720 PROGRESS: Protein Summary:
1:36:30.885570 PROGRESS: Channel   0:	 0.050 FDR: 1,484; 0.010 FDR: 1,484; 0.001 FDR: 1,071
1:36:30.885665 PROGRESS: =========================================================================
1:36:30.898832 INFO: Target number of precursors reached.
1:36:31.339315 INFO: fragments_df: keeping 5000 of 4025260 [sum(precursor_idx_mask)=41521 sum(mass_error_mask)=4025260 stop_rank=5000
1:36:31.768927 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:31.991355 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:32.644148 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:32.644622 INFO: Using score_cutoff 10.306013060474395 (fac=0.99, q=1)
1:36:32.644935 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:32.645012 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:32.645066 INFO: Updating optimization_manager: score_cutoff        : 12.673598047256469 -> 10.306013060474395
1:36:32.645122 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:32.796952 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:33.141522 INFO: === checking if optimization conditions were reached ===
1:36:33.143784 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:36:33.143943 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:36:33.144013 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:36:33.144084 INFO: ==============================================
1:36:33.144159 INFO: Starting optimization step 10.
1:36:33.144224 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:33.144301 INFO: Using rust extraction backend
1:36:33.144373 PROGRESS: Extracting batch of 250330 precursors
1:36:33.570640 INFO: === Search parameters used ===
1:36:33.570927 INFO: rt_error       : 805.6004638671875
1:36:33.570990 INFO: mobility_error : 0.1
1:36:33.571041 INFO: num_candidates : 3
1:36:33.571099 INFO: ms1_error      : 30
1:36:33.571146 INFO: ms2_error      : 10.0
1:36:33.571194 INFO: fwhm_rt        : 3.0
1:36:33.571236 INFO: quant_window   : 3
1:36:33.571275 INFO: ==============================================
1:36:36.837827 INFO: performing precursor FDR with 40 features
1:36:36.837952 INFO: Decoy channel: -1
1:36:36.837978 INFO: competitive: True
1:36:37.027578 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:37.317261 INFO: Estimating optimal hyperparameters - samples: 599,374, batch_size: 2,455, learning_rate: 7.74e-04
1:36:37.318342 INFO: Using random state 651555 for train-test-split
1:36:50.063398 INFO: Test AUC: 0.614
1:36:50.063556 INFO: Train AUC: 0.617
1:36:50.063591 INFO: AUC difference: 0.50%
1:36:50.542229 INFO: Resetting torch num_threads to 24
1:36:50.569335 PROGRESS: === Extracted 749218 precursors and 4024619 fragments ===
1:36:50.569813 INFO: === FDR correction performed with classifier version 9 ===
1:36:50.570540 PROGRESS: ============================= Precursor FDR =============================
1:36:50.570643 PROGRESS: Total precursors accumulated: 1,924
1:36:50.570704 PROGRESS: Target precursors: 1,905 (99.01%)
1:36:50.570756 PROGRESS: Decoy precursors: 19 (0.99%)
1:36:50.570802 PROGRESS: 
1:36:50.570849 PROGRESS: Precursor Summary:
1:36:50.572282 PROGRESS: Channel   0:	 0.050 FDR: 1,905; 0.010 FDR: 1,905; 0.001 FDR: 1,189
1:36:50.572375 PROGRESS: 
1:36:50.572432 PROGRESS: Protein Summary:
1:36:50.574308 PROGRESS: Channel   0:	 0.050 FDR: 1,607; 0.010 FDR: 1,607; 0.001 FDR: 1,026
1:36:50.574399 PROGRESS: =========================================================================
1:36:50.587914 INFO: Target number of precursors reached.
1:36:51.025390 INFO: fragments_df: keeping 5000 of 4024619 [sum(precursor_idx_mask)=44366 sum(mass_error_mask)=4024619 stop_rank=5000
1:36:51.436131 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:51.690833 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:52.342151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:52.342596 INFO: Using score_cutoff 10.18675633392334 (fac=0.99, q=1)
1:36:52.342897 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:52.342972 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:52.343025 INFO: Updating optimization_manager: score_cutoff        : 10.306013060474395 -> 10.18675633392334
1:36:52.343076 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:52.491162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:52.824588 INFO: === checking if optimization conditions were reached ===
1:36:52.827248 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:36:52.827412 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:36:52.827510 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:36:52.827588 INFO: ==============================================
1:36:52.827671 INFO: Starting optimization step 11.
1:36:52.827742 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:52.827815 INFO: Using rust extraction backend
1:36:52.827888 PROGRESS: Extracting batch of 250330 precursors
1:36:53.257636 INFO: === Search parameters used ===
1:36:53.257910 INFO: rt_error       : 805.6004638671875
1:36:53.257968 INFO: mobility_error : 0.1
1:36:53.258029 INFO: num_candidates : 3
1:36:53.258079 INFO: ms1_error      : 30
1:36:53.258123 INFO: ms2_error      : 10.0
1:36:53.258166 INFO: fwhm_rt        : 3.0
1:36:53.258207 INFO: quant_window   : 3
1:36:53.258251 INFO: ==============================================
1:36:56.544519 INFO: performing precursor FDR with 40 features
1:36:56.544643 INFO: Decoy channel: -1
1:36:56.544670 INFO: competitive: True
1:36:56.734840 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:57.025800 INFO: Estimating optimal hyperparameters - samples: 599,382, batch_size: 2,455, learning_rate: 7.74e-04
1:36:57.026890 INFO: Using random state 63600 for train-test-split
1:37:09.659146 INFO: Test AUC: 0.607
1:37:09.659282 INFO: Train AUC: 0.617
1:37:09.659329 INFO: AUC difference: 1.66%
1:37:10.133858 INFO: Resetting torch num_threads to 24
1:37:10.160746 PROGRESS: === Extracted 749228 precursors and 4024348 fragments ===
1:37:10.161222 INFO: === FDR correction performed with classifier version 10 ===
1:37:10.161906 PROGRESS: ============================= Precursor FDR =============================
1:37:10.161997 PROGRESS: Total precursors accumulated: 1,778
1:37:10.162058 PROGRESS: Target precursors: 1,761 (99.04%)
1:37:10.162110 PROGRESS: Decoy precursors: 17 (0.96%)
1:37:10.162156 PROGRESS: 
1:37:10.162202 PROGRESS: Precursor Summary:
1:37:10.163637 PROGRESS: Channel   0:	 0.050 FDR: 1,761; 0.010 FDR: 1,761; 0.001 FDR: 1,374
1:37:10.163745 PROGRESS: 
1:37:10.163806 PROGRESS: Protein Summary:
1:37:10.165682 PROGRESS: Channel   0:	 0.050 FDR: 1,495; 0.010 FDR: 1,495; 0.001 FDR: 1,176
1:37:10.165772 PROGRESS: =========================================================================
1:37:10.178915 INFO: Target number of precursors reached.
1:37:10.622204 INFO: fragments_df: keeping 5000 of 4024348 [sum(precursor_idx_mask)=41169 sum(mass_error_mask)=4024348 stop_rank=5000
1:37:11.033727 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:11.271009 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:11.926783 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:11.927252 INFO: Using score_cutoff 10.17895790863037 (fac=0.99, q=1)
1:37:11.927569 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:11.927652 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:11.927709 INFO: Updating optimization_manager: score_cutoff        : 10.18675633392334 -> 10.17895790863037
1:37:11.927765 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:12.076900 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:12.420413 INFO: === checking if optimization conditions were reached ===
1:37:12.422590 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:37:12.422691 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:37:12.422758 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:37:12.422818 INFO: ==============================================
1:37:12.422884 INFO: Starting optimization step 12.
1:37:12.422945 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:37:12.423006 INFO: Using rust extraction backend
1:37:12.423066 PROGRESS: Extracting batch of 250330 precursors
1:37:12.849426 INFO: === Search parameters used ===
1:37:12.849713 INFO: rt_error       : 805.6004638671875
1:37:12.849772 INFO: mobility_error : 0.1
1:37:12.849821 INFO: num_candidates : 3
1:37:12.849866 INFO: ms1_error      : 30
1:37:12.849909 INFO: ms2_error      : 10.0
1:37:12.849952 INFO: fwhm_rt        : 3.0
1:37:12.849993 INFO: quant_window   : 3
1:37:12.850034 INFO: ==============================================
1:37:16.118306 INFO: performing precursor FDR with 40 features
1:37:16.118434 INFO: Decoy channel: -1
1:37:16.118460 INFO: competitive: True
1:37:16.298572 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:16.585318 INFO: Estimating optimal hyperparameters - samples: 599,366, batch_size: 2,455, learning_rate: 7.74e-04
1:37:16.586323 INFO: Using random state 230827 for train-test-split
1:37:28.901464 INFO: Test AUC: 0.613
1:37:28.901613 INFO: Train AUC: 0.623
1:37:28.901646 INFO: AUC difference: 1.50%
1:37:29.386935 INFO: Resetting torch num_threads to 24
1:37:29.414612 PROGRESS: === Extracted 749208 precursors and 4024183 fragments ===
1:37:29.415105 INFO: === FDR correction performed with classifier version 11 ===
1:37:29.415847 PROGRESS: ============================= Precursor FDR =============================
1:37:29.415940 PROGRESS: Total precursors accumulated: 2,077
1:37:29.416002 PROGRESS: Target precursors: 2,057 (99.04%)
1:37:29.416054 PROGRESS: Decoy precursors: 20 (0.96%)
1:37:29.416101 PROGRESS: 
1:37:29.416147 PROGRESS: Precursor Summary:
1:37:29.417649 PROGRESS: Channel   0:	 0.050 FDR: 2,057; 0.010 FDR: 2,057; 0.001 FDR: 1,468
1:37:29.417744 PROGRESS: 
1:37:29.417803 PROGRESS: Protein Summary:
1:37:29.419806 PROGRESS: Channel   0:	 0.050 FDR: 1,733; 0.010 FDR: 1,733; 0.001 FDR: 1,249
1:37:29.419901 PROGRESS: =========================================================================
1:37:29.432684 INFO: Target number of precursors reached.
1:37:29.862602 INFO: fragments_df: keeping 5000 of 4024183 [sum(precursor_idx_mask)=47173 sum(mass_error_mask)=4024183 stop_rank=5000
1:37:30.119701 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:30.375943 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:31.025797 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:31.026253 INFO: Using score_cutoff 9.452112464904785 (fac=0.99, q=1)
1:37:31.026556 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:31.026634 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:31.026689 INFO: Updating optimization_manager: score_cutoff        : 10.17895790863037 -> 9.452112464904785
1:37:31.026743 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:31.101558 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:31.271054 INFO: === checking if optimization conditions were reached ===
1:37:31.273232 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:37:31.273337 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:37:31.273402 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:37:31.273459 INFO: ==============================================
1:37:31.273537 PROGRESS: Optimization finished for ms2_error.
1:37:31.514748 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:31.590572 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:31.757990 INFO: Starting optimization step 0.
1:37:31.758252 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:37:31.758333 INFO: Using rust extraction backend
1:37:31.758396 PROGRESS: Extracting batch of 124183 precursors
1:37:31.972043 INFO: === Search parameters used ===
1:37:31.972317 INFO: rt_error       : 805.6004638671875
1:37:31.972375 INFO: mobility_error : 0.1
1:37:31.972426 INFO: num_candidates : 3
1:37:31.972471 INFO: ms1_error      : 30
1:37:31.972513 INFO: ms2_error      : 10.0
1:37:31.972554 INFO: fwhm_rt        : 3.0
1:37:31.972595 INFO: quant_window   : 3
1:37:31.972635 INFO: ==============================================
1:37:33.610233 INFO: performing precursor FDR with 40 features
1:37:33.610363 INFO: Decoy channel: -1
1:37:33.610392 INFO: competitive: True
1:37:33.697834 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:33.821666 INFO: Estimating optimal hyperparameters - samples: 297,343, batch_size: 1,217, learning_rate: 5.45e-04
1:37:33.822248 INFO: Using random state 337299 for train-test-split
1:37:41.486623 INFO: Test AUC: 0.610
1:37:41.486746 INFO: Train AUC: 0.628
1:37:41.486778 INFO: AUC difference: 2.83%
1:37:41.857140 INFO: Resetting torch num_threads to 24
1:37:41.870428 PROGRESS: === Extracted 371679 precursors and 1998083 fragments ===
1:37:41.870853 INFO: === FDR correction performed with classifier version 12 ===
1:37:41.871470 PROGRESS: ============================= Precursor FDR =============================
1:37:41.871570 PROGRESS: Total precursors accumulated: 1,018
1:37:41.871633 PROGRESS: Target precursors: 1,008 (99.02%)
1:37:41.871684 PROGRESS: Decoy precursors: 10 (0.98%)
1:37:41.871731 PROGRESS: 
1:37:41.871776 PROGRESS: Precursor Summary:
1:37:41.872958 PROGRESS: Channel   0:	 0.050 FDR: 1,008; 0.010 FDR: 1,008; 0.001 FDR:   431
1:37:41.873062 PROGRESS: 
1:37:41.873119 PROGRESS: Protein Summary:
1:37:41.874574 PROGRESS: Channel   0:	 0.050 FDR:   920; 0.010 FDR:   920; 0.001 FDR:   402
1:37:41.874662 PROGRESS: =========================================================================
1:37:41.880409 INFO: Target number of precursors reached.
1:37:42.102449 INFO: fragments_df: keeping 5000 of 1998083 [sum(precursor_idx_mask)=23477 sum(mass_error_mask)=1998083 stop_rank=5000
1:37:42.350275 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:42.544074 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:43.261150 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:43.261597 INFO: Using score_cutoff 10.670861845493317 (fac=0.99, q=1)
1:37:43.261900 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:43.261980 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:43.262038 INFO: Updating optimization_manager: score_cutoff        : 9.452112464904785 -> 10.670861845493317
1:37:43.262095 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:43.336460 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:43.515608 INFO: === checking if optimization conditions were reached ===
1:37:43.516849 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:37:43.519232 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 580.9539923812374
1:37:43.519340 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 580.9540.
1:37:43.519421 INFO: ==============================================
1:37:43.519508 INFO: Starting optimization step 1.
1:37:43.519573 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:37:43.519636 INFO: Using rust extraction backend
1:37:43.519696 PROGRESS: Extracting batch of 124183 precursors
1:37:43.733417 INFO: === Search parameters used ===
1:37:43.733702 INFO: rt_error       : 580.9539923812374
1:37:43.733761 INFO: mobility_error : 0.1
1:37:43.733810 INFO: num_candidates : 3
1:37:43.733858 INFO: ms1_error      : 30
1:37:43.733902 INFO: ms2_error      : 10.0
1:37:43.733947 INFO: fwhm_rt        : 3.0
1:37:43.733992 INFO: quant_window   : 3
1:37:43.734034 INFO: ==============================================
1:37:45.265818 INFO: performing precursor FDR with 40 features
1:37:45.265948 INFO: Decoy channel: -1
1:37:45.265974 INFO: competitive: True
1:37:45.355144 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:45.478662 INFO: Estimating optimal hyperparameters - samples: 297,176, batch_size: 1,217, learning_rate: 5.45e-04
1:37:45.479241 INFO: Using random state 337299 for train-test-split
1:37:53.385282 INFO: Test AUC: 0.614
1:37:53.385412 INFO: Train AUC: 0.624
1:37:53.385445 INFO: AUC difference: 1.71%
1:37:53.769829 INFO: Resetting torch num_threads to 24
1:37:53.784312 PROGRESS: === Extracted 371470 precursors and 1985999 fragments ===
1:37:53.784753 INFO: === FDR correction performed with classifier version 12 ===
1:37:53.785336 PROGRESS: ============================= Precursor FDR =============================
1:37:53.785423 PROGRESS: Total precursors accumulated: 979
1:37:53.785481 PROGRESS: Target precursors: 970 (99.08%)
1:37:53.785533 PROGRESS: Decoy precursors: 9 (0.92%)
1:37:53.785583 PROGRESS: 
1:37:53.785629 PROGRESS: Precursor Summary:
1:37:53.786845 PROGRESS: Channel   0:	 0.050 FDR:   970; 0.010 FDR:   970; 0.001 FDR:   767
1:37:53.786933 PROGRESS: 
1:37:53.786988 PROGRESS: Protein Summary:
1:37:53.788516 PROGRESS: Channel   0:	 0.050 FDR:   887; 0.010 FDR:   887; 0.001 FDR:   700
1:37:53.788611 PROGRESS: =========================================================================
1:37:53.794448 INFO: Target number of precursors not reached yet.
1:37:54.038800 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:54.115234 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:54.283472 INFO: === skipping optimization until target number of precursors are found ===
1:37:54.283738 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:37:54.283838 INFO: Starting optimization step 2.
1:37:54.283903 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:37:54.283970 INFO: Using rust extraction backend
1:37:54.284028 PROGRESS: Extracting batch of 126147 precursors
1:37:54.501444 INFO: === Search parameters used ===
1:37:54.501731 INFO: rt_error       : 580.9539923812374
1:37:54.501789 INFO: mobility_error : 0.1
1:37:54.501840 INFO: num_candidates : 3
1:37:54.501885 INFO: ms1_error      : 30
1:37:54.501928 INFO: ms2_error      : 10.0
1:37:54.501983 INFO: fwhm_rt        : 3.0
1:37:54.502026 INFO: quant_window   : 3
1:37:54.502066 INFO: ==============================================
1:37:56.146664 INFO: performing precursor FDR with 40 features
1:37:56.146790 INFO: Decoy channel: -1
1:37:56.146816 INFO: competitive: True
1:37:56.393610 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:56.671024 INFO: Estimating optimal hyperparameters - samples: 599,044, batch_size: 2,453, learning_rate: 7.74e-04
1:37:56.671918 INFO: Using random state 337299 for train-test-split
1:38:09.839325 INFO: Test AUC: 0.611
1:38:09.839475 INFO: Train AUC: 0.623
1:38:09.839514 INFO: AUC difference: 1.93%
1:38:10.322967 INFO: Resetting torch num_threads to 24
1:38:10.420767 PROGRESS: === Extracted 748806 precursors and 3999732 fragments ===
1:38:10.421489 INFO: === FDR correction performed with classifier version 12 ===
1:38:10.422501 PROGRESS: ============================= Precursor FDR =============================
1:38:10.422596 PROGRESS: Total precursors accumulated: 1,979
1:38:10.422658 PROGRESS: Target precursors: 1,960 (99.04%)
1:38:10.422710 PROGRESS: Decoy precursors: 19 (0.96%)
1:38:10.422758 PROGRESS: 
1:38:10.422803 PROGRESS: Precursor Summary:
1:38:10.424327 PROGRESS: Channel   0:	 0.050 FDR: 1,960; 0.010 FDR: 1,960; 0.001 FDR: 1,383
1:38:10.424424 PROGRESS: 
1:38:10.424481 PROGRESS: Protein Summary:
1:38:10.426451 PROGRESS: Channel   0:	 0.050 FDR: 1,666; 0.010 FDR: 1,666; 0.001 FDR: 1,194
1:38:10.426545 PROGRESS: =========================================================================
1:38:10.435395 INFO: Target number of precursors reached.
1:38:10.886579 INFO: fragments_df: keeping 5000 of 3999732 [sum(precursor_idx_mask)=44191 sum(mass_error_mask)=3999732 stop_rank=5000
1:38:11.297631 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:11.583333 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:12.298667 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:12.299131 INFO: Using score_cutoff 7.699382745409012 (fac=0.99, q=1)
1:38:12.299444 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:12.299539 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:12.299594 INFO: Updating optimization_manager: score_cutoff        : 10.670861845493317 -> 7.699382745409012
1:38:12.299650 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:12.449237 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:12.797455 INFO: === checking if optimization conditions were reached ===
1:38:12.797737 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:38:12.800765 INFO: Updating optimization_manager: rt_error            : 580.9539923812374 -> 778.3491401673358
1:38:12.800875 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 778.3491.
1:38:12.800942 INFO: ==============================================
1:38:12.801014 INFO: Starting optimization step 3.
1:38:12.801076 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:12.801139 INFO: Using rust extraction backend
1:38:12.801198 PROGRESS: Extracting batch of 250330 precursors
1:38:13.227754 INFO: === Search parameters used ===
1:38:13.228035 INFO: rt_error       : 778.3491401673358
1:38:13.228095 INFO: mobility_error : 0.1
1:38:13.228143 INFO: num_candidates : 3
1:38:13.228202 INFO: ms1_error      : 30
1:38:13.228247 INFO: ms2_error      : 10.0
1:38:13.228291 INFO: fwhm_rt        : 3.0
1:38:13.228332 INFO: quant_window   : 3
1:38:13.228373 INFO: ==============================================
1:38:16.490776 INFO: performing precursor FDR with 40 features
1:38:16.490903 INFO: Decoy channel: -1
1:38:16.490942 INFO: competitive: True
1:38:16.672077 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:16.964199 INFO: Estimating optimal hyperparameters - samples: 599,388, batch_size: 2,455, learning_rate: 7.74e-04
1:38:16.965317 INFO: Using random state 337299 for train-test-split
1:38:29.966715 INFO: Test AUC: 0.615
1:38:29.966841 INFO: Train AUC: 0.625
1:38:29.966875 INFO: AUC difference: 1.56%
1:38:30.441409 INFO: Resetting torch num_threads to 24
1:38:30.468083 PROGRESS: === Extracted 749236 precursors and 4024643 fragments ===
1:38:30.468561 INFO: === FDR correction performed with classifier version 12 ===
1:38:30.469282 PROGRESS: ============================= Precursor FDR =============================
1:38:30.469372 PROGRESS: Total precursors accumulated: 1,997
1:38:30.469432 PROGRESS: Target precursors: 1,978 (99.05%)
1:38:30.469484 PROGRESS: Decoy precursors: 19 (0.95%)
1:38:30.469533 PROGRESS: 
1:38:30.469578 PROGRESS: Precursor Summary:
1:38:30.471049 PROGRESS: Channel   0:	 0.050 FDR: 1,978; 0.010 FDR: 1,978; 0.001 FDR: 1,436
1:38:30.471139 PROGRESS: 
1:38:30.471201 PROGRESS: Protein Summary:
1:38:30.473211 PROGRESS: Channel   0:	 0.050 FDR: 1,682; 0.010 FDR: 1,682; 0.001 FDR: 1,229
1:38:30.473306 PROGRESS: =========================================================================
1:38:30.486145 INFO: Target number of precursors reached.
1:38:30.919864 INFO: fragments_df: keeping 5000 of 4024643 [sum(precursor_idx_mask)=45164 sum(mass_error_mask)=4024643 stop_rank=5000
1:38:31.327233 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:31.613868 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:32.325560 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:32.326028 INFO: Using score_cutoff 7.8024349319458 (fac=0.99, q=1)
1:38:32.326341 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:32.326419 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:32.326476 INFO: Updating optimization_manager: score_cutoff        : 7.699382745409012 -> 7.8024349319458
1:38:32.326533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:32.475912 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:32.817230 INFO: === checking if optimization conditions were reached ===
1:38:32.817513 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:38:32.820663 INFO: Updating optimization_manager: rt_error            : 778.3491401673358 -> 976.5710276151747
1:38:32.820771 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 976.5710.
1:38:32.820837 INFO: ==============================================
1:38:32.820906 INFO: Starting optimization step 4.
1:38:32.820966 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:32.821031 INFO: Using rust extraction backend
1:38:32.821090 PROGRESS: Extracting batch of 250330 precursors
1:38:33.247663 INFO: === Search parameters used ===
1:38:33.250019 INFO: rt_error       : 976.5710276151747
1:38:33.250096 INFO: mobility_error : 0.1
1:38:33.250147 INFO: num_candidates : 3
1:38:33.250194 INFO: ms1_error      : 30
1:38:33.250239 INFO: ms2_error      : 10.0
1:38:33.250287 INFO: fwhm_rt        : 3.0
1:38:33.250331 INFO: quant_window   : 3
1:38:33.250373 INFO: ==============================================
1:38:36.708365 INFO: performing precursor FDR with 40 features
1:38:36.708494 INFO: Decoy channel: -1
1:38:36.708521 INFO: competitive: True
1:38:36.891520 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:37.178681 INFO: Estimating optimal hyperparameters - samples: 599,357, batch_size: 2,454, learning_rate: 7.74e-04
1:38:37.179885 INFO: Using random state 337299 for train-test-split
1:38:50.170362 INFO: Test AUC: 0.613
1:38:50.170490 INFO: Train AUC: 0.623
1:38:50.170525 INFO: AUC difference: 1.74%
1:38:51.543252 INFO: Resetting torch num_threads to 24
1:38:51.570313 PROGRESS: === Extracted 749197 precursors and 4024247 fragments ===
1:38:51.570856 INFO: === FDR correction performed with classifier version 12 ===
1:38:51.571626 PROGRESS: ============================= Precursor FDR =============================
1:38:51.571722 PROGRESS: Total precursors accumulated: 1,926
1:38:51.571783 PROGRESS: Target precursors: 1,907 (99.01%)
1:38:51.571836 PROGRESS: Decoy precursors: 19 (0.99%)
1:38:51.571884 PROGRESS: 
1:38:51.571929 PROGRESS: Precursor Summary:
1:38:51.573419 PROGRESS: Channel   0:	 0.050 FDR: 1,907; 0.010 FDR: 1,907; 0.001 FDR: 1,280
1:38:51.573510 PROGRESS: 
1:38:51.573565 PROGRESS: Protein Summary:
1:38:51.575520 PROGRESS: Channel   0:	 0.050 FDR: 1,643; 0.010 FDR: 1,643; 0.001 FDR: 1,100
1:38:51.575622 PROGRESS: =========================================================================
1:38:51.589370 INFO: Target number of precursors reached.
1:38:52.018462 INFO: fragments_df: keeping 5000 of 4024247 [sum(precursor_idx_mask)=42497 sum(mass_error_mask)=4024247 stop_rank=5000
1:38:52.425624 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:52.706923 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:53.420198 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:53.420645 INFO: Using score_cutoff 7.329884927845002 (fac=0.99, q=1)
1:38:53.420958 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:53.421036 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:53.421091 INFO: Updating optimization_manager: score_cutoff        : 7.8024349319458 -> 7.329884927845002
1:38:53.421147 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:53.570848 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:53.914503 INFO: === checking if optimization conditions were reached ===
1:38:53.914815 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:38:53.918486 INFO: Updating optimization_manager: rt_error            : 976.5710276151747 -> 1038.6013656069806
1:38:53.918612 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 1038.6014.
1:38:53.918690 INFO: ==============================================
1:38:53.918773 INFO: Starting optimization step 5.
1:38:53.918844 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:53.918925 INFO: Using rust extraction backend
1:38:53.918997 PROGRESS: Extracting batch of 250330 precursors
1:38:54.345896 INFO: === Search parameters used ===
1:38:54.346192 INFO: rt_error       : 1038.6013656069806
1:38:54.346256 INFO: mobility_error : 0.1
1:38:54.346309 INFO: num_candidates : 3
1:38:54.346354 INFO: ms1_error      : 30
1:38:54.346398 INFO: ms2_error      : 10.0
1:38:54.346443 INFO: fwhm_rt        : 3.0
1:38:54.346487 INFO: quant_window   : 3
1:38:54.346538 INFO: ==============================================
1:38:57.752028 INFO: performing precursor FDR with 40 features
1:38:57.752152 INFO: Decoy channel: -1
1:38:57.752179 INFO: competitive: True
1:38:57.941384 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:58.225685 INFO: Estimating optimal hyperparameters - samples: 599,354, batch_size: 2,454, learning_rate: 7.74e-04
1:38:58.226677 INFO: Using random state 337299 for train-test-split
1:39:11.204022 INFO: Test AUC: 0.613
1:39:11.204162 INFO: Train AUC: 0.624
1:39:11.204196 INFO: AUC difference: 1.79%
1:39:11.699851 INFO: Resetting torch num_threads to 24
1:39:11.727181 PROGRESS: === Extracted 749193 precursors and 4023880 fragments ===
1:39:11.727684 INFO: === FDR correction performed with classifier version 12 ===
1:39:11.728426 PROGRESS: ============================= Precursor FDR =============================
1:39:11.728518 PROGRESS: Total precursors accumulated: 1,947
1:39:11.728582 PROGRESS: Target precursors: 1,928 (99.02%)
1:39:11.728636 PROGRESS: Decoy precursors: 19 (0.98%)
1:39:11.728685 PROGRESS: 
1:39:11.728731 PROGRESS: Precursor Summary:
1:39:11.730216 PROGRESS: Channel   0:	 0.050 FDR: 1,928; 0.010 FDR: 1,928; 0.001 FDR: 1,444
1:39:11.730321 PROGRESS: 
1:39:11.730381 PROGRESS: Protein Summary:
1:39:11.732459 PROGRESS: Channel   0:	 0.050 FDR: 1,626; 0.010 FDR: 1,626; 0.001 FDR: 1,229
1:39:11.732558 PROGRESS: =========================================================================
1:39:11.745523 INFO: Target number of precursors reached.
1:39:12.179653 INFO: fragments_df: keeping 5000 of 4023880 [sum(precursor_idx_mask)=45202 sum(mass_error_mask)=4023880 stop_rank=5000
1:39:12.642998 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:12.934761 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:13.648706 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:13.649165 INFO: Using score_cutoff 10.659561075782776 (fac=0.99, q=1)
1:39:13.649487 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:13.649569 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:13.649624 INFO: Updating optimization_manager: score_cutoff        : 7.329884927845002 -> 10.659561075782776
1:39:13.649680 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:13.800417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:14.140295 INFO: === checking if optimization conditions were reached ===
1:39:14.140616 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:39:14.144280 INFO: Updating optimization_manager: rt_error            : 1038.6013656069806 -> 811.5538569780952
1:39:14.144405 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 811.5539.
1:39:14.144485 INFO: ==============================================
1:39:14.144575 INFO: Starting optimization step 6.
1:39:14.144648 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:39:14.144727 INFO: Using rust extraction backend
1:39:14.144817 PROGRESS: Extracting batch of 250330 precursors
1:39:14.572133 INFO: === Search parameters used ===
1:39:14.572422 INFO: rt_error       : 811.5538569780952
1:39:14.572479 INFO: mobility_error : 0.1
1:39:14.572527 INFO: num_candidates : 3
1:39:14.572571 INFO: ms1_error      : 30
1:39:14.572617 INFO: ms2_error      : 10.0
1:39:14.572661 INFO: fwhm_rt        : 3.0
1:39:14.572704 INFO: quant_window   : 3
1:39:14.572744 INFO: ==============================================
1:39:17.921381 INFO: performing precursor FDR with 40 features
1:39:17.921502 INFO: Decoy channel: -1
1:39:17.921529 INFO: competitive: True
1:39:18.103563 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:18.398162 INFO: Estimating optimal hyperparameters - samples: 599,378, batch_size: 2,455, learning_rate: 7.74e-04
1:39:18.399069 INFO: Using random state 337299 for train-test-split
1:39:31.085382 INFO: Test AUC: 0.617
1:39:31.085515 INFO: Train AUC: 0.624
1:39:31.085550 INFO: AUC difference: 1.16%
1:39:31.573034 INFO: Resetting torch num_threads to 24
1:39:31.601587 PROGRESS: === Extracted 749223 precursors and 4024847 fragments ===
1:39:31.602077 INFO: === FDR correction performed with classifier version 12 ===
1:39:31.602825 PROGRESS: ============================= Precursor FDR =============================
1:39:31.602916 PROGRESS: Total precursors accumulated: 2,068
1:39:31.602978 PROGRESS: Target precursors: 2,048 (99.03%)
1:39:31.603031 PROGRESS: Decoy precursors: 20 (0.97%)
1:39:31.603080 PROGRESS: 
1:39:31.603129 PROGRESS: Precursor Summary:
1:39:31.604744 PROGRESS: Channel   0:	 0.050 FDR: 2,048; 0.010 FDR: 2,048; 0.001 FDR: 1,438
1:39:31.604844 PROGRESS: 
1:39:31.604902 PROGRESS: Protein Summary:
1:39:31.606914 PROGRESS: Channel   0:	 0.050 FDR: 1,718; 0.010 FDR: 1,718; 0.001 FDR: 1,219
1:39:31.607019 PROGRESS: =========================================================================
1:39:31.619707 INFO: Target number of precursors reached.
1:39:32.052634 INFO: fragments_df: keeping 5000 of 4024847 [sum(precursor_idx_mask)=47505 sum(mass_error_mask)=4024847 stop_rank=5000
1:39:32.312884 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:32.569322 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:33.215070 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:33.215530 INFO: Using score_cutoff 10.122213654327393 (fac=0.99, q=1)
1:39:33.215845 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:33.215921 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:33.215975 INFO: Updating optimization_manager: score_cutoff        : 10.659561075782776 -> 10.122213654327393
1:39:33.216029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:33.290936 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:33.459721 INFO: === checking if optimization conditions were reached ===
1:39:33.460019 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:39:33.463741 INFO: Updating optimization_manager: rt_error            : 811.5538569780952 -> 807.8417836542524
1:39:33.463868 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 807.8418.
1:39:33.463963 INFO: ==============================================
1:39:33.464046 INFO: Starting optimization step 7.
1:39:33.464120 PROGRESS: === Extracting elution groups 0 to 63000 ===
1:39:33.464196 INFO: Using rust extraction backend
1:39:33.464266 PROGRESS: Extracting batch of 124183 precursors
1:39:33.681069 INFO: === Search parameters used ===
1:39:33.681350 INFO: rt_error       : 807.8417836542524
1:39:33.681407 INFO: mobility_error : 0.1
1:39:33.681454 INFO: num_candidates : 3
1:39:33.681496 INFO: ms1_error      : 30
1:39:33.681535 INFO: ms2_error      : 10.0
1:39:33.681575 INFO: fwhm_rt        : 3.0
1:39:33.681613 INFO: quant_window   : 3
1:39:33.681651 INFO: ==============================================
1:39:35.338951 INFO: performing precursor FDR with 40 features
1:39:35.339081 INFO: Decoy channel: -1
1:39:35.339108 INFO: competitive: True
1:39:35.427075 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:35.553110 INFO: Estimating optimal hyperparameters - samples: 297,338, batch_size: 1,217, learning_rate: 5.45e-04
1:39:35.553678 INFO: Using random state 337299 for train-test-split
1:39:43.403790 INFO: Test AUC: 0.612
1:39:43.403929 INFO: Train AUC: 0.628
1:39:43.403962 INFO: AUC difference: 2.49%
1:39:43.773875 INFO: Resetting torch num_threads to 24
1:39:43.787701 PROGRESS: === Extracted 371673 precursors and 1998168 fragments ===
1:39:43.788162 INFO: === FDR correction performed with classifier version 12 ===
1:39:43.788761 PROGRESS: ============================= Precursor FDR =============================
1:39:43.788851 PROGRESS: Total precursors accumulated: 1,056
1:39:43.788912 PROGRESS: Target precursors: 1,046 (99.05%)
1:39:43.788965 PROGRESS: Decoy precursors: 10 (0.95%)
1:39:43.789012 PROGRESS: 
1:39:43.789058 PROGRESS: Precursor Summary:
1:39:43.790294 PROGRESS: Channel   0:	 0.050 FDR: 1,046; 0.010 FDR: 1,046; 0.001 FDR:   762
1:39:43.790393 PROGRESS: 
1:39:43.790450 PROGRESS: Protein Summary:
1:39:43.792007 PROGRESS: Channel   0:	 0.050 FDR:   951; 0.010 FDR:   951; 0.001 FDR:   696
1:39:43.792102 PROGRESS: =========================================================================
1:39:43.797877 INFO: Target number of precursors reached.
1:39:44.014582 INFO: fragments_df: keeping 5000 of 1998168 [sum(precursor_idx_mask)=24252 sum(mass_error_mask)=1998168 stop_rank=5000
1:39:44.263760 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:44.449789 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:45.166758 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:45.167240 INFO: Using score_cutoff 10.689548499584198 (fac=0.99, q=1)
1:39:45.167587 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:45.167672 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:45.167731 INFO: Updating optimization_manager: score_cutoff        : 10.122213654327393 -> 10.689548499584198
1:39:45.167791 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:45.242861 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:45.416502 INFO: === checking if optimization conditions were reached ===
1:39:45.416820 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:39:45.417986 INFO: Updating optimization_manager: rt_error            : 807.8417836542524 -> 807.8417836542524
1:39:45.418137 INFO: Updating optimization_manager: classifier_version  : 12 -> 20
1:39:45.418267 INFO: Updating optimization_manager: score_cutoff        : 10.689548499584198 -> 10.689548499584198
1:39:45.418371 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:45.418470 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:45.418569 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 807.8418 found after 7 searches.
1:39:45.418639 INFO: ==============================================
1:39:45.418724 PROGRESS: Optimization finished for rt_error.
1:39:45.670992 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:45.746465 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:45.920333 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:39:45.920623 PROGRESS: ==============================================
1:39:45.920712 PROGRESS: ms2_error      : 10.0000
1:39:45.920782 PROGRESS: rt_error       : 807.8418
1:39:45.920839 PROGRESS: ==============================================
1:39:45.921645 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:53.531957 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:40:10.640248 INFO: Using rust extraction backend
1:40:10.640636 PROGRESS: Extracting batch of 11997144 precursors
1:40:26.857372 INFO: === Search parameters used ===
1:40:26.857654 INFO: rt_error       : 807.8417836542524
1:40:26.857720 INFO: mobility_error : 0.1
1:40:26.857780 INFO: num_candidates : 3
1:40:26.857830 INFO: ms1_error      : 30
1:40:26.857873 INFO: ms2_error      : 10.0
1:40:26.857916 INFO: fwhm_rt        : 3.0
1:40:26.857956 INFO: quant_window   : 3
1:40:26.857997 INFO: ==============================================
1:41:29.167342 INFO: Removed 8528822 precursors with score below cutoff 10.689548499584198
1:41:59.935090 INFO: performing precursor FDR with 40 features
1:41:59.935222 INFO: Decoy channel: -1
1:41:59.935250 INFO: competitive: True
1:42:02.855019 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:13.973053 INFO: Estimating optimal hyperparameters - samples: 21,969,784, batch_size: 4,096, learning_rate: 1.00e-03
1:42:14.039596 INFO: Using random state 750252 for train-test-split
1:49:16.201387 INFO: Test AUC: 0.621
1:49:16.201671 INFO: Train AUC: 0.622
1:49:16.201718 INFO: AUC difference: 0.12%
1:49:22.946284 INFO: Resetting torch num_threads to 24
1:49:25.110862 PROGRESS: ============================= Precursor FDR =============================
1:49:25.111186 PROGRESS: Total precursors accumulated: 91,330
1:49:25.111262 PROGRESS: Target precursors: 90,426 (99.01%)
1:49:25.111320 PROGRESS: Decoy precursors: 904 (0.99%)
1:49:25.111369 PROGRESS: 
1:49:25.111418 PROGRESS: Precursor Summary:
1:49:25.135438 PROGRESS: Channel   0:	 0.050 FDR: 90,426; 0.010 FDR: 90,426; 0.001 FDR: 59,124
1:49:25.135695 PROGRESS: 
1:49:25.135759 PROGRESS: Protein Summary:
1:49:25.169785 PROGRESS: Channel   0:	 0.050 FDR: 13,131; 0.010 FDR: 13,131; 0.001 FDR: 9,391
1:49:25.170038 PROGRESS: =========================================================================
1:49:25.352825 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
1:49:25.520742 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
1:49:25.767768 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:49:26.395857 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
1:49:26.396041 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:49:26.396141 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:49:26.396330 INFO: Initializing TimingManager
1:49:26.396785 INFO: Initializing RawFileManager
1:49:39.780704 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.
1:49:39.789269 INFO: Determining DIA cycle
1:49:39.805787 INFO: Found cycle with start 0.00 min and length 300.
1:49:39.981013 INFO: RT (min)            : 0.0 - 26.9
1:49:39.981203 INFO: RT duration (sec)   : 1611.2
1:49:39.981234 INFO: RT duration (min)   : 26.9
1:49:39.981259 INFO: Cycle len (scans)   : 300
1:49:39.981281 INFO: Cycle len (sec)     : 1.65
1:49:39.981301 INFO: Number of cycles    : 977
1:49:39.981321 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:49:39.981363 INFO: Creating DIA data object took: 13.58448076248169
1:49:41.910184 INFO: Creating DIA data NG object took: 1.9286630153656006
1:49:43.560229 INFO: Initializing CalibrationManager
1:49:43.560521 INFO: Setting up calibration estimators ..
1:49:43.560587 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:49:43.560670 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'}' ..
1:49:43.560777 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:49:43.560846 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:49:43.560901 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}}' ..
1:49:43.560958 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:49:43.561005 INFO: Done setting up calibration estimators.
1:49:43.561218 INFO: Initializing OptimizationManager
1:49:43.561363 INFO: initial parameter: ms1_error = 30
1:49:43.561418 INFO: initial parameter: ms2_error = 30
1:49:43.561466 INFO: initial parameter: rt_error = 805.5982666015625
1:49:43.561510 INFO: initial parameter: mobility_error = 0.1
1:49:43.561550 INFO: initial parameter: num_candidates = 1
1:49:43.561590 INFO: initial parameter: fwhm_rt = 5
1:49:43.561631 INFO: initial parameter: fwhm_mobility = 0.01
1:49:43.561671 INFO: initial parameter: score_cutoff = 0
1:49:43.561711 INFO: initial parameter: classifier_version = -1
1:49:43.561781 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:49:43.562104 INFO: FDRManager: loading saved state not requested, will be initialized.
1:49:43.562136 INFO: Initializing FDRManager
1:49:43.562179 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:49:44.966100 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:49:45.848469 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:49:45.848912 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
1:49:45.849022 PROGRESS: Starting initial search for precursors.
1:49:45.849111 INFO: Starting optimization step 0.
1:49:45.849179 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:49:45.849243 INFO: Using rust extraction backend
1:49:45.849316 PROGRESS: Extracting batch of 1972 precursors
1:49:45.854223 INFO: === Search parameters used ===
1:49:45.854337 INFO: rt_error       : 805.5982666015625
1:49:45.854388 INFO: mobility_error : 0.1
1:49:45.854444 INFO: num_candidates : 1
1:49:45.854487 INFO: ms1_error      : 30
1:49:45.854527 INFO: ms2_error      : 30
1:49:45.854565 INFO: fwhm_rt        : 5
1:49:45.854603 INFO: quant_window   : 3
1:49:45.854640 INFO: ==============================================
1:49:45.904926 INFO: performing precursor FDR with 40 features
1:49:45.905012 INFO: Decoy channel: -1
1:49:45.905036 INFO: competitive: True
1:49:45.906322 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:45.908342 INFO: Estimating optimal hyperparameters - samples: 1,567, batch_size: 128, learning_rate: 1.77e-04
1:49:45.909304 INFO: Using random state 600446 for train-test-split
1:49:46.061689 INFO: Test AUC: 0.513
1:49:46.061771 INFO: Train AUC: 0.515
1:49:46.061801 INFO: AUC difference: 0.29%
1:49:46.303802 INFO: Resetting torch num_threads to 24
1:49:46.305425 PROGRESS: === Extracted 1959 precursors and 9309 fragments ===
1:49:46.305788 INFO: === FDR correction performed with classifier version -1 ===
1:49:46.306278 PROGRESS: ============================= Precursor FDR =============================
1:49:46.306361 PROGRESS: Total precursors accumulated: 2
1:49:46.306418 PROGRESS: Target precursors: 2 (100.00%)
1:49:46.306467 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:46.306510 PROGRESS: 
1:49:46.306554 PROGRESS: Precursor Summary:
1:49:46.307616 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:49:46.307704 PROGRESS: 
1:49:46.307762 PROGRESS: Protein Summary:
1:49:46.308923 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:49:46.309007 PROGRESS: =========================================================================
1:49:46.309227 INFO: Target number of precursors not reached yet.
1:49:46.393381 INFO: Starting optimization step 1.
1:49:46.393609 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:49:46.393688 INFO: Using rust extraction backend
1:49:46.393747 PROGRESS: Extracting batch of 3939 precursors
1:49:46.402056 INFO: === Search parameters used ===
1:49:46.402183 INFO: rt_error       : 805.5982666015625
1:49:46.402237 INFO: mobility_error : 0.1
1:49:46.402284 INFO: num_candidates : 1
1:49:46.402327 INFO: ms1_error      : 30
1:49:46.402369 INFO: ms2_error      : 30
1:49:46.402408 INFO: fwhm_rt        : 5
1:49:46.402447 INFO: quant_window   : 3
1:49:46.402487 INFO: ==============================================
1:49:46.469832 INFO: performing precursor FDR with 40 features
1:49:46.469929 INFO: Decoy channel: -1
1:49:46.469953 INFO: competitive: True
1:49:46.474289 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:46.476625 INFO: Estimating optimal hyperparameters - samples: 4,696, batch_size: 128, learning_rate: 1.77e-04
1:49:46.476708 INFO: Using random state 178183 for train-test-split
1:49:46.944929 INFO: Test AUC: 0.505
1:49:46.945025 INFO: Train AUC: 0.553
1:49:46.945055 INFO: AUC difference: 8.80%
1:49:46.945080 WARNING: AUC difference > 5%. This may indicate overfitting.
1:49:47.183927 INFO: Resetting torch num_threads to 24
1:49:47.187039 PROGRESS: === Extracted 5870 precursors and 27958 fragments ===
1:49:47.187419 INFO: === FDR correction performed with classifier version -1 ===
1:49:47.187928 PROGRESS: ============================= Precursor FDR =============================
1:49:47.188017 PROGRESS: Total precursors accumulated: 6
1:49:47.188079 PROGRESS: Target precursors: 6 (100.00%)
1:49:47.188133 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:47.188181 PROGRESS: 
1:49:47.188226 PROGRESS: Precursor Summary:
1:49:47.189282 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:49:47.189367 PROGRESS: 
1:49:47.189423 PROGRESS: Protein Summary:
1:49:47.190569 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:49:47.190654 PROGRESS: =========================================================================
1:49:47.190951 INFO: Target number of precursors not reached yet.
1:49:47.285194 INFO: Starting optimization step 2.
1:49:47.285423 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:49:47.285517 INFO: Using rust extraction backend
1:49:47.285578 PROGRESS: Extracting batch of 7870 precursors
1:49:47.300822 INFO: === Search parameters used ===
1:49:47.300976 INFO: rt_error       : 805.5982666015625
1:49:47.301029 INFO: mobility_error : 0.1
1:49:47.301076 INFO: num_candidates : 1
1:49:47.301119 INFO: ms1_error      : 30
1:49:47.301162 INFO: ms2_error      : 30
1:49:47.301203 INFO: fwhm_rt        : 5
1:49:47.301244 INFO: quant_window   : 3
1:49:47.301285 INFO: ==============================================
1:49:47.418604 INFO: performing precursor FDR with 40 features
1:49:47.418710 INFO: Decoy channel: -1
1:49:47.418735 INFO: competitive: True
1:49:47.425892 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:47.429386 INFO: Estimating optimal hyperparameters - samples: 10,935, batch_size: 128, learning_rate: 1.77e-04
1:49:47.429500 INFO: Using random state 430328 for train-test-split
1:49:48.537856 INFO: Test AUC: 0.544
1:49:48.537967 INFO: Train AUC: 0.571
1:49:48.537996 INFO: AUC difference: 4.63%
1:49:48.781057 INFO: Resetting torch num_threads to 24
1:49:48.785364 PROGRESS: === Extracted 13669 precursors and 64866 fragments ===
1:49:48.785760 INFO: === FDR correction performed with classifier version -1 ===
1:49:48.786263 PROGRESS: ============================= Precursor FDR =============================
1:49:48.786346 PROGRESS: Total precursors accumulated: 40
1:49:48.786403 PROGRESS: Target precursors: 40 (100.00%)
1:49:48.786451 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:48.786495 PROGRESS: 
1:49:48.786537 PROGRESS: Precursor Summary:
1:49:48.787604 PROGRESS: Channel   0:	 0.050 FDR:    40; 0.010 FDR:    40; 0.001 FDR:    40
1:49:48.787693 PROGRESS: 
1:49:48.787748 PROGRESS: Protein Summary:
1:49:48.788933 PROGRESS: Channel   0:	 0.050 FDR:    40; 0.010 FDR:    40; 0.001 FDR:    40
1:49:48.789017 PROGRESS: =========================================================================
1:49:48.789371 INFO: Target number of precursors not reached yet.
1:49:48.889273 INFO: Starting optimization step 3.
1:49:48.889515 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:49:48.889593 INFO: Using rust extraction backend
1:49:48.889650 PROGRESS: Extracting batch of 15774 precursors
1:49:48.918112 INFO: === Search parameters used ===
1:49:48.918309 INFO: rt_error       : 805.5982666015625
1:49:48.918360 INFO: mobility_error : 0.1
1:49:48.918403 INFO: num_candidates : 1
1:49:48.918445 INFO: ms1_error      : 30
1:49:48.918486 INFO: ms2_error      : 30
1:49:48.918538 INFO: fwhm_rt        : 5
1:49:48.918579 INFO: quant_window   : 3
1:49:48.918618 INFO: ==============================================
1:49:49.086842 INFO: performing precursor FDR with 40 features
1:49:49.086957 INFO: Decoy channel: -1
1:49:49.086982 INFO: competitive: True
1:49:49.097750 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:49.104481 INFO: Estimating optimal hyperparameters - samples: 23,458, batch_size: 128, learning_rate: 1.77e-04
1:49:49.104647 INFO: Using random state 983368 for train-test-split
1:49:51.484777 INFO: Test AUC: 0.555
1:49:51.484868 INFO: Train AUC: 0.602
1:49:51.484896 INFO: AUC difference: 7.72%
1:49:51.484918 WARNING: AUC difference > 5%. This may indicate overfitting.
1:49:51.737130 INFO: Resetting torch num_threads to 24
1:49:51.743385 PROGRESS: === Extracted 29323 precursors and 139177 fragments ===
1:49:51.743908 INFO: === FDR correction performed with classifier version -1 ===
1:49:51.744416 PROGRESS: ============================= Precursor FDR =============================
1:49:51.744497 PROGRESS: Total precursors accumulated: 0
1:49:51.744553 PROGRESS: Target precursors: 0 (0.00%)
1:49:51.744600 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:51.744642 PROGRESS: 
1:49:51.744684 PROGRESS: Precursor Summary:
1:49:51.744798 PROGRESS: 
1:49:51.744854 PROGRESS: Protein Summary:
1:49:51.744924 PROGRESS: =========================================================================
1:49:51.745375 INFO: Target number of precursors not reached yet.
1:49:51.863640 INFO: Starting optimization step 4.
1:49:51.863920 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:49:51.864002 INFO: Using rust extraction backend
1:49:51.864063 PROGRESS: Extracting batch of 31503 precursors
1:49:51.919809 INFO: === Search parameters used ===
1:49:51.920077 INFO: rt_error       : 805.5982666015625
1:49:51.920144 INFO: mobility_error : 0.1
1:49:51.920192 INFO: num_candidates : 1
1:49:51.920234 INFO: ms1_error      : 30
1:49:51.920274 INFO: ms2_error      : 30
1:49:51.920312 INFO: fwhm_rt        : 5
1:49:51.920349 INFO: quant_window   : 3
1:49:51.920387 INFO: ==============================================
1:49:52.208583 INFO: performing precursor FDR with 40 features
1:49:52.208709 INFO: Decoy channel: -1
1:49:52.208740 INFO: competitive: True
1:49:52.231347 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:52.245380 INFO: Estimating optimal hyperparameters - samples: 48,410, batch_size: 198, learning_rate: 2.20e-04
1:49:52.245598 INFO: Using random state 798409 for train-test-split
1:49:55.873421 INFO: Test AUC: 0.577
1:49:55.873515 INFO: Train AUC: 0.607
1:49:55.873544 INFO: AUC difference: 4.87%
1:49:56.140741 INFO: Resetting torch num_threads to 24
1:49:56.151449 PROGRESS: === Extracted 60513 precursors and 287658 fragments ===
1:49:56.152120 INFO: === FDR correction performed with classifier version -1 ===
1:49:56.152668 PROGRESS: ============================= Precursor FDR =============================
1:49:56.152755 PROGRESS: Total precursors accumulated: 0
1:49:56.152816 PROGRESS: Target precursors: 0 (0.00%)
1:49:56.152869 PROGRESS: Decoy precursors: 0 (0.00%)
1:49:56.152917 PROGRESS: 
1:49:56.152965 PROGRESS: Precursor Summary:
1:49:56.153086 PROGRESS: 
1:49:56.153147 PROGRESS: Protein Summary:
1:49:56.153220 PROGRESS: =========================================================================
1:49:56.154138 INFO: Target number of precursors not reached yet.
1:49:56.314115 INFO: Starting optimization step 5.
1:49:56.314377 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:49:56.314512 INFO: Using rust extraction backend
1:49:56.314581 PROGRESS: Extracting batch of 63125 precursors
1:49:56.424175 INFO: === Search parameters used ===
1:49:56.424459 INFO: rt_error       : 805.5982666015625
1:49:56.424516 INFO: mobility_error : 0.1
1:49:56.424565 INFO: num_candidates : 1
1:49:56.424610 INFO: ms1_error      : 30
1:49:56.424653 INFO: ms2_error      : 30
1:49:56.424693 INFO: fwhm_rt        : 5
1:49:56.424733 INFO: quant_window   : 3
1:49:56.424773 INFO: ==============================================
1:49:56.986172 INFO: performing precursor FDR with 40 features
1:49:56.986293 INFO: Decoy channel: -1
1:49:56.986318 INFO: competitive: True
1:49:57.033283 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:57.063991 INFO: Estimating optimal hyperparameters - samples: 98,482, batch_size: 403, learning_rate: 3.14e-04
1:49:57.064286 INFO: Using random state 264031 for train-test-split
1:50:01.737299 INFO: Test AUC: 0.589
1:50:01.737416 INFO: Train AUC: 0.608
1:50:01.737448 INFO: AUC difference: 3.00%
1:50:02.021515 INFO: Resetting torch num_threads to 24
1:50:02.044278 PROGRESS: === Extracted 123103 precursors and 585063 fragments ===
1:50:02.044961 INFO: === FDR correction performed with classifier version -1 ===
1:50:02.045596 PROGRESS: ============================= Precursor FDR =============================
1:50:02.045694 PROGRESS: Total precursors accumulated: 384
1:50:02.045759 PROGRESS: Target precursors: 381 (99.22%)
1:50:02.045813 PROGRESS: Decoy precursors: 3 (0.78%)
1:50:02.045861 PROGRESS: 
1:50:02.045907 PROGRESS: Precursor Summary:
1:50:02.046956 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   381; 0.001 FDR:    56
1:50:02.047043 PROGRESS: 
1:50:02.047099 PROGRESS: Protein Summary:
1:50:02.048390 PROGRESS: Channel   0:	 0.050 FDR:   357; 0.010 FDR:   357; 0.001 FDR:    56
1:50:02.048489 PROGRESS: =========================================================================
1:50:02.050612 INFO: Target number of precursors not reached yet.
1:50:02.294272 INFO: Starting optimization step 6.
1:50:02.294573 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:50:02.294663 INFO: Using rust extraction backend
1:50:02.294734 PROGRESS: Extracting batch of 126147 precursors
1:50:02.511562 INFO: === Search parameters used ===
1:50:02.511852 INFO: rt_error       : 805.5982666015625
1:50:02.511911 INFO: mobility_error : 0.1
1:50:02.511961 INFO: num_candidates : 1
1:50:02.512007 INFO: ms1_error      : 30
1:50:02.512052 INFO: ms2_error      : 30
1:50:02.512096 INFO: fwhm_rt        : 5
1:50:02.512142 INFO: quant_window   : 3
1:50:02.512191 INFO: ==============================================
1:50:03.595562 INFO: performing precursor FDR with 40 features
1:50:03.595693 INFO: Decoy channel: -1
1:50:03.595719 INFO: competitive: True
1:50:03.691850 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:03.768678 INFO: Estimating optimal hyperparameters - samples: 198,507, batch_size: 813, learning_rate: 4.46e-04
1:50:03.769120 INFO: Using random state 435751 for train-test-split
1:50:10.179137 INFO: Test AUC: 0.585
1:50:10.179266 INFO: Train AUC: 0.609
1:50:10.179298 INFO: AUC difference: 3.86%
1:50:10.504995 INFO: Resetting torch num_threads to 24
1:50:10.548147 PROGRESS: === Extracted 248134 precursors and 1178305 fragments ===
1:50:10.548851 INFO: === FDR correction performed with classifier version -1 ===
1:50:10.549597 PROGRESS: ============================= Precursor FDR =============================
1:50:10.549688 PROGRESS: Total precursors accumulated: 870
1:50:10.549752 PROGRESS: Target precursors: 862 (99.08%)
1:50:10.549806 PROGRESS: Decoy precursors: 8 (0.92%)
1:50:10.549864 PROGRESS: 
1:50:10.549913 PROGRESS: Precursor Summary:
1:50:10.551104 PROGRESS: Channel   0:	 0.050 FDR:   862; 0.010 FDR:   862; 0.001 FDR:   708
1:50:10.551192 PROGRESS: 
1:50:10.551247 PROGRESS: Protein Summary:
1:50:10.552730 PROGRESS: Channel   0:	 0.050 FDR:   747; 0.010 FDR:   747; 0.001 FDR:   625
1:50:10.552823 PROGRESS: =========================================================================
1:50:10.557385 INFO: Target number of precursors not reached yet.
1:50:10.963692 INFO: Starting optimization step 7.
1:50:10.963972 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:50:10.964058 INFO: Using rust extraction backend
1:50:10.964126 PROGRESS: Extracting batch of 252313 precursors
1:50:11.398926 INFO: === Search parameters used ===
1:50:11.399203 INFO: rt_error       : 805.5982666015625
1:50:11.399260 INFO: mobility_error : 0.1
1:50:11.399308 INFO: num_candidates : 1
1:50:11.399356 INFO: ms1_error      : 30
1:50:11.399404 INFO: ms2_error      : 30
1:50:11.399446 INFO: fwhm_rt        : 5
1:50:11.399503 INFO: quant_window   : 3
1:50:11.399546 INFO: ==============================================
1:50:13.527869 INFO: performing precursor FDR with 40 features
1:50:13.527999 INFO: Decoy channel: -1
1:50:13.528026 INFO: competitive: True
1:50:13.717287 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:13.909660 INFO: Estimating optimal hyperparameters - samples: 398,528, batch_size: 1,632, learning_rate: 6.31e-04
1:50:13.910297 INFO: Using random state 949427 for train-test-split
1:50:23.755179 INFO: Test AUC: 0.593
1:50:23.755309 INFO: Train AUC: 0.605
1:50:23.755342 INFO: AUC difference: 1.97%
1:50:24.158449 INFO: Resetting torch num_threads to 24
1:50:24.245488 PROGRESS: === Extracted 498160 precursors and 2365344 fragments ===
1:50:24.246215 INFO: === FDR correction performed with classifier version -1 ===
1:50:24.247297 PROGRESS: ============================= Precursor FDR =============================
1:50:24.247399 PROGRESS: Total precursors accumulated: 1,950
1:50:24.247474 PROGRESS: Target precursors: 1,931 (99.03%)
1:50:24.247531 PROGRESS: Decoy precursors: 19 (0.97%)
1:50:24.247577 PROGRESS: 
1:50:24.247622 PROGRESS: Precursor Summary:
1:50:24.249107 PROGRESS: Channel   0:	 0.050 FDR: 1,931; 0.010 FDR: 1,931; 0.001 FDR: 1,405
1:50:24.249194 PROGRESS: 
1:50:24.249249 PROGRESS: Protein Summary:
1:50:24.251199 PROGRESS: Channel   0:	 0.050 FDR: 1,485; 0.010 FDR: 1,485; 0.001 FDR: 1,107
1:50:24.251297 PROGRESS: =========================================================================
1:50:24.259017 INFO: Target number of precursors reached.
1:50:24.531040 INFO: fragments_df: keeping 5000 of 2365344 [sum(precursor_idx_mask)=20702 sum(mass_error_mask)=2365344 stop_rank=5000
1:50:25.304179 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:25.588409 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:26.302049 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:50:26.302508 INFO: Using score_cutoff 12.87428534603119 (fac=0.99, q=1)
1:50:26.302828 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:50:26.302906 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:50:26.302964 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.87428534603119
1:50:26.303021 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:26.609691 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:27.289555 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:50:27.289805 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:50:27.289914 INFO: Starting optimization step 8.
1:50:27.289979 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:50:27.290047 INFO: Using rust extraction backend
1:50:27.290106 PROGRESS: Extracting batch of 502643 precursors
1:50:28.141450 INFO: === Search parameters used ===
1:50:28.141751 INFO: rt_error       : 805.5982666015625
1:50:28.141809 INFO: mobility_error : 0.1
1:50:28.141856 INFO: num_candidates : 3
1:50:28.141900 INFO: ms1_error      : 30
1:50:28.141942 INFO: ms2_error      : 30
1:50:28.141985 INFO: fwhm_rt        : 3.0
1:50:28.142028 INFO: quant_window   : 3
1:50:28.142069 INFO: ==============================================
1:50:35.451592 INFO: performing precursor FDR with 40 features
1:50:35.451737 INFO: Decoy channel: -1
1:50:35.451764 INFO: competitive: True
1:50:35.826154 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:36.418466 INFO: Estimating optimal hyperparameters - samples: 1,196,580, batch_size: 4,096, learning_rate: 1.00e-03
1:50:36.420493 INFO: Using random state 554976 for train-test-split
1:50:59.629919 INFO: Test AUC: 0.600
1:50:59.630096 INFO: Train AUC: 0.606
1:50:59.630132 INFO: AUC difference: 0.97%
1:51:00.352956 INFO: Resetting torch num_threads to 24
1:51:00.417766 PROGRESS: === Extracted 1495726 precursors and 6951332 fragments ===
1:51:00.418325 INFO: === FDR correction performed with classifier version 7 ===
1:51:00.419233 PROGRESS: ============================= Precursor FDR =============================
1:51:00.419355 PROGRESS: Total precursors accumulated: 2,151
1:51:00.419416 PROGRESS: Target precursors: 2,130 (99.02%)
1:51:00.419481 PROGRESS: Decoy precursors: 21 (0.98%)
1:51:00.419533 PROGRESS: 
1:51:00.419578 PROGRESS: Precursor Summary:
1:51:00.421284 PROGRESS: Channel   0:	 0.050 FDR: 2,130; 0.010 FDR: 2,130; 0.001 FDR: 1,577
1:51:00.421380 PROGRESS: 
1:51:00.421435 PROGRESS: Protein Summary:
1:51:00.423483 PROGRESS: Channel   0:	 0.050 FDR: 1,629; 0.010 FDR: 1,629; 0.001 FDR: 1,241
1:51:00.423579 PROGRESS: =========================================================================
1:51:00.453537 INFO: Target number of precursors reached.
1:51:01.220693 INFO: fragments_df: keeping 5000 of 6951332 [sum(precursor_idx_mask)=47852 sum(mass_error_mask)=6951332 stop_rank=5000
1:51:01.803812 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:02.126704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:02.850811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:02.851281 INFO: Using score_cutoff 12.793771172618866 (fac=0.99, q=1)
1:51:02.851613 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:02.851697 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:02.851753 INFO: Updating optimization_manager: score_cutoff        : 12.87428534603119 -> 12.793771172618866
1:51:02.851818 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:03.007885 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:03.360795 INFO: === checking if optimization conditions were reached ===
1:51:03.363075 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
1:51:03.363178 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:51:03.363249 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:51:03.363316 INFO: ==============================================
1:51:03.363390 INFO: Starting optimization step 9.
1:51:03.363464 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:51:03.363544 INFO: Using rust extraction backend
1:51:03.363607 PROGRESS: Extracting batch of 250330 precursors
1:51:03.795282 INFO: === Search parameters used ===
1:51:03.795575 INFO: rt_error       : 805.5982666015625
1:51:03.795641 INFO: mobility_error : 0.1
1:51:03.795692 INFO: num_candidates : 3
1:51:03.795736 INFO: ms1_error      : 30
1:51:03.795777 INFO: ms2_error      : 10.0
1:51:03.795819 INFO: fwhm_rt        : 3.0
1:51:03.795865 INFO: quant_window   : 3
1:51:03.795906 INFO: ==============================================
1:51:07.206133 INFO: performing precursor FDR with 40 features
1:51:07.206262 INFO: Decoy channel: -1
1:51:07.206288 INFO: competitive: True
1:51:07.381415 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:07.674863 INFO: Estimating optimal hyperparameters - samples: 599,660, batch_size: 2,456, learning_rate: 7.74e-04
1:51:07.676026 INFO: Using random state 846399 for train-test-split
1:51:20.006555 INFO: Test AUC: 0.605
1:51:20.006711 INFO: Train AUC: 0.614
1:51:20.006751 INFO: AUC difference: 1.41%
1:51:20.490584 INFO: Resetting torch num_threads to 24
1:51:20.516026 PROGRESS: === Extracted 749576 precursors and 4049846 fragments ===
1:51:20.516546 INFO: === FDR correction performed with classifier version 8 ===
1:51:20.517250 PROGRESS: ============================= Precursor FDR =============================
1:51:20.517342 PROGRESS: Total precursors accumulated: 1,660
1:51:20.517403 PROGRESS: Target precursors: 1,644 (99.04%)
1:51:20.517453 PROGRESS: Decoy precursors: 16 (0.96%)
1:51:20.517499 PROGRESS: 
1:51:20.517543 PROGRESS: Precursor Summary:
1:51:20.518951 PROGRESS: Channel   0:	 0.050 FDR: 1,644; 0.010 FDR: 1,644; 0.001 FDR: 1,294
1:51:20.519037 PROGRESS: 
1:51:20.519092 PROGRESS: Protein Summary:
1:51:20.520942 PROGRESS: Channel   0:	 0.050 FDR: 1,386; 0.010 FDR: 1,386; 0.001 FDR: 1,101
1:51:20.521039 PROGRESS: =========================================================================
1:51:20.534977 INFO: Target number of precursors reached.
1:51:20.975104 INFO: fragments_df: keeping 5000 of 4049846 [sum(precursor_idx_mask)=38622 sum(mass_error_mask)=4049846 stop_rank=5000
1:51:21.387641 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:21.639764 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:22.353204 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:22.353680 INFO: Using score_cutoff 8.982448245620727 (fac=0.99, q=1)
1:51:22.354000 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:22.354079 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:22.354135 INFO: Updating optimization_manager: score_cutoff        : 12.793771172618866 -> 8.982448245620727
1:51:22.354199 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:22.502948 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:22.830137 INFO: === checking if optimization conditions were reached ===
1:51:22.832421 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:51:22.832573 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:51:22.832645 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:51:22.832705 INFO: ==============================================
1:51:22.832795 INFO: Starting optimization step 10.
1:51:22.832861 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:51:22.832936 INFO: Using rust extraction backend
1:51:22.833007 PROGRESS: Extracting batch of 250330 precursors
1:51:23.261633 INFO: === Search parameters used ===
1:51:23.261906 INFO: rt_error       : 805.5982666015625
1:51:23.261965 INFO: mobility_error : 0.1
1:51:23.262012 INFO: num_candidates : 3
1:51:23.262053 INFO: ms1_error      : 30
1:51:23.262094 INFO: ms2_error      : 10.0
1:51:23.262133 INFO: fwhm_rt        : 3.0
1:51:23.262171 INFO: quant_window   : 3
1:51:23.262209 INFO: ==============================================
1:51:26.624219 INFO: performing precursor FDR with 40 features
1:51:26.624342 INFO: Decoy channel: -1
1:51:26.624368 INFO: competitive: True
1:51:26.791698 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:27.082074 INFO: Estimating optimal hyperparameters - samples: 599,669, batch_size: 2,456, learning_rate: 7.74e-04
1:51:27.083202 INFO: Using random state 156443 for train-test-split
1:51:39.236756 INFO: Test AUC: 0.609
1:51:39.236892 INFO: Train AUC: 0.619
1:51:39.236925 INFO: AUC difference: 1.55%
1:51:39.719749 INFO: Resetting torch num_threads to 24
1:51:39.745017 PROGRESS: === Extracted 749587 precursors and 4049953 fragments ===
1:51:39.745507 INFO: === FDR correction performed with classifier version 9 ===
1:51:39.746154 PROGRESS: ============================= Precursor FDR =============================
1:51:39.746243 PROGRESS: Total precursors accumulated: 1,580
1:51:39.746307 PROGRESS: Target precursors: 1,565 (99.05%)
1:51:39.746360 PROGRESS: Decoy precursors: 15 (0.95%)
1:51:39.746407 PROGRESS: 
1:51:39.746453 PROGRESS: Precursor Summary:
1:51:39.747831 PROGRESS: Channel   0:	 0.050 FDR: 1,565; 0.010 FDR: 1,565; 0.001 FDR: 1,277
1:51:39.747923 PROGRESS: 
1:51:39.747980 PROGRESS: Protein Summary:
1:51:39.749768 PROGRESS: Channel   0:	 0.050 FDR: 1,300; 0.010 FDR: 1,300; 0.001 FDR: 1,085
1:51:39.749861 PROGRESS: =========================================================================
1:51:39.762845 INFO: Target number of precursors reached.
1:51:40.219207 INFO: fragments_df: keeping 5000 of 4049953 [sum(precursor_idx_mask)=37241 sum(mass_error_mask)=4049953 stop_rank=5000
1:51:40.636003 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:40.873896 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:41.592752 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:41.593223 INFO: Using score_cutoff 11.628989016723633 (fac=0.99, q=1)
1:51:41.593548 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:41.593636 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:41.593693 INFO: Updating optimization_manager: score_cutoff        : 8.982448245620727 -> 11.628989016723633
1:51:41.593750 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:41.747753 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:42.078865 INFO: === checking if optimization conditions were reached ===
1:51:42.081174 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:51:42.081331 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:51:42.081400 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:51:42.081461 INFO: ==============================================
1:51:42.081533 INFO: Starting optimization step 11.
1:51:42.081597 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:51:42.081666 INFO: Using rust extraction backend
1:51:42.081735 PROGRESS: Extracting batch of 250330 precursors
1:51:42.511661 INFO: === Search parameters used ===
1:51:42.512063 INFO: rt_error       : 805.5982666015625
1:51:42.512125 INFO: mobility_error : 0.1
1:51:42.512178 INFO: num_candidates : 3
1:51:42.512232 INFO: ms1_error      : 30
1:51:42.512277 INFO: ms2_error      : 10.0
1:51:42.512321 INFO: fwhm_rt        : 3.0
1:51:42.512369 INFO: quant_window   : 3
1:51:42.512491 INFO: ==============================================
1:51:45.959143 INFO: performing precursor FDR with 40 features
1:51:45.959266 INFO: Decoy channel: -1
1:51:45.959292 INFO: competitive: True
1:51:46.126022 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:46.406573 INFO: Estimating optimal hyperparameters - samples: 599,648, batch_size: 2,456, learning_rate: 7.74e-04
1:51:46.407588 INFO: Using random state 266516 for train-test-split
1:51:58.874673 INFO: Test AUC: 0.610
1:51:58.874827 INFO: Train AUC: 0.623
1:51:58.874864 INFO: AUC difference: 2.11%
1:51:59.349378 INFO: Resetting torch num_threads to 24
1:51:59.375712 PROGRESS: === Extracted 749560 precursors and 4049608 fragments ===
1:51:59.376221 INFO: === FDR correction performed with classifier version 10 ===
1:51:59.376925 PROGRESS: ============================= Precursor FDR =============================
1:51:59.377017 PROGRESS: Total precursors accumulated: 1,729
1:51:59.377083 PROGRESS: Target precursors: 1,712 (99.02%)
1:51:59.377138 PROGRESS: Decoy precursors: 17 (0.98%)
1:51:59.377187 PROGRESS: 
1:51:59.377233 PROGRESS: Precursor Summary:
1:51:59.378637 PROGRESS: Channel   0:	 0.050 FDR: 1,712; 0.010 FDR: 1,712; 0.001 FDR: 1,359
1:51:59.378727 PROGRESS: 
1:51:59.378783 PROGRESS: Protein Summary:
1:51:59.380729 PROGRESS: Channel   0:	 0.050 FDR: 1,443; 0.010 FDR: 1,443; 0.001 FDR: 1,150
1:51:59.380831 PROGRESS: =========================================================================
1:51:59.393787 INFO: Target number of precursors reached.
1:51:59.817410 INFO: fragments_df: keeping 5000 of 4049608 [sum(precursor_idx_mask)=39192 sum(mass_error_mask)=4049608 stop_rank=5000
1:52:00.252713 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:00.516084 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:01.235977 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:52:01.236432 INFO: Using score_cutoff 7.536330512237549 (fac=0.99, q=1)
1:52:01.236768 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:52:01.236849 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:52:01.236907 INFO: Updating optimization_manager: score_cutoff        : 11.628989016723633 -> 7.536330512237549
1:52:01.236971 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:01.386754 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:01.721053 INFO: === checking if optimization conditions were reached ===
1:52:01.723811 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:52:01.723984 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:52:01.724070 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:52:01.724145 INFO: ==============================================
1:52:01.724234 INFO: Starting optimization step 12.
1:52:01.724312 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:01.724403 INFO: Using rust extraction backend
1:52:01.724485 PROGRESS: Extracting batch of 250330 precursors
1:52:02.160728 INFO: === Search parameters used ===
1:52:02.161029 INFO: rt_error       : 805.5982666015625
1:52:02.161089 INFO: mobility_error : 0.1
1:52:02.161146 INFO: num_candidates : 3
1:52:02.161202 INFO: ms1_error      : 30
1:52:02.161249 INFO: ms2_error      : 10.0
1:52:02.161303 INFO: fwhm_rt        : 3.0
1:52:02.161347 INFO: quant_window   : 3
1:52:02.161390 INFO: ==============================================
1:52:05.784462 INFO: performing precursor FDR with 40 features
1:52:05.784639 INFO: Decoy channel: -1
1:52:05.784667 INFO: competitive: True
1:52:05.954688 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:06.244054 INFO: Estimating optimal hyperparameters - samples: 599,677, batch_size: 2,456, learning_rate: 7.74e-04
1:52:06.245165 INFO: Using random state 601882 for train-test-split
1:52:18.404543 INFO: Test AUC: 0.614
1:52:18.404691 INFO: Train AUC: 0.625
1:52:18.404730 INFO: AUC difference: 1.74%
1:52:18.892113 INFO: Resetting torch num_threads to 24
1:52:18.918978 PROGRESS: === Extracted 749597 precursors and 4050142 fragments ===
1:52:18.919514 INFO: === FDR correction performed with classifier version 11 ===
1:52:18.920237 PROGRESS: ============================= Precursor FDR =============================
1:52:18.920331 PROGRESS: Total precursors accumulated: 1,922
1:52:18.920393 PROGRESS: Target precursors: 1,903 (99.01%)
1:52:18.920446 PROGRESS: Decoy precursors: 19 (0.99%)
1:52:18.920493 PROGRESS: 
1:52:18.920540 PROGRESS: Precursor Summary:
1:52:18.922030 PROGRESS: Channel   0:	 0.050 FDR: 1,903; 0.010 FDR: 1,903; 0.001 FDR: 1,241
1:52:18.922116 PROGRESS: 
1:52:18.922175 PROGRESS: Protein Summary:
1:52:18.924092 PROGRESS: Channel   0:	 0.050 FDR: 1,591; 0.010 FDR: 1,591; 0.001 FDR: 1,063
1:52:18.924190 PROGRESS: =========================================================================
1:52:18.936730 INFO: Target number of precursors reached.
1:52:19.367046 INFO: fragments_df: keeping 5000 of 4050142 [sum(precursor_idx_mask)=43288 sum(mass_error_mask)=4050142 stop_rank=5000
1:52:19.804870 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:20.048922 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:20.759589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:52:20.760071 INFO: Using score_cutoff 7.40034751996994 (fac=0.99, q=1)
1:52:20.760400 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:52:20.760479 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:52:20.760534 INFO: Updating optimization_manager: score_cutoff        : 7.536330512237549 -> 7.40034751996994
1:52:20.760591 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:20.916580 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:21.254589 INFO: === checking if optimization conditions were reached ===
1:52:21.257327 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:52:21.257492 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:52:21.257576 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:52:21.257651 INFO: ==============================================
1:52:21.257744 PROGRESS: Optimization finished for ms2_error.
1:52:21.742532 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:21.891205 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:22.228070 INFO: Starting optimization step 0.
1:52:22.228664 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:22.228800 INFO: Using rust extraction backend
1:52:22.228892 PROGRESS: Extracting batch of 250330 precursors
1:52:22.660532 INFO: === Search parameters used ===
1:52:22.660923 INFO: rt_error       : 805.5982666015625
1:52:22.660985 INFO: mobility_error : 0.1
1:52:22.661037 INFO: num_candidates : 3
1:52:22.661084 INFO: ms1_error      : 30
1:52:22.661127 INFO: ms2_error      : 10.0
1:52:22.661170 INFO: fwhm_rt        : 3.0
1:52:22.661212 INFO: quant_window   : 3
1:52:22.661256 INFO: ==============================================
1:52:26.096979 INFO: performing precursor FDR with 40 features
1:52:26.097106 INFO: Decoy channel: -1
1:52:26.097133 INFO: competitive: True
1:52:26.269069 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:26.556827 INFO: Estimating optimal hyperparameters - samples: 599,682, batch_size: 2,456, learning_rate: 7.74e-04
1:52:26.557834 INFO: Using random state 774573 for train-test-split
1:52:38.687546 INFO: Test AUC: 0.614
1:52:38.687692 INFO: Train AUC: 0.627
1:52:38.687727 INFO: AUC difference: 1.97%
1:52:39.179899 INFO: Resetting torch num_threads to 24
1:52:39.205718 PROGRESS: === Extracted 749603 precursors and 4050223 fragments ===
1:52:39.206209 INFO: === FDR correction performed with classifier version 12 ===
1:52:39.206906 PROGRESS: ============================= Precursor FDR =============================
1:52:39.206996 PROGRESS: Total precursors accumulated: 1,732
1:52:39.207058 PROGRESS: Target precursors: 1,715 (99.02%)
1:52:39.207111 PROGRESS: Decoy precursors: 17 (0.98%)
1:52:39.207169 PROGRESS: 
1:52:39.207214 PROGRESS: Precursor Summary:
1:52:39.208630 PROGRESS: Channel   0:	 0.050 FDR: 1,715; 0.010 FDR: 1,715; 0.001 FDR: 1,274
1:52:39.208722 PROGRESS: 
1:52:39.208778 PROGRESS: Protein Summary:
1:52:39.210622 PROGRESS: Channel   0:	 0.050 FDR: 1,431; 0.010 FDR: 1,431; 0.001 FDR: 1,077
1:52:39.210717 PROGRESS: =========================================================================
1:52:39.223873 INFO: Target number of precursors reached.
1:52:39.645947 INFO: fragments_df: keeping 5000 of 4050223 [sum(precursor_idx_mask)=40382 sum(mass_error_mask)=4050223 stop_rank=5000
1:52:40.058597 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:40.320052 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:41.038071 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:52:41.038519 INFO: Using score_cutoff 9.807796034431457 (fac=0.99, q=1)
1:52:41.038828 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:52:41.038908 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:52:41.038964 INFO: Updating optimization_manager: score_cutoff        : 7.40034751996994 -> 9.807796034431457
1:52:41.039019 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:41.190431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:41.529019 INFO: === checking if optimization conditions were reached ===
1:52:41.529285 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:52:41.532125 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 759.1539440215486
1:52:41.532232 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 759.1539.
1:52:41.532300 INFO: ==============================================
1:52:41.532375 INFO: Starting optimization step 1.
1:52:41.532437 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:41.532505 INFO: Using rust extraction backend
1:52:41.532568 PROGRESS: Extracting batch of 250330 precursors
1:52:41.966763 INFO: === Search parameters used ===
1:52:41.967046 INFO: rt_error       : 759.1539440215486
1:52:41.967105 INFO: mobility_error : 0.1
1:52:41.967155 INFO: num_candidates : 3
1:52:41.967200 INFO: ms1_error      : 30
1:52:41.967244 INFO: ms2_error      : 10.0
1:52:41.967300 INFO: fwhm_rt        : 3.0
1:52:41.967341 INFO: quant_window   : 3
1:52:41.967382 INFO: ==============================================
1:52:45.337073 INFO: performing precursor FDR with 40 features
1:52:45.337194 INFO: Decoy channel: -1
1:52:45.337220 INFO: competitive: True
1:52:45.505792 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:45.793235 INFO: Estimating optimal hyperparameters - samples: 599,668, batch_size: 2,456, learning_rate: 7.74e-04
1:52:45.794401 INFO: Using random state 774573 for train-test-split
1:52:57.828364 INFO: Test AUC: 0.615
1:52:57.828492 INFO: Train AUC: 0.626
1:52:57.828526 INFO: AUC difference: 1.83%
1:52:59.358547 INFO: Resetting torch num_threads to 24
1:52:59.384728 PROGRESS: === Extracted 749585 precursors and 4050042 fragments ===
1:52:59.385217 INFO: === FDR correction performed with classifier version 12 ===
1:52:59.385930 PROGRESS: ============================= Precursor FDR =============================
1:52:59.386021 PROGRESS: Total precursors accumulated: 1,784
1:52:59.386081 PROGRESS: Target precursors: 1,767 (99.05%)
1:52:59.386134 PROGRESS: Decoy precursors: 17 (0.95%)
1:52:59.386182 PROGRESS: 
1:52:59.386228 PROGRESS: Precursor Summary:
1:52:59.387775 PROGRESS: Channel   0:	 0.050 FDR: 1,767; 0.010 FDR: 1,767; 0.001 FDR: 1,174
1:52:59.387873 PROGRESS: 
1:52:59.387931 PROGRESS: Protein Summary:
1:52:59.389803 PROGRESS: Channel   0:	 0.050 FDR: 1,483; 0.010 FDR: 1,483; 0.001 FDR: 1,007
1:52:59.389907 PROGRESS: =========================================================================
1:52:59.403396 INFO: Target number of precursors reached.
1:52:59.843893 INFO: fragments_df: keeping 5000 of 4050042 [sum(precursor_idx_mask)=40398 sum(mass_error_mask)=4050042 stop_rank=5000
1:53:00.257725 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:00.527161 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:01.242614 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:01.243070 INFO: Using score_cutoff 7.47738085641861 (fac=0.99, q=1)
1:53:01.243383 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:01.243470 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:01.243536 INFO: Updating optimization_manager: score_cutoff        : 9.807796034431457 -> 7.47738085641861
1:53:01.243590 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:01.392861 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:01.734616 INFO: === checking if optimization conditions were reached ===
1:53:01.734877 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:53:01.737818 INFO: Updating optimization_manager: rt_error            : 759.1539440215486 -> 886.0521877064581
1:53:01.737926 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 886.0522.
1:53:01.737991 INFO: ==============================================
1:53:01.738060 INFO: Starting optimization step 2.
1:53:01.738117 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:53:01.738189 INFO: Using rust extraction backend
1:53:01.738254 PROGRESS: Extracting batch of 250330 precursors
1:53:02.166962 INFO: === Search parameters used ===
1:53:02.167239 INFO: rt_error       : 886.0521877064581
1:53:02.167296 INFO: mobility_error : 0.1
1:53:02.167344 INFO: num_candidates : 3
1:53:02.167386 INFO: ms1_error      : 30
1:53:02.167425 INFO: ms2_error      : 10.0
1:53:02.167501 INFO: fwhm_rt        : 3.0
1:53:02.167548 INFO: quant_window   : 3
1:53:02.167591 INFO: ==============================================
1:53:05.540430 INFO: performing precursor FDR with 40 features
1:53:05.540557 INFO: Decoy channel: -1
1:53:05.540584 INFO: competitive: True
1:53:05.710499 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:05.992967 INFO: Estimating optimal hyperparameters - samples: 599,645, batch_size: 2,456, learning_rate: 7.74e-04
1:53:05.994098 INFO: Using random state 774573 for train-test-split
1:53:18.129719 INFO: Test AUC: 0.613
1:53:18.129872 INFO: Train AUC: 0.626
1:53:18.129905 INFO: AUC difference: 2.09%
1:53:18.623087 INFO: Resetting torch num_threads to 24
1:53:18.652285 PROGRESS: === Extracted 749557 precursors and 4050123 fragments ===
1:53:18.652786 INFO: === FDR correction performed with classifier version 12 ===
1:53:18.653485 PROGRESS: ============================= Precursor FDR =============================
1:53:18.653575 PROGRESS: Total precursors accumulated: 1,656
1:53:18.653638 PROGRESS: Target precursors: 1,640 (99.03%)
1:53:18.653689 PROGRESS: Decoy precursors: 16 (0.97%)
1:53:18.653738 PROGRESS: 
1:53:18.653783 PROGRESS: Precursor Summary:
1:53:18.655167 PROGRESS: Channel   0:	 0.050 FDR: 1,640; 0.010 FDR: 1,640; 0.001 FDR:   377
1:53:18.655259 PROGRESS: 
1:53:18.655316 PROGRESS: Protein Summary:
1:53:18.657119 PROGRESS: Channel   0:	 0.050 FDR: 1,365; 0.010 FDR: 1,365; 0.001 FDR:   348
1:53:18.657215 PROGRESS: =========================================================================
1:53:18.670437 INFO: Target number of precursors reached.
1:53:19.098310 INFO: fragments_df: keeping 5000 of 4050123 [sum(precursor_idx_mask)=39090 sum(mass_error_mask)=4050123 stop_rank=5000
1:53:19.511870 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:19.756522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:20.406401 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:20.406863 INFO: Using score_cutoff 11.847207128047943 (fac=0.99, q=1)
1:53:20.407182 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:20.407261 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:20.407324 INFO: Updating optimization_manager: score_cutoff        : 7.47738085641861 -> 11.847207128047943
1:53:20.407378 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:20.560368 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:20.888007 INFO: === checking if optimization conditions were reached ===
1:53:20.888281 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:53:20.891272 INFO: Updating optimization_manager: rt_error            : 886.0521877064581 -> 593.0733599448013
1:53:20.891375 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 593.0734.
1:53:20.891464 INFO: ==============================================
1:53:20.891552 INFO: Starting optimization step 3.
1:53:20.891615 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:53:20.891682 INFO: Using rust extraction backend
1:53:20.891743 PROGRESS: Extracting batch of 250330 precursors
1:53:21.324931 INFO: === Search parameters used ===
1:53:21.325204 INFO: rt_error       : 593.0733599448013
1:53:21.325261 INFO: mobility_error : 0.1
1:53:21.325307 INFO: num_candidates : 3
1:53:21.325349 INFO: ms1_error      : 30
1:53:21.325388 INFO: ms2_error      : 10.0
1:53:21.325427 INFO: fwhm_rt        : 3.0
1:53:21.325464 INFO: quant_window   : 3
1:53:21.325503 INFO: ==============================================
1:53:24.518358 INFO: performing precursor FDR with 40 features
1:53:24.518485 INFO: Decoy channel: -1
1:53:24.518512 INFO: competitive: True
1:53:24.698056 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:25.001875 INFO: Estimating optimal hyperparameters - samples: 599,476, batch_size: 2,455, learning_rate: 7.74e-04
1:53:25.003020 INFO: Using random state 774573 for train-test-split
1:53:37.675215 INFO: Test AUC: 0.615
1:53:37.675355 INFO: Train AUC: 0.625
1:53:37.675389 INFO: AUC difference: 1.60%
1:53:38.159348 INFO: Resetting torch num_threads to 24
1:53:38.186583 PROGRESS: === Extracted 749346 precursors and 4033516 fragments ===
1:53:38.187080 INFO: === FDR correction performed with classifier version 12 ===
1:53:38.187798 PROGRESS: ============================= Precursor FDR =============================
1:53:38.187893 PROGRESS: Total precursors accumulated: 1,668
1:53:38.187955 PROGRESS: Target precursors: 1,652 (99.04%)
1:53:38.188007 PROGRESS: Decoy precursors: 16 (0.96%)
1:53:38.188055 PROGRESS: 
1:53:38.188100 PROGRESS: Precursor Summary:
1:53:38.189526 PROGRESS: Channel   0:	 0.050 FDR: 1,652; 0.010 FDR: 1,652; 0.001 FDR: 1,208
1:53:38.189626 PROGRESS: 
1:53:38.189687 PROGRESS: Protein Summary:
1:53:38.191542 PROGRESS: Channel   0:	 0.050 FDR: 1,371; 0.010 FDR: 1,371; 0.001 FDR: 1,031
1:53:38.191636 PROGRESS: =========================================================================
1:53:38.204885 INFO: Target number of precursors reached.
1:53:38.650820 INFO: fragments_df: keeping 5000 of 4033516 [sum(precursor_idx_mask)=39319 sum(mass_error_mask)=4033516 stop_rank=5000
1:53:39.064745 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:39.282067 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:39.929510 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:39.929970 INFO: Using score_cutoff 11.655903659820558 (fac=0.99, q=1)
1:53:39.930289 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:39.930369 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:39.930425 INFO: Updating optimization_manager: score_cutoff        : 11.847207128047943 -> 11.655903659820558
1:53:39.930479 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:40.082894 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:40.419672 INFO: === checking if optimization conditions were reached ===
1:53:40.419969 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:53:40.422935 INFO: Updating optimization_manager: rt_error            : 593.0733599448013 -> 605.5023363094413
1:53:40.423054 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 605.5023.
1:53:40.423119 INFO: ==============================================
1:53:40.423192 INFO: Starting optimization step 4.
1:53:40.423251 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:53:40.423317 INFO: Using rust extraction backend
1:53:40.423381 PROGRESS: Extracting batch of 250330 precursors
1:53:40.856698 INFO: === Search parameters used ===
1:53:40.856997 INFO: rt_error       : 605.5023363094413
1:53:40.857056 INFO: mobility_error : 0.1
1:53:40.857105 INFO: num_candidates : 3
1:53:40.857148 INFO: ms1_error      : 30
1:53:40.857190 INFO: ms2_error      : 10.0
1:53:40.857230 INFO: fwhm_rt        : 3.0
1:53:40.857270 INFO: quant_window   : 3
1:53:40.857308 INFO: ==============================================
1:53:44.046304 INFO: performing precursor FDR with 40 features
1:53:44.046426 INFO: Decoy channel: -1
1:53:44.046451 INFO: competitive: True
1:53:44.215662 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:44.507874 INFO: Estimating optimal hyperparameters - samples: 599,460, batch_size: 2,455, learning_rate: 7.74e-04
1:53:44.508999 INFO: Using random state 774573 for train-test-split
1:53:57.159332 INFO: Test AUC: 0.613
1:53:57.159520 INFO: Train AUC: 0.626
1:53:57.159557 INFO: AUC difference: 2.09%
1:53:57.636353 INFO: Resetting torch num_threads to 24
1:53:57.664495 PROGRESS: === Extracted 749325 precursors and 4032957 fragments ===
1:53:57.664989 INFO: === FDR correction performed with classifier version 12 ===
1:53:57.665673 PROGRESS: ============================= Precursor FDR =============================
1:53:57.665763 PROGRESS: Total precursors accumulated: 1,685
1:53:57.665825 PROGRESS: Target precursors: 1,669 (99.05%)
1:53:57.665879 PROGRESS: Decoy precursors: 16 (0.95%)
1:53:57.665927 PROGRESS: 
1:53:57.665983 PROGRESS: Precursor Summary:
1:53:57.667390 PROGRESS: Channel   0:	 0.050 FDR: 1,669; 0.010 FDR: 1,669; 0.001 FDR: 1,210
1:53:57.667496 PROGRESS: 
1:53:57.667555 PROGRESS: Protein Summary:
1:53:57.669383 PROGRESS: Channel   0:	 0.050 FDR: 1,397; 0.010 FDR: 1,397; 0.001 FDR: 1,034
1:53:57.669476 PROGRESS: =========================================================================
1:53:57.682610 INFO: Target number of precursors reached.
1:53:58.097999 INFO: fragments_df: keeping 5000 of 4032957 [sum(precursor_idx_mask)=39443 sum(mass_error_mask)=4032957 stop_rank=5000
1:53:58.519308 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:58.771094 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:59.482927 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:59.483377 INFO: Using score_cutoff 9.960761333084106 (fac=0.99, q=1)
1:53:59.483704 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:59.483786 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:59.483847 INFO: Updating optimization_manager: score_cutoff        : 11.655903659820558 -> 9.960761333084106
1:53:59.483902 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:59.634085 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:59.977038 INFO: === checking if optimization conditions were reached ===
1:53:59.977353 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:53:59.978563 INFO: Updating optimization_manager: rt_error            : 605.5023363094413 -> 759.1539440215486
1:53:59.978738 INFO: Updating optimization_manager: classifier_version  : 12 -> 14
1:53:59.978855 INFO: Updating optimization_manager: score_cutoff        : 9.960761333084106 -> 7.47738085641861
1:53:59.978961 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:59.979067 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:59.979174 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 759.1539 found after 5 searches.
1:53:59.979260 INFO: ==============================================
1:53:59.979345 PROGRESS: Optimization finished for rt_error.
1:54:00.392230 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:00.542790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:00.880937 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:54:00.881236 PROGRESS: ==============================================
1:54:00.881332 PROGRESS: ms2_error      : 10.0000
1:54:00.881401 PROGRESS: rt_error       : 759.1539
1:54:00.881460 PROGRESS: ==============================================
1:54:00.882406 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:08.432413 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:25.239099 INFO: Using rust extraction backend
1:54:25.239436 PROGRESS: Extracting batch of 11997144 precursors
1:54:41.528537 INFO: === Search parameters used ===
1:54:41.528879 INFO: rt_error       : 759.1539440215486
1:54:41.528949 INFO: mobility_error : 0.1
1:54:41.529007 INFO: num_candidates : 3
1:54:41.529055 INFO: ms1_error      : 30
1:54:41.529100 INFO: ms2_error      : 10.0
1:54:41.529145 INFO: fwhm_rt        : 3.0
1:54:41.529189 INFO: quant_window   : 3
1:54:41.529233 INFO: ==============================================
1:55:45.275847 INFO: Removed 2417345 precursors with score below cutoff 7.47738085641861
1:56:21.920985 INFO: performing precursor FDR with 40 features
1:56:21.921151 INFO: Decoy channel: -1
1:56:21.921179 INFO: competitive: True
1:56:25.451707 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:39.759421 INFO: Estimating optimal hyperparameters - samples: 26,859,008, batch_size: 4,096, learning_rate: 1.00e-03
1:56:39.840902 INFO: Using random state 965645 for train-test-split
2:06:06.344337 INFO: Test AUC: 0.621
2:06:06.344945 INFO: Train AUC: 0.622
2:06:06.345008 INFO: AUC difference: 0.11%
2:06:13.692481 INFO: Resetting torch num_threads to 24
2:06:16.978002 PROGRESS: ============================= Precursor FDR =============================
2:06:16.978457 PROGRESS: Total precursors accumulated: 93,813
2:06:16.978554 PROGRESS: Target precursors: 92,885 (99.01%)
2:06:16.978631 PROGRESS: Decoy precursors: 928 (0.99%)
2:06:16.978684 PROGRESS: 
2:06:16.978730 PROGRESS: Precursor Summary:
2:06:17.004983 PROGRESS: Channel   0:	 0.050 FDR: 92,885; 0.010 FDR: 92,885; 0.001 FDR: 64,401
2:06:17.005234 PROGRESS: 
2:06:17.005296 PROGRESS: Protein Summary:
2:06:17.043421 PROGRESS: Channel   0:	 0.050 FDR: 13,749; 0.010 FDR: 13,749; 0.001 FDR: 9,638
2:06:17.043695 PROGRESS: =========================================================================
2:06:17.304269 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
2:06:17.506144 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
2:06:17.765699 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:06:18.477873 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
2:06:18.478041 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
2:06:18.478128 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
2:06:18.478359 INFO: Initializing TimingManager
2:06:18.478869 INFO: Initializing RawFileManager
2:06:32.443427 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:06:32.451836 INFO: Determining DIA cycle
2:06:32.468733 INFO: Found cycle with start 0.00 min and length 300.
2:06:32.660588 INFO: RT (min)            : 0.0 - 26.9
2:06:32.660693 INFO: RT duration (sec)   : 1611.2
2:06:32.660724 INFO: RT duration (min)   : 26.9
2:06:32.660748 INFO: Cycle len (scans)   : 300
2:06:32.660769 INFO: Cycle len (sec)     : 1.65
2:06:32.660787 INFO: Number of cycles    : 977
2:06:32.660806 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:06:32.660842 INFO: Creating DIA data object took: 14.181878089904785
2:06:34.524055 INFO: Creating DIA data NG object took: 1.8630754947662354
2:06:35.955284 INFO: Initializing CalibrationManager
2:06:35.955577 INFO: Setting up calibration estimators ..
2:06:35.955667 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:06:35.955809 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:06:35.955958 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:06:35.956025 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:06:35.956092 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:06:35.956164 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:06:35.956218 INFO: Done setting up calibration estimators.
2:06:35.956473 INFO: Initializing OptimizationManager
2:06:35.956660 INFO: initial parameter: ms1_error = 30
2:06:35.956717 INFO: initial parameter: ms2_error = 30
2:06:35.956764 INFO: initial parameter: rt_error = 805.6002197265625
2:06:35.956808 INFO: initial parameter: mobility_error = 0.1
2:06:35.956849 INFO: initial parameter: num_candidates = 1
2:06:35.956890 INFO: initial parameter: fwhm_rt = 5
2:06:35.956931 INFO: initial parameter: fwhm_mobility = 0.01
2:06:35.956977 INFO: initial parameter: score_cutoff = 0
2:06:35.957019 INFO: initial parameter: classifier_version = -1
2:06:35.957093 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:06:35.957890 INFO: FDRManager: loading saved state not requested, will be initialized.
2:06:35.957931 INFO: Initializing FDRManager
2:06:35.957987 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:06:37.474348 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
2:06:38.505432 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:06:38.505953 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
2:06:38.506108 PROGRESS: Starting initial search for precursors.
2:06:38.506231 INFO: Starting optimization step 0.
2:06:38.506316 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:06:38.506397 INFO: Using rust extraction backend
2:06:38.506489 PROGRESS: Extracting batch of 1972 precursors
2:06:38.522191 INFO: === Search parameters used ===
2:06:38.522406 INFO: rt_error       : 805.6002197265625
2:06:38.522466 INFO: mobility_error : 0.1
2:06:38.522514 INFO: num_candidates : 1
2:06:38.522558 INFO: ms1_error      : 30
2:06:38.522602 INFO: ms2_error      : 30
2:06:38.522645 INFO: fwhm_rt        : 5
2:06:38.522686 INFO: quant_window   : 3
2:06:38.522726 INFO: ==============================================
2:06:38.564135 INFO: performing precursor FDR with 40 features
2:06:38.564322 INFO: Decoy channel: -1
2:06:38.564350 INFO: competitive: True
2:06:38.566230 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:38.569203 INFO: Estimating optimal hyperparameters - samples: 1,560, batch_size: 128, learning_rate: 1.77e-04
2:06:38.570675 INFO: Using random state 926538 for train-test-split
2:06:38.695558 INFO: Test AUC: 0.521
2:06:38.695658 INFO: Train AUC: 0.595
2:06:38.695689 INFO: AUC difference: 12.37%
2:06:38.695713 WARNING: AUC difference > 5%. This may indicate overfitting.
2:06:38.949995 INFO: Resetting torch num_threads to 24
2:06:38.951957 PROGRESS: === Extracted 1950 precursors and 9210 fragments ===
2:06:38.952427 INFO: === FDR correction performed with classifier version -1 ===
2:06:38.952939 PROGRESS: ============================= Precursor FDR =============================
2:06:38.953034 PROGRESS: Total precursors accumulated: 10
2:06:38.953093 PROGRESS: Target precursors: 10 (100.00%)
2:06:38.953141 PROGRESS: Decoy precursors: 0 (0.00%)
2:06:38.953185 PROGRESS: 
2:06:38.953227 PROGRESS: Precursor Summary:
2:06:38.954306 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
2:06:38.954387 PROGRESS: 
2:06:38.954441 PROGRESS: Protein Summary:
2:06:38.955672 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
2:06:38.955767 PROGRESS: =========================================================================
2:06:38.956172 INFO: Target number of precursors not reached yet.
2:06:39.044180 INFO: Starting optimization step 1.
2:06:39.044432 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:06:39.044545 INFO: Using rust extraction backend
2:06:39.044621 PROGRESS: Extracting batch of 3939 precursors
2:06:39.053424 INFO: === Search parameters used ===
2:06:39.053550 INFO: rt_error       : 805.6002197265625
2:06:39.053607 INFO: mobility_error : 0.1
2:06:39.053653 INFO: num_candidates : 1
2:06:39.053694 INFO: ms1_error      : 30
2:06:39.053734 INFO: ms2_error      : 30
2:06:39.053775 INFO: fwhm_rt        : 5
2:06:39.053815 INFO: quant_window   : 3
2:06:39.053855 INFO: ==============================================
2:06:39.117305 INFO: performing precursor FDR with 40 features
2:06:39.117412 INFO: Decoy channel: -1
2:06:39.117436 INFO: competitive: True
2:06:39.122624 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:39.125138 INFO: Estimating optimal hyperparameters - samples: 4,678, batch_size: 128, learning_rate: 1.77e-04
2:06:39.125243 INFO: Using random state 515088 for train-test-split
2:06:39.669484 INFO: Test AUC: 0.536
2:06:39.669591 INFO: Train AUC: 0.557
2:06:39.669618 INFO: AUC difference: 3.83%
2:06:39.915471 INFO: Resetting torch num_threads to 24
2:06:39.918521 PROGRESS: === Extracted 5848 precursors and 27669 fragments ===
2:06:39.918899 INFO: === FDR correction performed with classifier version -1 ===
2:06:39.919402 PROGRESS: ============================= Precursor FDR =============================
2:06:39.919501 PROGRESS: Total precursors accumulated: 11
2:06:39.919563 PROGRESS: Target precursors: 11 (100.00%)
2:06:39.919613 PROGRESS: Decoy precursors: 0 (0.00%)
2:06:39.919660 PROGRESS: 
2:06:39.919703 PROGRESS: Precursor Summary:
2:06:39.920753 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2:06:39.920834 PROGRESS: 
2:06:39.920886 PROGRESS: Protein Summary:
2:06:39.922042 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2:06:39.922124 PROGRESS: =========================================================================
2:06:39.922415 INFO: Target number of precursors not reached yet.
2:06:40.017583 INFO: Starting optimization step 2.
2:06:40.017818 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:06:40.017895 INFO: Using rust extraction backend
2:06:40.017952 PROGRESS: Extracting batch of 7870 precursors
2:06:40.033299 INFO: === Search parameters used ===
2:06:40.033479 INFO: rt_error       : 805.6002197265625
2:06:40.033531 INFO: mobility_error : 0.1
2:06:40.033575 INFO: num_candidates : 1
2:06:40.033617 INFO: ms1_error      : 30
2:06:40.033657 INFO: ms2_error      : 30
2:06:40.033696 INFO: fwhm_rt        : 5
2:06:40.033735 INFO: quant_window   : 3
2:06:40.033773 INFO: ==============================================
2:06:40.157267 INFO: performing precursor FDR with 40 features
2:06:40.157377 INFO: Decoy channel: -1
2:06:40.157399 INFO: competitive: True
2:06:40.163702 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:40.167692 INFO: Estimating optimal hyperparameters - samples: 10,922, batch_size: 128, learning_rate: 1.77e-04
2:06:40.167806 INFO: Using random state 799182 for train-test-split
2:06:41.506070 INFO: Test AUC: 0.531
2:06:41.506179 INFO: Train AUC: 0.594
2:06:41.506207 INFO: AUC difference: 10.69%
2:06:41.506226 WARNING: AUC difference > 5%. This may indicate overfitting.
2:06:41.755919 INFO: Resetting torch num_threads to 24
2:06:41.760409 PROGRESS: === Extracted 13653 precursors and 64377 fragments ===
2:06:41.760829 INFO: === FDR correction performed with classifier version -1 ===
2:06:41.761348 PROGRESS: ============================= Precursor FDR =============================
2:06:41.761432 PROGRESS: Total precursors accumulated: 59
2:06:41.761488 PROGRESS: Target precursors: 59 (100.00%)
2:06:41.761537 PROGRESS: Decoy precursors: 0 (0.00%)
2:06:41.761583 PROGRESS: 
2:06:41.761626 PROGRESS: Precursor Summary:
2:06:41.762701 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
2:06:41.762781 PROGRESS: 
2:06:41.762834 PROGRESS: Protein Summary:
2:06:41.764056 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
2:06:41.764143 PROGRESS: =========================================================================
2:06:41.764506 INFO: Target number of precursors not reached yet.
2:06:41.876620 INFO: Starting optimization step 3.
2:06:41.876857 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:06:41.876934 INFO: Using rust extraction backend
2:06:41.876992 PROGRESS: Extracting batch of 15774 precursors
2:06:41.906028 INFO: === Search parameters used ===
2:06:41.906221 INFO: rt_error       : 805.6002197265625
2:06:41.906272 INFO: mobility_error : 0.1
2:06:41.906317 INFO: num_candidates : 1
2:06:41.906360 INFO: ms1_error      : 30
2:06:41.906401 INFO: ms2_error      : 30
2:06:41.906451 INFO: fwhm_rt        : 5
2:06:41.906493 INFO: quant_window   : 3
2:06:41.906533 INFO: ==============================================
2:06:42.086300 INFO: performing precursor FDR with 40 features
2:06:42.086416 INFO: Decoy channel: -1
2:06:42.086440 INFO: competitive: True
2:06:42.099021 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:42.107014 INFO: Estimating optimal hyperparameters - samples: 23,438, batch_size: 128, learning_rate: 1.77e-04
2:06:42.107226 INFO: Using random state 239233 for train-test-split
2:06:45.035136 INFO: Test AUC: 0.578
2:06:45.035352 INFO: Train AUC: 0.607
2:06:45.035388 INFO: AUC difference: 4.77%
2:06:45.288271 INFO: Resetting torch num_threads to 24
2:06:45.296081 PROGRESS: === Extracted 29298 precursors and 138525 fragments ===
2:06:45.296689 INFO: === FDR correction performed with classifier version -1 ===
2:06:45.297277 PROGRESS: ============================= Precursor FDR =============================
2:06:45.297369 PROGRESS: Total precursors accumulated: 48
2:06:45.297432 PROGRESS: Target precursors: 48 (100.00%)
2:06:45.297489 PROGRESS: Decoy precursors: 0 (0.00%)
2:06:45.297538 PROGRESS: 
2:06:45.297585 PROGRESS: Precursor Summary:
2:06:45.298674 PROGRESS: Channel   0:	 0.050 FDR:    48; 0.010 FDR:    48; 0.001 FDR:    48
2:06:45.298763 PROGRESS: 
2:06:45.298821 PROGRESS: Protein Summary:
2:06:45.300035 PROGRESS: Channel   0:	 0.050 FDR:    48; 0.010 FDR:    48; 0.001 FDR:    48
2:06:45.300128 PROGRESS: =========================================================================
2:06:45.301135 INFO: Target number of precursors not reached yet.
2:06:45.449607 INFO: Starting optimization step 4.
2:06:45.449874 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:06:45.449983 INFO: Using rust extraction backend
2:06:45.450060 PROGRESS: Extracting batch of 31503 precursors
2:06:45.508866 INFO: === Search parameters used ===
2:06:45.509142 INFO: rt_error       : 805.6002197265625
2:06:45.509196 INFO: mobility_error : 0.1
2:06:45.509250 INFO: num_candidates : 1
2:06:45.509294 INFO: ms1_error      : 30
2:06:45.509336 INFO: ms2_error      : 30
2:06:45.509378 INFO: fwhm_rt        : 5
2:06:45.509419 INFO: quant_window   : 3
2:06:45.509459 INFO: ==============================================
2:06:45.829120 INFO: performing precursor FDR with 40 features
2:06:45.829236 INFO: Decoy channel: -1
2:06:45.829273 INFO: competitive: True
2:06:45.854290 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:45.870997 INFO: Estimating optimal hyperparameters - samples: 48,411, batch_size: 198, learning_rate: 2.20e-04
2:06:45.871246 INFO: Using random state 106817 for train-test-split
2:06:50.453812 INFO: Test AUC: 0.576
2:06:50.453914 INFO: Train AUC: 0.615
2:06:50.453944 INFO: AUC difference: 6.34%
2:06:50.453966 WARNING: AUC difference > 5%. This may indicate overfitting.
2:06:50.719929 INFO: Resetting torch num_threads to 24
2:06:50.733759 PROGRESS: === Extracted 60514 precursors and 286556 fragments ===
2:06:50.734356 INFO: === FDR correction performed with classifier version -1 ===
2:06:50.734926 PROGRESS: ============================= Precursor FDR =============================
2:06:50.735015 PROGRESS: Total precursors accumulated: 215
2:06:50.735076 PROGRESS: Target precursors: 213 (99.07%)
2:06:50.735130 PROGRESS: Decoy precursors: 2 (0.93%)
2:06:50.735178 PROGRESS: 
2:06:50.735223 PROGRESS: Precursor Summary:
2:06:50.736259 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:   149
2:06:50.736356 PROGRESS: 
2:06:50.736412 PROGRESS: Protein Summary:
2:06:50.737586 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:   145
2:06:50.737672 PROGRESS: =========================================================================
2:06:50.738784 INFO: Target number of precursors not reached yet.
2:06:50.930829 INFO: Starting optimization step 5.
2:06:50.931099 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:06:50.931179 INFO: Using rust extraction backend
2:06:50.931243 PROGRESS: Extracting batch of 63125 precursors
2:06:51.046193 INFO: === Search parameters used ===
2:06:51.046454 INFO: rt_error       : 805.6002197265625
2:06:51.046512 INFO: mobility_error : 0.1
2:06:51.046559 INFO: num_candidates : 1
2:06:51.046603 INFO: ms1_error      : 30
2:06:51.046645 INFO: ms2_error      : 30
2:06:51.046690 INFO: fwhm_rt        : 5
2:06:51.046739 INFO: quant_window   : 3
2:06:51.046783 INFO: ==============================================
2:06:51.664824 INFO: performing precursor FDR with 40 features
2:06:51.664937 INFO: Decoy channel: -1
2:06:51.664963 INFO: competitive: True
2:06:51.721820 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:51.765889 INFO: Estimating optimal hyperparameters - samples: 98,449, batch_size: 403, learning_rate: 3.14e-04
2:06:51.766246 INFO: Using random state 265865 for train-test-split
2:06:57.667855 INFO: Test AUC: 0.585
2:06:57.667986 INFO: Train AUC: 0.612
2:06:57.668017 INFO: AUC difference: 4.32%
2:06:57.956823 INFO: Resetting torch num_threads to 24
2:06:57.986439 PROGRESS: === Extracted 123062 precursors and 583209 fragments ===
2:06:57.987097 INFO: === FDR correction performed with classifier version -1 ===
2:06:57.988032 PROGRESS: ============================= Precursor FDR =============================
2:06:57.988132 PROGRESS: Total precursors accumulated: 516
2:06:57.988195 PROGRESS: Target precursors: 511 (99.03%)
2:06:57.988249 PROGRESS: Decoy precursors: 5 (0.97%)
2:06:57.988297 PROGRESS: 
2:06:57.988353 PROGRESS: Precursor Summary:
2:06:57.989476 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   511; 0.001 FDR:   306
2:06:57.989563 PROGRESS: 
2:06:57.989618 PROGRESS: Protein Summary:
2:06:57.990921 PROGRESS: Channel   0:	 0.050 FDR:   475; 0.010 FDR:   475; 0.001 FDR:   288
2:06:57.991008 PROGRESS: =========================================================================
2:06:57.993402 INFO: Target number of precursors not reached yet.
2:06:58.271554 INFO: Starting optimization step 6.
2:06:58.271832 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:06:58.271917 INFO: Using rust extraction backend
2:06:58.271988 PROGRESS: Extracting batch of 126147 precursors
2:06:58.495001 INFO: === Search parameters used ===
2:06:58.495248 INFO: rt_error       : 805.6002197265625
2:06:58.495306 INFO: mobility_error : 0.1
2:06:58.495358 INFO: num_candidates : 1
2:06:58.495404 INFO: ms1_error      : 30
2:06:58.495471 INFO: ms2_error      : 30
2:06:58.495522 INFO: fwhm_rt        : 5
2:06:58.495564 INFO: quant_window   : 3
2:06:58.495603 INFO: ==============================================
2:06:59.675232 INFO: performing precursor FDR with 40 features
2:06:59.675364 INFO: Decoy channel: -1
2:06:59.675390 INFO: competitive: True
2:06:59.793730 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:59.929581 INFO: Estimating optimal hyperparameters - samples: 198,449, batch_size: 812, learning_rate: 4.45e-04
2:06:59.930146 INFO: Using random state 242700 for train-test-split
2:07:07.814858 INFO: Test AUC: 0.592
2:07:07.814995 INFO: Train AUC: 0.610
2:07:07.815027 INFO: AUC difference: 2.99%
2:07:08.143340 INFO: Resetting torch num_threads to 24
2:07:08.197852 PROGRESS: === Extracted 248062 precursors and 1174058 fragments ===
2:07:08.198511 INFO: === FDR correction performed with classifier version -1 ===
2:07:08.199507 PROGRESS: ============================= Precursor FDR =============================
2:07:08.199607 PROGRESS: Total precursors accumulated: 887
2:07:08.199669 PROGRESS: Target precursors: 879 (99.10%)
2:07:08.199721 PROGRESS: Decoy precursors: 8 (0.90%)
2:07:08.199767 PROGRESS: 
2:07:08.199813 PROGRESS: Precursor Summary:
2:07:08.201010 PROGRESS: Channel   0:	 0.050 FDR:   879; 0.010 FDR:   879; 0.001 FDR:   715
2:07:08.201105 PROGRESS: 
2:07:08.201161 PROGRESS: Protein Summary:
2:07:08.202650 PROGRESS: Channel   0:	 0.050 FDR:   759; 0.010 FDR:   759; 0.001 FDR:   631
2:07:08.202741 PROGRESS: =========================================================================
2:07:08.207116 INFO: Target number of precursors not reached yet.
2:07:08.661175 INFO: Starting optimization step 7.
2:07:08.661457 PROGRESS: === Extracting elution groups 127000 to 255000 ===
2:07:08.661548 INFO: Using rust extraction backend
2:07:08.661617 PROGRESS: Extracting batch of 252313 precursors
2:07:09.104076 INFO: === Search parameters used ===
2:07:09.104328 INFO: rt_error       : 805.6002197265625
2:07:09.104388 INFO: mobility_error : 0.1
2:07:09.104437 INFO: num_candidates : 1
2:07:09.104483 INFO: ms1_error      : 30
2:07:09.104538 INFO: ms2_error      : 30
2:07:09.104584 INFO: fwhm_rt        : 5
2:07:09.104626 INFO: quant_window   : 3
2:07:09.104671 INFO: ==============================================
2:07:11.480506 INFO: performing precursor FDR with 40 features
2:07:11.480629 INFO: Decoy channel: -1
2:07:11.480656 INFO: competitive: True
2:07:11.726149 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:12.072252 INFO: Estimating optimal hyperparameters - samples: 398,423, batch_size: 1,631, learning_rate: 6.31e-04
2:07:12.073046 INFO: Using random state 743954 for train-test-split
2:07:24.526641 INFO: Test AUC: 0.591
2:07:24.526804 INFO: Train AUC: 0.608
2:07:24.526837 INFO: AUC difference: 2.78%
2:07:24.930460 INFO: Resetting torch num_threads to 24
2:07:25.043904 PROGRESS: === Extracted 498029 precursors and 2355178 fragments ===
2:07:25.044598 INFO: === FDR correction performed with classifier version -1 ===
2:07:25.045621 PROGRESS: ============================= Precursor FDR =============================
2:07:25.045710 PROGRESS: Total precursors accumulated: 2,054
2:07:25.045769 PROGRESS: Target precursors: 2,034 (99.03%)
2:07:25.045820 PROGRESS: Decoy precursors: 20 (0.97%)
2:07:25.045866 PROGRESS: 
2:07:25.045910 PROGRESS: Precursor Summary:
2:07:25.047406 PROGRESS: Channel   0:	 0.050 FDR: 2,034; 0.010 FDR: 2,034; 0.001 FDR: 1,417
2:07:25.047507 PROGRESS: 
2:07:25.047565 PROGRESS: Protein Summary:
2:07:25.049537 PROGRESS: Channel   0:	 0.050 FDR: 1,558; 0.010 FDR: 1,558; 0.001 FDR: 1,130
2:07:25.049627 PROGRESS: =========================================================================
2:07:25.057482 INFO: Target number of precursors reached.
2:07:25.344934 INFO: fragments_df: keeping 5000 of 2355178 [sum(precursor_idx_mask)=21763 sum(mass_error_mask)=2355178 stop_rank=5000
2:07:25.814801 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:07:26.078952 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:07:26.732589 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:07:26.733027 INFO: Using score_cutoff 12.531769219493867 (fac=0.99, q=1)
2:07:26.733406 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:07:26.733486 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:07:26.733542 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.531769219493867
2:07:26.733613 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:26.885099 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:27.248627 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
2:07:27.248904 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:07:27.249001 INFO: Starting optimization step 8.
2:07:27.249063 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:07:27.249131 INFO: Using rust extraction backend
2:07:27.249191 PROGRESS: Extracting batch of 250330 precursors
2:07:27.700901 INFO: === Search parameters used ===
2:07:27.701144 INFO: rt_error       : 805.6002197265625
2:07:27.701200 INFO: mobility_error : 0.1
2:07:27.701247 INFO: num_candidates : 3
2:07:27.701292 INFO: ms1_error      : 30
2:07:27.701333 INFO: ms2_error      : 30
2:07:27.701374 INFO: fwhm_rt        : 3.0
2:07:27.701420 INFO: quant_window   : 3
2:07:27.701462 INFO: ==============================================
2:07:32.523983 INFO: performing precursor FDR with 40 features
2:07:32.524141 INFO: Decoy channel: -1
2:07:32.524167 INFO: competitive: True
2:07:33.161247 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:34.551986 INFO: Estimating optimal hyperparameters - samples: 595,720, batch_size: 2,440, learning_rate: 7.72e-04
2:07:34.553305 INFO: Using random state 294415 for train-test-split
2:07:52.104011 INFO: Test AUC: 0.597
2:07:52.104402 INFO: Train AUC: 0.609
2:07:52.104446 INFO: AUC difference: 2.05%
2:07:52.640051 INFO: Resetting torch num_threads to 24
2:07:52.675043 PROGRESS: === Extracted 744651 precursors and 3448283 fragments ===
2:07:52.675697 INFO: === FDR correction performed with classifier version 7 ===
2:07:52.676583 PROGRESS: ============================= Precursor FDR =============================
2:07:52.676699 PROGRESS: Total precursors accumulated: 1,135
2:07:52.676770 PROGRESS: Target precursors: 1,124 (99.03%)
2:07:52.676825 PROGRESS: Decoy precursors: 11 (0.97%)
2:07:52.676882 PROGRESS: 
2:07:52.676931 PROGRESS: Precursor Summary:
2:07:52.678284 PROGRESS: Channel   0:	 0.050 FDR: 1,124; 0.010 FDR: 1,124; 0.001 FDR:   560
2:07:52.678382 PROGRESS: 
2:07:52.678440 PROGRESS: Protein Summary:
2:07:52.680062 PROGRESS: Channel   0:	 0.050 FDR:   953; 0.010 FDR:   953; 0.001 FDR:   501
2:07:52.680166 PROGRESS: =========================================================================
2:07:52.698178 INFO: Target number of precursors reached.
2:07:53.072538 INFO: fragments_df: keeping 5000 of 3448283 [sum(precursor_idx_mask)=25332 sum(mass_error_mask)=3448283 stop_rank=5000
2:07:54.197839 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:07:54.405529 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:07:55.135589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:07:55.136193 INFO: Using score_cutoff 12.703996038722993 (fac=0.99, q=1)
2:07:55.136570 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:07:55.136647 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:07:55.136701 INFO: Updating optimization_manager: score_cutoff        : 12.531769219493867 -> 12.703996038722993
2:07:55.136770 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:07:55.292254 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:55.671943 INFO: === checking if optimization conditions were reached ===
2:07:55.674447 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:07:55.674558 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
2:07:55.674649 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:07:55.674719 INFO: ==============================================
2:07:55.674797 INFO: Starting optimization step 9.
2:07:55.674872 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:07:55.674951 INFO: Using rust extraction backend
2:07:55.675027 PROGRESS: Extracting batch of 250330 precursors
2:07:56.123994 INFO: === Search parameters used ===
2:07:56.124268 INFO: rt_error       : 805.6002197265625
2:07:56.124322 INFO: mobility_error : 0.1
2:07:56.124369 INFO: num_candidates : 3
2:07:56.124414 INFO: ms1_error      : 30
2:07:56.124457 INFO: ms2_error      : 10.0
2:07:56.124761 INFO: fwhm_rt        : 3.0
2:07:56.124806 INFO: quant_window   : 3
2:07:56.124846 INFO: ==============================================
2:08:03.403358 INFO: performing precursor FDR with 40 features
2:08:03.403542 INFO: Decoy channel: -1
2:08:03.403572 INFO: competitive: True
2:08:03.848150 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:05.752620 INFO: Estimating optimal hyperparameters - samples: 599,636, batch_size: 2,456, learning_rate: 7.74e-04
2:08:05.755702 INFO: Using random state 538547 for train-test-split
2:08:27.183217 INFO: Test AUC: 0.605
2:08:27.183450 INFO: Train AUC: 0.613
2:08:27.183514 INFO: AUC difference: 1.32%
2:08:27.692297 INFO: Resetting torch num_threads to 24
2:08:27.722901 PROGRESS: === Extracted 749545 precursors and 4036768 fragments ===
2:08:27.723438 INFO: === FDR correction performed with classifier version 8 ===
2:08:27.724167 PROGRESS: ============================= Precursor FDR =============================
2:08:27.724263 PROGRESS: Total precursors accumulated: 1,606
2:08:27.724332 PROGRESS: Target precursors: 1,591 (99.07%)
2:08:27.724386 PROGRESS: Decoy precursors: 15 (0.93%)
2:08:27.724435 PROGRESS: 
2:08:27.724480 PROGRESS: Precursor Summary:
2:08:27.725834 PROGRESS: Channel   0:	 0.050 FDR: 1,591; 0.010 FDR: 1,591; 0.001 FDR:   712
2:08:27.725923 PROGRESS: 
2:08:27.725979 PROGRESS: Protein Summary:
2:08:27.727716 PROGRESS: Channel   0:	 0.050 FDR: 1,338; 0.010 FDR: 1,338; 0.001 FDR:   632
2:08:27.727820 PROGRESS: =========================================================================
2:08:27.750080 INFO: Target number of precursors reached.
2:08:28.194424 INFO: fragments_df: keeping 5000 of 4036768 [sum(precursor_idx_mask)=37720 sum(mass_error_mask)=4036768 stop_rank=5000
2:08:28.718518 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:08:28.979171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:08:29.716272 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:08:29.716691 INFO: Using score_cutoff 11.537060720443726 (fac=0.99, q=1)
2:08:29.717019 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:08:29.717097 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:08:29.717152 INFO: Updating optimization_manager: score_cutoff        : 12.703996038722993 -> 11.537060720443726
2:08:29.717211 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:08:29.883554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:08:30.260000 INFO: === checking if optimization conditions were reached ===
2:08:30.262278 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:08:30.262392 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:08:30.262466 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:08:30.262527 INFO: ==============================================
2:08:30.262604 INFO: Starting optimization step 10.
2:08:30.262680 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:08:30.262759 INFO: Using rust extraction backend
2:08:30.262834 PROGRESS: Extracting batch of 250330 precursors
2:08:30.714246 INFO: === Search parameters used ===
2:08:30.714715 INFO: rt_error       : 805.6002197265625
2:08:30.714779 INFO: mobility_error : 0.1
2:08:30.714828 INFO: num_candidates : 3
2:08:30.714885 INFO: ms1_error      : 30
2:08:30.714937 INFO: ms2_error      : 10.0
2:08:30.714978 INFO: fwhm_rt        : 3.0
2:08:30.715017 INFO: quant_window   : 3
2:08:30.715056 INFO: ==============================================
2:08:38.086465 INFO: performing precursor FDR with 40 features
2:08:38.086584 INFO: Decoy channel: -1
2:08:38.086613 INFO: competitive: True
2:08:39.787555 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:42.337428 INFO: Estimating optimal hyperparameters - samples: 599,634, batch_size: 2,456, learning_rate: 7.74e-04
2:08:42.339056 INFO: Using random state 610474 for train-test-split
2:08:57.927882 INFO: Test AUC: 0.608
2:08:57.928100 INFO: Train AUC: 0.619
2:08:57.928137 INFO: AUC difference: 1.65%
2:08:58.431865 INFO: Resetting torch num_threads to 24
2:08:58.485054 PROGRESS: === Extracted 749543 precursors and 4036468 fragments ===
2:08:58.485669 INFO: === FDR correction performed with classifier version 9 ===
2:08:58.486664 PROGRESS: ============================= Precursor FDR =============================
2:08:58.486804 PROGRESS: Total precursors accumulated: 1,588
2:08:58.486871 PROGRESS: Target precursors: 1,573 (99.06%)
2:08:58.486925 PROGRESS: Decoy precursors: 15 (0.94%)
2:08:58.486975 PROGRESS: 
2:08:58.487022 PROGRESS: Precursor Summary:
2:08:58.488583 PROGRESS: Channel   0:	 0.050 FDR: 1,573; 0.010 FDR: 1,573; 0.001 FDR:     0
2:08:58.488697 PROGRESS: 
2:08:58.488756 PROGRESS: Protein Summary:
2:08:58.490594 PROGRESS: Channel   0:	 0.050 FDR: 1,324; 0.010 FDR: 1,324; 0.001 FDR:     0
2:08:58.490707 PROGRESS: =========================================================================
2:08:58.516875 INFO: Target number of precursors reached.
2:08:58.983916 INFO: fragments_df: keeping 5000 of 4036468 [sum(precursor_idx_mask)=37155 sum(mass_error_mask)=4036468 stop_rank=5000
2:08:59.490638 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:08:59.746742 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:00.472467 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:09:00.472936 INFO: Using score_cutoff 8.332916717147826 (fac=0.99, q=1)
2:09:00.473292 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:09:00.473372 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:09:00.473428 INFO: Updating optimization_manager: score_cutoff        : 11.537060720443726 -> 8.332916717147826
2:09:00.473489 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:00.634943 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:01.022754 INFO: === checking if optimization conditions were reached ===
2:09:01.024973 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:09:01.025085 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:09:01.025159 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:09:01.025221 INFO: ==============================================
2:09:01.025296 INFO: Starting optimization step 11.
2:09:01.025361 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:09:01.025441 INFO: Using rust extraction backend
2:09:01.025518 PROGRESS: Extracting batch of 250330 precursors
2:09:01.465414 INFO: === Search parameters used ===
2:09:01.465678 INFO: rt_error       : 805.6002197265625
2:09:01.465740 INFO: mobility_error : 0.1
2:09:01.465804 INFO: num_candidates : 3
2:09:01.465851 INFO: ms1_error      : 30
2:09:01.465894 INFO: ms2_error      : 10.0
2:09:01.465937 INFO: fwhm_rt        : 3.0
2:09:01.465978 INFO: quant_window   : 3
2:09:01.466019 INFO: ==============================================
2:09:05.196777 INFO: performing precursor FDR with 40 features
2:09:05.196896 INFO: Decoy channel: -1
2:09:05.196922 INFO: competitive: True
2:09:05.422137 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:05.753683 INFO: Estimating optimal hyperparameters - samples: 599,656, batch_size: 2,456, learning_rate: 7.74e-04
2:09:05.755355 INFO: Using random state 263985 for train-test-split
2:09:21.173068 INFO: Test AUC: 0.609
2:09:21.173435 INFO: Train AUC: 0.622
2:09:21.173481 INFO: AUC difference: 2.08%
2:09:21.685916 INFO: Resetting torch num_threads to 24
2:09:21.719003 PROGRESS: === Extracted 749570 precursors and 4037255 fragments ===
2:09:21.719664 INFO: === FDR correction performed with classifier version 10 ===
2:09:21.720367 PROGRESS: ============================= Precursor FDR =============================
2:09:21.720458 PROGRESS: Total precursors accumulated: 1,585
2:09:21.720519 PROGRESS: Target precursors: 1,570 (99.05%)
2:09:21.720572 PROGRESS: Decoy precursors: 15 (0.95%)
2:09:21.720621 PROGRESS: 
2:09:21.720668 PROGRESS: Precursor Summary:
2:09:21.721912 PROGRESS: Channel   0:	 0.050 FDR: 1,570; 0.010 FDR: 1,570; 0.001 FDR:     0
2:09:21.722001 PROGRESS: 
2:09:21.722056 PROGRESS: Protein Summary:
2:09:21.723702 PROGRESS: Channel   0:	 0.050 FDR: 1,331; 0.010 FDR: 1,331; 0.001 FDR:     0
2:09:21.723797 PROGRESS: =========================================================================
2:09:21.742491 INFO: Target number of precursors reached.
2:09:22.181971 INFO: fragments_df: keeping 5000 of 4037255 [sum(precursor_idx_mask)=36604 sum(mass_error_mask)=4037255 stop_rank=5000
2:09:22.760484 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:09:23.005152 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:23.730624 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:09:23.731184 INFO: Using score_cutoff 7.993285657882691 (fac=0.99, q=1)
2:09:23.731584 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:09:23.731669 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:09:23.731725 INFO: Updating optimization_manager: score_cutoff        : 8.332916717147826 -> 7.993285657882691
2:09:23.731790 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:23.889404 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:24.227063 INFO: === checking if optimization conditions were reached ===
2:09:24.230072 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:09:24.230262 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:09:24.230349 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:09:24.230433 INFO: ==============================================
2:09:24.230526 INFO: Starting optimization step 12.
2:09:24.230608 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:09:24.230717 INFO: Using rust extraction backend
2:09:24.230818 PROGRESS: Extracting batch of 250330 precursors
2:09:24.671584 INFO: === Search parameters used ===
2:09:24.672046 INFO: rt_error       : 805.6002197265625
2:09:24.672117 INFO: mobility_error : 0.1
2:09:24.672167 INFO: num_candidates : 3
2:09:24.672211 INFO: ms1_error      : 30
2:09:24.672255 INFO: ms2_error      : 10.0
2:09:24.672296 INFO: fwhm_rt        : 3.0
2:09:24.672340 INFO: quant_window   : 3
2:09:24.672382 INFO: ==============================================
2:09:28.240056 INFO: performing precursor FDR with 40 features
2:09:28.240196 INFO: Decoy channel: -1
2:09:28.240223 INFO: competitive: True
2:09:28.459061 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:28.782310 INFO: Estimating optimal hyperparameters - samples: 599,649, batch_size: 2,456, learning_rate: 7.74e-04
2:09:28.783505 INFO: Using random state 581318 for train-test-split
2:09:41.469084 INFO: Test AUC: 0.613
2:09:41.469313 INFO: Train AUC: 0.624
2:09:41.469351 INFO: AUC difference: 1.72%
2:09:41.974380 INFO: Resetting torch num_threads to 24
2:09:42.007735 PROGRESS: === Extracted 749562 precursors and 4037150 fragments ===
2:09:42.008379 INFO: === FDR correction performed with classifier version 11 ===
2:09:42.009193 PROGRESS: ============================= Precursor FDR =============================
2:09:42.009304 PROGRESS: Total precursors accumulated: 1,640
2:09:42.009368 PROGRESS: Target precursors: 1,624 (99.02%)
2:09:42.009422 PROGRESS: Decoy precursors: 16 (0.98%)
2:09:42.009470 PROGRESS: 
2:09:42.009527 PROGRESS: Precursor Summary:
2:09:42.010895 PROGRESS: Channel   0:	 0.050 FDR: 1,624; 0.010 FDR: 1,624; 0.001 FDR:     2
2:09:42.010994 PROGRESS: 
2:09:42.011062 PROGRESS: Protein Summary:
2:09:42.012775 PROGRESS: Channel   0:	 0.050 FDR: 1,385; 0.010 FDR: 1,385; 0.001 FDR:     2
2:09:42.012873 PROGRESS: =========================================================================
2:09:42.030565 INFO: Target number of precursors reached.
2:09:42.474499 INFO: fragments_df: keeping 5000 of 4037150 [sum(precursor_idx_mask)=37519 sum(mass_error_mask)=4037150 stop_rank=5000
2:09:43.273468 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:09:43.542843 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:44.193586 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:09:44.194307 INFO: Using score_cutoff 8.062774315452575 (fac=0.99, q=1)
2:09:44.194732 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:09:44.194811 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:09:44.194866 INFO: Updating optimization_manager: score_cutoff        : 7.993285657882691 -> 8.062774315452575
2:09:44.194941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:44.345240 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:44.676786 INFO: === checking if optimization conditions were reached ===
2:09:44.679738 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:09:44.679938 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:09:44.680037 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:09:44.680141 INFO: ==============================================
2:09:44.680256 PROGRESS: Optimization finished for ms2_error.
2:09:45.413364 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:45.566090 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:45.898427 INFO: Starting optimization step 0.
2:09:45.898771 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:09:45.898946 INFO: Using rust extraction backend
2:09:45.899068 PROGRESS: Extracting batch of 250330 precursors
2:09:46.342575 INFO: === Search parameters used ===
2:09:46.342999 INFO: rt_error       : 805.6002197265625
2:09:46.343058 INFO: mobility_error : 0.1
2:09:46.343108 INFO: num_candidates : 3
2:09:46.343151 INFO: ms1_error      : 30
2:09:46.343197 INFO: ms2_error      : 10.0
2:09:46.343237 INFO: fwhm_rt        : 3.0
2:09:46.343284 INFO: quant_window   : 3
2:09:46.343324 INFO: ==============================================
2:09:49.829452 INFO: performing precursor FDR with 40 features
2:09:49.829581 INFO: Decoy channel: -1
2:09:49.829613 INFO: competitive: True
2:09:50.024308 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:50.335066 INFO: Estimating optimal hyperparameters - samples: 599,672, batch_size: 2,456, learning_rate: 7.74e-04
2:09:50.336264 INFO: Using random state 177110 for train-test-split
2:10:02.660968 INFO: Test AUC: 0.610
2:10:02.661217 INFO: Train AUC: 0.627
2:10:02.661263 INFO: AUC difference: 2.66%
2:10:03.144648 INFO: Resetting torch num_threads to 24
2:10:03.172445 PROGRESS: === Extracted 749590 precursors and 4037125 fragments ===
2:10:03.173043 INFO: === FDR correction performed with classifier version 12 ===
2:10:03.173750 PROGRESS: ============================= Precursor FDR =============================
2:10:03.173848 PROGRESS: Total precursors accumulated: 1,662
2:10:03.173922 PROGRESS: Target precursors: 1,646 (99.04%)
2:10:03.173978 PROGRESS: Decoy precursors: 16 (0.96%)
2:10:03.174027 PROGRESS: 
2:10:03.174074 PROGRESS: Precursor Summary:
2:10:03.175381 PROGRESS: Channel   0:	 0.050 FDR: 1,646; 0.010 FDR: 1,646; 0.001 FDR:     4
2:10:03.175490 PROGRESS: 
2:10:03.175550 PROGRESS: Protein Summary:
2:10:03.177183 PROGRESS: Channel   0:	 0.050 FDR: 1,401; 0.010 FDR: 1,401; 0.001 FDR:     4
2:10:03.177287 PROGRESS: =========================================================================
2:10:03.192048 INFO: Target number of precursors reached.
2:10:03.635147 INFO: fragments_df: keeping 5000 of 4037125 [sum(precursor_idx_mask)=38371 sum(mass_error_mask)=4037125 stop_rank=5000
2:10:04.227540 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:10:04.453706 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:10:05.100537 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:10:05.101032 INFO: Using score_cutoff 8.378600003242491 (fac=0.99, q=1)
2:10:05.101393 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:10:05.101470 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:10:05.101525 INFO: Updating optimization_manager: score_cutoff        : 8.062774315452575 -> 8.378600003242491
2:10:05.101591 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:10:05.250863 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:10:05.581378 INFO: === checking if optimization conditions were reached ===
2:10:05.581787 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:10:05.585762 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 868.6716924897097
2:10:05.585928 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 868.6717.
2:10:05.586018 INFO: ==============================================
2:10:05.586160 INFO: Starting optimization step 1.
2:10:05.586254 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:10:05.586396 INFO: Using rust extraction backend
2:10:05.586515 PROGRESS: Extracting batch of 250330 precursors
2:10:06.024441 INFO: === Search parameters used ===
2:10:06.024748 INFO: rt_error       : 868.6716924897097
2:10:06.024805 INFO: mobility_error : 0.1
2:10:06.024852 INFO: num_candidates : 3
2:10:06.024894 INFO: ms1_error      : 30
2:10:06.024934 INFO: ms2_error      : 10.0
2:10:06.024973 INFO: fwhm_rt        : 3.0
2:10:06.025011 INFO: quant_window   : 3
2:10:06.025048 INFO: ==============================================
2:10:09.529859 INFO: performing precursor FDR with 40 features
2:10:09.529998 INFO: Decoy channel: -1
2:10:09.530025 INFO: competitive: True
2:10:09.734931 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:10.042779 INFO: Estimating optimal hyperparameters - samples: 599,649, batch_size: 2,456, learning_rate: 7.74e-04
2:10:10.044031 INFO: Using random state 177110 for train-test-split
2:10:21.772447 INFO: Test AUC: 0.615
2:10:21.772630 INFO: Train AUC: 0.628
2:10:21.772669 INFO: AUC difference: 2.06%
2:10:22.258872 INFO: Resetting torch num_threads to 24
2:10:22.289469 PROGRESS: === Extracted 749562 precursors and 4036346 fragments ===
2:10:22.290006 INFO: === FDR correction performed with classifier version 12 ===
2:10:22.290699 PROGRESS: ============================= Precursor FDR =============================
2:10:22.290792 PROGRESS: Total precursors accumulated: 1,447
2:10:22.290856 PROGRESS: Target precursors: 1,433 (99.03%)
2:10:22.290910 PROGRESS: Decoy precursors: 14 (0.97%)
2:10:22.290960 PROGRESS: 
2:10:22.291006 PROGRESS: Precursor Summary:
2:10:22.292274 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR:     0
2:10:22.292365 PROGRESS: 
2:10:22.292421 PROGRESS: Protein Summary:
2:10:22.293990 PROGRESS: Channel   0:	 0.050 FDR: 1,217; 0.010 FDR: 1,217; 0.001 FDR:     0
2:10:22.294082 PROGRESS: =========================================================================
2:10:22.308745 INFO: Target number of precursors reached.
2:10:22.762336 INFO: fragments_df: keeping 5000 of 4036346 [sum(precursor_idx_mask)=33909 sum(mass_error_mask)=4036346 stop_rank=5000
2:10:23.299325 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:10:23.532027 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:10:24.245781 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:10:24.246294 INFO: Using score_cutoff 9.63141389579773 (fac=0.99, q=1)
2:10:24.246641 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:10:24.246725 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:10:24.246779 INFO: Updating optimization_manager: score_cutoff        : 8.378600003242491 -> 9.63141389579773
2:10:24.246835 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:10:24.395786 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:10:24.730715 INFO: === checking if optimization conditions were reached ===
2:10:24.731054 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:10:24.734602 INFO: Updating optimization_manager: rt_error            : 868.6716924897097 -> 794.1921230754427
2:10:24.734772 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 794.1921.
2:10:24.734855 INFO: ==============================================
2:10:24.734948 INFO: Starting optimization step 2.
2:10:24.735029 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:10:24.735116 INFO: Using rust extraction backend
2:10:24.735197 PROGRESS: Extracting batch of 250330 precursors
2:10:25.167646 INFO: === Search parameters used ===
2:10:25.167941 INFO: rt_error       : 794.1921230754427
2:10:25.168001 INFO: mobility_error : 0.1
2:10:25.168049 INFO: num_candidates : 3
2:10:25.168092 INFO: ms1_error      : 30
2:10:25.168133 INFO: ms2_error      : 10.0
2:10:25.168177 INFO: fwhm_rt        : 3.0
2:10:25.168221 INFO: quant_window   : 3
2:10:25.168267 INFO: ==============================================
2:10:28.579206 INFO: performing precursor FDR with 40 features
2:10:28.579332 INFO: Decoy channel: -1
2:10:28.579360 INFO: competitive: True
2:10:28.767729 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:29.059301 INFO: Estimating optimal hyperparameters - samples: 599,660, batch_size: 2,456, learning_rate: 7.74e-04
2:10:29.060738 INFO: Using random state 177110 for train-test-split
2:10:41.063699 INFO: Test AUC: 0.613
2:10:41.063843 INFO: Train AUC: 0.627
2:10:41.063892 INFO: AUC difference: 2.12%
2:10:42.836823 INFO: Resetting torch num_threads to 24
2:10:42.868512 PROGRESS: === Extracted 749576 precursors and 4036962 fragments ===
2:10:42.869012 INFO: === FDR correction performed with classifier version 12 ===
2:10:42.869699 PROGRESS: ============================= Precursor FDR =============================
2:10:42.869788 PROGRESS: Total precursors accumulated: 1,560
2:10:42.869849 PROGRESS: Target precursors: 1,545 (99.04%)
2:10:42.869901 PROGRESS: Decoy precursors: 15 (0.96%)
2:10:42.869958 PROGRESS: 
2:10:42.870005 PROGRESS: Precursor Summary:
2:10:42.871368 PROGRESS: Channel   0:	 0.050 FDR: 1,545; 0.010 FDR: 1,545; 0.001 FDR: 1,050
2:10:42.871467 PROGRESS: 
2:10:42.871528 PROGRESS: Protein Summary:
2:10:42.873345 PROGRESS: Channel   0:	 0.050 FDR: 1,305; 0.010 FDR: 1,305; 0.001 FDR:   907
2:10:42.873442 PROGRESS: =========================================================================
2:10:42.887990 INFO: Target number of precursors reached.
2:10:43.338238 INFO: fragments_df: keeping 5000 of 4036962 [sum(precursor_idx_mask)=36663 sum(mass_error_mask)=4036962 stop_rank=5000
2:10:43.864274 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:10:44.102985 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:10:44.811129 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:10:44.811605 INFO: Using score_cutoff 10.704375830841066 (fac=0.99, q=1)
2:10:44.811915 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:10:44.811991 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:10:44.812045 INFO: Updating optimization_manager: score_cutoff        : 9.63141389579773 -> 10.704375830841066
2:10:44.812098 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:10:44.961938 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:10:45.296625 INFO: === checking if optimization conditions were reached ===
2:10:45.296951 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:10:45.300609 INFO: Updating optimization_manager: rt_error            : 794.1921230754427 -> 654.2825861064016
2:10:45.300769 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 654.2826.
2:10:45.300848 INFO: ==============================================
2:10:45.300931 INFO: Starting optimization step 3.
2:10:45.301000 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:10:45.301074 INFO: Using rust extraction backend
2:10:45.301141 PROGRESS: Extracting batch of 250330 precursors
2:10:45.730152 INFO: === Search parameters used ===
2:10:45.730433 INFO: rt_error       : 654.2825861064016
2:10:45.730486 INFO: mobility_error : 0.1
2:10:45.730533 INFO: num_candidates : 3
2:10:45.730575 INFO: ms1_error      : 30
2:10:45.730617 INFO: ms2_error      : 10.0
2:10:45.730657 INFO: fwhm_rt        : 3.0
2:10:45.730698 INFO: quant_window   : 3
2:10:45.730738 INFO: ==============================================
2:10:49.070244 INFO: performing precursor FDR with 40 features
2:10:49.070374 INFO: Decoy channel: -1
2:10:49.070401 INFO: competitive: True
2:10:49.272299 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:49.580426 INFO: Estimating optimal hyperparameters - samples: 599,559, batch_size: 2,455, learning_rate: 7.74e-04
2:10:49.581594 INFO: Using random state 177110 for train-test-split
2:11:02.004364 INFO: Test AUC: 0.612
2:11:02.004521 INFO: Train AUC: 0.627
2:11:02.004556 INFO: AUC difference: 2.43%
2:11:02.505116 INFO: Resetting torch num_threads to 24
2:11:02.535938 PROGRESS: === Extracted 749449 precursors and 4030186 fragments ===
2:11:02.536438 INFO: === FDR correction performed with classifier version 12 ===
2:11:02.537152 PROGRESS: ============================= Precursor FDR =============================
2:11:02.537253 PROGRESS: Total precursors accumulated: 1,444
2:11:02.537322 PROGRESS: Target precursors: 1,430 (99.03%)
2:11:02.537373 PROGRESS: Decoy precursors: 14 (0.97%)
2:11:02.537419 PROGRESS: 
2:11:02.537462 PROGRESS: Precursor Summary:
2:11:02.538722 PROGRESS: Channel   0:	 0.050 FDR: 1,430; 0.010 FDR: 1,430; 0.001 FDR:     0
2:11:02.538809 PROGRESS: 
2:11:02.538864 PROGRESS: Protein Summary:
2:11:02.540472 PROGRESS: Channel   0:	 0.050 FDR: 1,213; 0.010 FDR: 1,213; 0.001 FDR:     0
2:11:02.540566 PROGRESS: =========================================================================
2:11:02.554922 INFO: Target number of precursors reached.
2:11:03.008043 INFO: fragments_df: keeping 5000 of 4030186 [sum(precursor_idx_mask)=34038 sum(mass_error_mask)=4030186 stop_rank=5000
2:11:03.583899 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:11:03.790956 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:11:04.441866 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:11:04.442336 INFO: Using score_cutoff 11.026253506565094 (fac=0.99, q=1)
2:11:04.442653 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:11:04.442729 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:11:04.442784 INFO: Updating optimization_manager: score_cutoff        : 10.704375830841066 -> 11.026253506565094
2:11:04.442840 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:04.593117 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:04.936737 INFO: === checking if optimization conditions were reached ===
2:11:04.937073 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:11:04.940812 INFO: Updating optimization_manager: rt_error            : 654.2825861064016 -> 721.49091309447
2:11:04.940974 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 721.4909.
2:11:04.941054 INFO: ==============================================
2:11:04.941144 INFO: Starting optimization step 4.
2:11:04.941219 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:11:04.941304 INFO: Using rust extraction backend
2:11:04.941384 PROGRESS: Extracting batch of 250330 precursors
2:11:05.374940 INFO: === Search parameters used ===
2:11:05.375218 INFO: rt_error       : 721.49091309447
2:11:05.375276 INFO: mobility_error : 0.1
2:11:05.375324 INFO: num_candidates : 3
2:11:05.375368 INFO: ms1_error      : 30
2:11:05.375408 INFO: ms2_error      : 10.0
2:11:05.375448 INFO: fwhm_rt        : 3.0
2:11:05.375513 INFO: quant_window   : 3
2:11:05.375553 INFO: ==============================================
2:11:08.754634 INFO: performing precursor FDR with 40 features
2:11:08.754760 INFO: Decoy channel: -1
2:11:08.754786 INFO: competitive: True
2:11:08.952168 INFO: Setting torch num_threads to 2 for FDR classification task
2:11:09.259460 INFO: Estimating optimal hyperparameters - samples: 599,624, batch_size: 2,456, learning_rate: 7.74e-04
2:11:09.260601 INFO: Using random state 177110 for train-test-split
2:11:22.530949 INFO: Test AUC: 0.614
2:11:22.531075 INFO: Train AUC: 0.627
2:11:22.531109 INFO: AUC difference: 2.14%
2:11:23.014398 INFO: Resetting torch num_threads to 24
2:11:23.041252 PROGRESS: === Extracted 749531 precursors and 4035768 fragments ===
2:11:23.041737 INFO: === FDR correction performed with classifier version 12 ===
2:11:23.042429 PROGRESS: ============================= Precursor FDR =============================
2:11:23.042518 PROGRESS: Total precursors accumulated: 1,603
2:11:23.042576 PROGRESS: Target precursors: 1,588 (99.06%)
2:11:23.042625 PROGRESS: Decoy precursors: 15 (0.94%)
2:11:23.042669 PROGRESS: 
2:11:23.042712 PROGRESS: Precursor Summary:
2:11:23.044020 PROGRESS: Channel   0:	 0.050 FDR: 1,588; 0.010 FDR: 1,588; 0.001 FDR:     0
2:11:23.044114 PROGRESS: 
2:11:23.044171 PROGRESS: Protein Summary:
2:11:23.045777 PROGRESS: Channel   0:	 0.050 FDR: 1,342; 0.010 FDR: 1,342; 0.001 FDR:     0
2:11:23.045867 PROGRESS: =========================================================================
2:11:23.060773 INFO: Target number of precursors reached.
2:11:23.506614 INFO: fragments_df: keeping 5000 of 4035768 [sum(precursor_idx_mask)=37890 sum(mass_error_mask)=4035768 stop_rank=5000
2:11:24.116874 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:11:24.389251 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:11:25.033906 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:11:25.034381 INFO: Using score_cutoff 12.12853887233734 (fac=0.99, q=1)
2:11:25.034704 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:11:25.034787 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:11:25.034845 INFO: Updating optimization_manager: score_cutoff        : 11.026253506565094 -> 12.12853887233734
2:11:25.034910 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:25.186901 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:25.518788 INFO: === checking if optimization conditions were reached ===
2:11:25.519112 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:11:25.522820 INFO: Updating optimization_manager: rt_error            : 721.49091309447 -> 642.914589202579
2:11:25.522983 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 642.9146.
2:11:25.523063 INFO: ==============================================
2:11:25.523149 INFO: Starting optimization step 5.
2:11:25.523220 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:11:25.523299 INFO: Using rust extraction backend
2:11:25.523369 PROGRESS: Extracting batch of 250330 precursors
2:11:25.956097 INFO: === Search parameters used ===
2:11:25.956382 INFO: rt_error       : 642.914589202579
2:11:25.956440 INFO: mobility_error : 0.1
2:11:25.956491 INFO: num_candidates : 3
2:11:25.956536 INFO: ms1_error      : 30
2:11:25.956579 INFO: ms2_error      : 10.0
2:11:25.956620 INFO: fwhm_rt        : 3.0
2:11:25.956661 INFO: quant_window   : 3
2:11:25.956701 INFO: ==============================================
2:11:29.291437 INFO: performing precursor FDR with 40 features
2:11:29.291581 INFO: Decoy channel: -1
2:11:29.291607 INFO: competitive: True
2:11:29.484847 INFO: Setting torch num_threads to 2 for FDR classification task
2:11:29.794176 INFO: Estimating optimal hyperparameters - samples: 599,528, batch_size: 2,455, learning_rate: 7.74e-04
2:11:29.795217 INFO: Using random state 177110 for train-test-split
2:11:42.607050 INFO: Test AUC: 0.614
2:11:42.607195 INFO: Train AUC: 0.627
2:11:42.607228 INFO: AUC difference: 2.15%
2:11:43.090392 INFO: Resetting torch num_threads to 24
2:11:43.156178 PROGRESS: === Extracted 749410 precursors and 4027567 fragments ===
2:11:43.156687 INFO: === FDR correction performed with classifier version 12 ===
2:11:43.157438 PROGRESS: ============================= Precursor FDR =============================
2:11:43.157537 PROGRESS: Total precursors accumulated: 1,556
2:11:43.157597 PROGRESS: Target precursors: 1,541 (99.04%)
2:11:43.157647 PROGRESS: Decoy precursors: 15 (0.96%)
2:11:43.157692 PROGRESS: 
2:11:43.157738 PROGRESS: Precursor Summary:
2:11:43.159000 PROGRESS: Channel   0:	 0.050 FDR: 1,541; 0.010 FDR: 1,541; 0.001 FDR:     0
2:11:43.159086 PROGRESS: 
2:11:43.159142 PROGRESS: Protein Summary:
2:11:43.160742 PROGRESS: Channel   0:	 0.050 FDR: 1,298; 0.010 FDR: 1,298; 0.001 FDR:     0
2:11:43.160833 PROGRESS: =========================================================================
2:11:43.175391 INFO: Target number of precursors reached.
2:11:43.622332 INFO: fragments_df: keeping 5000 of 4027567 [sum(precursor_idx_mask)=36668 sum(mass_error_mask)=4027567 stop_rank=5000
2:11:44.157126 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:11:44.398186 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:11:45.116157 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:11:45.116628 INFO: Using score_cutoff 11.223214662551879 (fac=0.99, q=1)
2:11:45.116938 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:11:45.117017 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:11:45.117082 INFO: Updating optimization_manager: score_cutoff        : 12.12853887233734 -> 11.223214662551879
2:11:45.117140 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:45.267516 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:45.616877 INFO: === checking if optimization conditions were reached ===
2:11:45.617240 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:11:45.620919 INFO: Updating optimization_manager: rt_error            : 642.914589202579 -> 673.2090968211673
2:11:45.621046 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 673.2091.
2:11:45.621124 INFO: ==============================================
2:11:45.621212 INFO: Starting optimization step 6.
2:11:45.621288 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:11:45.621369 INFO: Using rust extraction backend
2:11:45.621449 PROGRESS: Extracting batch of 250330 precursors
2:11:46.052288 INFO: === Search parameters used ===
2:11:46.052579 INFO: rt_error       : 673.2090968211673
2:11:46.052639 INFO: mobility_error : 0.1
2:11:46.052689 INFO: num_candidates : 3
2:11:46.052735 INFO: ms1_error      : 30
2:11:46.052779 INFO: ms2_error      : 10.0
2:11:46.052822 INFO: fwhm_rt        : 3.0
2:11:46.052863 INFO: quant_window   : 3
2:11:46.052917 INFO: ==============================================
2:11:49.432966 INFO: performing precursor FDR with 40 features
2:11:49.433099 INFO: Decoy channel: -1
2:11:49.433125 INFO: competitive: True
2:11:49.643341 INFO: Setting torch num_threads to 2 for FDR classification task
2:11:49.970664 INFO: Estimating optimal hyperparameters - samples: 599,583, batch_size: 2,455, learning_rate: 7.74e-04
2:11:49.971720 INFO: Using random state 177110 for train-test-split
2:12:02.755949 INFO: Test AUC: 0.613
2:12:02.756074 INFO: Train AUC: 0.626
2:12:02.756108 INFO: AUC difference: 2.06%
2:12:03.240770 INFO: Resetting torch num_threads to 24
2:12:03.269773 PROGRESS: === Extracted 749479 precursors and 4031839 fragments ===
2:12:03.270288 INFO: === FDR correction performed with classifier version 12 ===
2:12:03.271027 PROGRESS: ============================= Precursor FDR =============================
2:12:03.271120 PROGRESS: Total precursors accumulated: 1,677
2:12:03.271196 PROGRESS: Target precursors: 1,661 (99.05%)
2:12:03.271262 PROGRESS: Decoy precursors: 16 (0.95%)
2:12:03.271314 PROGRESS: 
2:12:03.271361 PROGRESS: Precursor Summary:
2:12:03.272764 PROGRESS: Channel   0:	 0.050 FDR: 1,661; 0.010 FDR: 1,661; 0.001 FDR:     0
2:12:03.272882 PROGRESS: 
2:12:03.272959 PROGRESS: Protein Summary:
2:12:03.275056 PROGRESS: Channel   0:	 0.050 FDR: 1,392; 0.010 FDR: 1,392; 0.001 FDR:     0
2:12:03.275156 PROGRESS: =========================================================================
2:12:03.290675 INFO: Target number of precursors reached.
2:12:03.729039 INFO: fragments_df: keeping 5000 of 4031839 [sum(precursor_idx_mask)=39351 sum(mass_error_mask)=4031839 stop_rank=5000
2:12:04.263532 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:12:04.515252 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:12:05.228962 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:12:05.229441 INFO: Using score_cutoff 11.562081499099731 (fac=0.99, q=1)
2:12:05.229759 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:12:05.229834 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:12:05.229889 INFO: Updating optimization_manager: score_cutoff        : 11.223214662551879 -> 11.562081499099731
2:12:05.229942 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:05.386091 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:05.719127 INFO: === checking if optimization conditions were reached ===
2:12:05.719408 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:12:05.720531 INFO: Updating optimization_manager: rt_error            : 673.2090968211673 -> 673.2090968211673
2:12:05.720688 INFO: Updating optimization_manager: classifier_version  : 12 -> 19
2:12:05.720789 INFO: Updating optimization_manager: score_cutoff        : 11.562081499099731 -> 11.562081499099731
2:12:05.720880 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:12:05.720979 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:12:05.721066 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 673.2091 found after 7 searches.
2:12:05.721134 INFO: ==============================================
2:12:05.721207 PROGRESS: Optimization finished for rt_error.
2:12:06.297484 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:06.449415 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:06.787432 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:12:06.787750 PROGRESS: ==============================================
2:12:06.787829 PROGRESS: ms2_error      : 10.0000
2:12:06.787894 PROGRESS: rt_error       : 673.2091
2:12:06.787943 PROGRESS: ==============================================
2:12:06.788808 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:15.293133 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:57.569904 INFO: Using rust extraction backend
2:12:57.570291 PROGRESS: Extracting batch of 11997144 precursors
2:13:18.321342 INFO: === Search parameters used ===
2:13:18.321823 INFO: rt_error       : 673.2090968211673
2:13:18.321899 INFO: mobility_error : 0.1
2:13:18.321954 INFO: num_candidates : 3
2:13:18.322002 INFO: ms1_error      : 30
2:13:18.322047 INFO: ms2_error      : 10.0
2:13:18.322089 INFO: fwhm_rt        : 3.0
2:13:18.322134 INFO: quant_window   : 3
2:13:18.322178 INFO: ==============================================
2:14:38.926866 INFO: Removed 10470334 precursors with score below cutoff 11.562081499099731
2:15:09.252133 INFO: performing precursor FDR with 40 features
2:15:09.252318 INFO: Decoy channel: -1
2:15:09.252347 INFO: competitive: True
2:15:11.981619 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:22.243077 INFO: Estimating optimal hyperparameters - samples: 20,416,427, batch_size: 4,096, learning_rate: 1.00e-03
2:15:22.304517 INFO: Using random state 708646 for train-test-split
2:21:52.097171 INFO: Test AUC: 0.619
2:21:52.097466 INFO: Train AUC: 0.620
2:21:52.097515 INFO: AUC difference: 0.07%
2:21:58.423694 INFO: Resetting torch num_threads to 24
2:22:00.664041 PROGRESS: ============================= Precursor FDR =============================
2:22:00.664496 PROGRESS: Total precursors accumulated: 93,231
2:22:00.664569 PROGRESS: Target precursors: 92,308 (99.01%)
2:22:00.664632 PROGRESS: Decoy precursors: 923 (0.99%)
2:22:00.664695 PROGRESS: 
2:22:00.664743 PROGRESS: Precursor Summary:
2:22:00.690621 PROGRESS: Channel   0:	 0.050 FDR: 92,308; 0.010 FDR: 92,308; 0.001 FDR: 59,316
2:22:00.690879 PROGRESS: 
2:22:00.690939 PROGRESS: Protein Summary:
2:22:00.726881 PROGRESS: Channel   0:	 0.050 FDR: 13,028; 0.010 FDR: 13,028; 0.001 FDR: 9,078
2:22:00.727124 PROGRESS: =========================================================================
2:22:01.191848 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
2:22:01.367706 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
2:22:01.606612 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:22:02.188105 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:22:02.188260 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
2:22:02.188347 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
2:22:02.188531 INFO: Initializing TimingManager
2:22:02.188966 INFO: Initializing RawFileManager
2:22:16.274106 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.
2:22:16.283853 INFO: Determining DIA cycle
2:22:16.301558 INFO: Found cycle with start 0.00 min and length 300.
2:22:16.480791 INFO: RT (min)            : 0.0 - 26.9
2:22:16.480886 INFO: RT duration (sec)   : 1611.2
2:22:16.480916 INFO: RT duration (min)   : 26.9
2:22:16.480942 INFO: Cycle len (scans)   : 300
2:22:16.480962 INFO: Cycle len (sec)     : 1.65
2:22:16.480981 INFO: Number of cycles    : 978
2:22:16.481000 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:22:16.481033 INFO: Creating DIA data object took: 14.291975498199463
2:22:18.346518 INFO: Creating DIA data NG object took: 1.865347146987915
2:22:19.591750 INFO: Initializing CalibrationManager
2:22:19.592043 INFO: Setting up calibration estimators ..
2:22:19.592107 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:22:19.592196 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'}' ..
2:22:19.592275 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:22:19.592336 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:22:19.592391 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}}' ..
2:22:19.592453 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:22:19.592499 INFO: Done setting up calibration estimators.
2:22:19.592713 INFO: Initializing OptimizationManager
2:22:19.592857 INFO: initial parameter: ms1_error = 30
2:22:19.592908 INFO: initial parameter: ms2_error = 30
2:22:19.592953 INFO: initial parameter: rt_error = 805.611083984375
2:22:19.592994 INFO: initial parameter: mobility_error = 0.1
2:22:19.593033 INFO: initial parameter: num_candidates = 1
2:22:19.593073 INFO: initial parameter: fwhm_rt = 5
2:22:19.593115 INFO: initial parameter: fwhm_mobility = 0.01
2:22:19.593155 INFO: initial parameter: score_cutoff = 0
2:22:19.593194 INFO: initial parameter: classifier_version = -1
2:22:19.593264 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:22:19.593590 INFO: FDRManager: loading saved state not requested, will be initialized.
2:22:19.593622 INFO: Initializing FDRManager
2:22:19.593660 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:22:21.021629 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
2:22:21.933079 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:22:21.933512 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:22:21.933621 PROGRESS: Starting initial search for precursors.
2:22:21.933710 INFO: Starting optimization step 0.
2:22:21.933772 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:22:21.933830 INFO: Using rust extraction backend
2:22:21.933890 PROGRESS: Extracting batch of 1972 precursors
2:22:21.938943 INFO: === Search parameters used ===
2:22:21.939050 INFO: rt_error       : 805.611083984375
2:22:21.939102 INFO: mobility_error : 0.1
2:22:21.939146 INFO: num_candidates : 1
2:22:21.939187 INFO: ms1_error      : 30
2:22:21.939228 INFO: ms2_error      : 30
2:22:21.939267 INFO: fwhm_rt        : 5
2:22:21.939305 INFO: quant_window   : 3
2:22:21.939343 INFO: ==============================================
2:22:21.980504 INFO: performing precursor FDR with 40 features
2:22:21.980585 INFO: Decoy channel: -1
2:22:21.980609 INFO: competitive: True
2:22:21.982001 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:21.984437 INFO: Estimating optimal hyperparameters - samples: 1,562, batch_size: 128, learning_rate: 1.77e-04
2:22:21.987042 INFO: Using random state 446170 for train-test-split
2:22:22.144542 INFO: Test AUC: 0.509
2:22:22.144631 INFO: Train AUC: 0.599
2:22:22.144661 INFO: AUC difference: 15.03%
2:22:22.144683 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:22.387130 INFO: Resetting torch num_threads to 24
2:22:22.388826 PROGRESS: === Extracted 1953 precursors and 9283 fragments ===
2:22:22.389203 INFO: === FDR correction performed with classifier version -1 ===
2:22:22.389699 PROGRESS: ============================= Precursor FDR =============================
2:22:22.389787 PROGRESS: Total precursors accumulated: 1
2:22:22.389849 PROGRESS: Target precursors: 1 (100.00%)
2:22:22.389902 PROGRESS: Decoy precursors: 0 (0.00%)
2:22:22.389951 PROGRESS: 
2:22:22.389997 PROGRESS: Precursor Summary:
2:22:22.391053 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2:22:22.391138 PROGRESS: 
2:22:22.391195 PROGRESS: Protein Summary:
2:22:22.392365 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2:22:22.392457 PROGRESS: =========================================================================
2:22:22.392692 INFO: Target number of precursors not reached yet.
2:22:22.478557 INFO: Starting optimization step 1.
2:22:22.478795 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:22:22.478880 INFO: Using rust extraction backend
2:22:22.478944 PROGRESS: Extracting batch of 3939 precursors
2:22:22.487427 INFO: === Search parameters used ===
2:22:22.487566 INFO: rt_error       : 805.611083984375
2:22:22.487618 INFO: mobility_error : 0.1
2:22:22.487665 INFO: num_candidates : 1
2:22:22.487708 INFO: ms1_error      : 30
2:22:22.487749 INFO: ms2_error      : 30
2:22:22.487789 INFO: fwhm_rt        : 5
2:22:22.487829 INFO: quant_window   : 3
2:22:22.487868 INFO: ==============================================
2:22:22.555377 INFO: performing precursor FDR with 40 features
2:22:22.555483 INFO: Decoy channel: -1
2:22:22.555507 INFO: competitive: True
2:22:22.559833 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:22.562253 INFO: Estimating optimal hyperparameters - samples: 4,688, batch_size: 128, learning_rate: 1.77e-04
2:22:22.562338 INFO: Using random state 790351 for train-test-split
2:22:23.031044 INFO: Test AUC: 0.536
2:22:23.031138 INFO: Train AUC: 0.594
2:22:23.031168 INFO: AUC difference: 9.73%
2:22:23.031188 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:23.272946 INFO: Resetting torch num_threads to 24
2:22:23.276030 PROGRESS: === Extracted 5860 precursors and 27760 fragments ===
2:22:23.276414 INFO: === FDR correction performed with classifier version -1 ===
2:22:23.276899 PROGRESS: ============================= Precursor FDR =============================
2:22:23.276980 PROGRESS: Total precursors accumulated: 4
2:22:23.277035 PROGRESS: Target precursors: 4 (100.00%)
2:22:23.277083 PROGRESS: Decoy precursors: 0 (0.00%)
2:22:23.277128 PROGRESS: 
2:22:23.277171 PROGRESS: Precursor Summary:
2:22:23.278235 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2:22:23.278317 PROGRESS: 
2:22:23.278371 PROGRESS: Protein Summary:
2:22:23.279532 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2:22:23.279619 PROGRESS: =========================================================================
2:22:23.279895 INFO: Target number of precursors not reached yet.
2:22:23.370495 INFO: Starting optimization step 2.
2:22:23.370729 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:22:23.370809 INFO: Using rust extraction backend
2:22:23.370866 PROGRESS: Extracting batch of 7870 precursors
2:22:23.385984 INFO: === Search parameters used ===
2:22:23.386140 INFO: rt_error       : 805.611083984375
2:22:23.386191 INFO: mobility_error : 0.1
2:22:23.386236 INFO: num_candidates : 1
2:22:23.386278 INFO: ms1_error      : 30
2:22:23.386318 INFO: ms2_error      : 30
2:22:23.386358 INFO: fwhm_rt        : 5
2:22:23.386396 INFO: quant_window   : 3
2:22:23.386434 INFO: ==============================================
2:22:23.494806 INFO: performing precursor FDR with 40 features
2:22:23.494914 INFO: Decoy channel: -1
2:22:23.494937 INFO: competitive: True
2:22:23.501097 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:23.504755 INFO: Estimating optimal hyperparameters - samples: 10,924, batch_size: 128, learning_rate: 1.77e-04
2:22:23.504876 INFO: Using random state 258537 for train-test-split
2:22:24.605968 INFO: Test AUC: 0.549
2:22:24.606079 INFO: Train AUC: 0.598
2:22:24.606107 INFO: AUC difference: 8.14%
2:22:24.606127 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:24.852403 INFO: Resetting torch num_threads to 24
2:22:24.856787 PROGRESS: === Extracted 13656 precursors and 64483 fragments ===
2:22:24.857228 INFO: === FDR correction performed with classifier version -1 ===
2:22:24.857777 PROGRESS: ============================= Precursor FDR =============================
2:22:24.857861 PROGRESS: Total precursors accumulated: 31
2:22:24.857917 PROGRESS: Target precursors: 31 (100.00%)
2:22:24.857965 PROGRESS: Decoy precursors: 0 (0.00%)
2:22:24.858007 PROGRESS: 
2:22:24.858049 PROGRESS: Precursor Summary:
2:22:24.859098 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
2:22:24.859177 PROGRESS: 
2:22:24.859230 PROGRESS: Protein Summary:
2:22:24.860419 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
2:22:24.860510 PROGRESS: =========================================================================
2:22:24.860875 INFO: Target number of precursors not reached yet.
2:22:24.960667 INFO: Starting optimization step 3.
2:22:24.960914 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:22:24.960995 INFO: Using rust extraction backend
2:22:24.961055 PROGRESS: Extracting batch of 15774 precursors
2:22:24.992347 INFO: === Search parameters used ===
2:22:24.992562 INFO: rt_error       : 805.611083984375
2:22:24.992615 INFO: mobility_error : 0.1
2:22:24.992659 INFO: num_candidates : 1
2:22:24.992701 INFO: ms1_error      : 30
2:22:24.992741 INFO: ms2_error      : 30
2:22:24.992785 INFO: fwhm_rt        : 5
2:22:24.992836 INFO: quant_window   : 3
2:22:24.992882 INFO: ==============================================
2:22:25.168782 INFO: performing precursor FDR with 40 features
2:22:25.168902 INFO: Decoy channel: -1
2:22:25.168927 INFO: competitive: True
2:22:25.180047 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:25.186872 INFO: Estimating optimal hyperparameters - samples: 23,441, batch_size: 128, learning_rate: 1.77e-04
2:22:25.187066 INFO: Using random state 997788 for train-test-split
2:22:27.540439 INFO: Test AUC: 0.576
2:22:27.540564 INFO: Train AUC: 0.608
2:22:27.540595 INFO: AUC difference: 5.24%
2:22:27.540618 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:27.786097 INFO: Resetting torch num_threads to 24
2:22:27.792760 PROGRESS: === Extracted 29302 precursors and 138964 fragments ===
2:22:27.793280 INFO: === FDR correction performed with classifier version -1 ===
2:22:27.793845 PROGRESS: ============================= Precursor FDR =============================
2:22:27.793934 PROGRESS: Total precursors accumulated: 61
2:22:27.794008 PROGRESS: Target precursors: 61 (100.00%)
2:22:27.794061 PROGRESS: Decoy precursors: 0 (0.00%)
2:22:27.794109 PROGRESS: 
2:22:27.794155 PROGRESS: Precursor Summary:
2:22:27.795224 PROGRESS: Channel   0:	 0.050 FDR:    61; 0.010 FDR:    61; 0.001 FDR:    61
2:22:27.795310 PROGRESS: 
2:22:27.795365 PROGRESS: Protein Summary:
2:22:27.796563 PROGRESS: Channel   0:	 0.050 FDR:    61; 0.010 FDR:    61; 0.001 FDR:    61
2:22:27.796656 PROGRESS: =========================================================================
2:22:27.797172 INFO: Target number of precursors not reached yet.
2:22:27.921430 INFO: Starting optimization step 4.
2:22:27.921710 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:22:27.921796 INFO: Using rust extraction backend
2:22:27.921861 PROGRESS: Extracting batch of 31503 precursors
2:22:27.977564 INFO: === Search parameters used ===
2:22:27.977818 INFO: rt_error       : 805.611083984375
2:22:27.977873 INFO: mobility_error : 0.1
2:22:27.977918 INFO: num_candidates : 1
2:22:27.977961 INFO: ms1_error      : 30
2:22:27.978002 INFO: ms2_error      : 30
2:22:27.978043 INFO: fwhm_rt        : 5
2:22:27.978082 INFO: quant_window   : 3
2:22:27.978121 INFO: ==============================================
2:22:28.276111 INFO: performing precursor FDR with 40 features
2:22:28.276232 INFO: Decoy channel: -1
2:22:28.276257 INFO: competitive: True
2:22:28.298426 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:28.312883 INFO: Estimating optimal hyperparameters - samples: 48,405, batch_size: 198, learning_rate: 2.20e-04
2:22:28.313096 INFO: Using random state 752492 for train-test-split
2:22:32.020979 INFO: Test AUC: 0.573
2:22:32.021093 INFO: Train AUC: 0.609
2:22:32.021123 INFO: AUC difference: 5.90%
2:22:32.021148 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:32.277598 INFO: Resetting torch num_threads to 24
2:22:32.289121 PROGRESS: === Extracted 60507 precursors and 286543 fragments ===
2:22:32.289745 INFO: === FDR correction performed with classifier version -1 ===
2:22:32.290574 PROGRESS: ============================= Precursor FDR =============================
2:22:32.290667 PROGRESS: Total precursors accumulated: 165
2:22:32.290730 PROGRESS: Target precursors: 164 (99.39%)
2:22:32.290783 PROGRESS: Decoy precursors: 1 (0.61%)
2:22:32.290831 PROGRESS: 
2:22:32.290878 PROGRESS: Precursor Summary:
2:22:32.291910 PROGRESS: Channel   0:	 0.050 FDR:   164; 0.010 FDR:   164; 0.001 FDR:    56
2:22:32.292002 PROGRESS: 
2:22:32.292060 PROGRESS: Protein Summary:
2:22:32.293222 PROGRESS: Channel   0:	 0.050 FDR:   156; 0.010 FDR:   156; 0.001 FDR:    55
2:22:32.293314 PROGRESS: =========================================================================
2:22:32.294363 INFO: Target number of precursors not reached yet.
2:22:32.454382 INFO: Starting optimization step 5.
2:22:32.454642 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:22:32.454731 INFO: Using rust extraction backend
2:22:32.454793 PROGRESS: Extracting batch of 63125 precursors
2:22:32.564960 INFO: === Search parameters used ===
2:22:32.565253 INFO: rt_error       : 805.611083984375
2:22:32.565306 INFO: mobility_error : 0.1
2:22:32.565350 INFO: num_candidates : 1
2:22:32.565392 INFO: ms1_error      : 30
2:22:32.565432 INFO: ms2_error      : 30
2:22:32.565473 INFO: fwhm_rt        : 5
2:22:32.565515 INFO: quant_window   : 3
2:22:32.565555 INFO: ==============================================
2:22:33.128979 INFO: performing precursor FDR with 40 features
2:22:33.129104 INFO: Decoy channel: -1
2:22:33.129128 INFO: competitive: True
2:22:33.173504 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:33.206996 INFO: Estimating optimal hyperparameters - samples: 98,492, batch_size: 403, learning_rate: 3.14e-04
2:22:33.207324 INFO: Using random state 822212 for train-test-split
2:22:37.951594 INFO: Test AUC: 0.583
2:22:37.951722 INFO: Train AUC: 0.615
2:22:37.951754 INFO: AUC difference: 5.23%
2:22:37.951779 WARNING: AUC difference > 5%. This may indicate overfitting.
2:22:38.237330 INFO: Resetting torch num_threads to 24
2:22:38.259888 PROGRESS: === Extracted 123116 precursors and 583143 fragments ===
2:22:38.260561 INFO: === FDR correction performed with classifier version -1 ===
2:22:38.261242 PROGRESS: ============================= Precursor FDR =============================
2:22:38.261347 PROGRESS: Total precursors accumulated: 346
2:22:38.261409 PROGRESS: Target precursors: 343 (99.13%)
2:22:38.261461 PROGRESS: Decoy precursors: 3 (0.87%)
2:22:38.261509 PROGRESS: 
2:22:38.261573 PROGRESS: Precursor Summary:
2:22:38.262640 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   343; 0.001 FDR:   264
2:22:38.262726 PROGRESS: 
2:22:38.262780 PROGRESS: Protein Summary:
2:22:38.264027 PROGRESS: Channel   0:	 0.050 FDR:   316; 0.010 FDR:   316; 0.001 FDR:   246
2:22:38.264118 PROGRESS: =========================================================================
2:22:38.266079 INFO: Target number of precursors not reached yet.
2:22:38.509235 INFO: Starting optimization step 6.
2:22:38.509523 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:22:38.509611 INFO: Using rust extraction backend
2:22:38.509679 PROGRESS: Extracting batch of 126147 precursors
2:22:38.727786 INFO: === Search parameters used ===
2:22:38.728074 INFO: rt_error       : 805.611083984375
2:22:38.728130 INFO: mobility_error : 0.1
2:22:38.728179 INFO: num_candidates : 1
2:22:38.728223 INFO: ms1_error      : 30
2:22:38.728267 INFO: ms2_error      : 30
2:22:38.728308 INFO: fwhm_rt        : 5
2:22:38.728349 INFO: quant_window   : 3
2:22:38.728389 INFO: ==============================================
2:22:39.810107 INFO: performing precursor FDR with 40 features
2:22:39.810235 INFO: Decoy channel: -1
2:22:39.810261 INFO: competitive: True
2:22:39.910758 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:39.989234 INFO: Estimating optimal hyperparameters - samples: 198,523, batch_size: 813, learning_rate: 4.46e-04
2:22:39.989621 INFO: Using random state 859170 for train-test-split
2:22:46.358518 INFO: Test AUC: 0.588
2:22:46.358642 INFO: Train AUC: 0.611
2:22:46.358673 INFO: AUC difference: 3.83%
2:22:46.673864 INFO: Resetting torch num_threads to 24
2:22:46.716867 PROGRESS: === Extracted 248154 precursors and 1172491 fragments ===
2:22:46.717559 INFO: === FDR correction performed with classifier version -1 ===
2:22:46.718317 PROGRESS: ============================= Precursor FDR =============================
2:22:46.718408 PROGRESS: Total precursors accumulated: 962
2:22:46.718469 PROGRESS: Target precursors: 953 (99.06%)
2:22:46.718523 PROGRESS: Decoy precursors: 9 (0.94%)
2:22:46.718570 PROGRESS: 
2:22:46.718615 PROGRESS: Precursor Summary:
2:22:46.719833 PROGRESS: Channel   0:	 0.050 FDR:   953; 0.010 FDR:   953; 0.001 FDR:   635
2:22:46.719932 PROGRESS: 
2:22:46.719987 PROGRESS: Protein Summary:
2:22:46.721499 PROGRESS: Channel   0:	 0.050 FDR:   819; 0.010 FDR:   819; 0.001 FDR:   565
2:22:46.721592 PROGRESS: =========================================================================
2:22:46.725403 INFO: Target number of precursors not reached yet.
2:22:47.122736 INFO: Starting optimization step 7.
2:22:47.123017 PROGRESS: === Extracting elution groups 127000 to 255000 ===
2:22:47.123102 INFO: Using rust extraction backend
2:22:47.123164 PROGRESS: Extracting batch of 252313 precursors
2:22:47.555175 INFO: === Search parameters used ===
2:22:47.555435 INFO: rt_error       : 805.611083984375
2:22:47.555498 INFO: mobility_error : 0.1
2:22:47.555546 INFO: num_candidates : 1
2:22:47.555589 INFO: ms1_error      : 30
2:22:47.555644 INFO: ms2_error      : 30
2:22:47.555688 INFO: fwhm_rt        : 5
2:22:47.555729 INFO: quant_window   : 3
2:22:47.555771 INFO: ==============================================
2:22:49.700053 INFO: performing precursor FDR with 40 features
2:22:49.700186 INFO: Decoy channel: -1
2:22:49.700213 INFO: competitive: True
2:22:49.890234 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:50.086394 INFO: Estimating optimal hyperparameters - samples: 398,462, batch_size: 1,632, learning_rate: 6.31e-04
2:22:50.087113 INFO: Using random state 207089 for train-test-split
2:22:59.861198 INFO: Test AUC: 0.590
2:22:59.861343 INFO: Train AUC: 0.610
2:22:59.861378 INFO: AUC difference: 3.25%
2:23:00.259968 INFO: Resetting torch num_threads to 24
2:23:00.350569 PROGRESS: === Extracted 498078 precursors and 2354828 fragments ===
2:23:00.351316 INFO: === FDR correction performed with classifier version -1 ===
2:23:00.352364 PROGRESS: ============================= Precursor FDR =============================
2:23:00.352461 PROGRESS: Total precursors accumulated: 2,167
2:23:00.352523 PROGRESS: Target precursors: 2,146 (99.03%)
2:23:00.352591 PROGRESS: Decoy precursors: 21 (0.97%)
2:23:00.352639 PROGRESS: 
2:23:00.352684 PROGRESS: Precursor Summary:
2:23:00.354217 PROGRESS: Channel   0:	 0.050 FDR: 2,146; 0.010 FDR: 2,146; 0.001 FDR: 1,532
2:23:00.354309 PROGRESS: 
2:23:00.354365 PROGRESS: Protein Summary:
2:23:00.356433 PROGRESS: Channel   0:	 0.050 FDR: 1,640; 0.010 FDR: 1,640; 0.001 FDR: 1,226
2:23:00.356529 PROGRESS: =========================================================================
2:23:00.363845 INFO: Target number of precursors reached.
2:23:00.639250 INFO: fragments_df: keeping 5000 of 2354828 [sum(precursor_idx_mask)=22990 sum(mass_error_mask)=2354828 stop_rank=5000
2:23:01.050272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:23:01.317550 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:23:01.964112 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:23:01.964597 INFO: Using score_cutoff 12.9318940243721 (fac=0.99, q=1)
2:23:01.964931 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:23:01.965007 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:23:01.965061 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.9318940243721
2:23:01.965114 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:23:02.114568 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:23:02.448378 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
2:23:02.448675 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:23:02.448790 INFO: Starting optimization step 8.
2:23:02.448865 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:23:02.448949 INFO: Using rust extraction backend
2:23:02.449024 PROGRESS: Extracting batch of 250330 precursors
2:23:02.881352 INFO: === Search parameters used ===
2:23:02.881620 INFO: rt_error       : 805.611083984375
2:23:02.881678 INFO: mobility_error : 0.1
2:23:02.881727 INFO: num_candidates : 3
2:23:02.881781 INFO: ms1_error      : 30
2:23:02.881828 INFO: ms2_error      : 30
2:23:02.881871 INFO: fwhm_rt        : 3.0
2:23:02.881929 INFO: quant_window   : 3
2:23:02.881969 INFO: ==============================================
2:23:06.552109 INFO: performing precursor FDR with 40 features
2:23:06.552247 INFO: Decoy channel: -1
2:23:06.552273 INFO: competitive: True
2:23:06.766093 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:07.083725 INFO: Estimating optimal hyperparameters - samples: 595,861, batch_size: 2,440, learning_rate: 7.72e-04
2:23:07.084903 INFO: Using random state 973793 for train-test-split
2:23:19.076572 INFO: Test AUC: 0.598
2:23:19.076704 INFO: Train AUC: 0.609
2:23:19.076738 INFO: AUC difference: 1.83%
2:23:19.552815 INFO: Resetting torch num_threads to 24
2:23:19.582272 PROGRESS: === Extracted 744827 precursors and 3446934 fragments ===
2:23:19.582765 INFO: === FDR correction performed with classifier version 7 ===
2:23:19.583408 PROGRESS: ============================= Precursor FDR =============================
2:23:19.583516 PROGRESS: Total precursors accumulated: 1,292
2:23:19.583581 PROGRESS: Target precursors: 1,280 (99.07%)
2:23:19.583647 PROGRESS: Decoy precursors: 12 (0.93%)
2:23:19.583694 PROGRESS: 
2:23:19.583739 PROGRESS: Precursor Summary:
2:23:19.584996 PROGRESS: Channel   0:	 0.050 FDR: 1,280; 0.010 FDR: 1,280; 0.001 FDR:   770
2:23:19.585090 PROGRESS: 
2:23:19.585155 PROGRESS: Protein Summary:
2:23:19.586770 PROGRESS: Channel   0:	 0.050 FDR: 1,084; 0.010 FDR: 1,084; 0.001 FDR:   662
2:23:19.586859 PROGRESS: =========================================================================
2:23:19.601020 INFO: Target number of precursors reached.
2:23:19.986423 INFO: fragments_df: keeping 5000 of 3446934 [sum(precursor_idx_mask)=28232 sum(mass_error_mask)=3446934 stop_rank=5000
2:23:20.522962 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:23:20.710708 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:23:21.356515 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:23:21.357001 INFO: Using score_cutoff 12.537545490932464 (fac=0.99, q=1)
2:23:21.357335 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:23:21.357414 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:23:21.357469 INFO: Updating optimization_manager: score_cutoff        : 12.9318940243721 -> 12.537545490932464
2:23:21.357526 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:23:21.507943 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:23:21.860635 INFO: === checking if optimization conditions were reached ===
2:23:21.863334 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:23:21.863435 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
2:23:21.863518 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:23:21.863578 INFO: ==============================================
2:23:21.863650 INFO: Starting optimization step 9.
2:23:21.863711 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:23:21.863779 INFO: Using rust extraction backend
2:23:21.863845 PROGRESS: Extracting batch of 250330 precursors
2:23:22.297182 INFO: === Search parameters used ===
2:23:22.297472 INFO: rt_error       : 805.611083984375
2:23:22.297532 INFO: mobility_error : 0.1
2:23:22.297580 INFO: num_candidates : 3
2:23:22.297625 INFO: ms1_error      : 30
2:23:22.297667 INFO: ms2_error      : 10.0
2:23:22.297721 INFO: fwhm_rt        : 3.0
2:23:22.297764 INFO: quant_window   : 3
2:23:22.297806 INFO: ==============================================
2:23:25.743360 INFO: performing precursor FDR with 40 features
2:23:25.743500 INFO: Decoy channel: -1
2:23:25.743527 INFO: competitive: True
2:23:25.938752 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:26.241358 INFO: Estimating optimal hyperparameters - samples: 599,669, batch_size: 2,456, learning_rate: 7.74e-04
2:23:26.242517 INFO: Using random state 438829 for train-test-split
2:23:38.655305 INFO: Test AUC: 0.602
2:23:38.655434 INFO: Train AUC: 0.614
2:23:38.655483 INFO: AUC difference: 1.94%
2:23:39.139056 INFO: Resetting torch num_threads to 24
2:23:39.165221 PROGRESS: === Extracted 749587 precursors and 4034324 fragments ===
2:23:39.165704 INFO: === FDR correction performed with classifier version 8 ===
2:23:39.166365 PROGRESS: ============================= Precursor FDR =============================
2:23:39.166467 PROGRESS: Total precursors accumulated: 1,594
2:23:39.166526 PROGRESS: Target precursors: 1,579 (99.06%)
2:23:39.166575 PROGRESS: Decoy precursors: 15 (0.94%)
2:23:39.166619 PROGRESS: 
2:23:39.166662 PROGRESS: Precursor Summary:
2:23:39.168045 PROGRESS: Channel   0:	 0.050 FDR: 1,579; 0.010 FDR: 1,579; 0.001 FDR: 1,339
2:23:39.168135 PROGRESS: 
2:23:39.168189 PROGRESS: Protein Summary:
2:23:39.169996 PROGRESS: Channel   0:	 0.050 FDR: 1,311; 0.010 FDR: 1,311; 0.001 FDR: 1,123
2:23:39.170087 PROGRESS: =========================================================================
2:23:39.184216 INFO: Target number of precursors reached.
2:23:39.600036 INFO: fragments_df: keeping 5000 of 4034324 [sum(precursor_idx_mask)=37530 sum(mass_error_mask)=4034324 stop_rank=5000
2:23:40.024999 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:23:40.238141 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:23:40.880984 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:23:40.881466 INFO: Using score_cutoff 12.141171772956847 (fac=0.99, q=1)
2:23:40.881774 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:23:40.881849 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:23:40.881901 INFO: Updating optimization_manager: score_cutoff        : 12.537545490932464 -> 12.141171772956847
2:23:40.881952 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:23:41.032848 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:23:41.374207 INFO: === checking if optimization conditions were reached ===
2:23:41.376478 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:23:41.376583 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:23:41.376652 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:23:41.376714 INFO: ==============================================
2:23:41.376780 INFO: Starting optimization step 10.
2:23:41.376840 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:23:41.376903 INFO: Using rust extraction backend
2:23:41.376964 PROGRESS: Extracting batch of 250330 precursors
2:23:41.804627 INFO: === Search parameters used ===
2:23:41.804932 INFO: rt_error       : 805.611083984375
2:23:41.804993 INFO: mobility_error : 0.1
2:23:41.805043 INFO: num_candidates : 3
2:23:41.805088 INFO: ms1_error      : 30
2:23:41.805145 INFO: ms2_error      : 10.0
2:23:41.805190 INFO: fwhm_rt        : 3.0
2:23:41.805231 INFO: quant_window   : 3
2:23:41.805271 INFO: ==============================================
2:23:45.177918 INFO: performing precursor FDR with 40 features
2:23:45.178037 INFO: Decoy channel: -1
2:23:45.178063 INFO: competitive: True
2:23:45.375395 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:45.678530 INFO: Estimating optimal hyperparameters - samples: 599,663, batch_size: 2,456, learning_rate: 7.74e-04
2:23:45.679690 INFO: Using random state 746654 for train-test-split
2:23:58.881390 INFO: Test AUC: 0.609
2:23:58.881522 INFO: Train AUC: 0.618
2:23:58.881557 INFO: AUC difference: 1.39%
2:23:59.362340 INFO: Resetting torch num_threads to 24
2:23:59.389261 PROGRESS: === Extracted 749579 precursors and 4034155 fragments ===
2:23:59.389743 INFO: === FDR correction performed with classifier version 9 ===
2:23:59.390441 PROGRESS: ============================= Precursor FDR =============================
2:23:59.390529 PROGRESS: Total precursors accumulated: 1,832
2:23:59.390588 PROGRESS: Target precursors: 1,814 (99.02%)
2:23:59.390638 PROGRESS: Decoy precursors: 18 (0.98%)
2:23:59.390684 PROGRESS: 
2:23:59.390729 PROGRESS: Precursor Summary:
2:23:59.392181 PROGRESS: Channel   0:	 0.050 FDR: 1,814; 0.010 FDR: 1,814; 0.001 FDR: 1,388
2:23:59.392286 PROGRESS: 
2:23:59.392341 PROGRESS: Protein Summary:
2:23:59.394228 PROGRESS: Channel   0:	 0.050 FDR: 1,514; 0.010 FDR: 1,514; 0.001 FDR: 1,165
2:23:59.394319 PROGRESS: =========================================================================
2:23:59.408031 INFO: Target number of precursors reached.
2:23:59.852879 INFO: fragments_df: keeping 5000 of 4034155 [sum(precursor_idx_mask)=42101 sum(mass_error_mask)=4034155 stop_rank=5000
2:24:00.269478 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:24:00.540436 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:24:01.253309 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:24:01.253782 INFO: Using score_cutoff 9.356685478019715 (fac=0.99, q=1)
2:24:01.254093 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:24:01.254165 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:24:01.254219 INFO: Updating optimization_manager: score_cutoff        : 12.141171772956847 -> 9.356685478019715
2:24:01.254277 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:24:01.403980 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:24:01.755686 INFO: === checking if optimization conditions were reached ===
2:24:01.757935 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:24:01.758031 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:24:01.758096 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:24:01.758157 INFO: ==============================================
2:24:01.758221 INFO: Starting optimization step 11.
2:24:01.758277 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:24:01.758337 INFO: Using rust extraction backend
2:24:01.758395 PROGRESS: Extracting batch of 250330 precursors
2:24:02.188960 INFO: === Search parameters used ===
2:24:02.189250 INFO: rt_error       : 805.611083984375
2:24:02.189309 INFO: mobility_error : 0.1
2:24:02.189372 INFO: num_candidates : 3
2:24:02.189418 INFO: ms1_error      : 30
2:24:02.189460 INFO: ms2_error      : 10.0
2:24:02.189500 INFO: fwhm_rt        : 3.0
2:24:02.189538 INFO: quant_window   : 3
2:24:02.189576 INFO: ==============================================
2:24:05.591178 INFO: performing precursor FDR with 40 features
2:24:05.591328 INFO: Decoy channel: -1
2:24:05.591358 INFO: competitive: True
2:24:05.788209 INFO: Setting torch num_threads to 2 for FDR classification task
2:24:06.105514 INFO: Estimating optimal hyperparameters - samples: 599,680, batch_size: 2,456, learning_rate: 7.74e-04
2:24:06.106664 INFO: Using random state 818408 for train-test-split
2:24:18.309104 INFO: Test AUC: 0.608
2:24:18.309261 INFO: Train AUC: 0.621
2:24:18.309296 INFO: AUC difference: 2.14%
2:24:18.793320 INFO: Resetting torch num_threads to 24
2:24:18.840269 PROGRESS: === Extracted 749601 precursors and 4034371 fragments ===
2:24:18.840785 INFO: === FDR correction performed with classifier version 10 ===
2:24:18.841492 PROGRESS: ============================= Precursor FDR =============================
2:24:18.841582 PROGRESS: Total precursors accumulated: 1,721
2:24:18.841644 PROGRESS: Target precursors: 1,704 (99.01%)
2:24:18.841697 PROGRESS: Decoy precursors: 17 (0.99%)
2:24:18.841745 PROGRESS: 
2:24:18.841790 PROGRESS: Precursor Summary:
2:24:18.843179 PROGRESS: Channel   0:	 0.050 FDR: 1,704; 0.010 FDR: 1,704; 0.001 FDR: 1,279
2:24:18.843271 PROGRESS: 
2:24:18.843329 PROGRESS: Protein Summary:
2:24:18.845171 PROGRESS: Channel   0:	 0.050 FDR: 1,422; 0.010 FDR: 1,422; 0.001 FDR: 1,081
2:24:18.845264 PROGRESS: =========================================================================
2:24:18.859901 INFO: Target number of precursors reached.
2:24:19.297570 INFO: fragments_df: keeping 5000 of 4034371 [sum(precursor_idx_mask)=40596 sum(mass_error_mask)=4034371 stop_rank=5000
2:24:19.725571 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:24:19.974414 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:24:20.691478 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:24:20.691985 INFO: Using score_cutoff 11.863465696334838 (fac=0.99, q=1)
2:24:20.692313 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:24:20.692389 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:24:20.692444 INFO: Updating optimization_manager: score_cutoff        : 9.356685478019715 -> 11.863465696334838
2:24:20.692503 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:24:20.842693 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:24:21.168912 INFO: === checking if optimization conditions were reached ===
2:24:21.171167 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:24:21.171269 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:24:21.171334 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:24:21.171392 INFO: ==============================================
2:24:21.171470 INFO: Starting optimization step 12.
2:24:21.171540 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:24:21.171607 INFO: Using rust extraction backend
2:24:21.171672 PROGRESS: Extracting batch of 250330 precursors
2:24:21.603656 INFO: === Search parameters used ===
2:24:21.604022 INFO: rt_error       : 805.611083984375
2:24:21.604111 INFO: mobility_error : 0.1
2:24:21.604162 INFO: num_candidates : 3
2:24:21.604207 INFO: ms1_error      : 30
2:24:21.604249 INFO: ms2_error      : 10.0
2:24:21.604290 INFO: fwhm_rt        : 3.0
2:24:21.604330 INFO: quant_window   : 3
2:24:21.604370 INFO: ==============================================
2:24:25.012338 INFO: performing precursor FDR with 40 features
2:24:25.012467 INFO: Decoy channel: -1
2:24:25.012501 INFO: competitive: True
2:24:25.203856 INFO: Setting torch num_threads to 2 for FDR classification task
2:24:25.493784 INFO: Estimating optimal hyperparameters - samples: 599,655, batch_size: 2,456, learning_rate: 7.74e-04
2:24:25.494921 INFO: Using random state 412310 for train-test-split
2:24:42.691125 INFO: Test AUC: 0.611
2:24:42.691326 INFO: Train AUC: 0.623
2:24:42.691367 INFO: AUC difference: 1.91%
2:24:43.733326 INFO: Resetting torch num_threads to 24
2:24:43.905280 PROGRESS: === Extracted 749569 precursors and 4033513 fragments ===
2:24:43.908551 INFO: === FDR correction performed with classifier version 11 ===
2:24:43.917076 PROGRESS: ============================= Precursor FDR =============================
2:24:43.918087 PROGRESS: Total precursors accumulated: 1,919
2:24:43.918498 PROGRESS: Target precursors: 1,900 (99.01%)
2:24:43.918882 PROGRESS: Decoy precursors: 19 (0.99%)
2:24:43.919197 PROGRESS: 
2:24:43.919659 PROGRESS: Precursor Summary:
2:24:43.938470 PROGRESS: Channel   0:	 0.050 FDR: 1,900; 0.010 FDR: 1,899; 0.001 FDR: 1,395
2:24:43.939609 PROGRESS: 
2:24:43.940004 PROGRESS: Protein Summary:
2:24:43.965218 PROGRESS: Channel   0:	 0.050 FDR: 1,578; 0.010 FDR: 1,577; 0.001 FDR: 1,163
2:24:43.966299 PROGRESS: =========================================================================
2:24:44.090986 INFO: Target number of precursors reached.
2:24:45.594188 INFO: fragments_df: keeping 5000 of 4033513 [sum(precursor_idx_mask)=44041 sum(mass_error_mask)=4033513 stop_rank=5000
2:24:47.543638 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:24:48.371147 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:24:49.939425 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:24:49.941790 INFO: Using score_cutoff 10.107210911750792 (fac=0.99, q=1)
2:24:49.943766 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:24:49.943943 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:24:49.944014 INFO: Updating optimization_manager: score_cutoff        : 11.863465696334838 -> 10.107210911750792
2:24:49.944102 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:24:50.183573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:24:50.747265 INFO: === checking if optimization conditions were reached ===
2:24:50.750875 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:24:50.751183 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:24:50.751266 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:24:50.751352 INFO: ==============================================
2:24:50.751450 PROGRESS: Optimization finished for ms2_error.
2:24:51.798239 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:24:52.012116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:24:52.582721 INFO: Starting optimization step 0.
2:24:52.583222 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:24:52.583370 INFO: Using rust extraction backend
2:24:52.583483 PROGRESS: Extracting batch of 250330 precursors
2:24:53.552776 INFO: === Search parameters used ===
2:24:53.553397 INFO: rt_error       : 805.611083984375
2:24:53.553463 INFO: mobility_error : 0.1
2:24:53.553515 INFO: num_candidates : 3
2:24:53.553561 INFO: ms1_error      : 30
2:24:53.553604 INFO: ms2_error      : 10.0
2:24:53.553647 INFO: fwhm_rt        : 3.0
2:24:53.553699 INFO: quant_window   : 3
2:24:53.553741 INFO: ==============================================
2:25:03.464681 INFO: performing precursor FDR with 40 features
2:25:03.465182 INFO: Decoy channel: -1
2:25:03.465293 INFO: competitive: True
2:25:04.605051 INFO: Setting torch num_threads to 2 for FDR classification task
2:25:05.894351 INFO: Estimating optimal hyperparameters - samples: 599,660, batch_size: 2,456, learning_rate: 7.74e-04
2:25:05.904113 INFO: Using random state 835843 for train-test-split
2:25:52.442442 INFO: Test AUC: 0.613
2:25:52.443052 INFO: Train AUC: 0.625
2:25:52.443156 INFO: AUC difference: 1.96%
2:25:54.277915 INFO: Resetting torch num_threads to 24
2:25:54.423845 PROGRESS: === Extracted 749575 precursors and 4033660 fragments ===
2:25:54.426355 INFO: === FDR correction performed with classifier version 12 ===
2:25:54.431911 PROGRESS: ============================= Precursor FDR =============================
2:25:54.432733 PROGRESS: Total precursors accumulated: 1,887
2:25:54.433009 PROGRESS: Target precursors: 1,869 (99.05%)
2:25:54.433252 PROGRESS: Decoy precursors: 18 (0.95%)
2:25:54.433492 PROGRESS: 
2:25:54.433751 PROGRESS: Precursor Summary:
2:25:54.444679 PROGRESS: Channel   0:	 0.050 FDR: 1,869; 0.010 FDR: 1,869; 0.001 FDR: 1,437
2:25:54.445515 PROGRESS: 
2:25:54.445873 PROGRESS: Protein Summary:
2:25:54.459783 PROGRESS: Channel   0:	 0.050 FDR: 1,555; 0.010 FDR: 1,555; 0.001 FDR: 1,200
2:25:54.460609 PROGRESS: =========================================================================
2:25:54.549884 INFO: Target number of precursors reached.
2:25:55.973890 INFO: fragments_df: keeping 5000 of 4033660 [sum(precursor_idx_mask)=43067 sum(mass_error_mask)=4033660 stop_rank=5000
2:25:57.884585 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:25:59.207923 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:26:00.828814 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:26:00.830087 INFO: Using score_cutoff 9.254754856109619 (fac=0.99, q=1)
2:26:00.830699 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:26:00.830788 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:26:00.830849 INFO: Updating optimization_manager: score_cutoff        : 10.107210911750792 -> 9.254754856109619
2:26:00.830932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:26:01.079288 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:26:01.784781 INFO: === checking if optimization conditions were reached ===
2:26:01.785357 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:26:01.791397 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 865.4611168826518
2:26:01.791870 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 865.4611.
2:26:01.792022 INFO: ==============================================
2:26:01.792168 INFO: Starting optimization step 1.
2:26:01.792270 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:26:01.792399 INFO: Using rust extraction backend
2:26:01.792493 PROGRESS: Extracting batch of 250330 precursors
2:26:02.791831 INFO: === Search parameters used ===
2:26:02.792455 INFO: rt_error       : 865.4611168826518
2:26:02.792573 INFO: mobility_error : 0.1
2:26:02.792629 INFO: num_candidates : 3
2:26:02.792687 INFO: ms1_error      : 30
2:26:02.792732 INFO: ms2_error      : 10.0
2:26:02.792774 INFO: fwhm_rt        : 3.0
2:26:02.792816 INFO: quant_window   : 3
2:26:02.792859 INFO: ==============================================
2:26:12.717617 INFO: performing precursor FDR with 40 features
2:26:12.717929 INFO: Decoy channel: -1
2:26:12.717960 INFO: competitive: True
2:26:13.529420 INFO: Setting torch num_threads to 2 for FDR classification task
2:26:14.825442 INFO: Estimating optimal hyperparameters - samples: 599,674, batch_size: 2,456, learning_rate: 7.74e-04
2:26:14.833165 INFO: Using random state 835843 for train-test-split
2:26:42.649450 INFO: Test AUC: 0.612
2:26:42.649792 INFO: Train AUC: 0.628
2:26:42.649838 INFO: AUC difference: 2.58%
2:26:43.493281 INFO: Resetting torch num_threads to 24
2:26:43.636822 PROGRESS: === Extracted 749593 precursors and 4034081 fragments ===
2:26:43.638086 INFO: === FDR correction performed with classifier version 12 ===
2:26:43.640136 PROGRESS: ============================= Precursor FDR =============================
2:26:43.640292 PROGRESS: Total precursors accumulated: 1,945
2:26:43.640360 PROGRESS: Target precursors: 1,926 (99.02%)
2:26:43.640420 PROGRESS: Decoy precursors: 19 (0.98%)
2:26:43.640474 PROGRESS: 
2:26:43.640523 PROGRESS: Precursor Summary:
2:26:43.642852 PROGRESS: Channel   0:	 0.050 FDR: 1,926; 0.010 FDR: 1,926; 0.001 FDR: 1,367
2:26:43.643003 PROGRESS: 
2:26:43.643062 PROGRESS: Protein Summary:
2:26:43.645778 PROGRESS: Channel   0:	 0.050 FDR: 1,606; 0.010 FDR: 1,606; 0.001 FDR: 1,144
2:26:43.645936 PROGRESS: =========================================================================
2:26:43.702860 INFO: Target number of precursors reached.
2:26:44.199517 INFO: fragments_df: keeping 5000 of 4034081 [sum(precursor_idx_mask)=43874 sum(mass_error_mask)=4034081 stop_rank=5000
2:26:45.582380 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:26:46.099580 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:26:46.908175 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:26:46.909197 INFO: Using score_cutoff 8.06373975276947 (fac=0.99, q=1)
2:26:46.909814 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:26:46.909908 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:26:46.909967 INFO: Updating optimization_manager: score_cutoff        : 9.254754856109619 -> 8.06373975276947
2:26:46.910038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:26:47.154050 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:26:47.846016 INFO: === checking if optimization conditions were reached ===
2:26:47.846660 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:26:47.853270 INFO: Updating optimization_manager: rt_error            : 865.4611168826518 -> 750.2082681823217
2:26:47.853662 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 750.2083.
2:26:47.853783 INFO: ==============================================
2:26:47.853905 INFO: Starting optimization step 2.
2:26:47.853998 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:26:47.854112 INFO: Using rust extraction backend
2:26:47.854202 PROGRESS: Extracting batch of 250330 precursors
2:26:48.868930 INFO: === Search parameters used ===
2:26:48.869724 INFO: rt_error       : 750.2082681823217
2:26:48.869856 INFO: mobility_error : 0.1
2:26:48.869915 INFO: num_candidates : 3
2:26:48.869967 INFO: ms1_error      : 30
2:26:48.870016 INFO: ms2_error      : 10.0
2:26:48.870079 INFO: fwhm_rt        : 3.0
2:26:48.870126 INFO: quant_window   : 3
2:26:48.870170 INFO: ==============================================
2:27:00.226544 INFO: performing precursor FDR with 40 features
2:27:00.227136 INFO: Decoy channel: -1
2:27:00.227247 INFO: competitive: True
2:27:01.584840 INFO: Setting torch num_threads to 2 for FDR classification task
2:27:02.908659 INFO: Estimating optimal hyperparameters - samples: 599,662, batch_size: 2,456, learning_rate: 7.74e-04
2:27:02.920239 INFO: Using random state 835843 for train-test-split
2:27:28.791807 INFO: Test AUC: 0.614
2:27:28.792134 INFO: Train AUC: 0.628
2:27:28.792179 INFO: AUC difference: 2.24%
2:27:29.641334 INFO: Resetting torch num_threads to 24
2:27:29.792095 PROGRESS: === Extracted 749578 precursors and 4033896 fragments ===
2:27:29.793273 INFO: === FDR correction performed with classifier version 12 ===
2:27:29.795104 PROGRESS: ============================= Precursor FDR =============================
2:27:29.795261 PROGRESS: Total precursors accumulated: 1,864
2:27:29.795334 PROGRESS: Target precursors: 1,846 (99.03%)
2:27:29.795388 PROGRESS: Decoy precursors: 18 (0.97%)
2:27:29.795483 PROGRESS: 
2:27:29.795543 PROGRESS: Precursor Summary:
2:27:29.797576 PROGRESS: Channel   0:	 0.050 FDR: 1,846; 0.010 FDR: 1,846; 0.001 FDR: 1,074
2:27:29.797705 PROGRESS: 
2:27:29.797764 PROGRESS: Protein Summary:
2:27:29.800127 PROGRESS: Channel   0:	 0.050 FDR: 1,539; 0.010 FDR: 1,539; 0.001 FDR:   920
2:27:29.800268 PROGRESS: =========================================================================
2:27:29.885282 INFO: Target number of precursors reached.
2:27:30.415535 INFO: fragments_df: keeping 5000 of 4033896 [sum(precursor_idx_mask)=42777 sum(mass_error_mask)=4033896 stop_rank=5000
2:27:31.864293 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:27:32.266965 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:27:33.152412 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:27:33.153403 INFO: Using score_cutoff 9.873069278240203 (fac=0.99, q=1)
2:27:33.153987 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:27:33.154086 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:27:33.154146 INFO: Updating optimization_manager: score_cutoff        : 8.06373975276947 -> 9.873069278240203
2:27:33.154212 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:27:33.402089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:27:34.122686 INFO: === checking if optimization conditions were reached ===
2:27:34.123307 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:27:34.130204 INFO: Updating optimization_manager: rt_error            : 750.2082681823217 -> 893.2568751414999
2:27:34.130560 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 893.2569.
2:27:34.130689 INFO: ==============================================
2:27:34.130835 INFO: Starting optimization step 3.
2:27:34.130933 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:27:34.131049 INFO: Using rust extraction backend
2:27:34.131138 PROGRESS: Extracting batch of 250330 precursors
2:27:35.063999 INFO: === Search parameters used ===
2:27:35.064593 INFO: rt_error       : 893.2568751414999
2:27:35.064730 INFO: mobility_error : 0.1
2:27:35.064791 INFO: num_candidates : 3
2:27:35.064841 INFO: ms1_error      : 30
2:27:35.064893 INFO: ms2_error      : 10.0
2:27:35.064946 INFO: fwhm_rt        : 3.0
2:27:35.064998 INFO: quant_window   : 3
2:27:35.065044 INFO: ==============================================
2:27:44.446123 INFO: performing precursor FDR with 40 features
2:27:44.446416 INFO: Decoy channel: -1
2:27:44.446446 INFO: competitive: True
2:27:45.299035 INFO: Setting torch num_threads to 2 for FDR classification task
2:27:46.573220 INFO: Estimating optimal hyperparameters - samples: 599,660, batch_size: 2,456, learning_rate: 7.74e-04
2:27:46.582855 INFO: Using random state 835843 for train-test-split
2:28:22.729613 INFO: Test AUC: 0.613
2:28:22.729960 INFO: Train AUC: 0.629
2:28:22.730009 INFO: AUC difference: 2.51%
2:28:23.510981 INFO: Resetting torch num_threads to 24
2:28:23.623019 PROGRESS: === Extracted 749576 precursors and 4034183 fragments ===
2:28:23.624249 INFO: === FDR correction performed with classifier version 12 ===
2:28:23.626125 PROGRESS: ============================= Precursor FDR =============================
2:28:23.626273 PROGRESS: Total precursors accumulated: 1,825
2:28:23.626376 PROGRESS: Target precursors: 1,807 (99.01%)
2:28:23.626438 PROGRESS: Decoy precursors: 18 (0.99%)
2:28:23.626488 PROGRESS: 
2:28:23.626536 PROGRESS: Precursor Summary:
2:28:23.628757 PROGRESS: Channel   0:	 0.050 FDR: 1,807; 0.010 FDR: 1,807; 0.001 FDR: 1,344
2:28:23.628900 PROGRESS: 
2:28:23.628963 PROGRESS: Protein Summary:
2:28:23.632609 PROGRESS: Channel   0:	 0.050 FDR: 1,514; 0.010 FDR: 1,514; 0.001 FDR: 1,129
2:28:23.632839 PROGRESS: =========================================================================
2:28:23.679988 INFO: Target number of precursors reached.
2:28:24.177244 INFO: fragments_df: keeping 5000 of 4034183 [sum(precursor_idx_mask)=41747 sum(mass_error_mask)=4034183 stop_rank=5000
2:28:25.552027 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:28:26.017375 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:28:26.907028 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:28:26.908022 INFO: Using score_cutoff 9.346227096176149 (fac=0.99, q=1)
2:28:26.908584 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:28:26.908672 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:28:26.908730 INFO: Updating optimization_manager: score_cutoff        : 9.873069278240203 -> 9.346227096176149
2:28:26.908792 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:28:27.167248 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:28:27.929502 INFO: === checking if optimization conditions were reached ===
2:28:27.930088 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:28:27.935260 INFO: Updating optimization_manager: rt_error            : 893.2568751414999 -> 882.8331785570778
2:28:27.935721 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 882.8332.
2:28:27.935809 INFO: ==============================================
2:28:27.935908 INFO: Starting optimization step 4.
2:28:27.935987 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:28:27.936082 INFO: Using rust extraction backend
2:28:27.936167 PROGRESS: Extracting batch of 250330 precursors
2:28:29.448405 INFO: === Search parameters used ===
2:28:29.449316 INFO: rt_error       : 882.8331785570778
2:28:29.449455 INFO: mobility_error : 0.1
2:28:29.449550 INFO: num_candidates : 3
2:28:29.449663 INFO: ms1_error      : 30
2:28:29.449793 INFO: ms2_error      : 10.0
2:28:29.449910 INFO: fwhm_rt        : 3.0
2:28:29.450021 INFO: quant_window   : 3
2:28:29.450109 INFO: ==============================================
2:28:39.476588 INFO: performing precursor FDR with 40 features
2:28:39.477169 INFO: Decoy channel: -1
2:28:39.477384 INFO: competitive: True
2:28:41.048620 INFO: Setting torch num_threads to 2 for FDR classification task
2:28:43.217136 INFO: Estimating optimal hyperparameters - samples: 599,669, batch_size: 2,456, learning_rate: 7.74e-04
2:28:43.232939 INFO: Using random state 835843 for train-test-split
2:29:12.795761 INFO: Test AUC: 0.613
2:29:12.796154 INFO: Train AUC: 0.628
2:29:12.796203 INFO: AUC difference: 2.29%
2:29:13.531285 INFO: Resetting torch num_threads to 24
2:29:13.605120 PROGRESS: === Extracted 749587 precursors and 4034347 fragments ===
2:29:13.606390 INFO: === FDR correction performed with classifier version 12 ===
2:29:13.608325 PROGRESS: ============================= Precursor FDR =============================
2:29:13.608526 PROGRESS: Total precursors accumulated: 1,820
2:29:13.608602 PROGRESS: Target precursors: 1,802 (99.01%)
2:29:13.608678 PROGRESS: Decoy precursors: 18 (0.99%)
2:29:13.608735 PROGRESS: 
2:29:13.608783 PROGRESS: Precursor Summary:
2:29:13.611019 PROGRESS: Channel   0:	 0.050 FDR: 1,802; 0.010 FDR: 1,802; 0.001 FDR: 1,341
2:29:13.611170 PROGRESS: 
2:29:13.611231 PROGRESS: Protein Summary:
2:29:13.613618 PROGRESS: Channel   0:	 0.050 FDR: 1,493; 0.010 FDR: 1,493; 0.001 FDR: 1,122
2:29:13.613770 PROGRESS: =========================================================================
2:29:13.666470 INFO: Target number of precursors reached.
2:29:14.150607 INFO: fragments_df: keeping 5000 of 4034347 [sum(precursor_idx_mask)=42101 sum(mass_error_mask)=4034347 stop_rank=5000
2:29:15.516350 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:29:22.193873 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:29:23.118383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:29:23.119673 INFO: Using score_cutoff 10.071778967571259 (fac=0.99, q=1)
2:29:23.120874 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:29:23.121130 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:29:23.121206 INFO: Updating optimization_manager: score_cutoff        : 9.346227096176149 -> 10.071778967571259
2:29:23.121324 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:29:23.362636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:29:24.078180 INFO: === checking if optimization conditions were reached ===
2:29:24.078816 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:29:24.081483 INFO: Updating optimization_manager: rt_error            : 882.8331785570778 -> 865.4611168826518
2:29:24.082037 INFO: Updating optimization_manager: classifier_version  : 12 -> 14
2:29:24.082270 INFO: Updating optimization_manager: score_cutoff        : 10.071778967571259 -> 8.06373975276947
2:29:24.082438 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:29:24.082558 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:29:24.082680 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 865.4611 found after 5 searches.
2:29:24.082764 INFO: ==============================================
2:29:24.082891 PROGRESS: Optimization finished for rt_error.
2:29:25.470252 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:29:25.702823 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:29:26.400118 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:29:26.400870 PROGRESS: ==============================================
2:29:26.401062 PROGRESS: ms2_error      : 10.0000
2:29:26.401205 PROGRESS: rt_error       : 865.4611
2:29:26.401310 PROGRESS: ==============================================
2:29:26.404741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:29:38.657337 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:30:16.375218 INFO: Using rust extraction backend
2:30:16.376117 PROGRESS: Extracting batch of 11997144 precursors
2:30:57.879364 INFO: === Search parameters used ===
2:30:57.880404 INFO: rt_error       : 865.4611168826518
2:30:57.880550 INFO: mobility_error : 0.1
2:30:57.880619 INFO: num_candidates : 3
2:30:57.880682 INFO: ms1_error      : 30
2:30:57.880734 INFO: ms2_error      : 10.0
2:30:57.880780 INFO: fwhm_rt        : 3.0
2:30:57.880822 INFO: quant_window   : 3
2:30:57.880865 INFO: ==============================================
2:33:29.458489 INFO: Removed 3269950 precursors with score below cutoff 8.06373975276947
2:34:53.259145 INFO: performing precursor FDR with 40 features
2:34:53.259605 INFO: Decoy channel: -1
2:34:53.259643 INFO: competitive: True
2:35:16.156516 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:28.544563 INFO: Estimating optimal hyperparameters - samples: 26,176,961, batch_size: 4,096, learning_rate: 1.00e-03
2:36:29.154362 INFO: Using random state 765147 for train-test-split
2:46:16.631508 INFO: Test AUC: 0.621
2:46:16.631954 INFO: Train AUC: 0.622
2:46:16.632011 INFO: AUC difference: 0.14%
2:46:24.007118 INFO: Resetting torch num_threads to 24
2:46:26.179336 PROGRESS: ============================= Precursor FDR =============================
2:46:26.179873 PROGRESS: Total precursors accumulated: 93,881
2:46:26.179974 PROGRESS: Target precursors: 92,952 (99.01%)
2:46:26.180037 PROGRESS: Decoy precursors: 929 (0.99%)
2:46:26.180095 PROGRESS: 
2:46:26.180140 PROGRESS: Precursor Summary:
2:46:26.205659 PROGRESS: Channel   0:	 0.050 FDR: 92,952; 0.010 FDR: 92,952; 0.001 FDR: 60,843
2:46:26.205925 PROGRESS: 
2:46:26.206004 PROGRESS: Protein Summary:
2:46:26.240413 PROGRESS: Channel   0:	 0.050 FDR: 13,506; 0.010 FDR: 13,506; 0.001 FDR: 9,225
2:46:26.240670 PROGRESS: =========================================================================
2:46:26.447621 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
2:46:26.637800 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
2:46:26.886943 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:47:04.785666 PROGRESS: Processing search outputs
2:47:04.785966 PROGRESS: === Performing protein grouping and FDR ===
2:47:04.786022 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:47:04.877687 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:47:04.958673 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:47:05.044195 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:47:05.105754 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:47:05.195215 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:47:05.297956 INFO: Performing protein inference
2:47:06.108548 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2:47:57.599209 INFO: Performing protein FDR
2:48:04.605613 INFO: Normalizing q-values using 19,586 targets and 3,929 decoys
2:48:04.610788 INFO: Test AUC: 0.861
2:48:04.610851 INFO: Train AUC: 0.856
2:48:04.610893 INFO: AUC difference: 0.56%
2:48:05.300397 INFO: ================ Protein FDR =================
2:48:05.300552 INFO: Unique protein groups in output
2:48:05.300584 INFO:   1% protein FDR: 10,386
2:48:05.300606 INFO: 
2:48:05.300628 INFO: Unique precursor in output
2:48:05.300647 INFO:   1% protein FDR: 132,778
2:48:05.300667 INFO: ================================================
2:48:05.365084 PROGRESS: Building search statistics
2:48:05.464571 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
2:48:05.464913 INFO: Initializing OptimizationManager
2:48:05.465344 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
2:48:05.465429 INFO: Initializing CalibrationManager
2:48:05.465816 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
2:48:05.465901 INFO: Initializing RawFileManager
2:48:05.498596 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
2:48:05.498976 INFO: Initializing OptimizationManager
2:48:05.499395 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
2:48:05.499500 INFO: Initializing CalibrationManager
2:48:05.499946 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
2:48:05.500036 INFO: Initializing RawFileManager
2:48:05.532727 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
2:48:05.533112 INFO: Initializing OptimizationManager
2:48:05.533490 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
2:48:05.533573 INFO: Initializing CalibrationManager
2:48:05.533993 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
2:48:05.534074 INFO: Initializing RawFileManager
2:48:05.567282 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
2:48:05.567477 INFO: Initializing OptimizationManager
2:48:05.567828 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
2:48:05.567908 INFO: Initializing CalibrationManager
2:48:05.568299 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
2:48:05.568379 INFO: Initializing RawFileManager
2:48:05.601774 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
2:48:05.602087 INFO: Initializing OptimizationManager
2:48:05.602435 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
2:48:05.602513 INFO: Initializing CalibrationManager
2:48:05.602721 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
2:48:05.602801 INFO: Initializing RawFileManager
2:48:05.636599 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
2:48:05.636785 INFO: Initializing OptimizationManager
2:48:05.637157 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
2:48:05.637236 INFO: Initializing CalibrationManager
2:48:05.637630 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
2:48:05.637710 INFO: Initializing RawFileManager
2:48:05.640815 INFO: Writing stat output to disk
2:48:05.640892 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/stat.tsv to disk
2:48:05.650683 PROGRESS: Building internal statistics
2:48:05.651249 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
2:48:05.651297 INFO: Initializing TimingManager
2:48:05.651937 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
2:48:05.651983 INFO: Initializing TimingManager
2:48:05.652354 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
2:48:05.652401 INFO: Initializing TimingManager
2:48:05.652607 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
2:48:05.652653 INFO: Initializing TimingManager
2:48:05.652978 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
2:48:05.653015 INFO: Initializing TimingManager
2:48:05.653214 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
2:48:05.653247 INFO: Initializing TimingManager
2:48:05.653704 INFO: Writing internal output to disk
2:48:05.653745 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/internal.tsv to disk
2:48:05.718693 INFO: Performing label free quantification
2:48:05.718866 INFO: Accumulating fragment data
2:48:05.718927 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:48:05.998333 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:48:08.627094 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:48:10.635751 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:48:12.128278 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:48:13.777559 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:48:15.846733 INFO: Performing label free quantification on the precursor level
2:48:15.846900 INFO: Filtering fragments by quality
2:48:16.287121 INFO: Performing label-free quantification with directlfq normalization
2:48:16.913455 INFO: 132778 lfq-groups total
2:48:59.691649 INFO: using 24 processes
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2:50:40.729389 INFO: Performing label free quantification on the peptide level
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2:52:30.082373 INFO: lfq-object 107000
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2:52:39.783960 INFO: lfq-object 115200
2:52:39.852840 INFO: lfq-object 117900
2:52:39.870288 INFO: lfq-object 116200
2:52:39.881204 INFO: lfq-object 117100
2:52:39.963914 INFO: lfq-object 118000
2:52:39.981233 INFO: lfq-object 116300
2:52:40.001495 INFO: lfq-object 117200
2:52:40.076663 INFO: lfq-object 118100
2:52:40.090544 INFO: lfq-object 116400
2:52:40.116396 INFO: lfq-object 117300
2:52:40.154551 INFO: lfq-object 119100
2:52:40.193561 INFO: lfq-object 118200
2:52:40.230929 INFO: lfq-object 117400
2:52:40.269457 INFO: lfq-object 119200
2:52:40.306931 INFO: lfq-object 118300
2:52:40.349538 INFO: lfq-object 117500
2:52:40.381773 INFO: lfq-object 119300
2:52:40.419972 INFO: lfq-object 118400
2:52:40.461831 INFO: lfq-object 117600
2:52:40.494942 INFO: lfq-object 119400
2:52:40.527328 INFO: lfq-object 118500
2:52:40.577068 INFO: lfq-object 117700
2:52:40.613393 INFO: lfq-object 119500
2:52:40.622163 INFO: lfq-object 120300
2:52:40.645394 INFO: lfq-object 118600
2:52:40.729502 INFO: lfq-object 119600
2:52:40.735032 INFO: lfq-object 120400
2:52:40.760614 INFO: lfq-object 118700
2:52:40.844597 INFO: lfq-object 119700
2:52:40.852502 INFO: lfq-object 120500
2:52:40.872704 INFO: lfq-object 118800
2:52:40.965120 INFO: lfq-object 120600
2:52:40.972084 INFO: lfq-object 119800
2:52:40.982621 INFO: lfq-object 118900
2:52:41.070268 INFO: lfq-object 120700
2:52:41.076271 INFO: lfq-object 119900
2:52:41.094273 INFO: lfq-object 119000
2:52:41.183702 INFO: lfq-object 120800
2:52:41.189989 INFO: lfq-object 120000
2:52:41.298949 INFO: lfq-object 120900
2:52:41.302805 INFO: lfq-object 120100
2:52:41.415191 INFO: lfq-object 121000
2:52:41.421600 INFO: lfq-object 120200
2:52:41.527450 INFO: lfq-object 121100
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2:52:41.749714 INFO: lfq-object 121300
2:52:41.866879 INFO: lfq-object 121400
2:52:47.746806 INFO: Performing label free quantification on the pg level
2:52:47.747211 INFO: Filtering fragments by quality
2:52:48.165716 INFO: Performing label-free quantification with directlfq normalization
2:52:48.375982 INFO: 10386 lfq-groups total
2:53:00.933193 INFO: using 24 processes
2:53:01.092480 INFO: lfq-object 0
2:53:02.312356 INFO: lfq-object 1200
2:53:02.355344 INFO: lfq-object 100
2:53:02.373308 INFO: lfq-object 800
2:53:02.408592 INFO: lfq-object 400
2:53:02.421101 INFO: lfq-object 1000
2:53:02.440422 INFO: lfq-object 900
2:53:02.447542 INFO: lfq-object 1100
2:53:02.457693 INFO: lfq-object 700
2:53:02.476014 INFO: lfq-object 500
2:53:02.575577 INFO: lfq-object 300
2:53:02.618565 INFO: lfq-object 200
2:53:02.660655 INFO: lfq-object 600
2:53:02.764208 INFO: lfq-object 1900
2:53:02.770817 INFO: lfq-object 1800
2:53:02.777327 INFO: lfq-object 2000
2:53:02.818213 INFO: lfq-object 2400
2:53:02.877420 INFO: lfq-object 2100
2:53:02.935204 INFO: lfq-object 1700
2:53:03.034596 INFO: lfq-object 2200
2:53:03.038039 INFO: lfq-object 2300
2:53:03.100405 INFO: lfq-object 1500
2:53:03.145379 INFO: lfq-object 1600
2:53:03.160319 INFO: lfq-object 1300
2:53:03.192495 INFO: lfq-object 2700
2:53:03.410688 INFO: lfq-object 1400
2:53:03.662433 INFO: lfq-object 2500
2:53:03.703420 INFO: lfq-object 2600
2:53:04.479629 INFO: lfq-object 2800
2:53:04.526653 INFO: lfq-object 3000
2:53:04.713717 INFO: lfq-object 3200
2:53:04.724190 INFO: lfq-object 3400
2:53:04.773638 INFO: lfq-object 3300
2:53:04.815464 INFO: lfq-object 2900
2:53:04.832472 INFO: lfq-object 3500
2:53:04.849199 INFO: lfq-object 3600
2:53:04.917210 INFO: lfq-object 3100
2:53:05.291781 INFO: lfq-object 3800
2:53:05.292150 INFO: lfq-object 4000
2:53:05.348050 INFO: lfq-object 4200
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2:53:05.375221 INFO: lfq-object 4100
2:53:05.387856 INFO: lfq-object 4500
2:53:05.401178 INFO: lfq-object 4800
2:53:05.417988 INFO: lfq-object 4700
2:53:05.457476 INFO: lfq-object 3900
2:53:05.503089 INFO: lfq-object 4400
2:53:05.534366 INFO: lfq-object 3700
2:53:05.565884 INFO: lfq-object 4600
2:53:05.789904 INFO: lfq-object 5100
2:53:05.847647 INFO: lfq-object 5200
2:53:05.941823 INFO: lfq-object 5700
2:53:05.978651 INFO: lfq-object 5600
2:53:06.024628 INFO: lfq-object 6000
2:53:06.050405 INFO: lfq-object 5900
2:53:06.091364 INFO: lfq-object 5800
2:53:06.123176 INFO: lfq-object 5000
2:53:06.157433 INFO: lfq-object 5400
2:53:06.278075 INFO: lfq-object 4900
2:53:06.325741 INFO: lfq-object 5500
2:53:06.360103 INFO: lfq-object 6100
2:53:06.384660 INFO: lfq-object 6400
2:53:06.401259 INFO: lfq-object 6500
2:53:06.405991 INFO: lfq-object 5300
2:53:06.430992 INFO: lfq-object 6200
2:53:06.455340 INFO: lfq-object 6300
2:53:06.541220 INFO: lfq-object 6700
2:53:06.571893 INFO: lfq-object 7100
2:53:06.572661 INFO: lfq-object 7200
2:53:06.588298 INFO: lfq-object 7000
2:53:06.655766 INFO: lfq-object 6800
2:53:06.657768 INFO: lfq-object 6600
2:53:06.707795 INFO: lfq-object 6900
2:53:06.783552 INFO: lfq-object 7400
2:53:06.881301 INFO: lfq-object 7300
2:53:06.925213 INFO: lfq-object 7800
2:53:06.939863 INFO: lfq-object 7500
2:53:06.965606 INFO: lfq-object 7700
2:53:07.016740 INFO: lfq-object 8000
2:53:07.017988 INFO: lfq-object 8100
2:53:07.078149 INFO: lfq-object 7900
2:53:07.105431 INFO: lfq-object 7600
2:53:07.123975 INFO: lfq-object 8200
2:53:07.135113 INFO: lfq-object 8400
2:53:07.185813 INFO: lfq-object 8300
2:53:07.383174 INFO: lfq-object 8500
2:53:07.425420 INFO: lfq-object 8700
2:53:07.502956 INFO: lfq-object 8600
2:53:07.521595 INFO: lfq-object 9100
2:53:07.537189 INFO: lfq-object 9000
2:53:07.549682 INFO: lfq-object 9200
2:53:07.576105 INFO: lfq-object 8900
2:53:07.644925 INFO: lfq-object 9500
2:53:07.651559 INFO: lfq-object 9300
2:53:07.682315 INFO: lfq-object 8800
2:53:07.683848 INFO: lfq-object 9400
2:53:07.722754 INFO: lfq-object 9600
2:53:08.014455 INFO: lfq-object 9700
2:53:08.055844 INFO: lfq-object 9800
2:53:08.096515 INFO: lfq-object 9900
2:53:08.164579 INFO: lfq-object 10000
2:53:08.208746 INFO: lfq-object 10100
2:53:08.283252 INFO: lfq-object 10200
2:53:08.388910 INFO: lfq-object 10300
2:53:12.672621 INFO: Writing psm output to disk
2:53:12.772877 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/precursors.parquet to disk
2:53:13.563098 INFO: Writing precursor output to disk
2:53:13.568296 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/precursor.matrix.parquet to disk
2:53:13.655024 INFO: Writing peptide output to disk
2:53:13.660454 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/peptide.matrix.parquet to disk
2:53:13.736710 INFO: Writing pg output to disk
2:53:13.740632 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/pg.matrix.parquet to disk
2:53:13.815121 PROGRESS: Building MBR spectral library
2:53:13.815311 INFO: Running MbrLibraryBuilder
2:53:15.880198 INFO: MBR spectral library contains 132,778 precursors, 10,386 proteins
2:53:15.880340 INFO: Writing MBR spectral library to disk
2:53:17.131322 PROGRESS: =================== Search step 'library' finished ===================
2:53:18.323848 INFO: =================== Running step 'mbr' ===================
2:53:18.326912 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 10.0}})
2:53:18.327065 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
2:53:18.340058 INFO: loading additional config provided via CLI
2:53:18.340117 INFO: loading additional config provided via CLI parameters
2:53:18.340482 INFO: Updating config with 'user defined'
2:53:18.340544 INFO: Updating config with 'user defined (cli)'
2:53:18.340631 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}}, {'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 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'}]
2:53:18.340863 INFO: Updating config with 'user defined'
2:53:18.340907 INFO: Updating config with 'user defined (cli)'
2:53:18.340927 INFO: Updating config with 'multistep search'
2:53:18.340970 INFO: ├──version: None
2:53:18.340993 INFO: ├──workflow_name: None
2:53:18.341013 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1 [multistep search, default: None][0m
2:53:18.341032 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
2:53:18.341050 INFO: ├──raw_paths:
2:53:18.341068 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
2:53:18.341087 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
2:53:18.341107 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
2:53:18.341125 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
2:53:18.341141 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
2:53:18.341158 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
2:53:18.341175 INFO: ├──fasta_paths:
2:53:18.341193 INFO: ├──quant_directory: None
2:53:18.341209 INFO: ├──general
2:53:18.341228 INFO: │   [32;20m├──thread_count: 24 [user defined, default: 10][0m
2:53:18.341246 INFO: │   ├──transfer_step_enabled: False
2:53:18.341264 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
2:53:18.341282 INFO: │   ├──reuse_calibration: False
2:53:18.341300 INFO: │   ├──reuse_quant: False
2:53:18.341317 INFO: │   ├──log_level: INFO
2:53:18.341335 INFO: │   ├──use_gpu: True
2:53:18.341353 INFO: │   ├──save_figures: True
2:53:18.341371 INFO: │   ├──save_library: True
2:53:18.341389 INFO: │   ├──save_flat_library: False
2:53:18.341407 INFO: │   ├──input_library_type: base
2:53:18.341425 INFO: │   ├──save_mbr_library: True
2:53:18.341442 INFO: │   ├──random_state: None
2:53:18.341460 INFO: │   └──fail_fast: False
2:53:18.341476 INFO: ├──library_loading
2:53:18.341494 INFO: │   └──drop_decoys: False
2:53:18.341510 INFO: ├──library_prediction
2:53:18.341527 INFO: │   ├──enabled: False
2:53:18.341544 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
2:53:18.341561 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
2:53:18.341578 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
2:53:18.341600 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
2:53:18.341618 INFO: │   ├──missed_cleavages: 1
2:53:18.341634 INFO: │   ├──precursor_len:
2:53:18.341654 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
2:53:18.341671 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
2:53:18.341688 INFO: │   ├──precursor_charge:
2:53:18.341705 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
2:53:18.341721 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
2:53:18.341738 INFO: │   ├──precursor_mz:
2:53:18.341756 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
2:53:18.341773 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
2:53:18.341789 INFO: │   ├──fragment_mz:
2:53:18.341806 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
2:53:18.341822 INFO: │   │   - 2000.0
2:53:18.341840 INFO: │   ├──nce: 25.0
2:53:18.341857 INFO: │   ├──fragment_types:
2:53:18.341873 INFO: │   │   - b
2:53:18.341889 INFO: │   │   - y
2:53:18.341906 INFO: │   ├──max_fragment_charge: 2
2:53:18.341923 INFO: │   ├──instrument: Lumos
2:53:18.341939 INFO: │   ├──peptdeep_model_path: None
2:53:18.341957 INFO: │   ├──peptdeep_model_type: generic
2:53:18.341974 INFO: │   ├──predict_charge: False
2:53:18.341992 INFO: │   └──min_charge_probability: 0.1
2:53:18.342008 INFO: ├──custom_modifications:
2:53:18.342026 INFO: │   ├──name: Dimethyl:d12@K
2:53:18.342043 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:53:18.342060 INFO: │   ├──name: Dimethyl:d12@Any_N-term
2:53:18.342077 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:53:18.342093 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
2:53:18.342110 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:53:18.342128 INFO: │   ├──name: mTRAQ:d12@K
2:53:18.342144 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
2:53:18.342161 INFO: │   ├──name: mTRAQ:d12@Any_N-term
2:53:18.342179 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:53:18.342196 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
2:53:18.342213 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:53:18.342230 INFO: │   ├──name: Label:13C(12)@K
2:53:18.342246 INFO: │   └──composition: C(12)
2:53:18.342262 INFO: ├──search
2:53:18.342281 INFO: │   ├──extraction_backend: rust
2:53:18.342300 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
2:53:18.342318 INFO: │   ├──target_ms2_tolerance: 10.0
2:53:18.342336 INFO: │   ├──target_rt_tolerance: 0.0
2:53:18.342354 INFO: │   ├──target_mobility_tolerance: 0.0
2:53:18.342373 INFO: │   ├──quant_window: 3
2:53:18.342396 INFO: │   ├──target_num_candidates: 3
2:53:18.342418 INFO: │   ├──channel_filter: 
2:53:18.342436 INFO: │   ├──compete_for_fragments: True
2:53:18.342454 INFO: │   ├──top_k_fragments_selection: 12
2:53:18.342472 INFO: │   ├──top_k_fragments_scoring: 12
2:53:18.342489 INFO: │   ├──min_fragment_intensity: 0.01
2:53:18.342507 INFO: │   ├──optimized_peak_group_score: False
2:53:18.342524 INFO: │   ├──exclude_shared_ions: True
2:53:18.342541 INFO: │   ├──quant_all: True
2:53:18.342559 INFO: │   └──experimental_xic: True
2:53:18.342577 INFO: ├──calibration
2:53:18.342595 INFO: │   ├──batch_size: 1000
2:53:18.342612 INFO: │   ├──optimization_lock_target: 1000
2:53:18.342629 INFO: │   ├──max_steps: 20
2:53:18.342646 INFO: │   ├──min_steps: 5
2:53:18.342663 INFO: │   ├──max_skips: 1
2:53:18.342680 INFO: │   ├──max_fragments: 5000
2:53:18.342698 INFO: │   └──min_correlation: 0.7
2:53:18.342714 INFO: ├──search_initial
2:53:18.342731 INFO: │   ├──num_candidates: 1
2:53:18.342751 INFO: │   ├──ms1_tolerance: 30
2:53:18.342768 INFO: │   ├──ms2_tolerance: 30
2:53:18.342786 INFO: │   ├──mobility_tolerance: 0.1
2:53:18.342803 INFO: │   └──rt_tolerance: 0.5
2:53:18.342819 INFO: ├──library_multiplexing
2:53:18.342839 INFO: │   ├──enabled: False
2:53:18.342856 INFO: │   ├──input_channel: 0
2:53:18.342873 INFO: │   └──multiplex_mapping:
2:53:18.342892 INFO: ├──multiplexing
2:53:18.342909 INFO: │   ├──enabled: False
2:53:18.342926 INFO: │   ├──target_channels: 4,8
2:53:18.342942 INFO: │   ├──decoy_channel: 12
2:53:18.342959 INFO: │   ├──reference_channel: 0
2:53:18.342976 INFO: │   └──competitive_scoring: True
2:53:18.342992 INFO: ├──fdr
2:53:18.343009 INFO: │   ├──fdr: 0.01
2:53:18.343026 INFO: │   ├──group_level: proteins
2:53:18.343043 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
2:53:18.343059 INFO: │   ├──competitive_scoring: True
2:53:18.343076 INFO: │   ├──keep_decoys: False
2:53:18.343093 INFO: │   ├──keep_decoys_in_mbr_library: False
2:53:18.343110 INFO: │   ├──channel_wise_fdr: False
2:53:18.343127 INFO: │   └──enable_nn_hyperparameter_tuning: True
2:53:18.343143 INFO: ├──search_output
2:53:18.343160 INFO: │   ├──file_format: parquet
2:53:18.343177 INFO: │   ├──precursor_level_lfq: True
2:53:18.343194 INFO: │   ├──peptide_level_lfq: True
2:53:18.343211 INFO: │   ├──save_fragment_quant_matrix: False
2:53:18.343228 INFO: │   ├──min_k_fragments: 12
2:53:18.343245 INFO: │   ├──min_correlation: 0.9
2:53:18.343262 INFO: │   ├──num_samples_quadratic: 50
2:53:18.343280 INFO: │   ├──min_nonnan: 3
2:53:18.343297 INFO: │   ├──normalization_method: directlfq
2:53:18.343314 INFO: │   [32;20m└──normalize_directlfq: False [user defined, default: True][0m
2:53:18.343331 INFO: ├──optimization
2:53:18.343348 INFO: │   ├──order_of_optimization: None
2:53:18.343364 INFO: │   ├──ms2_error
2:53:18.343382 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:53:18.343401 INFO: │   │   ├──targeted_update_factor: 1.0
2:53:18.343419 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:53:18.343437 INFO: │   │   ├──automatic_update_factor: 1.1
2:53:18.343491 INFO: │   │   ├──try_narrower_values: True
2:53:18.343514 INFO: │   │   ├──maximal_decrease: 0.5
2:53:18.343532 INFO: │   │   ├──favour_narrower_optimum: False
2:53:18.343551 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:53:18.343569 INFO: │   ├──ms1_error
2:53:18.343587 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:53:18.343605 INFO: │   │   ├──targeted_update_factor: 1.0
2:53:18.343622 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:53:18.343641 INFO: │   │   ├──automatic_update_factor: 1.1
2:53:18.343658 INFO: │   │   ├──try_narrower_values: False
2:53:18.343676 INFO: │   │   ├──maximal_decrease: 0.2
2:53:18.343693 INFO: │   │   ├──favour_narrower_optimum: False
2:53:18.343710 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:53:18.343727 INFO: │   ├──mobility_error
2:53:18.343745 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:53:18.343762 INFO: │   │   ├──targeted_update_factor: 1.0
2:53:18.343779 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:53:18.343797 INFO: │   │   ├──automatic_update_factor: 1.1
2:53:18.343815 INFO: │   │   ├──try_narrower_values: False
2:53:18.343832 INFO: │   │   ├──maximal_decrease: 0.2
2:53:18.343849 INFO: │   │   ├──favour_narrower_optimum: False
2:53:18.343866 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:53:18.343883 INFO: │   └──rt_error
2:53:18.343904 INFO: │       ├──targeted_update_percentile_range: 0.95
2:53:18.343922 INFO: │       ├──targeted_update_factor: 1.0
2:53:18.343940 INFO: │       ├──automatic_update_percentile_range: 0.999
2:53:18.343957 INFO: │       ├──automatic_update_factor: 1.5
2:53:18.343977 INFO: │       ├──try_narrower_values: True
2:53:18.343994 INFO: │       ├──maximal_decrease: 0.1
2:53:18.344012 INFO: │       ├──favour_narrower_optimum: False
2:53:18.344029 INFO: │       └──maximum_decrease_from_maximum: 0.5
2:53:18.344046 INFO: ├──optimization_manager
2:53:18.344064 INFO: │   ├──fwhm_rt: 5
2:53:18.344081 INFO: │   ├──fwhm_mobility: 0.01
2:53:18.344099 INFO: │   └──score_cutoff: 0
2:53:18.344115 INFO: ├──transfer_library
2:53:18.344131 INFO: │   ├──enabled: False
2:53:18.344147 INFO: │   ├──fragment_types:
2:53:18.344163 INFO: │   │   - b
2:53:18.344180 INFO: │   │   - y
2:53:18.344197 INFO: │   ├──max_charge: 2
2:53:18.344213 INFO: │   ├──top_k_samples: 3
2:53:18.344230 INFO: │   ├──norm_delta_max: True
2:53:18.344247 INFO: │   ├──precursor_correlation_cutoff: 0.5
2:53:18.344264 INFO: │   └──fragment_correlation_ratio: 0.75
2:53:18.344280 INFO: └──transfer_learning
2:53:18.344297 INFO:     ├──enabled: False
2:53:18.344315 INFO:     ├──batch_size: 2000
2:53:18.344332 INFO:     ├──max_lr: 0.0001
2:53:18.344349 INFO:     ├──train_fraction: 0.7
2:53:18.344366 INFO:     ├──validation_fraction: 0.2
2:53:18.344383 INFO:     ├──test_fraction: 0.1
2:53:18.344400 INFO:     ├──test_interval: 1
2:53:18.344417 INFO:     ├──lr_patience: 3
2:53:18.344434 INFO:     ├──epochs: 51
2:53:18.344450 INFO:     ├──warmup_epochs: 5
2:53:18.344467 INFO:     ├──nce: 25
2:53:18.344485 INFO:     └──instrument: Lumos
2:53:18.349861 INFO: Registering 7 custom modifications
2:53:18.373914 INFO: Searching 6 files:
2:53:18.373989 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
2:53:18.374012 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
2:53:18.374030 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
2:53:18.374047 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
2:53:18.374063 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
2:53:18.374080 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
2:53:18.374098 INFO: Using 0 fasta files:
2:53:18.374115 INFO: Using library: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:53:18.374131 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1
2:53:18.374160 PROGRESS: Loading spectral library
2:53:18.374192 PROGRESS: Loading library (type: base) from disk..
2:53:18.374216 INFO: Running DynamicLoader
2:53:18.374277 INFO: Loading .hdf library from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:53:19.026684 INFO: Running PrecursorInitializer
2:53:19.027117 INFO: Channel column already present, skipping initialization
2:53:19.027152 INFO: Elution group indices already present, skipping initialization
2:53:19.027173 INFO: Precursor indices already present, skipping initialization
2:53:19.027290 INFO: Running AnnotateFasta
2:53:19.045734 INFO: Running IsotopeGenerator
2:53:19.046025 INFO: Isotope information already present, skipping isotope generation
2:53:19.046059 INFO: Running RTNormalization
2:53:19.050646 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/speclib.hdf
2:53:19.957247 INFO: Running DecoyGenerator
2:53:25.989906 INFO: Running FlattenLibrary
2:53:27.202162 INFO: Running InitFlatColumns
2:53:27.209280 INFO: Running LogFlatLibraryStats
2:53:27.209405 INFO: ============ Library Stats ============
2:53:27.209438 INFO: Number of precursors: 265,524
2:53:27.263431 INFO: 	thereof targets:132,778
2:53:27.263589 INFO: 	thereof decoys: 132,746
2:53:27.265877 INFO: Number of elution groups: 132,778
2:53:27.265952 INFO: 	average size: 2.00
2:53:27.277235 INFO: Number of proteins: 10,386
2:53:27.278333 INFO: Number of channels: 1 ([0])
2:53:27.278437 INFO: Isotopes Distribution for 4 isotopes
2:53:27.278461 INFO: =======================================
2:53:27.278595 PROGRESS: =================== Starting Search Workflows for step mbr ===================
2:53:27.278663 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
2:53:27.278720 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:53:27.278793 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
2:53:27.279017 INFO: Initializing TimingManager
2:53:27.279469 INFO: Initializing RawFileManager
2:53:43.301387 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.
2:53:43.309022 INFO: Determining DIA cycle
2:53:43.325616 INFO: Found cycle with start 0.00 min and length 300.
2:53:43.499525 INFO: RT (min)            : 0.0 - 26.9
2:53:43.499625 INFO: RT duration (sec)   : 1611.2
2:53:43.499654 INFO: RT duration (min)   : 26.9
2:53:43.499677 INFO: Cycle len (scans)   : 300
2:53:43.499698 INFO: Cycle len (sec)     : 1.65
2:53:43.499717 INFO: Number of cycles    : 977
2:53:43.499737 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:53:43.499767 INFO: Creating DIA data object took: 16.220200061798096
2:53:45.357839 INFO: Creating DIA data NG object took: 1.8579363822937012
2:53:45.406344 INFO: Initializing CalibrationManager
2:53:45.406654 INFO: Setting up calibration estimators ..
2:53:45.406716 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:53:45.406806 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'}' ..
2:53:45.406893 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:53:45.406942 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:53:45.406995 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}}' ..
2:53:45.407050 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:53:45.407097 INFO: Done setting up calibration estimators.
2:53:45.407327 INFO: Initializing OptimizationManager
2:53:45.407470 INFO: initial parameter: ms1_error = 30
2:53:45.407530 INFO: initial parameter: ms2_error = 30
2:53:45.407577 INFO: initial parameter: rt_error = 805.5992431640625
2:53:45.407620 INFO: initial parameter: mobility_error = 0.1
2:53:45.407661 INFO: initial parameter: num_candidates = 1
2:53:45.407701 INFO: initial parameter: fwhm_rt = 5
2:53:45.407741 INFO: initial parameter: fwhm_mobility = 0.01
2:53:45.407781 INFO: initial parameter: score_cutoff = 0
2:53:45.407820 INFO: initial parameter: classifier_version = -1
2:53:45.407890 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:53:45.408315 INFO: FDRManager: loading saved state not requested, will be initialized.
2:53:45.408354 INFO: Initializing FDRManager
2:53:45.408389 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:53:45.448138 PROGRESS: Initializing spectral library: 132,778 target precursors potentially observable (0 removed)
2:53:45.474065 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:53:45.474469 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
2:53:45.474576 PROGRESS: Starting initial search for precursors.
2:53:45.474683 INFO: Starting optimization step 0.
2:53:45.474746 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:53:45.474805 INFO: Using rust extraction backend
2:53:45.474875 PROGRESS: Extracting batch of 1980 precursors
2:53:45.479844 INFO: === Search parameters used ===
2:53:45.479946 INFO: rt_error       : 805.5992431640625
2:53:45.479996 INFO: mobility_error : 0.1
2:53:45.480039 INFO: num_candidates : 1
2:53:45.480079 INFO: ms1_error      : 30
2:53:45.480119 INFO: ms2_error      : 30
2:53:45.480158 INFO: fwhm_rt        : 5
2:53:45.480196 INFO: quant_window   : 3
2:53:45.480235 INFO: ==============================================
2:53:45.514308 INFO: performing precursor FDR with 40 features
2:53:45.514384 INFO: Decoy channel: -1
2:53:45.514406 INFO: competitive: True
2:53:45.515761 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:45.517901 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
2:53:45.518741 INFO: Using random state 864539 for train-test-split
2:53:45.674482 INFO: Test AUC: 0.786
2:53:45.674563 INFO: Train AUC: 0.779
2:53:45.674594 INFO: AUC difference: 0.93%
2:53:45.972663 INFO: Resetting torch num_threads to 24
2:53:45.974420 PROGRESS: === Extracted 1976 precursors and 13487 fragments ===
2:53:45.974798 INFO: === FDR correction performed with classifier version -1 ===
2:53:45.975293 PROGRESS: ============================= Precursor FDR =============================
2:53:45.975383 PROGRESS: Total precursors accumulated: 271
2:53:45.975440 PROGRESS: Target precursors: 269 (99.26%)
2:53:45.975507 PROGRESS: Decoy precursors: 2 (0.74%)
2:53:45.975553 PROGRESS: 
2:53:45.975595 PROGRESS: Precursor Summary:
2:53:45.976640 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   269; 0.001 FDR:   187
2:53:45.976725 PROGRESS: 
2:53:45.976776 PROGRESS: Protein Summary:
2:53:45.977971 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   254; 0.001 FDR:   179
2:53:45.978058 PROGRESS: =========================================================================
2:53:45.978248 INFO: Target number of precursors not reached yet.
2:53:45.986346 INFO: Starting optimization step 1.
2:53:45.986453 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:53:45.986522 INFO: Using rust extraction backend
2:53:45.986579 PROGRESS: Extracting batch of 3976 precursors
2:53:45.994619 INFO: === Search parameters used ===
2:53:45.994730 INFO: rt_error       : 805.5992431640625
2:53:45.994778 INFO: mobility_error : 0.1
2:53:45.994821 INFO: num_candidates : 1
2:53:45.994862 INFO: ms1_error      : 30
2:53:45.994901 INFO: ms2_error      : 30
2:53:45.994940 INFO: fwhm_rt        : 5
2:53:45.994978 INFO: quant_window   : 3
2:53:45.995017 INFO: ==============================================
2:53:46.056065 INFO: performing precursor FDR with 40 features
2:53:46.056170 INFO: Decoy channel: -1
2:53:46.056194 INFO: competitive: True
2:53:46.061821 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:46.064883 INFO: Estimating optimal hyperparameters - samples: 4,756, batch_size: 128, learning_rate: 1.77e-04
2:53:46.064973 INFO: Using random state 596189 for train-test-split
2:53:46.546186 INFO: Test AUC: 0.802
2:53:46.546277 INFO: Train AUC: 0.829
2:53:46.546304 INFO: AUC difference: 3.18%
2:53:46.809646 INFO: Resetting torch num_threads to 24
2:53:46.813416 PROGRESS: === Extracted 5945 precursors and 40854 fragments ===
2:53:46.813835 INFO: === FDR correction performed with classifier version -1 ===
2:53:46.814479 PROGRESS: ============================= Precursor FDR =============================
2:53:46.814561 PROGRESS: Total precursors accumulated: 1,389
2:53:46.814616 PROGRESS: Target precursors: 1,376 (99.06%)
2:53:46.814665 PROGRESS: Decoy precursors: 13 (0.94%)
2:53:46.814713 PROGRESS: 
2:53:46.814756 PROGRESS: Precursor Summary:
2:53:46.816169 PROGRESS: Channel   0:	 0.050 FDR: 1,376; 0.010 FDR: 1,376; 0.001 FDR:   862
2:53:46.816268 PROGRESS: 
2:53:46.816322 PROGRESS: Protein Summary:
2:53:46.818079 PROGRESS: Channel   0:	 0.050 FDR: 1,156; 0.010 FDR: 1,156; 0.001 FDR:   754
2:53:46.818177 PROGRESS: =========================================================================
2:53:46.818428 INFO: Target number of precursors reached.
2:53:46.827235 INFO: fragments_df: keeping 5000 of 40854 [sum(precursor_idx_mask)=14268 sum(mass_error_mask)=40854 stop_rank=5000
2:53:46.838451 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:53:47.125679 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:53:47.854805 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:53:47.855330 INFO: Using score_cutoff 12.553108484745026 (fac=0.99, q=1)
2:53:47.855737 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:53:47.855820 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:53:47.855875 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.553108484745026
2:53:47.855936 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:53:47.860056 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:53:47.868357 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:53:47.868464 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:53:47.868546 INFO: Starting optimization step 2.
2:53:47.868615 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:53:47.868684 INFO: Using rust extraction backend
2:53:47.868746 PROGRESS: Extracting batch of 5956 precursors
2:53:47.880356 INFO: === Search parameters used ===
2:53:47.880492 INFO: rt_error       : 805.5992431640625
2:53:47.880543 INFO: mobility_error : 0.1
2:53:47.880589 INFO: num_candidates : 3
2:53:47.880630 INFO: ms1_error      : 30
2:53:47.880671 INFO: ms2_error      : 30
2:53:47.880711 INFO: fwhm_rt        : 3.0
2:53:47.880750 INFO: quant_window   : 3
2:53:47.880788 INFO: ==============================================
2:53:48.011447 INFO: performing precursor FDR with 40 features
2:53:48.011584 INFO: Decoy channel: -1
2:53:48.011608 INFO: competitive: True
2:53:48.017582 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:48.022046 INFO: Estimating optimal hyperparameters - samples: 14,262, batch_size: 128, learning_rate: 1.77e-04
2:53:48.022185 INFO: Using random state 351113 for train-test-split
2:53:49.469882 INFO: Test AUC: 0.674
2:53:49.470004 INFO: Train AUC: 0.701
2:53:49.470032 INFO: AUC difference: 3.75%
2:53:49.722545 INFO: Resetting torch num_threads to 24
2:53:49.725173 PROGRESS: === Extracted 17828 precursors and 106704 fragments ===
2:53:49.725543 INFO: === FDR correction performed with classifier version 1 ===
2:53:49.726203 PROGRESS: ============================= Precursor FDR =============================
2:53:49.726284 PROGRESS: Total precursors accumulated: 1,755
2:53:49.726338 PROGRESS: Target precursors: 1,738 (99.03%)
2:53:49.726386 PROGRESS: Decoy precursors: 17 (0.97%)
2:53:49.726428 PROGRESS: 
2:53:49.726470 PROGRESS: Precursor Summary:
2:53:49.727930 PROGRESS: Channel   0:	 0.050 FDR: 1,738; 0.010 FDR: 1,738; 0.001 FDR: 1,233
2:53:49.728027 PROGRESS: 
2:53:49.728085 PROGRESS: Protein Summary:
2:53:49.729981 PROGRESS: Channel   0:	 0.050 FDR: 1,432; 0.010 FDR: 1,432; 0.001 FDR: 1,054
2:53:49.730070 PROGRESS: =========================================================================
2:53:49.730456 INFO: Target number of precursors reached.
2:53:49.749768 INFO: fragments_df: keeping 5000 of 106704 [sum(precursor_idx_mask)=37683 sum(mass_error_mask)=106704 stop_rank=5000
2:53:49.761029 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:53:50.033167 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:53:50.751809 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:53:50.752274 INFO: Using score_cutoff 12.216539603519438 (fac=0.99, q=1)
2:53:50.752599 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:53:50.752680 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:53:50.752738 INFO: Updating optimization_manager: score_cutoff        : 12.553108484745026 -> 12.216539603519438
2:53:50.752800 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:53:50.756787 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:53:50.765181 INFO: === checking if optimization conditions were reached ===
2:53:50.766899 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:53:50.767000 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:53:50.767066 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:53:50.767124 INFO: ==============================================
2:53:50.767195 INFO: Starting optimization step 3.
2:53:50.767253 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:53:50.767312 INFO: Using rust extraction backend
2:53:50.767368 PROGRESS: Extracting batch of 5956 precursors
2:53:50.778773 INFO: === Search parameters used ===
2:53:50.778904 INFO: rt_error       : 805.5992431640625
2:53:50.778957 INFO: mobility_error : 0.1
2:53:50.779004 INFO: num_candidates : 3
2:53:50.779048 INFO: ms1_error      : 30
2:53:50.779102 INFO: ms2_error      : 10.0
2:53:50.779142 INFO: fwhm_rt        : 3.0
2:53:50.779181 INFO: quant_window   : 3
2:53:50.779222 INFO: ==============================================
2:53:50.892696 INFO: performing precursor FDR with 40 features
2:53:50.892807 INFO: Decoy channel: -1
2:53:50.892830 INFO: competitive: True
2:53:50.899916 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:50.904398 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:53:50.904534 INFO: Using random state 566819 for train-test-split
2:53:52.346896 INFO: Test AUC: 0.740
2:53:52.347004 INFO: Train AUC: 0.747
2:53:52.347032 INFO: AUC difference: 0.92%
2:53:52.605272 INFO: Resetting torch num_threads to 24
2:53:52.607950 PROGRESS: === Extracted 17861 precursors and 120137 fragments ===
2:53:52.608322 INFO: === FDR correction performed with classifier version 2 ===
2:53:52.609223 PROGRESS: ============================= Precursor FDR =============================
2:53:52.609306 PROGRESS: Total precursors accumulated: 2,450
2:53:52.609362 PROGRESS: Target precursors: 2,426 (99.02%)
2:53:52.609410 PROGRESS: Decoy precursors: 24 (0.98%)
2:53:52.609453 PROGRESS: 
2:53:52.609495 PROGRESS: Precursor Summary:
2:53:52.611111 PROGRESS: Channel   0:	 0.050 FDR: 2,426; 0.010 FDR: 2,426; 0.001 FDR: 1,617
2:53:52.611203 PROGRESS: 
2:53:52.611257 PROGRESS: Protein Summary:
2:53:52.613475 PROGRESS: Channel   0:	 0.050 FDR: 1,914; 0.010 FDR: 1,914; 0.001 FDR: 1,353
2:53:52.613578 PROGRESS: =========================================================================
2:53:52.613955 INFO: Target number of precursors reached.
2:53:52.639942 INFO: fragments_df: keeping 5000 of 120137 [sum(precursor_idx_mask)=55397 sum(mass_error_mask)=120137 stop_rank=5000
2:53:52.651178 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:53:53.020380 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:53:53.736277 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:53:53.736745 INFO: Using score_cutoff 10.639897248744964 (fac=0.99, q=1)
2:53:53.737068 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:53:53.737142 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:53:53.737195 INFO: Updating optimization_manager: score_cutoff        : 12.216539603519438 -> 10.639897248744964
2:53:53.737245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:53:53.742525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:53:53.750190 INFO: === checking if optimization conditions were reached ===
2:53:53.751967 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:53:53.752069 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:53:53.752131 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:53:53.752193 INFO: ==============================================
2:53:53.752264 INFO: Starting optimization step 4.
2:53:53.752318 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:53:53.752377 INFO: Using rust extraction backend
2:53:53.752429 PROGRESS: Extracting batch of 5956 precursors
2:53:53.766634 INFO: === Search parameters used ===
2:53:53.766762 INFO: rt_error       : 805.5992431640625
2:53:53.766812 INFO: mobility_error : 0.1
2:53:53.766856 INFO: num_candidates : 3
2:53:53.766899 INFO: ms1_error      : 30
2:53:53.766940 INFO: ms2_error      : 10.0
2:53:53.766979 INFO: fwhm_rt        : 3.0
2:53:53.767020 INFO: quant_window   : 3
2:53:53.767061 INFO: ==============================================
2:53:53.882161 INFO: performing precursor FDR with 40 features
2:53:53.882276 INFO: Decoy channel: -1
2:53:53.882299 INFO: competitive: True
2:53:53.887489 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:53.891627 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:53:53.891756 INFO: Using random state 896044 for train-test-split
2:53:55.337722 INFO: Test AUC: 0.752
2:53:55.337830 INFO: Train AUC: 0.756
2:53:55.337857 INFO: AUC difference: 0.48%
2:53:55.597564 INFO: Resetting torch num_threads to 24
2:53:55.600401 PROGRESS: === Extracted 17861 precursors and 120117 fragments ===
2:53:55.600770 INFO: === FDR correction performed with classifier version 3 ===
2:53:55.601572 PROGRESS: ============================= Precursor FDR =============================
2:53:55.601655 PROGRESS: Total precursors accumulated: 2,471
2:53:55.601711 PROGRESS: Target precursors: 2,447 (99.03%)
2:53:55.601759 PROGRESS: Decoy precursors: 24 (0.97%)
2:53:55.601805 PROGRESS: 
2:53:55.601854 PROGRESS: Precursor Summary:
2:53:55.603480 PROGRESS: Channel   0:	 0.050 FDR: 2,447; 0.010 FDR: 2,447; 0.001 FDR: 1,728
2:53:55.603575 PROGRESS: 
2:53:55.603630 PROGRESS: Protein Summary:
2:53:55.605825 PROGRESS: Channel   0:	 0.050 FDR: 1,933; 0.010 FDR: 1,933; 0.001 FDR: 1,425
2:53:55.605914 PROGRESS: =========================================================================
2:53:55.606338 INFO: Target number of precursors reached.
2:53:55.632638 INFO: fragments_df: keeping 5000 of 120117 [sum(precursor_idx_mask)=55778 sum(mass_error_mask)=120117 stop_rank=5000
2:53:55.643978 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:53:56.015070 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:53:56.738412 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:53:56.738871 INFO: Using score_cutoff 10.61330156364441 (fac=0.99, q=1)
2:53:56.739187 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:53:56.739261 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:53:56.739314 INFO: Updating optimization_manager: score_cutoff        : 10.639897248744964 -> 10.61330156364441
2:53:56.739365 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:53:56.743373 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:53:56.751427 INFO: === checking if optimization conditions were reached ===
2:53:56.753116 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:53:56.753217 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:53:56.753278 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:53:56.753332 INFO: ==============================================
2:53:56.753393 INFO: Starting optimization step 5.
2:53:56.753454 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:53:56.753510 INFO: Using rust extraction backend
2:53:56.753563 PROGRESS: Extracting batch of 5956 precursors
2:53:56.765016 INFO: === Search parameters used ===
2:53:56.765146 INFO: rt_error       : 805.5992431640625
2:53:56.765198 INFO: mobility_error : 0.1
2:53:56.765242 INFO: num_candidates : 3
2:53:56.765282 INFO: ms1_error      : 30
2:53:56.765321 INFO: ms2_error      : 10.0
2:53:56.765360 INFO: fwhm_rt        : 3.0
2:53:56.765398 INFO: quant_window   : 3
2:53:56.765435 INFO: ==============================================
2:53:56.872931 INFO: performing precursor FDR with 40 features
2:53:56.873040 INFO: Decoy channel: -1
2:53:56.873063 INFO: competitive: True
2:53:56.878547 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:56.883287 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:53:56.883420 INFO: Using random state 520438 for train-test-split
2:53:58.336271 INFO: Test AUC: 0.754
2:53:58.336378 INFO: Train AUC: 0.769
2:53:58.336407 INFO: AUC difference: 1.94%
2:53:58.594117 INFO: Resetting torch num_threads to 24
2:53:58.597975 PROGRESS: === Extracted 17861 precursors and 120121 fragments ===
2:53:58.598348 INFO: === FDR correction performed with classifier version 4 ===
2:53:58.599192 PROGRESS: ============================= Precursor FDR =============================
2:53:58.599277 PROGRESS: Total precursors accumulated: 2,471
2:53:58.599332 PROGRESS: Target precursors: 2,447 (99.03%)
2:53:58.599388 PROGRESS: Decoy precursors: 24 (0.97%)
2:53:58.599436 PROGRESS: 
2:53:58.599503 PROGRESS: Precursor Summary:
2:53:58.600929 PROGRESS: Channel   0:	 0.050 FDR: 2,447; 0.010 FDR: 2,447; 0.001 FDR:    35
2:53:58.601012 PROGRESS: 
2:53:58.601066 PROGRESS: Protein Summary:
2:53:58.602974 PROGRESS: Channel   0:	 0.050 FDR: 1,929; 0.010 FDR: 1,929; 0.001 FDR:    35
2:53:58.603060 PROGRESS: =========================================================================
2:53:58.603606 INFO: Target number of precursors reached.
2:53:58.630914 INFO: fragments_df: keeping 5000 of 120121 [sum(precursor_idx_mask)=55691 sum(mass_error_mask)=120121 stop_rank=5000
2:53:58.646541 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:53:59.019796 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:01.177460 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:01.177939 INFO: Using score_cutoff 10.324440463829042 (fac=0.99, q=1)
2:54:01.178265 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:01.178343 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:01.178400 INFO: Updating optimization_manager: score_cutoff        : 10.61330156364441 -> 10.324440463829042
2:54:01.178457 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:01.182533 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:01.190878 INFO: === checking if optimization conditions were reached ===
2:54:01.192648 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:54:01.192749 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:54:01.192819 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:54:01.192875 INFO: ==============================================
2:54:01.192937 INFO: Starting optimization step 6.
2:54:01.192994 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:01.193051 INFO: Using rust extraction backend
2:54:01.193105 PROGRESS: Extracting batch of 5956 precursors
2:54:01.205306 INFO: === Search parameters used ===
2:54:01.205437 INFO: rt_error       : 805.5992431640625
2:54:01.205489 INFO: mobility_error : 0.1
2:54:01.205536 INFO: num_candidates : 3
2:54:01.205580 INFO: ms1_error      : 30
2:54:01.205623 INFO: ms2_error      : 10.0
2:54:01.205666 INFO: fwhm_rt        : 3.0
2:54:01.205707 INFO: quant_window   : 3
2:54:01.205748 INFO: ==============================================
2:54:01.327524 INFO: performing precursor FDR with 40 features
2:54:01.327639 INFO: Decoy channel: -1
2:54:01.327664 INFO: competitive: True
2:54:01.332890 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:01.337308 INFO: Estimating optimal hyperparameters - samples: 14,289, batch_size: 128, learning_rate: 1.77e-04
2:54:01.337450 INFO: Using random state 29053 for train-test-split
2:54:02.784516 INFO: Test AUC: 0.752
2:54:02.784650 INFO: Train AUC: 0.779
2:54:02.784682 INFO: AUC difference: 3.43%
2:54:03.044273 INFO: Resetting torch num_threads to 24
2:54:03.047167 PROGRESS: === Extracted 17862 precursors and 120102 fragments ===
2:54:03.047575 INFO: === FDR correction performed with classifier version 5 ===
2:54:03.048467 PROGRESS: ============================= Precursor FDR =============================
2:54:03.048556 PROGRESS: Total precursors accumulated: 2,599
2:54:03.048622 PROGRESS: Target precursors: 2,574 (99.04%)
2:54:03.048671 PROGRESS: Decoy precursors: 25 (0.96%)
2:54:03.048715 PROGRESS: 
2:54:03.048756 PROGRESS: Precursor Summary:
2:54:03.050278 PROGRESS: Channel   0:	 0.050 FDR: 2,574; 0.010 FDR: 2,574; 0.001 FDR:   272
2:54:03.050363 PROGRESS: 
2:54:03.050419 PROGRESS: Protein Summary:
2:54:03.052484 PROGRESS: Channel   0:	 0.050 FDR: 2,017; 0.010 FDR: 2,017; 0.001 FDR:   259
2:54:03.052581 PROGRESS: =========================================================================
2:54:03.053080 INFO: Target number of precursors reached.
2:54:03.079740 INFO: fragments_df: keeping 5000 of 120102 [sum(precursor_idx_mask)=58141 sum(mass_error_mask)=120102 stop_rank=5000
2:54:03.092987 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:03.478549 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:04.200284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:04.200852 INFO: Using score_cutoff 9.919473866558075 (fac=0.99, q=1)
2:54:04.201237 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:04.201314 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:04.201367 INFO: Updating optimization_manager: score_cutoff        : 10.324440463829042 -> 9.919473866558075
2:54:04.201428 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:04.205523 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:04.213535 INFO: === checking if optimization conditions were reached ===
2:54:04.215218 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:54:04.215318 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:54:04.215384 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:54:04.215442 INFO: ==============================================
2:54:04.215531 PROGRESS: Optimization finished for ms2_error.
2:54:04.226402 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:04.230242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:04.238167 INFO: Starting optimization step 0.
2:54:04.238280 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:04.238368 INFO: Using rust extraction backend
2:54:04.238440 PROGRESS: Extracting batch of 5956 precursors
2:54:04.249807 INFO: === Search parameters used ===
2:54:04.249930 INFO: rt_error       : 805.5992431640625
2:54:04.249982 INFO: mobility_error : 0.1
2:54:04.250028 INFO: num_candidates : 3
2:54:04.250071 INFO: ms1_error      : 30
2:54:04.250111 INFO: ms2_error      : 10.0
2:54:04.250151 INFO: fwhm_rt        : 3.0
2:54:04.250190 INFO: quant_window   : 3
2:54:04.250229 INFO: ==============================================
2:54:04.364530 INFO: performing precursor FDR with 40 features
2:54:04.364640 INFO: Decoy channel: -1
2:54:04.364665 INFO: competitive: True
2:54:04.370152 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:04.374449 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:54:04.374606 INFO: Using random state 107067 for train-test-split
2:54:05.800325 INFO: Test AUC: 0.776
2:54:05.800434 INFO: Train AUC: 0.782
2:54:05.800463 INFO: AUC difference: 0.80%
2:54:06.056547 INFO: Resetting torch num_threads to 24
2:54:06.059279 PROGRESS: === Extracted 17860 precursors and 120088 fragments ===
2:54:06.059672 INFO: === FDR correction performed with classifier version 6 ===
2:54:06.060401 PROGRESS: ============================= Precursor FDR =============================
2:54:06.060485 PROGRESS: Total precursors accumulated: 2,612
2:54:06.060539 PROGRESS: Target precursors: 2,587 (99.04%)
2:54:06.060587 PROGRESS: Decoy precursors: 25 (0.96%)
2:54:06.060631 PROGRESS: 
2:54:06.060672 PROGRESS: Precursor Summary:
2:54:06.062295 PROGRESS: Channel   0:	 0.050 FDR: 2,587; 0.010 FDR: 2,587; 0.001 FDR: 1,743
2:54:06.062386 PROGRESS: 
2:54:06.062438 PROGRESS: Protein Summary:
2:54:06.064705 PROGRESS: Channel   0:	 0.050 FDR: 2,027; 0.010 FDR: 2,027; 0.001 FDR: 1,436
2:54:06.064803 PROGRESS: =========================================================================
2:54:06.065217 INFO: Target number of precursors reached.
2:54:06.092375 INFO: fragments_df: keeping 5000 of 120088 [sum(precursor_idx_mask)=58262 sum(mass_error_mask)=120088 stop_rank=5000
2:54:06.104061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:06.497814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:07.219578 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:07.220048 INFO: Using score_cutoff 9.406764102172852 (fac=0.99, q=1)
2:54:07.220373 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:07.220463 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:07.220519 INFO: Updating optimization_manager: score_cutoff        : 9.919473866558075 -> 9.406764102172852
2:54:07.220572 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:07.224569 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:07.232275 INFO: === checking if optimization conditions were reached ===
2:54:07.232391 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:54:07.235142 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 392.6141253507079
2:54:07.235240 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 392.6141.
2:54:07.235301 INFO: ==============================================
2:54:07.235366 INFO: Starting optimization step 1.
2:54:07.235422 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:07.235494 INFO: Using rust extraction backend
2:54:07.235553 PROGRESS: Extracting batch of 5956 precursors
2:54:07.246906 INFO: === Search parameters used ===
2:54:07.247036 INFO: rt_error       : 392.6141253507079
2:54:07.247086 INFO: mobility_error : 0.1
2:54:07.247131 INFO: num_candidates : 3
2:54:07.247180 INFO: ms1_error      : 30
2:54:07.247222 INFO: ms2_error      : 10.0
2:54:07.247270 INFO: fwhm_rt        : 3.0
2:54:07.247313 INFO: quant_window   : 3
2:54:07.247364 INFO: ==============================================
2:54:07.346241 INFO: performing precursor FDR with 40 features
2:54:07.346355 INFO: Decoy channel: -1
2:54:07.346380 INFO: competitive: True
2:54:07.351768 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:07.356065 INFO: Estimating optimal hyperparameters - samples: 14,287, batch_size: 128, learning_rate: 1.77e-04
2:54:07.356208 INFO: Using random state 107067 for train-test-split
2:54:08.843256 INFO: Test AUC: 0.758
2:54:08.843395 INFO: Train AUC: 0.784
2:54:08.843424 INFO: AUC difference: 3.35%
2:54:09.105150 INFO: Resetting torch num_threads to 24
2:54:09.107999 PROGRESS: === Extracted 17859 precursors and 119565 fragments ===
2:54:09.108384 INFO: === FDR correction performed with classifier version 6 ===
2:54:09.109121 PROGRESS: ============================= Precursor FDR =============================
2:54:09.109204 PROGRESS: Total precursors accumulated: 2,629
2:54:09.109259 PROGRESS: Target precursors: 2,603 (99.01%)
2:54:09.109307 PROGRESS: Decoy precursors: 26 (0.99%)
2:54:09.109351 PROGRESS: 
2:54:09.109392 PROGRESS: Precursor Summary:
2:54:09.111019 PROGRESS: Channel   0:	 0.050 FDR: 2,603; 0.010 FDR: 2,603; 0.001 FDR: 1,600
2:54:09.111108 PROGRESS: 
2:54:09.111161 PROGRESS: Protein Summary:
2:54:09.113389 PROGRESS: Channel   0:	 0.050 FDR: 2,041; 0.010 FDR: 2,041; 0.001 FDR: 1,334
2:54:09.113484 PROGRESS: =========================================================================
2:54:09.113884 INFO: Target number of precursors reached.
2:54:09.141241 INFO: fragments_df: keeping 5000 of 119565 [sum(precursor_idx_mask)=58648 sum(mass_error_mask)=119565 stop_rank=5000
2:54:09.153128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:09.533687 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:10.258668 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:10.259129 INFO: Using score_cutoff 9.886873334312439 (fac=0.99, q=1)
2:54:10.259490 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:10.259573 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:10.259629 INFO: Updating optimization_manager: score_cutoff        : 9.406764102172852 -> 9.886873334312439
2:54:10.259682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:10.263678 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:10.271633 INFO: === checking if optimization conditions were reached ===
2:54:10.271754 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:54:10.274600 INFO: Updating optimization_manager: rt_error            : 392.6141253507079 -> 361.2131190385641
2:54:10.274704 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 361.2131.
2:54:10.274769 INFO: ==============================================
2:54:10.274840 INFO: Starting optimization step 2.
2:54:10.274900 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:10.274965 INFO: Using rust extraction backend
2:54:10.275026 PROGRESS: Extracting batch of 5956 precursors
2:54:10.286489 INFO: === Search parameters used ===
2:54:10.286616 INFO: rt_error       : 361.2131190385641
2:54:10.286668 INFO: mobility_error : 0.1
2:54:10.286714 INFO: num_candidates : 3
2:54:10.286757 INFO: ms1_error      : 30
2:54:10.286799 INFO: ms2_error      : 10.0
2:54:10.286849 INFO: fwhm_rt        : 3.0
2:54:10.286891 INFO: quant_window   : 3
2:54:10.286932 INFO: ==============================================
2:54:10.389525 INFO: performing precursor FDR with 40 features
2:54:10.389638 INFO: Decoy channel: -1
2:54:10.389664 INFO: competitive: True
2:54:10.394947 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:10.399098 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:54:10.399230 INFO: Using random state 107067 for train-test-split
2:54:11.828052 INFO: Test AUC: 0.775
2:54:11.828160 INFO: Train AUC: 0.783
2:54:11.828190 INFO: AUC difference: 1.03%
2:54:12.086823 INFO: Resetting torch num_threads to 24
2:54:12.089959 PROGRESS: === Extracted 17861 precursors and 119358 fragments ===
2:54:12.090343 INFO: === FDR correction performed with classifier version 6 ===
2:54:12.091102 PROGRESS: ============================= Precursor FDR =============================
2:54:12.091192 PROGRESS: Total precursors accumulated: 2,626
2:54:12.091251 PROGRESS: Target precursors: 2,600 (99.01%)
2:54:12.091302 PROGRESS: Decoy precursors: 26 (0.99%)
2:54:12.091349 PROGRESS: 
2:54:12.091394 PROGRESS: Precursor Summary:
2:54:12.093034 PROGRESS: Channel   0:	 0.050 FDR: 2,600; 0.010 FDR: 2,595; 0.001 FDR: 1,840
2:54:12.093129 PROGRESS: 
2:54:12.093184 PROGRESS: Protein Summary:
2:54:12.095435 PROGRESS: Channel   0:	 0.050 FDR: 2,042; 0.010 FDR: 2,040; 0.001 FDR: 1,499
2:54:12.095547 PROGRESS: =========================================================================
2:54:12.095984 INFO: Target number of precursors reached.
2:54:12.123149 INFO: fragments_df: keeping 5000 of 119358 [sum(precursor_idx_mask)=58527 sum(mass_error_mask)=119358 stop_rank=5000
2:54:12.136319 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:12.518523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:13.264052 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:13.264520 INFO: Using score_cutoff 9.885082513046266 (fac=0.99, q=1)
2:54:13.264836 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:13.264915 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:13.264971 INFO: Updating optimization_manager: score_cutoff        : 9.886873334312439 -> 9.885082513046266
2:54:13.265033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:13.269038 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:13.276677 INFO: === checking if optimization conditions were reached ===
2:54:13.276788 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:54:13.279745 INFO: Updating optimization_manager: rt_error            : 361.2131190385641 -> 312.7476135233276
2:54:13.279850 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 312.7476.
2:54:13.279912 INFO: ==============================================
2:54:13.279977 INFO: Starting optimization step 3.
2:54:13.280033 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:13.280092 INFO: Using rust extraction backend
2:54:13.280146 PROGRESS: Extracting batch of 5956 precursors
2:54:13.291601 INFO: === Search parameters used ===
2:54:13.291728 INFO: rt_error       : 312.7476135233276
2:54:13.291781 INFO: mobility_error : 0.1
2:54:13.291825 INFO: num_candidates : 3
2:54:13.291877 INFO: ms1_error      : 30
2:54:13.291919 INFO: ms2_error      : 10.0
2:54:13.291959 INFO: fwhm_rt        : 3.0
2:54:13.291998 INFO: quant_window   : 3
2:54:13.292037 INFO: ==============================================
2:54:13.393739 INFO: performing precursor FDR with 40 features
2:54:13.393847 INFO: Decoy channel: -1
2:54:13.393871 INFO: competitive: True
2:54:13.399150 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:13.403536 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:54:13.403675 INFO: Using random state 107067 for train-test-split
2:54:14.825918 INFO: Test AUC: 0.776
2:54:14.826025 INFO: Train AUC: 0.780
2:54:14.826053 INFO: AUC difference: 0.60%
2:54:15.083446 INFO: Resetting torch num_threads to 24
2:54:15.086453 PROGRESS: === Extracted 17860 precursors and 118698 fragments ===
2:54:15.086819 INFO: === FDR correction performed with classifier version 6 ===
2:54:15.087541 PROGRESS: ============================= Precursor FDR =============================
2:54:15.087630 PROGRESS: Total precursors accumulated: 2,629
2:54:15.087686 PROGRESS: Target precursors: 2,603 (99.01%)
2:54:15.087734 PROGRESS: Decoy precursors: 26 (0.99%)
2:54:15.087777 PROGRESS: 
2:54:15.087818 PROGRESS: Precursor Summary:
2:54:15.089422 PROGRESS: Channel   0:	 0.050 FDR: 2,603; 0.010 FDR: 2,603; 0.001 FDR: 2,091
2:54:15.089506 PROGRESS: 
2:54:15.089560 PROGRESS: Protein Summary:
2:54:15.091809 PROGRESS: Channel   0:	 0.050 FDR: 2,040; 0.010 FDR: 2,040; 0.001 FDR: 1,668
2:54:15.091900 PROGRESS: =========================================================================
2:54:15.092386 INFO: Target number of precursors reached.
2:54:15.119268 INFO: fragments_df: keeping 5000 of 118698 [sum(precursor_idx_mask)=58442 sum(mass_error_mask)=118698 stop_rank=5000
2:54:15.133312 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:15.518463 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:16.171043 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:16.171524 INFO: Using score_cutoff 9.871704234695434 (fac=0.99, q=1)
2:54:16.171840 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:16.171920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:16.171974 INFO: Updating optimization_manager: score_cutoff        : 9.885082513046266 -> 9.871704234695434
2:54:16.172027 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:16.176055 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:16.184064 INFO: === checking if optimization conditions were reached ===
2:54:16.184179 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:54:16.187071 INFO: Updating optimization_manager: rt_error            : 312.7476135233276 -> 327.15874183669916
2:54:16.187172 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 327.1587.
2:54:16.187247 INFO: ==============================================
2:54:16.187317 INFO: Starting optimization step 4.
2:54:16.187375 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:16.187435 INFO: Using rust extraction backend
2:54:16.187513 PROGRESS: Extracting batch of 5956 precursors
2:54:16.199286 INFO: === Search parameters used ===
2:54:16.199450 INFO: rt_error       : 327.15874183669916
2:54:16.199533 INFO: mobility_error : 0.1
2:54:16.199586 INFO: num_candidates : 3
2:54:16.199630 INFO: ms1_error      : 30
2:54:16.199672 INFO: ms2_error      : 10.0
2:54:16.199713 INFO: fwhm_rt        : 3.0
2:54:16.199752 INFO: quant_window   : 3
2:54:16.199790 INFO: ==============================================
2:54:16.293572 INFO: performing precursor FDR with 40 features
2:54:16.293686 INFO: Decoy channel: -1
2:54:16.293710 INFO: competitive: True
2:54:16.298631 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:16.303069 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
2:54:16.303201 INFO: Using random state 107067 for train-test-split
2:54:17.720897 INFO: Test AUC: 0.760
2:54:17.721009 INFO: Train AUC: 0.785
2:54:17.721039 INFO: AUC difference: 3.17%
2:54:17.977242 INFO: Resetting torch num_threads to 24
2:54:17.979799 PROGRESS: === Extracted 17860 precursors and 118900 fragments ===
2:54:17.980169 INFO: === FDR correction performed with classifier version 6 ===
2:54:17.980900 PROGRESS: ============================= Precursor FDR =============================
2:54:17.980997 PROGRESS: Total precursors accumulated: 2,608
2:54:17.981053 PROGRESS: Target precursors: 2,583 (99.04%)
2:54:17.981100 PROGRESS: Decoy precursors: 25 (0.96%)
2:54:17.981143 PROGRESS: 
2:54:17.981184 PROGRESS: Precursor Summary:
2:54:17.982780 PROGRESS: Channel   0:	 0.050 FDR: 2,583; 0.010 FDR: 2,583; 0.001 FDR: 1,810
2:54:17.982868 PROGRESS: 
2:54:17.982920 PROGRESS: Protein Summary:
2:54:17.985146 PROGRESS: Channel   0:	 0.050 FDR: 2,028; 0.010 FDR: 2,028; 0.001 FDR: 1,476
2:54:17.985239 PROGRESS: =========================================================================
2:54:17.985612 INFO: Target number of precursors reached.
2:54:18.011979 INFO: fragments_df: keeping 5000 of 118900 [sum(precursor_idx_mask)=58087 sum(mass_error_mask)=118900 stop_rank=5000
2:54:18.022948 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:18.394326 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:19.113547 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:19.114013 INFO: Using score_cutoff 9.883337520217896 (fac=0.99, q=1)
2:54:19.114321 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:19.114395 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:19.114447 INFO: Updating optimization_manager: score_cutoff        : 9.871704234695434 -> 9.883337520217896
2:54:19.114497 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:19.118474 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:19.126283 INFO: === checking if optimization conditions were reached ===
2:54:19.126394 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:54:19.127149 INFO: Updating optimization_manager: rt_error            : 327.15874183669916 -> 392.6141253507079
2:54:19.127269 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
2:54:19.127363 INFO: Updating optimization_manager: score_cutoff        : 9.883337520217896 -> 9.886873334312439
2:54:19.127449 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:19.127553 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:19.127636 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 392.6141 found after 5 searches.
2:54:19.127699 INFO: ==============================================
2:54:19.127765 PROGRESS: Optimization finished for rt_error.
2:54:19.138251 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:19.142043 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:19.149810 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:54:19.149925 PROGRESS: ==============================================
2:54:19.149994 PROGRESS: ms2_error      : 10.0000
2:54:19.150047 PROGRESS: rt_error       : 392.6141
2:54:19.150091 PROGRESS: ==============================================
2:54:19.150667 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:19.288502 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:19.657859 INFO: Using rust extraction backend
2:54:19.658191 PROGRESS: Extracting batch of 262809 precursors
2:54:20.090865 INFO: === Search parameters used ===
2:54:20.091161 INFO: rt_error       : 392.6141253507079
2:54:20.091217 INFO: mobility_error : 0.1
2:54:20.091263 INFO: num_candidates : 3
2:54:20.091307 INFO: ms1_error      : 30
2:54:20.091350 INFO: ms2_error      : 10.0
2:54:20.091392 INFO: fwhm_rt        : 3.0
2:54:20.091432 INFO: quant_window   : 3
2:54:20.091504 INFO: ==============================================
2:54:21.018251 INFO: Removed 86508 precursors with score below cutoff 9.886873334312439
2:54:21.714206 INFO: performing precursor FDR with 40 features
2:54:21.714341 INFO: Decoy channel: -1
2:54:21.714367 INFO: competitive: True
2:54:21.770983 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:21.806053 WARNING: FDR calculation for 368900 target and 333019 decoy PSMs
2:54:21.806188 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:54:21.987068 INFO: Estimating optimal hyperparameters - samples: 561,535, batch_size: 2,300, learning_rate: 7.49e-04
2:54:21.988080 INFO: Using random state 332521 for train-test-split
2:54:33.084688 INFO: Test AUC: 0.775
2:54:33.084818 INFO: Train AUC: 0.779
2:54:33.084853 INFO: AUC difference: 0.46%
2:54:33.588338 INFO: Resetting torch num_threads to 24
2:54:33.918743 PROGRESS: ============================= Precursor FDR =============================
2:54:33.919015 PROGRESS: Total precursors accumulated: 121,545
2:54:33.919086 PROGRESS: Target precursors: 120,342 (99.01%)
2:54:33.919141 PROGRESS: Decoy precursors: 1,203 (0.99%)
2:54:33.919188 PROGRESS: 
2:54:33.919234 PROGRESS: Precursor Summary:
2:54:33.956105 PROGRESS: Channel   0:	 0.050 FDR: 120,342; 0.010 FDR: 120,342; 0.001 FDR: 105,417
2:54:33.956366 PROGRESS: 
2:54:33.956430 PROGRESS: Protein Summary:
2:54:34.016640 PROGRESS: Channel   0:	 0.050 FDR: 10,349; 0.010 FDR: 10,349; 0.001 FDR: 10,128
2:54:34.016895 PROGRESS: =========================================================================
2:54:34.019536 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
2:54:34.249107 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
2:54:34.537910 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:54:34.654813 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
2:54:34.655005 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:54:34.655094 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
2:54:34.655269 INFO: Initializing TimingManager
2:54:34.655837 INFO: Initializing RawFileManager
2:54:48.420566 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.
2:54:48.428483 INFO: Determining DIA cycle
2:54:48.445065 INFO: Found cycle with start 0.00 min and length 300.
2:54:48.613558 INFO: RT (min)            : 0.0 - 26.9
2:54:48.613655 INFO: RT duration (sec)   : 1611.2
2:54:48.613684 INFO: RT duration (min)   : 26.9
2:54:48.613710 INFO: Cycle len (scans)   : 300
2:54:48.613729 INFO: Cycle len (sec)     : 1.65
2:54:48.613747 INFO: Number of cycles    : 978
2:54:48.613766 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:54:48.613802 INFO: Creating DIA data object took: 13.95786190032959
2:54:50.368465 INFO: Creating DIA data NG object took: 1.754530429840088
2:54:50.411579 INFO: Initializing CalibrationManager
2:54:50.411871 INFO: Setting up calibration estimators ..
2:54:50.411931 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:54:50.412024 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'}' ..
2:54:50.412110 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:54:50.412165 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:54:50.412222 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}}' ..
2:54:50.412277 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:54:50.412323 INFO: Done setting up calibration estimators.
2:54:50.412524 INFO: Initializing OptimizationManager
2:54:50.412657 INFO: initial parameter: ms1_error = 30
2:54:50.412709 INFO: initial parameter: ms2_error = 30
2:54:50.412756 INFO: initial parameter: rt_error = 805.6019897460938
2:54:50.412799 INFO: initial parameter: mobility_error = 0.1
2:54:50.412843 INFO: initial parameter: num_candidates = 1
2:54:50.412883 INFO: initial parameter: fwhm_rt = 5
2:54:50.412923 INFO: initial parameter: fwhm_mobility = 0.01
2:54:50.412963 INFO: initial parameter: score_cutoff = 0
2:54:50.413003 INFO: initial parameter: classifier_version = -1
2:54:50.413073 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:54:50.413362 INFO: FDRManager: loading saved state not requested, will be initialized.
2:54:50.413396 INFO: Initializing FDRManager
2:54:50.413429 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:54:50.451787 PROGRESS: Initializing spectral library: 132,778 target precursors potentially observable (0 removed)
2:54:50.477028 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:54:50.477417 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
2:54:50.477518 PROGRESS: Starting initial search for precursors.
2:54:50.477602 INFO: Starting optimization step 0.
2:54:50.477679 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:54:50.477736 INFO: Using rust extraction backend
2:54:50.477794 PROGRESS: Extracting batch of 1980 precursors
2:54:50.482621 INFO: === Search parameters used ===
2:54:50.482729 INFO: rt_error       : 805.6019897460938
2:54:50.482779 INFO: mobility_error : 0.1
2:54:50.482823 INFO: num_candidates : 1
2:54:50.482863 INFO: ms1_error      : 30
2:54:50.482903 INFO: ms2_error      : 30
2:54:50.482942 INFO: fwhm_rt        : 5
2:54:50.482980 INFO: quant_window   : 3
2:54:50.483018 INFO: ==============================================
2:54:50.514561 INFO: performing precursor FDR with 40 features
2:54:50.514635 INFO: Decoy channel: -1
2:54:50.514658 INFO: competitive: True
2:54:50.516186 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:50.518060 INFO: Estimating optimal hyperparameters - samples: 1,582, batch_size: 128, learning_rate: 1.77e-04
2:54:50.518858 INFO: Using random state 107057 for train-test-split
2:54:50.670700 INFO: Test AUC: 0.787
2:54:50.670780 INFO: Train AUC: 0.788
2:54:50.670809 INFO: AUC difference: 0.13%
2:54:50.931230 INFO: Resetting torch num_threads to 24
2:54:50.932965 PROGRESS: === Extracted 1978 precursors and 13461 fragments ===
2:54:50.933344 INFO: === FDR correction performed with classifier version -1 ===
2:54:50.933865 PROGRESS: ============================= Precursor FDR =============================
2:54:50.933949 PROGRESS: Total precursors accumulated: 404
2:54:50.934005 PROGRESS: Target precursors: 400 (99.01%)
2:54:50.934053 PROGRESS: Decoy precursors: 4 (0.99%)
2:54:50.934097 PROGRESS: 
2:54:50.934139 PROGRESS: Precursor Summary:
2:54:50.935192 PROGRESS: Channel   0:	 0.050 FDR:   400; 0.010 FDR:   257; 0.001 FDR:   201
2:54:50.935275 PROGRESS: 
2:54:50.935327 PROGRESS: Protein Summary:
2:54:50.936611 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   245; 0.001 FDR:   195
2:54:50.936702 PROGRESS: =========================================================================
2:54:50.936914 INFO: Target number of precursors not reached yet.
2:54:50.944791 INFO: Starting optimization step 1.
2:54:50.944903 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:54:50.944976 INFO: Using rust extraction backend
2:54:50.945032 PROGRESS: Extracting batch of 3976 precursors
2:54:50.953054 INFO: === Search parameters used ===
2:54:50.953155 INFO: rt_error       : 805.6019897460938
2:54:50.953204 INFO: mobility_error : 0.1
2:54:50.953248 INFO: num_candidates : 1
2:54:50.953291 INFO: ms1_error      : 30
2:54:50.953335 INFO: ms2_error      : 30
2:54:50.953376 INFO: fwhm_rt        : 5
2:54:50.953415 INFO: quant_window   : 3
2:54:50.953453 INFO: ==============================================
2:54:51.026401 INFO: performing precursor FDR with 40 features
2:54:51.026498 INFO: Decoy channel: -1
2:54:51.026522 INFO: competitive: True
2:54:51.030761 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:51.033762 INFO: Estimating optimal hyperparameters - samples: 4,760, batch_size: 128, learning_rate: 1.77e-04
2:54:51.033864 INFO: Using random state 320520 for train-test-split
2:54:51.508132 INFO: Test AUC: 0.831
2:54:51.508229 INFO: Train AUC: 0.827
2:54:51.508257 INFO: AUC difference: 0.58%
2:54:51.758258 INFO: Resetting torch num_threads to 24
2:54:51.761408 PROGRESS: === Extracted 5951 precursors and 40535 fragments ===
2:54:51.761790 INFO: === FDR correction performed with classifier version -1 ===
2:54:51.762407 PROGRESS: ============================= Precursor FDR =============================
2:54:51.762489 PROGRESS: Total precursors accumulated: 1,433
2:54:51.762546 PROGRESS: Target precursors: 1,419 (99.02%)
2:54:51.762594 PROGRESS: Decoy precursors: 14 (0.98%)
2:54:51.762637 PROGRESS: 
2:54:51.762678 PROGRESS: Precursor Summary:
2:54:51.764096 PROGRESS: Channel   0:	 0.050 FDR: 1,419; 0.010 FDR: 1,419; 0.001 FDR: 1,079
2:54:51.764195 PROGRESS: 
2:54:51.764250 PROGRESS: Protein Summary:
2:54:51.765995 PROGRESS: Channel   0:	 0.050 FDR: 1,187; 0.010 FDR: 1,187; 0.001 FDR:   928
2:54:51.766081 PROGRESS: =========================================================================
2:54:51.766343 INFO: Target number of precursors reached.
2:54:51.774935 INFO: fragments_df: keeping 5000 of 40535 [sum(precursor_idx_mask)=14669 sum(mass_error_mask)=40535 stop_rank=5000
2:54:51.786008 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:52.021035 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:52.738558 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:54:52.739123 INFO: Using score_cutoff 12.540014344596862 (fac=0.99, q=1)
2:54:52.739476 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:54:52.739559 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:54:52.739615 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.540014344596862
2:54:52.739679 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:52.743811 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:52.751940 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:54:52.752055 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:54:52.752151 INFO: Starting optimization step 2.
2:54:52.752222 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:52.752292 INFO: Using rust extraction backend
2:54:52.752359 PROGRESS: Extracting batch of 5956 precursors
2:54:52.763725 INFO: === Search parameters used ===
2:54:52.763849 INFO: rt_error       : 805.6019897460938
2:54:52.763901 INFO: mobility_error : 0.1
2:54:52.763947 INFO: num_candidates : 3
2:54:52.763989 INFO: ms1_error      : 30
2:54:52.764030 INFO: ms2_error      : 30
2:54:52.764070 INFO: fwhm_rt        : 3.0
2:54:52.764110 INFO: quant_window   : 3
2:54:52.764149 INFO: ==============================================
2:54:52.894885 INFO: performing precursor FDR with 40 features
2:54:52.894993 INFO: Decoy channel: -1
2:54:52.895018 INFO: competitive: True
2:54:52.900171 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:52.904340 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:54:52.904475 INFO: Using random state 395633 for train-test-split
2:54:54.327758 INFO: Test AUC: 0.695
2:54:54.327864 INFO: Train AUC: 0.713
2:54:54.327893 INFO: AUC difference: 2.51%
2:54:54.581993 INFO: Resetting torch num_threads to 24
2:54:54.584461 PROGRESS: === Extracted 17812 precursors and 105677 fragments ===
2:54:54.584832 INFO: === FDR correction performed with classifier version 1 ===
2:54:54.585562 PROGRESS: ============================= Precursor FDR =============================
2:54:54.585647 PROGRESS: Total precursors accumulated: 1,863
2:54:54.585703 PROGRESS: Target precursors: 1,845 (99.03%)
2:54:54.585752 PROGRESS: Decoy precursors: 18 (0.97%)
2:54:54.585799 PROGRESS: 
2:54:54.585842 PROGRESS: Precursor Summary:
2:54:54.587230 PROGRESS: Channel   0:	 0.050 FDR: 1,845; 0.010 FDR: 1,845; 0.001 FDR: 1,150
2:54:54.587317 PROGRESS: 
2:54:54.587379 PROGRESS: Protein Summary:
2:54:54.589235 PROGRESS: Channel   0:	 0.050 FDR: 1,499; 0.010 FDR: 1,499; 0.001 FDR:   978
2:54:54.589328 PROGRESS: =========================================================================
2:54:54.589748 INFO: Target number of precursors reached.
2:54:54.609136 INFO: fragments_df: keeping 5000 of 105677 [sum(precursor_idx_mask)=39741 sum(mass_error_mask)=105677 stop_rank=5000
2:54:54.620323 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:54.898376 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:55.609673 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:55.610120 INFO: Using score_cutoff 12.672026662445068 (fac=0.99, q=1)
2:54:55.610422 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:55.610497 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:55.610550 INFO: Updating optimization_manager: score_cutoff        : 12.540014344596862 -> 12.672026662445068
2:54:55.610602 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:55.614532 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:55.622594 INFO: === checking if optimization conditions were reached ===
2:54:55.624278 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:54:55.624378 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:54:55.624438 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:54:55.624492 INFO: ==============================================
2:54:55.624561 INFO: Starting optimization step 3.
2:54:55.624618 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:55.624673 INFO: Using rust extraction backend
2:54:55.624726 PROGRESS: Extracting batch of 5956 precursors
2:54:55.638884 INFO: === Search parameters used ===
2:54:55.639020 INFO: rt_error       : 805.6019897460938
2:54:55.639071 INFO: mobility_error : 0.1
2:54:55.639115 INFO: num_candidates : 3
2:54:55.639158 INFO: ms1_error      : 30
2:54:55.639199 INFO: ms2_error      : 10.0
2:54:55.639238 INFO: fwhm_rt        : 3.0
2:54:55.639278 INFO: quant_window   : 3
2:54:55.639317 INFO: ==============================================
2:54:55.758015 INFO: performing precursor FDR with 40 features
2:54:55.759309 INFO: Decoy channel: -1
2:54:55.759338 INFO: competitive: True
2:54:55.764167 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:55.768275 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:54:55.768409 INFO: Using random state 631597 for train-test-split
2:54:57.213295 INFO: Test AUC: 0.730
2:54:57.213478 INFO: Train AUC: 0.747
2:54:57.213513 INFO: AUC difference: 2.33%
2:54:57.471955 INFO: Resetting torch num_threads to 24
2:54:57.474485 PROGRESS: === Extracted 17855 precursors and 119295 fragments ===
2:54:57.474892 INFO: === FDR correction performed with classifier version 2 ===
2:54:57.475637 PROGRESS: ============================= Precursor FDR =============================
2:54:57.475732 PROGRESS: Total precursors accumulated: 2,378
2:54:57.475794 PROGRESS: Target precursors: 2,355 (99.03%)
2:54:57.475846 PROGRESS: Decoy precursors: 23 (0.97%)
2:54:57.475891 PROGRESS: 
2:54:57.475936 PROGRESS: Precursor Summary:
2:54:57.477473 PROGRESS: Channel   0:	 0.050 FDR: 2,355; 0.010 FDR: 2,355; 0.001 FDR: 1,463
2:54:57.477560 PROGRESS: 
2:54:57.477615 PROGRESS: Protein Summary:
2:54:57.479716 PROGRESS: Channel   0:	 0.050 FDR: 1,868; 0.010 FDR: 1,868; 0.001 FDR: 1,214
2:54:57.479814 PROGRESS: =========================================================================
2:54:57.480280 INFO: Target number of precursors reached.
2:54:57.505702 INFO: fragments_df: keeping 5000 of 119295 [sum(precursor_idx_mask)=53767 sum(mass_error_mask)=119295 stop_rank=5000
2:54:57.520286 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:54:57.868373 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:54:58.583797 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:54:58.584258 INFO: Using score_cutoff 10.737328422546385 (fac=0.99, q=1)
2:54:58.584583 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:54:58.584659 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:54:58.584713 INFO: Updating optimization_manager: score_cutoff        : 12.672026662445068 -> 10.737328422546385
2:54:58.584772 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:58.588784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:58.596496 INFO: === checking if optimization conditions were reached ===
2:54:58.598202 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:54:58.598303 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:54:58.598371 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:54:58.598435 INFO: ==============================================
2:54:58.598511 INFO: Starting optimization step 4.
2:54:58.598574 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:54:58.598648 INFO: Using rust extraction backend
2:54:58.598712 PROGRESS: Extracting batch of 5956 precursors
2:54:58.610995 INFO: === Search parameters used ===
2:54:58.611125 INFO: rt_error       : 805.6019897460938
2:54:58.611180 INFO: mobility_error : 0.1
2:54:58.611227 INFO: num_candidates : 3
2:54:58.611271 INFO: ms1_error      : 30
2:54:58.611314 INFO: ms2_error      : 10.0
2:54:58.611355 INFO: fwhm_rt        : 3.0
2:54:58.611396 INFO: quant_window   : 3
2:54:58.611435 INFO: ==============================================
2:54:58.720057 INFO: performing precursor FDR with 40 features
2:54:58.720167 INFO: Decoy channel: -1
2:54:58.720193 INFO: competitive: True
2:54:58.725326 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:58.729526 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:54:58.729661 INFO: Using random state 465613 for train-test-split
2:55:00.149318 INFO: Test AUC: 0.740
2:55:00.149425 INFO: Train AUC: 0.758
2:55:00.149456 INFO: AUC difference: 2.30%
2:55:00.403939 INFO: Resetting torch num_threads to 24
2:55:00.406383 PROGRESS: === Extracted 17855 precursors and 119280 fragments ===
2:55:00.406754 INFO: === FDR correction performed with classifier version 3 ===
2:55:00.407423 PROGRESS: ============================= Precursor FDR =============================
2:55:00.407520 PROGRESS: Total precursors accumulated: 2,360
2:55:00.407578 PROGRESS: Target precursors: 2,337 (99.03%)
2:55:00.407626 PROGRESS: Decoy precursors: 23 (0.97%)
2:55:00.407670 PROGRESS: 
2:55:00.407717 PROGRESS: Precursor Summary:
2:55:00.409219 PROGRESS: Channel   0:	 0.050 FDR: 2,337; 0.010 FDR: 2,337; 0.001 FDR: 1,589
2:55:00.409303 PROGRESS: 
2:55:00.409355 PROGRESS: Protein Summary:
2:55:00.411441 PROGRESS: Channel   0:	 0.050 FDR: 1,848; 0.010 FDR: 1,848; 0.001 FDR: 1,319
2:55:00.411545 PROGRESS: =========================================================================
2:55:00.411917 INFO: Target number of precursors reached.
2:55:00.436621 INFO: fragments_df: keeping 5000 of 119280 [sum(precursor_idx_mask)=53281 sum(mass_error_mask)=119280 stop_rank=5000
2:55:00.447528 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:00.787452 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:01.507857 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:01.508313 INFO: Using score_cutoff 10.68254782333374 (fac=0.99, q=1)
2:55:01.508616 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:01.508689 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:01.508741 INFO: Updating optimization_manager: score_cutoff        : 10.737328422546385 -> 10.68254782333374
2:55:01.508791 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:01.512736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:01.520638 INFO: === checking if optimization conditions were reached ===
2:55:01.522274 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:55:01.522375 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:55:01.522439 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:55:01.522494 INFO: ==============================================
2:55:01.522555 INFO: Starting optimization step 5.
2:55:01.522609 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:01.522664 INFO: Using rust extraction backend
2:55:01.522715 PROGRESS: Extracting batch of 5956 precursors
2:55:01.533932 INFO: === Search parameters used ===
2:55:01.534060 INFO: rt_error       : 805.6019897460938
2:55:01.534119 INFO: mobility_error : 0.1
2:55:01.534164 INFO: num_candidates : 3
2:55:01.534205 INFO: ms1_error      : 30
2:55:01.534247 INFO: ms2_error      : 10.0
2:55:01.534290 INFO: fwhm_rt        : 3.0
2:55:01.534331 INFO: quant_window   : 3
2:55:01.534371 INFO: ==============================================
2:55:01.638719 INFO: performing precursor FDR with 40 features
2:55:01.638832 INFO: Decoy channel: -1
2:55:01.638855 INFO: competitive: True
2:55:01.643927 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:01.647967 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:55:01.648100 INFO: Using random state 590379 for train-test-split
2:55:03.073273 INFO: Test AUC: 0.756
2:55:03.073408 INFO: Train AUC: 0.764
2:55:03.073438 INFO: AUC difference: 1.04%
2:55:03.330992 INFO: Resetting torch num_threads to 24
2:55:03.333500 PROGRESS: === Extracted 17855 precursors and 119292 fragments ===
2:55:03.333882 INFO: === FDR correction performed with classifier version 4 ===
2:55:03.334582 PROGRESS: ============================= Precursor FDR =============================
2:55:03.334668 PROGRESS: Total precursors accumulated: 2,486
2:55:03.334727 PROGRESS: Target precursors: 2,462 (99.03%)
2:55:03.334778 PROGRESS: Decoy precursors: 24 (0.97%)
2:55:03.334830 PROGRESS: 
2:55:03.334876 PROGRESS: Precursor Summary:
2:55:03.336447 PROGRESS: Channel   0:	 0.050 FDR: 2,462; 0.010 FDR: 2,462; 0.001 FDR: 1,593
2:55:03.336539 PROGRESS: 
2:55:03.336594 PROGRESS: Protein Summary:
2:55:03.338717 PROGRESS: Channel   0:	 0.050 FDR: 1,944; 0.010 FDR: 1,944; 0.001 FDR: 1,316
2:55:03.338815 PROGRESS: =========================================================================
2:55:03.339197 INFO: Target number of precursors reached.
2:55:03.364859 INFO: fragments_df: keeping 5000 of 119292 [sum(precursor_idx_mask)=55767 sum(mass_error_mask)=119292 stop_rank=5000
2:55:03.375929 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:03.734706 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:04.453323 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:04.453785 INFO: Using score_cutoff 10.122483205604553 (fac=0.99, q=1)
2:55:04.454118 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:04.454191 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:04.454243 INFO: Updating optimization_manager: score_cutoff        : 10.68254782333374 -> 10.122483205604553
2:55:04.454293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:04.458251 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:04.466023 INFO: === checking if optimization conditions were reached ===
2:55:04.467706 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:55:04.467806 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:55:04.467868 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:55:04.467924 INFO: ==============================================
2:55:04.467988 INFO: Starting optimization step 6.
2:55:04.468044 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:04.468106 INFO: Using rust extraction backend
2:55:04.468168 PROGRESS: Extracting batch of 5956 precursors
2:55:04.482160 INFO: === Search parameters used ===
2:55:04.482284 INFO: rt_error       : 805.6019897460938
2:55:04.482337 INFO: mobility_error : 0.1
2:55:04.482381 INFO: num_candidates : 3
2:55:04.482421 INFO: ms1_error      : 30
2:55:04.482461 INFO: ms2_error      : 10.0
2:55:04.482501 INFO: fwhm_rt        : 3.0
2:55:04.482541 INFO: quant_window   : 3
2:55:04.482581 INFO: ==============================================
2:55:04.594067 INFO: performing precursor FDR with 40 features
2:55:04.594176 INFO: Decoy channel: -1
2:55:04.594199 INFO: competitive: True
2:55:04.600668 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:04.604749 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:55:04.604875 INFO: Using random state 563758 for train-test-split
2:55:06.028272 INFO: Test AUC: 0.748
2:55:06.028379 INFO: Train AUC: 0.774
2:55:06.028408 INFO: AUC difference: 3.37%
2:55:06.283017 INFO: Resetting torch num_threads to 24
2:55:06.285540 PROGRESS: === Extracted 17855 precursors and 119326 fragments ===
2:55:06.285906 INFO: === FDR correction performed with classifier version 5 ===
2:55:06.286599 PROGRESS: ============================= Precursor FDR =============================
2:55:06.286685 PROGRESS: Total precursors accumulated: 2,483
2:55:06.286748 PROGRESS: Target precursors: 2,459 (99.03%)
2:55:06.286800 PROGRESS: Decoy precursors: 24 (0.97%)
2:55:06.286845 PROGRESS: 
2:55:06.286888 PROGRESS: Precursor Summary:
2:55:06.288494 PROGRESS: Channel   0:	 0.050 FDR: 2,459; 0.010 FDR: 2,459; 0.001 FDR: 2,111
2:55:06.288588 PROGRESS: 
2:55:06.288642 PROGRESS: Protein Summary:
2:55:06.290828 PROGRESS: Channel   0:	 0.050 FDR: 1,939; 0.010 FDR: 1,939; 0.001 FDR: 1,675
2:55:06.290915 PROGRESS: =========================================================================
2:55:06.291301 INFO: Target number of precursors reached.
2:55:06.317657 INFO: fragments_df: keeping 5000 of 119326 [sum(precursor_idx_mask)=55653 sum(mass_error_mask)=119326 stop_rank=5000
2:55:06.330345 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:06.689301 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:07.410022 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:07.410491 INFO: Using score_cutoff 10.186230487060547 (fac=0.99, q=1)
2:55:07.410814 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:07.410892 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:07.410949 INFO: Updating optimization_manager: score_cutoff        : 10.122483205604553 -> 10.186230487060547
2:55:07.411003 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:07.415031 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:07.423377 INFO: === checking if optimization conditions were reached ===
2:55:07.425108 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:55:07.425209 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:55:07.425273 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:55:07.425329 INFO: ==============================================
2:55:07.425400 PROGRESS: Optimization finished for ms2_error.
2:55:07.438982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:07.442729 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:07.450523 INFO: Starting optimization step 0.
2:55:07.450632 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:07.450706 INFO: Using rust extraction backend
2:55:07.450765 PROGRESS: Extracting batch of 5956 precursors
2:55:07.462085 INFO: === Search parameters used ===
2:55:07.462205 INFO: rt_error       : 805.6019897460938
2:55:07.462257 INFO: mobility_error : 0.1
2:55:07.462304 INFO: num_candidates : 3
2:55:07.462354 INFO: ms1_error      : 30
2:55:07.462399 INFO: ms2_error      : 10.0
2:55:07.462440 INFO: fwhm_rt        : 3.0
2:55:07.462480 INFO: quant_window   : 3
2:55:07.462520 INFO: ==============================================
2:55:07.613789 INFO: performing precursor FDR with 40 features
2:55:07.613921 INFO: Decoy channel: -1
2:55:07.613947 INFO: competitive: True
2:55:07.619260 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:07.623467 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:55:07.623593 INFO: Using random state 849362 for train-test-split
2:55:09.038502 INFO: Test AUC: 0.751
2:55:09.038610 INFO: Train AUC: 0.784
2:55:09.038639 INFO: AUC difference: 4.19%
2:55:09.292215 INFO: Resetting torch num_threads to 24
2:55:09.294823 PROGRESS: === Extracted 17855 precursors and 119309 fragments ===
2:55:09.295189 INFO: === FDR correction performed with classifier version 6 ===
2:55:09.295908 PROGRESS: ============================= Precursor FDR =============================
2:55:09.295999 PROGRESS: Total precursors accumulated: 2,542
2:55:09.296055 PROGRESS: Target precursors: 2,517 (99.02%)
2:55:09.296103 PROGRESS: Decoy precursors: 25 (0.98%)
2:55:09.296146 PROGRESS: 
2:55:09.296188 PROGRESS: Precursor Summary:
2:55:09.297807 PROGRESS: Channel   0:	 0.050 FDR: 2,517; 0.010 FDR: 2,517; 0.001 FDR: 2,244
2:55:09.297895 PROGRESS: 
2:55:09.297947 PROGRESS: Protein Summary:
2:55:09.300190 PROGRESS: Channel   0:	 0.050 FDR: 1,978; 0.010 FDR: 1,978; 0.001 FDR: 1,785
2:55:09.300286 PROGRESS: =========================================================================
2:55:09.300726 INFO: Target number of precursors reached.
2:55:09.327624 INFO: fragments_df: keeping 5000 of 119309 [sum(precursor_idx_mask)=56776 sum(mass_error_mask)=119309 stop_rank=5000
2:55:09.343824 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:09.712438 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:10.433778 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:10.434411 INFO: Using score_cutoff 10.185625370407104 (fac=0.99, q=1)
2:55:10.434763 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:10.434843 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:10.434900 INFO: Updating optimization_manager: score_cutoff        : 10.186230487060547 -> 10.185625370407104
2:55:10.434965 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:10.439138 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:10.447116 INFO: === checking if optimization conditions were reached ===
2:55:10.447260 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:55:10.450030 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 419.66377176611286
2:55:10.450138 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 419.6638.
2:55:10.450200 INFO: ==============================================
2:55:10.450278 INFO: Starting optimization step 1.
2:55:10.450347 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:10.450420 INFO: Using rust extraction backend
2:55:10.450489 PROGRESS: Extracting batch of 5956 precursors
2:55:10.462500 INFO: === Search parameters used ===
2:55:10.462620 INFO: rt_error       : 419.66377176611286
2:55:10.462674 INFO: mobility_error : 0.1
2:55:10.462718 INFO: num_candidates : 3
2:55:10.462769 INFO: ms1_error      : 30
2:55:10.462809 INFO: ms2_error      : 10.0
2:55:10.462850 INFO: fwhm_rt        : 3.0
2:55:10.462894 INFO: quant_window   : 3
2:55:10.462934 INFO: ==============================================
2:55:10.560102 INFO: performing precursor FDR with 40 features
2:55:10.560213 INFO: Decoy channel: -1
2:55:10.560236 INFO: competitive: True
2:55:10.565525 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:10.569688 INFO: Estimating optimal hyperparameters - samples: 14,283, batch_size: 128, learning_rate: 1.77e-04
2:55:10.569818 INFO: Using random state 849362 for train-test-split
2:55:11.982539 INFO: Test AUC: 0.756
2:55:11.982663 INFO: Train AUC: 0.781
2:55:11.982692 INFO: AUC difference: 3.15%
2:55:12.236907 INFO: Resetting torch num_threads to 24
2:55:12.239437 PROGRESS: === Extracted 17854 precursors and 118913 fragments ===
2:55:12.239839 INFO: === FDR correction performed with classifier version 6 ===
2:55:12.240553 PROGRESS: ============================= Precursor FDR =============================
2:55:12.240636 PROGRESS: Total precursors accumulated: 2,566
2:55:12.240693 PROGRESS: Target precursors: 2,541 (99.03%)
2:55:12.240740 PROGRESS: Decoy precursors: 25 (0.97%)
2:55:12.240783 PROGRESS: 
2:55:12.240824 PROGRESS: Precursor Summary:
2:55:12.242431 PROGRESS: Channel   0:	 0.050 FDR: 2,541; 0.010 FDR: 2,541; 0.001 FDR: 2,167
2:55:12.242515 PROGRESS: 
2:55:12.242568 PROGRESS: Protein Summary:
2:55:12.244826 PROGRESS: Channel   0:	 0.050 FDR: 1,994; 0.010 FDR: 1,994; 0.001 FDR: 1,724
2:55:12.244923 PROGRESS: =========================================================================
2:55:12.245339 INFO: Target number of precursors reached.
2:55:12.271888 INFO: fragments_df: keeping 5000 of 118913 [sum(precursor_idx_mask)=57149 sum(mass_error_mask)=118913 stop_rank=5000
2:55:12.283598 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:12.645063 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:13.365164 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:13.365619 INFO: Using score_cutoff 10.11431809616089 (fac=0.99, q=1)
2:55:13.365945 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:13.366023 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:13.366076 INFO: Updating optimization_manager: score_cutoff        : 10.185625370407104 -> 10.11431809616089
2:55:13.366129 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:13.370184 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:13.377885 INFO: === checking if optimization conditions were reached ===
2:55:13.378013 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:55:13.380814 INFO: Updating optimization_manager: rt_error            : 419.66377176611286 -> 312.9692122538337
2:55:13.380919 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 312.9692.
2:55:13.380982 INFO: ==============================================
2:55:13.381054 INFO: Starting optimization step 2.
2:55:13.381124 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:13.381192 INFO: Using rust extraction backend
2:55:13.381249 PROGRESS: Extracting batch of 5956 precursors
2:55:13.392512 INFO: === Search parameters used ===
2:55:13.392636 INFO: rt_error       : 312.9692122538337
2:55:13.392688 INFO: mobility_error : 0.1
2:55:13.392733 INFO: num_candidates : 3
2:55:13.392775 INFO: ms1_error      : 30
2:55:13.392815 INFO: ms2_error      : 10.0
2:55:13.392863 INFO: fwhm_rt        : 3.0
2:55:13.392904 INFO: quant_window   : 3
2:55:13.392944 INFO: ==============================================
2:55:13.484835 INFO: performing precursor FDR with 40 features
2:55:13.484947 INFO: Decoy channel: -1
2:55:13.484970 INFO: competitive: True
2:55:13.489979 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:13.494204 INFO: Estimating optimal hyperparameters - samples: 14,279, batch_size: 128, learning_rate: 1.77e-04
2:55:13.494335 INFO: Using random state 849362 for train-test-split
2:55:14.923348 INFO: Test AUC: 0.762
2:55:14.923467 INFO: Train AUC: 0.779
2:55:14.923498 INFO: AUC difference: 2.29%
2:55:15.176935 INFO: Resetting torch num_threads to 24
2:55:15.179410 PROGRESS: === Extracted 17849 precursors and 117826 fragments ===
2:55:15.179779 INFO: === FDR correction performed with classifier version 6 ===
2:55:15.180480 PROGRESS: ============================= Precursor FDR =============================
2:55:15.180562 PROGRESS: Total precursors accumulated: 2,613
2:55:15.180618 PROGRESS: Target precursors: 2,588 (99.04%)
2:55:15.180667 PROGRESS: Decoy precursors: 25 (0.96%)
2:55:15.180710 PROGRESS: 
2:55:15.180753 PROGRESS: Precursor Summary:
2:55:15.182362 PROGRESS: Channel   0:	 0.050 FDR: 2,588; 0.010 FDR: 2,588; 0.001 FDR: 2,168
2:55:15.182447 PROGRESS: 
2:55:15.182500 PROGRESS: Protein Summary:
2:55:15.184769 PROGRESS: Channel   0:	 0.050 FDR: 2,020; 0.010 FDR: 2,020; 0.001 FDR: 1,723
2:55:15.184863 PROGRESS: =========================================================================
2:55:15.185226 INFO: Target number of precursors reached.
2:55:15.211214 INFO: fragments_df: keeping 5000 of 117826 [sum(precursor_idx_mask)=57846 sum(mass_error_mask)=117826 stop_rank=5000
2:55:15.222252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:15.589408 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:16.308688 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:16.309149 INFO: Using score_cutoff 10.13259238872528 (fac=0.99, q=1)
2:55:16.309469 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:16.309543 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:16.309593 INFO: Updating optimization_manager: score_cutoff        : 10.11431809616089 -> 10.13259238872528
2:55:16.309646 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:16.313606 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:16.321631 INFO: === checking if optimization conditions were reached ===
2:55:16.321753 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:55:16.324694 INFO: Updating optimization_manager: rt_error            : 312.9692122538337 -> 290.70391735132023
2:55:16.324808 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 290.7039.
2:55:16.324870 INFO: ==============================================
2:55:16.324935 INFO: Starting optimization step 3.
2:55:16.324992 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:16.325049 INFO: Using rust extraction backend
2:55:16.325102 PROGRESS: Extracting batch of 5956 precursors
2:55:16.336449 INFO: === Search parameters used ===
2:55:16.336560 INFO: rt_error       : 290.70391735132023
2:55:16.336610 INFO: mobility_error : 0.1
2:55:16.336653 INFO: num_candidates : 3
2:55:16.336702 INFO: ms1_error      : 30
2:55:16.336744 INFO: ms2_error      : 10.0
2:55:16.336784 INFO: fwhm_rt        : 3.0
2:55:16.336823 INFO: quant_window   : 3
2:55:16.336867 INFO: ==============================================
2:55:16.431256 INFO: performing precursor FDR with 40 features
2:55:16.431372 INFO: Decoy channel: -1
2:55:16.431396 INFO: competitive: True
2:55:16.436447 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:16.440675 INFO: Estimating optimal hyperparameters - samples: 14,279, batch_size: 128, learning_rate: 1.77e-04
2:55:16.440810 INFO: Using random state 849362 for train-test-split
2:55:17.854203 INFO: Test AUC: 0.755
2:55:17.854317 INFO: Train AUC: 0.781
2:55:17.854350 INFO: AUC difference: 3.33%
2:55:18.107476 INFO: Resetting torch num_threads to 24
2:55:18.109960 PROGRESS: === Extracted 17849 precursors and 117368 fragments ===
2:55:18.110327 INFO: === FDR correction performed with classifier version 6 ===
2:55:18.111035 PROGRESS: ============================= Precursor FDR =============================
2:55:18.111123 PROGRESS: Total precursors accumulated: 2,653
2:55:18.111185 PROGRESS: Target precursors: 2,627 (99.02%)
2:55:18.111238 PROGRESS: Decoy precursors: 26 (0.98%)
2:55:18.111285 PROGRESS: 
2:55:18.111331 PROGRESS: Precursor Summary:
2:55:18.112967 PROGRESS: Channel   0:	 0.050 FDR: 2,627; 0.010 FDR: 2,627; 0.001 FDR: 2,273
2:55:18.113067 PROGRESS: 
2:55:18.113126 PROGRESS: Protein Summary:
2:55:18.115399 PROGRESS: Channel   0:	 0.050 FDR: 2,050; 0.010 FDR: 2,050; 0.001 FDR: 1,801
2:55:18.115503 PROGRESS: =========================================================================
2:55:18.115873 INFO: Target number of precursors reached.
2:55:18.142114 INFO: fragments_df: keeping 5000 of 117368 [sum(precursor_idx_mask)=58615 sum(mass_error_mask)=117368 stop_rank=5000
2:55:18.153004 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:18.526291 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:19.241824 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:19.242277 INFO: Using score_cutoff 9.847551741600036 (fac=0.99, q=1)
2:55:19.242584 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:19.242663 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:19.242718 INFO: Updating optimization_manager: score_cutoff        : 10.13259238872528 -> 9.847551741600036
2:55:19.242772 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:19.246722 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:19.254810 INFO: === checking if optimization conditions were reached ===
2:55:19.254931 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:55:19.257861 INFO: Updating optimization_manager: rt_error            : 290.70391735132023 -> 335.841773832326
2:55:19.257968 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 335.8418.
2:55:19.258034 INFO: ==============================================
2:55:19.258102 INFO: Starting optimization step 4.
2:55:19.258161 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:19.258222 INFO: Using rust extraction backend
2:55:19.258276 PROGRESS: Extracting batch of 5956 precursors
2:55:19.269479 INFO: === Search parameters used ===
2:55:19.269593 INFO: rt_error       : 335.841773832326
2:55:19.269654 INFO: mobility_error : 0.1
2:55:19.269704 INFO: num_candidates : 3
2:55:19.269747 INFO: ms1_error      : 30
2:55:19.269788 INFO: ms2_error      : 10.0
2:55:19.269828 INFO: fwhm_rt        : 3.0
2:55:19.269868 INFO: quant_window   : 3
2:55:19.269910 INFO: ==============================================
2:55:19.426760 INFO: performing precursor FDR with 40 features
2:55:19.426872 INFO: Decoy channel: -1
2:55:19.426896 INFO: competitive: True
2:55:19.431836 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:19.435891 INFO: Estimating optimal hyperparameters - samples: 14,280, batch_size: 128, learning_rate: 1.77e-04
2:55:19.436026 INFO: Using random state 849362 for train-test-split
2:55:20.849932 INFO: Test AUC: 0.759
2:55:20.850039 INFO: Train AUC: 0.780
2:55:20.850081 INFO: AUC difference: 2.67%
2:55:21.102047 INFO: Resetting torch num_threads to 24
2:55:21.104524 PROGRESS: === Extracted 17850 precursors and 118166 fragments ===
2:55:21.104884 INFO: === FDR correction performed with classifier version 6 ===
2:55:21.105579 PROGRESS: ============================= Precursor FDR =============================
2:55:21.105662 PROGRESS: Total precursors accumulated: 2,603
2:55:21.105720 PROGRESS: Target precursors: 2,578 (99.04%)
2:55:21.105767 PROGRESS: Decoy precursors: 25 (0.96%)
2:55:21.105810 PROGRESS: 
2:55:21.105853 PROGRESS: Precursor Summary:
2:55:21.107451 PROGRESS: Channel   0:	 0.050 FDR: 2,578; 0.010 FDR: 2,578; 0.001 FDR: 2,176
2:55:21.107581 PROGRESS: 
2:55:21.107635 PROGRESS: Protein Summary:
2:55:21.109863 PROGRESS: Channel   0:	 0.050 FDR: 2,014; 0.010 FDR: 2,014; 0.001 FDR: 1,727
2:55:21.109950 PROGRESS: =========================================================================
2:55:21.110295 INFO: Target number of precursors reached.
2:55:21.136580 INFO: fragments_df: keeping 5000 of 118166 [sum(precursor_idx_mask)=57792 sum(mass_error_mask)=118166 stop_rank=5000
2:55:21.147422 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:21.512677 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:22.228153 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:22.228609 INFO: Using score_cutoff 10.128704241371155 (fac=0.99, q=1)
2:55:22.228919 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:22.228994 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:22.229054 INFO: Updating optimization_manager: score_cutoff        : 9.847551741600036 -> 10.128704241371155
2:55:22.229104 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:22.233031 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:22.240976 INFO: === checking if optimization conditions were reached ===
2:55:22.241090 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:55:22.243979 INFO: Updating optimization_manager: rt_error            : 335.841773832326 -> 307.57101144116336
2:55:22.244080 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 307.5710.
2:55:22.244142 INFO: ==============================================
2:55:22.244208 INFO: Starting optimization step 5.
2:55:22.244266 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:22.244326 INFO: Using rust extraction backend
2:55:22.244380 PROGRESS: Extracting batch of 5956 precursors
2:55:22.255630 INFO: === Search parameters used ===
2:55:22.255752 INFO: rt_error       : 307.57101144116336
2:55:22.255802 INFO: mobility_error : 0.1
2:55:22.255845 INFO: num_candidates : 3
2:55:22.255887 INFO: ms1_error      : 30
2:55:22.255926 INFO: ms2_error      : 10.0
2:55:22.255967 INFO: fwhm_rt        : 3.0
2:55:22.256005 INFO: quant_window   : 3
2:55:22.256043 INFO: ==============================================
2:55:22.351590 INFO: performing precursor FDR with 40 features
2:55:22.351702 INFO: Decoy channel: -1
2:55:22.351727 INFO: competitive: True
2:55:22.356630 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:22.360681 INFO: Estimating optimal hyperparameters - samples: 14,279, batch_size: 128, learning_rate: 1.77e-04
2:55:22.360814 INFO: Using random state 849362 for train-test-split
2:55:23.768055 INFO: Test AUC: 0.769
2:55:23.768170 INFO: Train AUC: 0.777
2:55:23.768201 INFO: AUC difference: 0.96%
2:55:24.020242 INFO: Resetting torch num_threads to 24
2:55:24.022714 PROGRESS: === Extracted 17849 precursors and 117694 fragments ===
2:55:24.023077 INFO: === FDR correction performed with classifier version 6 ===
2:55:24.023798 PROGRESS: ============================= Precursor FDR =============================
2:55:24.023888 PROGRESS: Total precursors accumulated: 2,590
2:55:24.023947 PROGRESS: Target precursors: 2,565 (99.03%)
2:55:24.023998 PROGRESS: Decoy precursors: 25 (0.97%)
2:55:24.024045 PROGRESS: 
2:55:24.024107 PROGRESS: Precursor Summary:
2:55:24.025722 PROGRESS: Channel   0:	 0.050 FDR: 2,565; 0.010 FDR: 2,565; 0.001 FDR: 2,284
2:55:24.025815 PROGRESS: 
2:55:24.025872 PROGRESS: Protein Summary:
2:55:24.028125 PROGRESS: Channel   0:	 0.050 FDR: 2,002; 0.010 FDR: 2,002; 0.001 FDR: 1,813
2:55:24.028221 PROGRESS: =========================================================================
2:55:24.028586 INFO: Target number of precursors reached.
2:55:24.054204 INFO: fragments_df: keeping 5000 of 117694 [sum(precursor_idx_mask)=57307 sum(mass_error_mask)=117694 stop_rank=5000
2:55:24.065023 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:24.428514 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:25.106055 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:25.106512 INFO: Using score_cutoff 9.833437130355835 (fac=0.99, q=1)
2:55:25.106817 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:25.106892 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:25.106944 INFO: Updating optimization_manager: score_cutoff        : 10.128704241371155 -> 9.833437130355835
2:55:25.106994 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:25.110928 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:25.118872 INFO: === checking if optimization conditions were reached ===
2:55:25.118985 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:55:25.121863 INFO: Updating optimization_manager: rt_error            : 307.57101144116336 -> 281.59082027276355
2:55:25.121970 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 281.5908.
2:55:25.122032 INFO: ==============================================
2:55:25.122099 INFO: Starting optimization step 6.
2:55:25.122159 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:25.122231 INFO: Using rust extraction backend
2:55:25.122289 PROGRESS: Extracting batch of 5956 precursors
2:55:25.133617 INFO: === Search parameters used ===
2:55:25.133740 INFO: rt_error       : 281.59082027276355
2:55:25.133792 INFO: mobility_error : 0.1
2:55:25.133835 INFO: num_candidates : 3
2:55:25.133876 INFO: ms1_error      : 30
2:55:25.133916 INFO: ms2_error      : 10.0
2:55:25.133955 INFO: fwhm_rt        : 3.0
2:55:25.133993 INFO: quant_window   : 3
2:55:25.134031 INFO: ==============================================
2:55:25.228223 INFO: performing precursor FDR with 40 features
2:55:25.228336 INFO: Decoy channel: -1
2:55:25.228360 INFO: competitive: True
2:55:25.233147 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:25.237123 INFO: Estimating optimal hyperparameters - samples: 14,279, batch_size: 128, learning_rate: 1.77e-04
2:55:25.237251 INFO: Using random state 849362 for train-test-split
2:55:26.671113 INFO: Test AUC: 0.770
2:55:26.671216 INFO: Train AUC: 0.776
2:55:26.671244 INFO: AUC difference: 0.88%
2:55:26.923827 INFO: Resetting torch num_threads to 24
2:55:26.926467 PROGRESS: === Extracted 17849 precursors and 117190 fragments ===
2:55:26.926866 INFO: === FDR correction performed with classifier version 6 ===
2:55:26.927630 PROGRESS: ============================= Precursor FDR =============================
2:55:26.927728 PROGRESS: Total precursors accumulated: 2,635
2:55:26.927787 PROGRESS: Target precursors: 2,609 (99.01%)
2:55:26.927836 PROGRESS: Decoy precursors: 26 (0.99%)
2:55:26.927880 PROGRESS: 
2:55:26.927922 PROGRESS: Precursor Summary:
2:55:26.929563 PROGRESS: Channel   0:	 0.050 FDR: 2,609; 0.010 FDR: 2,609; 0.001 FDR: 2,275
2:55:26.929657 PROGRESS: 
2:55:26.929712 PROGRESS: Protein Summary:
2:55:26.932023 PROGRESS: Channel   0:	 0.050 FDR: 2,033; 0.010 FDR: 2,033; 0.001 FDR: 1,802
2:55:26.932118 PROGRESS: =========================================================================
2:55:26.932493 INFO: Target number of precursors reached.
2:55:26.958313 INFO: fragments_df: keeping 5000 of 117190 [sum(precursor_idx_mask)=58101 sum(mass_error_mask)=117190 stop_rank=5000
2:55:26.969469 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:27.293541 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:27.942375 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:27.942835 INFO: Using score_cutoff 10.018473328399658 (fac=0.99, q=1)
2:55:27.943141 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:27.943215 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:27.943267 INFO: Updating optimization_manager: score_cutoff        : 9.833437130355835 -> 10.018473328399658
2:55:27.943320 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:27.947252 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:27.955171 INFO: === checking if optimization conditions were reached ===
2:55:27.955293 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:55:27.958234 INFO: Updating optimization_manager: rt_error            : 281.59082027276355 -> 291.9505988887882
2:55:27.958335 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 291.9506.
2:55:27.958399 INFO: ==============================================
2:55:27.958466 INFO: Starting optimization step 7.
2:55:27.958530 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:55:27.958590 INFO: Using rust extraction backend
2:55:27.958644 PROGRESS: Extracting batch of 5956 precursors
2:55:27.969904 INFO: === Search parameters used ===
2:55:27.970024 INFO: rt_error       : 291.9505988887882
2:55:27.970077 INFO: mobility_error : 0.1
2:55:27.970122 INFO: num_candidates : 3
2:55:27.970163 INFO: ms1_error      : 30
2:55:27.970203 INFO: ms2_error      : 10.0
2:55:27.970242 INFO: fwhm_rt        : 3.0
2:55:27.970280 INFO: quant_window   : 3
2:55:27.970318 INFO: ==============================================
2:55:28.080667 INFO: performing precursor FDR with 40 features
2:55:28.080782 INFO: Decoy channel: -1
2:55:28.080810 INFO: competitive: True
2:55:28.085527 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:28.089662 INFO: Estimating optimal hyperparameters - samples: 14,279, batch_size: 128, learning_rate: 1.77e-04
2:55:28.089793 INFO: Using random state 849362 for train-test-split
2:55:29.515226 INFO: Test AUC: 0.757
2:55:29.515314 INFO: Train AUC: 0.782
2:55:29.515345 INFO: AUC difference: 3.14%
2:55:29.770852 INFO: Resetting torch num_threads to 24
2:55:29.773359 PROGRESS: === Extracted 17849 precursors and 117388 fragments ===
2:55:29.773730 INFO: === FDR correction performed with classifier version 6 ===
2:55:29.774439 PROGRESS: ============================= Precursor FDR =============================
2:55:29.774528 PROGRESS: Total precursors accumulated: 2,628
2:55:29.774596 PROGRESS: Target precursors: 2,602 (99.01%)
2:55:29.774648 PROGRESS: Decoy precursors: 26 (0.99%)
2:55:29.774693 PROGRESS: 
2:55:29.774738 PROGRESS: Precursor Summary:
2:55:29.776365 PROGRESS: Channel   0:	 0.050 FDR: 2,602; 0.010 FDR: 2,602; 0.001 FDR: 2,182
2:55:29.776466 PROGRESS: 
2:55:29.776523 PROGRESS: Protein Summary:
2:55:29.778766 PROGRESS: Channel   0:	 0.050 FDR: 2,026; 0.010 FDR: 2,026; 0.001 FDR: 1,734
2:55:29.778855 PROGRESS: =========================================================================
2:55:29.779232 INFO: Target number of precursors reached.
2:55:29.805555 INFO: fragments_df: keeping 5000 of 117388 [sum(precursor_idx_mask)=58146 sum(mass_error_mask)=117388 stop_rank=5000
2:55:29.816763 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:30.129081 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:30.777183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:30.777659 INFO: Using score_cutoff 10.18540925731659 (fac=0.99, q=1)
2:55:30.777978 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:30.778056 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:30.778112 INFO: Updating optimization_manager: score_cutoff        : 10.018473328399658 -> 10.18540925731659
2:55:30.778174 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:30.782115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:30.790120 INFO: === checking if optimization conditions were reached ===
2:55:30.790236 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:55:30.790995 INFO: Updating optimization_manager: rt_error            : 291.9505988887882 -> 290.70391735132023
2:55:30.791112 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:55:30.791212 INFO: Updating optimization_manager: score_cutoff        : 10.18540925731659 -> 9.847551741600036
2:55:30.791297 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:30.791377 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:30.791464 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 290.7039 found after 8 searches.
2:55:30.791529 INFO: ==============================================
2:55:30.791598 PROGRESS: Optimization finished for rt_error.
2:55:30.802148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:30.806007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:30.813944 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:55:30.814050 PROGRESS: ==============================================
2:55:30.814118 PROGRESS: ms2_error      : 10.0000
2:55:30.814170 PROGRESS: rt_error       : 290.7039
2:55:30.814214 PROGRESS: ==============================================
2:55:30.814806 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:30.952979 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:31.320697 INFO: Using rust extraction backend
2:55:31.320959 PROGRESS: Extracting batch of 262809 precursors
2:55:31.748733 INFO: === Search parameters used ===
2:55:31.749017 INFO: rt_error       : 290.70391735132023
2:55:31.749076 INFO: mobility_error : 0.1
2:55:31.749134 INFO: num_candidates : 3
2:55:31.749180 INFO: ms1_error      : 30
2:55:31.749221 INFO: ms2_error      : 10.0
2:55:31.749260 INFO: fwhm_rt        : 3.0
2:55:31.749298 INFO: quant_window   : 3
2:55:31.749336 INFO: ==============================================
2:55:32.486183 INFO: Removed 100909 precursors with score below cutoff 9.847551741600036
2:55:33.158602 INFO: performing precursor FDR with 40 features
2:55:33.158724 INFO: Decoy channel: -1
2:55:33.158748 INFO: competitive: True
2:55:33.215399 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:33.252444 WARNING: FDR calculation for 364287 target and 323231 decoy PSMs
2:55:33.252580 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:55:33.428181 INFO: Estimating optimal hyperparameters - samples: 550,014, batch_size: 2,252, learning_rate: 7.41e-04
2:55:33.429733 INFO: Using random state 505670 for train-test-split
2:55:44.160951 INFO: Test AUC: 0.777
2:55:44.161085 INFO: Train AUC: 0.782
2:55:44.161122 INFO: AUC difference: 0.57%
2:55:44.686698 INFO: Resetting torch num_threads to 24
2:55:44.986023 PROGRESS: ============================= Precursor FDR =============================
2:55:44.986309 PROGRESS: Total precursors accumulated: 121,834
2:55:44.986380 PROGRESS: Target precursors: 120,628 (99.01%)
2:55:44.986436 PROGRESS: Decoy precursors: 1,206 (0.99%)
2:55:44.986487 PROGRESS: 
2:55:44.986535 PROGRESS: Precursor Summary:
2:55:45.023018 PROGRESS: Channel   0:	 0.050 FDR: 120,628; 0.010 FDR: 120,628; 0.001 FDR: 104,412
2:55:45.023274 PROGRESS: 
2:55:45.023340 PROGRESS: Protein Summary:
2:55:45.082340 PROGRESS: Channel   0:	 0.050 FDR: 10,358; 0.010 FDR: 10,358; 0.001 FDR: 10,122
2:55:45.082599 PROGRESS: =========================================================================
2:55:45.084891 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
2:55:45.296120 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
2:55:45.587635 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:55:45.814954 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
2:55:45.815105 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:55:45.815194 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
2:55:45.815356 INFO: Initializing TimingManager
2:55:45.815859 INFO: Initializing RawFileManager
2:55:59.200670 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.
2:55:59.208366 INFO: Determining DIA cycle
2:55:59.224913 INFO: Found cycle with start 0.00 min and length 300.
2:55:59.389348 INFO: RT (min)            : 0.0 - 26.9
2:55:59.389445 INFO: RT duration (sec)   : 1611.2
2:55:59.389474 INFO: RT duration (min)   : 26.9
2:55:59.389497 INFO: Cycle len (scans)   : 300
2:55:59.389516 INFO: Cycle len (sec)     : 1.65
2:55:59.389535 INFO: Number of cycles    : 977
2:55:59.389555 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:55:59.389585 INFO: Creating DIA data object took: 13.573624610900879
2:56:01.132298 INFO: Creating DIA data NG object took: 1.742579460144043
2:56:01.167383 INFO: Initializing CalibrationManager
2:56:01.167690 INFO: Setting up calibration estimators ..
2:56:01.167750 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:56:01.167835 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'}' ..
2:56:01.167908 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:56:01.167959 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:56:01.168015 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}}' ..
2:56:01.168068 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:56:01.168114 INFO: Done setting up calibration estimators.
2:56:01.168325 INFO: Initializing OptimizationManager
2:56:01.168460 INFO: initial parameter: ms1_error = 30
2:56:01.168514 INFO: initial parameter: ms2_error = 30
2:56:01.168562 INFO: initial parameter: rt_error = 805.6004638671875
2:56:01.168607 INFO: initial parameter: mobility_error = 0.1
2:56:01.168650 INFO: initial parameter: num_candidates = 1
2:56:01.168691 INFO: initial parameter: fwhm_rt = 5
2:56:01.168734 INFO: initial parameter: fwhm_mobility = 0.01
2:56:01.168774 INFO: initial parameter: score_cutoff = 0
2:56:01.168815 INFO: initial parameter: classifier_version = -1
2:56:01.168883 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:56:01.169128 INFO: FDRManager: loading saved state not requested, will be initialized.
2:56:01.169163 INFO: Initializing FDRManager
2:56:01.169195 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:56:01.208695 PROGRESS: Initializing spectral library: 132,778 target precursors potentially observable (0 removed)
2:56:01.237047 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:56:01.237424 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
2:56:01.237522 PROGRESS: Starting initial search for precursors.
2:56:01.237606 INFO: Starting optimization step 0.
2:56:01.237683 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:56:01.237751 INFO: Using rust extraction backend
2:56:01.237803 PROGRESS: Extracting batch of 1980 precursors
2:56:01.242587 INFO: === Search parameters used ===
2:56:01.242693 INFO: rt_error       : 805.6004638671875
2:56:01.242745 INFO: mobility_error : 0.1
2:56:01.242791 INFO: num_candidates : 1
2:56:01.242833 INFO: ms1_error      : 30
2:56:01.242873 INFO: ms2_error      : 30
2:56:01.242914 INFO: fwhm_rt        : 5
2:56:01.242954 INFO: quant_window   : 3
2:56:01.242994 INFO: ==============================================
2:56:01.274471 INFO: performing precursor FDR with 40 features
2:56:01.274544 INFO: Decoy channel: -1
2:56:01.274567 INFO: competitive: True
2:56:01.275815 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:01.277715 INFO: Estimating optimal hyperparameters - samples: 1,581, batch_size: 128, learning_rate: 1.77e-04
2:56:01.278599 INFO: Using random state 95413 for train-test-split
2:56:01.430265 INFO: Test AUC: 0.777
2:56:01.430348 INFO: Train AUC: 0.789
2:56:01.430377 INFO: AUC difference: 1.55%
2:56:01.670170 INFO: Resetting torch num_threads to 24
2:56:01.671852 PROGRESS: === Extracted 1977 precursors and 13410 fragments ===
2:56:01.672220 INFO: === FDR correction performed with classifier version -1 ===
2:56:01.672711 PROGRESS: ============================= Precursor FDR =============================
2:56:01.672792 PROGRESS: Total precursors accumulated: 345
2:56:01.672848 PROGRESS: Target precursors: 342 (99.13%)
2:56:01.672896 PROGRESS: Decoy precursors: 3 (0.87%)
2:56:01.672939 PROGRESS: 
2:56:01.672980 PROGRESS: Precursor Summary:
2:56:01.674029 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   342; 0.001 FDR:   303
2:56:01.674111 PROGRESS: 
2:56:01.674163 PROGRESS: Protein Summary:
2:56:01.675384 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   287
2:56:01.675484 PROGRESS: =========================================================================
2:56:01.675692 INFO: Target number of precursors not reached yet.
2:56:01.683336 INFO: Starting optimization step 1.
2:56:01.683443 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:56:01.683560 INFO: Using rust extraction backend
2:56:01.683619 PROGRESS: Extracting batch of 3976 precursors
2:56:01.691620 INFO: === Search parameters used ===
2:56:01.691723 INFO: rt_error       : 805.6004638671875
2:56:01.691773 INFO: mobility_error : 0.1
2:56:01.691817 INFO: num_candidates : 1
2:56:01.691857 INFO: ms1_error      : 30
2:56:01.691897 INFO: ms2_error      : 30
2:56:01.691937 INFO: fwhm_rt        : 5
2:56:01.691978 INFO: quant_window   : 3
2:56:01.692016 INFO: ==============================================
2:56:01.754707 INFO: performing precursor FDR with 40 features
2:56:01.754801 INFO: Decoy channel: -1
2:56:01.754824 INFO: competitive: True
2:56:01.760254 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:01.762559 INFO: Estimating optimal hyperparameters - samples: 4,757, batch_size: 128, learning_rate: 1.77e-04
2:56:01.762640 INFO: Using random state 983051 for train-test-split
2:56:02.227031 INFO: Test AUC: 0.820
2:56:02.227115 INFO: Train AUC: 0.836
2:56:02.227144 INFO: AUC difference: 1.94%
2:56:02.476833 INFO: Resetting torch num_threads to 24
2:56:02.479891 PROGRESS: === Extracted 5947 precursors and 40641 fragments ===
2:56:02.480274 INFO: === FDR correction performed with classifier version -1 ===
2:56:02.480882 PROGRESS: ============================= Precursor FDR =============================
2:56:02.480967 PROGRESS: Total precursors accumulated: 1,494
2:56:02.481023 PROGRESS: Target precursors: 1,480 (99.06%)
2:56:02.481071 PROGRESS: Decoy precursors: 14 (0.94%)
2:56:02.481115 PROGRESS: 
2:56:02.481157 PROGRESS: Precursor Summary:
2:56:02.482479 PROGRESS: Channel   0:	 0.050 FDR: 1,480; 0.010 FDR: 1,480; 0.001 FDR:   823
2:56:02.482564 PROGRESS: 
2:56:02.482618 PROGRESS: Protein Summary:
2:56:02.484343 PROGRESS: Channel   0:	 0.050 FDR: 1,242; 0.010 FDR: 1,242; 0.001 FDR:   722
2:56:02.484437 PROGRESS: =========================================================================
2:56:02.484708 INFO: Target number of precursors reached.
2:56:02.493376 INFO: fragments_df: keeping 5000 of 40641 [sum(precursor_idx_mask)=15326 sum(mass_error_mask)=40641 stop_rank=5000
2:56:02.503938 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:02.740890 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:03.465868 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:56:03.466326 INFO: Using score_cutoff 12.534228490161896 (fac=0.99, q=1)
2:56:03.466645 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:56:03.466720 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:56:03.466773 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.534228490161896
2:56:03.466824 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:03.470757 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:03.478596 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:56:03.478699 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:56:03.478776 INFO: Starting optimization step 2.
2:56:03.478839 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:03.478901 INFO: Using rust extraction backend
2:56:03.478955 PROGRESS: Extracting batch of 5956 precursors
2:56:03.490286 INFO: === Search parameters used ===
2:56:03.490407 INFO: rt_error       : 805.6004638671875
2:56:03.490458 INFO: mobility_error : 0.1
2:56:03.490500 INFO: num_candidates : 3
2:56:03.490541 INFO: ms1_error      : 30
2:56:03.490580 INFO: ms2_error      : 30
2:56:03.490620 INFO: fwhm_rt        : 3.0
2:56:03.490658 INFO: quant_window   : 3
2:56:03.490696 INFO: ==============================================
2:56:03.614092 INFO: performing precursor FDR with 40 features
2:56:03.614200 INFO: Decoy channel: -1
2:56:03.614223 INFO: competitive: True
2:56:03.619159 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:03.623276 INFO: Estimating optimal hyperparameters - samples: 14,256, batch_size: 128, learning_rate: 1.77e-04
2:56:03.623405 INFO: Using random state 121861 for train-test-split
2:56:05.045148 INFO: Test AUC: 0.689
2:56:05.045276 INFO: Train AUC: 0.716
2:56:05.045306 INFO: AUC difference: 3.77%
2:56:05.298586 INFO: Resetting torch num_threads to 24
2:56:05.301016 PROGRESS: === Extracted 17820 precursors and 105975 fragments ===
2:56:05.301400 INFO: === FDR correction performed with classifier version 1 ===
2:56:05.302045 PROGRESS: ============================= Precursor FDR =============================
2:56:05.302132 PROGRESS: Total precursors accumulated: 1,852
2:56:05.302198 PROGRESS: Target precursors: 1,834 (99.03%)
2:56:05.302251 PROGRESS: Decoy precursors: 18 (0.97%)
2:56:05.302298 PROGRESS: 
2:56:05.302343 PROGRESS: Precursor Summary:
2:56:05.303779 PROGRESS: Channel   0:	 0.050 FDR: 1,834; 0.010 FDR: 1,834; 0.001 FDR: 1,373
2:56:05.303875 PROGRESS: 
2:56:05.303937 PROGRESS: Protein Summary:
2:56:05.305841 PROGRESS: Channel   0:	 0.050 FDR: 1,499; 0.010 FDR: 1,499; 0.001 FDR: 1,141
2:56:05.305933 PROGRESS: =========================================================================
2:56:05.306306 INFO: Target number of precursors reached.
2:56:05.325517 INFO: fragments_df: keeping 5000 of 105975 [sum(precursor_idx_mask)=39375 sum(mass_error_mask)=105975 stop_rank=5000
2:56:05.336459 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:05.602580 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:08.154453 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:08.154929 INFO: Using score_cutoff 12.724998954963684 (fac=0.99, q=1)
2:56:08.155250 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:08.155327 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:08.155382 INFO: Updating optimization_manager: score_cutoff        : 12.534228490161896 -> 12.724998954963684
2:56:08.155435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:08.159416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:08.172724 INFO: === checking if optimization conditions were reached ===
2:56:08.174529 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:56:08.174628 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:56:08.174697 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:56:08.174759 INFO: ==============================================
2:56:08.174841 INFO: Starting optimization step 3.
2:56:08.174913 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:08.174991 INFO: Using rust extraction backend
2:56:08.175060 PROGRESS: Extracting batch of 5956 precursors
2:56:08.187347 INFO: === Search parameters used ===
2:56:08.187489 INFO: rt_error       : 805.6004638671875
2:56:08.187550 INFO: mobility_error : 0.1
2:56:08.187595 INFO: num_candidates : 3
2:56:08.187637 INFO: ms1_error      : 30
2:56:08.187677 INFO: ms2_error      : 10.0
2:56:08.187720 INFO: fwhm_rt        : 3.0
2:56:08.187760 INFO: quant_window   : 3
2:56:08.187801 INFO: ==============================================
2:56:08.314511 INFO: performing precursor FDR with 40 features
2:56:08.314623 INFO: Decoy channel: -1
2:56:08.314646 INFO: competitive: True
2:56:08.320000 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:08.324265 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:56:08.324403 INFO: Using random state 495025 for train-test-split
2:56:09.764495 INFO: Test AUC: 0.734
2:56:09.764600 INFO: Train AUC: 0.751
2:56:09.764650 INFO: AUC difference: 2.19%
2:56:10.023059 INFO: Resetting torch num_threads to 24
2:56:10.025691 PROGRESS: === Extracted 17858 precursors and 119669 fragments ===
2:56:10.026076 INFO: === FDR correction performed with classifier version 2 ===
2:56:10.026812 PROGRESS: ============================= Precursor FDR =============================
2:56:10.026898 PROGRESS: Total precursors accumulated: 2,467
2:56:10.026956 PROGRESS: Target precursors: 2,443 (99.03%)
2:56:10.027003 PROGRESS: Decoy precursors: 24 (0.97%)
2:56:10.027046 PROGRESS: 
2:56:10.027089 PROGRESS: Precursor Summary:
2:56:10.028701 PROGRESS: Channel   0:	 0.050 FDR: 2,443; 0.010 FDR: 2,443; 0.001 FDR: 1,630
2:56:10.028799 PROGRESS: 
2:56:10.028853 PROGRESS: Protein Summary:
2:56:10.031070 PROGRESS: Channel   0:	 0.050 FDR: 1,930; 0.010 FDR: 1,930; 0.001 FDR: 1,342
2:56:10.031175 PROGRESS: =========================================================================
2:56:10.031596 INFO: Target number of precursors reached.
2:56:10.057075 INFO: fragments_df: keeping 5000 of 119669 [sum(precursor_idx_mask)=55756 sum(mass_error_mask)=119669 stop_rank=5000
2:56:10.069240 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:10.423664 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:11.138621 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:11.139085 INFO: Using score_cutoff 10.193990334892273 (fac=0.99, q=1)
2:56:11.139405 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:11.139496 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:11.139554 INFO: Updating optimization_manager: score_cutoff        : 12.724998954963684 -> 10.193990334892273
2:56:11.139608 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:11.143549 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:11.150951 INFO: === checking if optimization conditions were reached ===
2:56:11.152640 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:56:11.152744 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:56:11.152816 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:56:11.152875 INFO: ==============================================
2:56:11.152939 INFO: Starting optimization step 4.
2:56:11.152996 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:11.153061 INFO: Using rust extraction backend
2:56:11.153116 PROGRESS: Extracting batch of 5956 precursors
2:56:11.164446 INFO: === Search parameters used ===
2:56:11.164581 INFO: rt_error       : 805.6004638671875
2:56:11.164632 INFO: mobility_error : 0.1
2:56:11.164679 INFO: num_candidates : 3
2:56:11.164721 INFO: ms1_error      : 30
2:56:11.164763 INFO: ms2_error      : 10.0
2:56:11.164803 INFO: fwhm_rt        : 3.0
2:56:11.164844 INFO: quant_window   : 3
2:56:11.164883 INFO: ==============================================
2:56:11.278203 INFO: performing precursor FDR with 40 features
2:56:11.278316 INFO: Decoy channel: -1
2:56:11.278341 INFO: competitive: True
2:56:11.283419 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:11.287513 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:56:11.287641 INFO: Using random state 758270 for train-test-split
2:56:12.709155 INFO: Test AUC: 0.735
2:56:12.709302 INFO: Train AUC: 0.766
2:56:12.709333 INFO: AUC difference: 4.09%
2:56:12.965009 INFO: Resetting torch num_threads to 24
2:56:12.967657 PROGRESS: === Extracted 17858 precursors and 119683 fragments ===
2:56:12.968045 INFO: === FDR correction performed with classifier version 3 ===
2:56:12.968785 PROGRESS: ============================= Precursor FDR =============================
2:56:12.968868 PROGRESS: Total precursors accumulated: 2,532
2:56:12.968925 PROGRESS: Target precursors: 2,507 (99.01%)
2:56:12.968973 PROGRESS: Decoy precursors: 25 (0.99%)
2:56:12.969016 PROGRESS: 
2:56:12.969098 PROGRESS: Precursor Summary:
2:56:12.970660 PROGRESS: Channel   0:	 0.050 FDR: 2,507; 0.010 FDR: 2,507; 0.001 FDR: 1,601
2:56:12.970752 PROGRESS: 
2:56:12.970805 PROGRESS: Protein Summary:
2:56:12.973020 PROGRESS: Channel   0:	 0.050 FDR: 1,975; 0.010 FDR: 1,975; 0.001 FDR: 1,322
2:56:12.973121 PROGRESS: =========================================================================
2:56:12.973515 INFO: Target number of precursors reached.
2:56:12.999521 INFO: fragments_df: keeping 5000 of 119683 [sum(precursor_idx_mask)=56949 sum(mass_error_mask)=119683 stop_rank=5000
2:56:13.010593 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:13.372860 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:14.089365 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:14.089832 INFO: Using score_cutoff 10.0100337392807 (fac=0.99, q=1)
2:56:14.090152 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:14.090227 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:14.090280 INFO: Updating optimization_manager: score_cutoff        : 10.193990334892273 -> 10.0100337392807
2:56:14.090332 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:14.094275 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:14.101680 INFO: === checking if optimization conditions were reached ===
2:56:14.103362 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:56:14.103471 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:56:14.103543 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:56:14.103601 INFO: ==============================================
2:56:14.103665 INFO: Starting optimization step 5.
2:56:14.103720 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:14.103777 INFO: Using rust extraction backend
2:56:14.103829 PROGRESS: Extracting batch of 5956 precursors
2:56:14.115211 INFO: === Search parameters used ===
2:56:14.115348 INFO: rt_error       : 805.6004638671875
2:56:14.115399 INFO: mobility_error : 0.1
2:56:14.115444 INFO: num_candidates : 3
2:56:14.115501 INFO: ms1_error      : 30
2:56:14.115541 INFO: ms2_error      : 10.0
2:56:14.115581 INFO: fwhm_rt        : 3.0
2:56:14.115619 INFO: quant_window   : 3
2:56:14.115658 INFO: ==============================================
2:56:14.225435 INFO: performing precursor FDR with 40 features
2:56:14.225548 INFO: Decoy channel: -1
2:56:14.225584 INFO: competitive: True
2:56:14.230710 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:14.234757 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:56:14.234894 INFO: Using random state 434248 for train-test-split
2:56:15.664876 INFO: Test AUC: 0.748
2:56:15.664986 INFO: Train AUC: 0.773
2:56:15.665016 INFO: AUC difference: 3.21%
2:56:15.923206 INFO: Resetting torch num_threads to 24
2:56:15.925926 PROGRESS: === Extracted 17858 precursors and 119690 fragments ===
2:56:15.926295 INFO: === FDR correction performed with classifier version 4 ===
2:56:15.927058 PROGRESS: ============================= Precursor FDR =============================
2:56:15.927149 PROGRESS: Total precursors accumulated: 2,595
2:56:15.927209 PROGRESS: Target precursors: 2,570 (99.04%)
2:56:15.927269 PROGRESS: Decoy precursors: 25 (0.96%)
2:56:15.927319 PROGRESS: 
2:56:15.927365 PROGRESS: Precursor Summary:
2:56:15.929005 PROGRESS: Channel   0:	 0.050 FDR: 2,570; 0.010 FDR: 2,570; 0.001 FDR: 1,542
2:56:15.929108 PROGRESS: 
2:56:15.929164 PROGRESS: Protein Summary:
2:56:15.931417 PROGRESS: Channel   0:	 0.050 FDR: 2,016; 0.010 FDR: 2,016; 0.001 FDR: 1,279
2:56:15.931530 PROGRESS: =========================================================================
2:56:15.931920 INFO: Target number of precursors reached.
2:56:15.958086 INFO: fragments_df: keeping 5000 of 119690 [sum(precursor_idx_mask)=58142 sum(mass_error_mask)=119690 stop_rank=5000
2:56:15.969083 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:16.337864 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:17.053673 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:17.054142 INFO: Using score_cutoff 9.653204921436311 (fac=0.99, q=1)
2:56:17.054462 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:17.054542 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:17.054599 INFO: Updating optimization_manager: score_cutoff        : 10.0100337392807 -> 9.653204921436311
2:56:17.054653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:17.058583 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:17.065948 INFO: === checking if optimization conditions were reached ===
2:56:17.067633 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:56:17.067734 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:56:17.067799 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:56:17.067858 INFO: ==============================================
2:56:17.067923 INFO: Starting optimization step 6.
2:56:17.067982 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:17.068042 INFO: Using rust extraction backend
2:56:17.068098 PROGRESS: Extracting batch of 5956 precursors
2:56:17.079419 INFO: === Search parameters used ===
2:56:17.079566 INFO: rt_error       : 805.6004638671875
2:56:17.079619 INFO: mobility_error : 0.1
2:56:17.079665 INFO: num_candidates : 3
2:56:17.079709 INFO: ms1_error      : 30
2:56:17.079752 INFO: ms2_error      : 10.0
2:56:17.079794 INFO: fwhm_rt        : 3.0
2:56:17.079834 INFO: quant_window   : 3
2:56:17.079876 INFO: ==============================================
2:56:17.185280 INFO: performing precursor FDR with 40 features
2:56:17.185391 INFO: Decoy channel: -1
2:56:17.185416 INFO: competitive: True
2:56:17.190533 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:17.194759 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:56:17.194891 INFO: Using random state 298054 for train-test-split
2:56:18.625557 INFO: Test AUC: 0.757
2:56:18.625688 INFO: Train AUC: 0.781
2:56:18.625717 INFO: AUC difference: 3.11%
2:56:18.887733 INFO: Resetting torch num_threads to 24
2:56:18.890517 PROGRESS: === Extracted 17858 precursors and 119723 fragments ===
2:56:18.890913 INFO: === FDR correction performed with classifier version 5 ===
2:56:18.891759 PROGRESS: ============================= Precursor FDR =============================
2:56:18.891864 PROGRESS: Total precursors accumulated: 2,647
2:56:18.891933 PROGRESS: Target precursors: 2,621 (99.02%)
2:56:18.891984 PROGRESS: Decoy precursors: 26 (0.98%)
2:56:18.892027 PROGRESS: 
2:56:18.892068 PROGRESS: Precursor Summary:
2:56:18.893719 PROGRESS: Channel   0:	 0.050 FDR: 2,621; 0.010 FDR: 2,621; 0.001 FDR: 1,782
2:56:18.893816 PROGRESS: 
2:56:18.893868 PROGRESS: Protein Summary:
2:56:18.896133 PROGRESS: Channel   0:	 0.050 FDR: 2,052; 0.010 FDR: 2,052; 0.001 FDR: 1,460
2:56:18.896230 PROGRESS: =========================================================================
2:56:18.896616 INFO: Target number of precursors reached.
2:56:18.923143 INFO: fragments_df: keeping 5000 of 119723 [sum(precursor_idx_mask)=59184 sum(mass_error_mask)=119723 stop_rank=5000
2:56:18.934206 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:19.308579 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:20.029811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:20.030265 INFO: Using score_cutoff 9.637092996597291 (fac=0.99, q=1)
2:56:20.030588 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:20.030663 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:20.030715 INFO: Updating optimization_manager: score_cutoff        : 9.653204921436311 -> 9.637092996597291
2:56:20.030766 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:20.034730 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:20.042624 INFO: === checking if optimization conditions were reached ===
2:56:20.044302 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:56:20.044403 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:56:20.044464 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:56:20.044518 INFO: ==============================================
2:56:20.044586 PROGRESS: Optimization finished for ms2_error.
2:56:20.055156 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:20.058926 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:20.066760 INFO: Starting optimization step 0.
2:56:20.066878 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:20.066953 INFO: Using rust extraction backend
2:56:20.067016 PROGRESS: Extracting batch of 5956 precursors
2:56:20.078570 INFO: === Search parameters used ===
2:56:20.078712 INFO: rt_error       : 805.6004638671875
2:56:20.078767 INFO: mobility_error : 0.1
2:56:20.078812 INFO: num_candidates : 3
2:56:20.078854 INFO: ms1_error      : 30
2:56:20.078895 INFO: ms2_error      : 10.0
2:56:20.078935 INFO: fwhm_rt        : 3.0
2:56:20.078975 INFO: quant_window   : 3
2:56:20.079014 INFO: ==============================================
2:56:20.200050 INFO: performing precursor FDR with 40 features
2:56:20.200197 INFO: Decoy channel: -1
2:56:20.200231 INFO: competitive: True
2:56:20.206393 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:20.210707 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:56:20.210846 INFO: Using random state 878889 for train-test-split
2:56:21.568219 INFO: Test AUC: 0.757
2:56:21.568322 INFO: Train AUC: 0.792
2:56:21.568352 INFO: AUC difference: 4.43%
2:56:21.827134 INFO: Resetting torch num_threads to 24
2:56:21.829762 PROGRESS: === Extracted 17858 precursors and 119735 fragments ===
2:56:21.830129 INFO: === FDR correction performed with classifier version 6 ===
2:56:21.830851 PROGRESS: ============================= Precursor FDR =============================
2:56:21.830938 PROGRESS: Total precursors accumulated: 2,687
2:56:21.831000 PROGRESS: Target precursors: 2,661 (99.03%)
2:56:21.831051 PROGRESS: Decoy precursors: 26 (0.97%)
2:56:21.831098 PROGRESS: 
2:56:21.831145 PROGRESS: Precursor Summary:
2:56:21.832752 PROGRESS: Channel   0:	 0.050 FDR: 2,661; 0.010 FDR: 2,661; 0.001 FDR: 1,717
2:56:21.832850 PROGRESS: 
2:56:21.832915 PROGRESS: Protein Summary:
2:56:21.835189 PROGRESS: Channel   0:	 0.050 FDR: 2,083; 0.010 FDR: 2,083; 0.001 FDR: 1,412
2:56:21.835284 PROGRESS: =========================================================================
2:56:21.835697 INFO: Target number of precursors reached.
2:56:21.862642 INFO: fragments_df: keeping 5000 of 119735 [sum(precursor_idx_mask)=59905 sum(mass_error_mask)=119735 stop_rank=5000
2:56:21.873696 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:22.256367 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:22.974144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:22.974618 INFO: Using score_cutoff 9.596387638092041 (fac=0.99, q=1)
2:56:22.974933 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:22.975018 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:22.975074 INFO: Updating optimization_manager: score_cutoff        : 9.637092996597291 -> 9.596387638092041
2:56:22.975127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:22.979077 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:22.986876 INFO: === checking if optimization conditions were reached ===
2:56:22.987007 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:56:22.989816 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 579.7788214551357
2:56:22.989919 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 579.7788.
2:56:22.989982 INFO: ==============================================
2:56:22.990048 INFO: Starting optimization step 1.
2:56:22.990108 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:22.990169 INFO: Using rust extraction backend
2:56:22.990224 PROGRESS: Extracting batch of 5956 precursors
2:56:23.001601 INFO: === Search parameters used ===
2:56:23.001725 INFO: rt_error       : 579.7788214551357
2:56:23.001777 INFO: mobility_error : 0.1
2:56:23.001837 INFO: num_candidates : 3
2:56:23.001879 INFO: ms1_error      : 30
2:56:23.001920 INFO: ms2_error      : 10.0
2:56:23.001962 INFO: fwhm_rt        : 3.0
2:56:23.002006 INFO: quant_window   : 3
2:56:23.002046 INFO: ==============================================
2:56:23.109929 INFO: performing precursor FDR with 40 features
2:56:23.110043 INFO: Decoy channel: -1
2:56:23.110067 INFO: competitive: True
2:56:23.115271 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:23.119751 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:56:23.119894 INFO: Using random state 878889 for train-test-split
2:56:24.541854 INFO: Test AUC: 0.766
2:56:24.541970 INFO: Train AUC: 0.789
2:56:24.541999 INFO: AUC difference: 2.86%
2:56:24.799939 INFO: Resetting torch num_threads to 24
2:56:24.802545 PROGRESS: === Extracted 17857 precursors and 119689 fragments ===
2:56:24.802911 INFO: === FDR correction performed with classifier version 6 ===
2:56:24.803640 PROGRESS: ============================= Precursor FDR =============================
2:56:24.803730 PROGRESS: Total precursors accumulated: 2,671
2:56:24.803789 PROGRESS: Target precursors: 2,645 (99.03%)
2:56:24.803837 PROGRESS: Decoy precursors: 26 (0.97%)
2:56:24.803881 PROGRESS: 
2:56:24.803923 PROGRESS: Precursor Summary:
2:56:24.805529 PROGRESS: Channel   0:	 0.050 FDR: 2,645; 0.010 FDR: 2,645; 0.001 FDR: 1,661
2:56:24.805620 PROGRESS: 
2:56:24.805676 PROGRESS: Protein Summary:
2:56:24.807904 PROGRESS: Channel   0:	 0.050 FDR: 2,067; 0.010 FDR: 2,067; 0.001 FDR: 1,369
2:56:24.807996 PROGRESS: =========================================================================
2:56:24.808386 INFO: Target number of precursors reached.
2:56:24.834970 INFO: fragments_df: keeping 5000 of 119689 [sum(precursor_idx_mask)=59473 sum(mass_error_mask)=119689 stop_rank=5000
2:56:24.846457 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:25.226764 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:25.941085 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:25.941576 INFO: Using score_cutoff 9.55594289932251 (fac=0.99, q=1)
2:56:25.941897 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:25.941975 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:25.942033 INFO: Updating optimization_manager: score_cutoff        : 9.596387638092041 -> 9.55594289932251
2:56:25.942088 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:25.946110 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:25.954099 INFO: === checking if optimization conditions were reached ===
2:56:25.954215 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:56:25.957119 INFO: Updating optimization_manager: rt_error            : 579.7788214551357 -> 497.0430232946943
2:56:25.957220 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 497.0430.
2:56:25.957284 INFO: ==============================================
2:56:25.957352 INFO: Starting optimization step 2.
2:56:25.957411 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:25.957483 INFO: Using rust extraction backend
2:56:25.957536 PROGRESS: Extracting batch of 5956 precursors
2:56:25.968994 INFO: === Search parameters used ===
2:56:25.969120 INFO: rt_error       : 497.0430232946943
2:56:25.969172 INFO: mobility_error : 0.1
2:56:25.969218 INFO: num_candidates : 3
2:56:25.969261 INFO: ms1_error      : 30
2:56:25.969304 INFO: ms2_error      : 10.0
2:56:25.969354 INFO: fwhm_rt        : 3.0
2:56:25.969398 INFO: quant_window   : 3
2:56:25.969438 INFO: ==============================================
2:56:26.071867 INFO: performing precursor FDR with 40 features
2:56:26.071980 INFO: Decoy channel: -1
2:56:26.072005 INFO: competitive: True
2:56:26.079328 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:26.083778 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:56:26.083925 INFO: Using random state 878889 for train-test-split
2:56:27.506791 INFO: Test AUC: 0.758
2:56:27.506902 INFO: Train AUC: 0.791
2:56:27.506931 INFO: AUC difference: 4.20%
2:56:27.764778 INFO: Resetting torch num_threads to 24
2:56:27.767462 PROGRESS: === Extracted 17857 precursors and 119535 fragments ===
2:56:27.767834 INFO: === FDR correction performed with classifier version 6 ===
2:56:27.768583 PROGRESS: ============================= Precursor FDR =============================
2:56:27.768670 PROGRESS: Total precursors accumulated: 2,693
2:56:27.768728 PROGRESS: Target precursors: 2,667 (99.03%)
2:56:27.768778 PROGRESS: Decoy precursors: 26 (0.97%)
2:56:27.768823 PROGRESS: 
2:56:27.768867 PROGRESS: Precursor Summary:
2:56:27.770532 PROGRESS: Channel   0:	 0.050 FDR: 2,667; 0.010 FDR: 2,667; 0.001 FDR: 1,951
2:56:27.770621 PROGRESS: 
2:56:27.770679 PROGRESS: Protein Summary:
2:56:27.772980 PROGRESS: Channel   0:	 0.050 FDR: 2,081; 0.010 FDR: 2,081; 0.001 FDR: 1,584
2:56:27.773077 PROGRESS: =========================================================================
2:56:27.773476 INFO: Target number of precursors reached.
2:56:27.800145 INFO: fragments_df: keeping 5000 of 119535 [sum(precursor_idx_mask)=59985 sum(mass_error_mask)=119535 stop_rank=5000
2:56:27.811475 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:28.198483 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:28.911744 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:28.912205 INFO: Using score_cutoff 9.65221847705841 (fac=0.99, q=1)
2:56:28.912517 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:28.912594 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:28.912649 INFO: Updating optimization_manager: score_cutoff        : 9.55594289932251 -> 9.65221847705841
2:56:28.912703 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:28.916677 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:28.924081 INFO: === checking if optimization conditions were reached ===
2:56:28.924198 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:56:28.927182 INFO: Updating optimization_manager: rt_error            : 497.0430232946943 -> 534.1748592976617
2:56:28.927287 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 534.1749.
2:56:28.927348 INFO: ==============================================
2:56:28.927412 INFO: Starting optimization step 3.
2:56:28.927481 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:28.927544 INFO: Using rust extraction backend
2:56:28.927596 PROGRESS: Extracting batch of 5956 precursors
2:56:28.938883 INFO: === Search parameters used ===
2:56:28.939004 INFO: rt_error       : 534.1748592976617
2:56:28.939056 INFO: mobility_error : 0.1
2:56:28.939099 INFO: num_candidates : 3
2:56:28.939147 INFO: ms1_error      : 30
2:56:28.939188 INFO: ms2_error      : 10.0
2:56:28.939227 INFO: fwhm_rt        : 3.0
2:56:28.939266 INFO: quant_window   : 3
2:56:28.939303 INFO: ==============================================
2:56:29.045854 INFO: performing precursor FDR with 40 features
2:56:29.045967 INFO: Decoy channel: -1
2:56:29.045989 INFO: competitive: True
2:56:29.053077 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:29.057354 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:56:29.057492 INFO: Using random state 878889 for train-test-split
2:56:30.485207 INFO: Test AUC: 0.768
2:56:30.485318 INFO: Train AUC: 0.786
2:56:30.485348 INFO: AUC difference: 2.30%
2:56:30.739641 INFO: Resetting torch num_threads to 24
2:56:30.742182 PROGRESS: === Extracted 17857 precursors and 119568 fragments ===
2:56:30.742546 INFO: === FDR correction performed with classifier version 6 ===
2:56:30.743248 PROGRESS: ============================= Precursor FDR =============================
2:56:30.743330 PROGRESS: Total precursors accumulated: 2,685
2:56:30.743385 PROGRESS: Target precursors: 2,659 (99.03%)
2:56:30.743433 PROGRESS: Decoy precursors: 26 (0.97%)
2:56:30.743489 PROGRESS: 
2:56:30.743535 PROGRESS: Precursor Summary:
2:56:30.745151 PROGRESS: Channel   0:	 0.050 FDR: 2,659; 0.010 FDR: 2,659; 0.001 FDR: 1,769
2:56:30.745238 PROGRESS: 
2:56:30.745291 PROGRESS: Protein Summary:
2:56:30.747548 PROGRESS: Channel   0:	 0.050 FDR: 2,077; 0.010 FDR: 2,077; 0.001 FDR: 1,456
2:56:30.747641 PROGRESS: =========================================================================
2:56:30.748023 INFO: Target number of precursors reached.
2:56:30.774747 INFO: fragments_df: keeping 5000 of 119568 [sum(precursor_idx_mask)=59752 sum(mass_error_mask)=119568 stop_rank=5000
2:56:30.785835 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:31.162444 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:31.877878 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:31.878337 INFO: Using score_cutoff 9.62012185935974 (fac=0.99, q=1)
2:56:31.878648 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:31.878725 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:31.878780 INFO: Updating optimization_manager: score_cutoff        : 9.65221847705841 -> 9.62012185935974
2:56:31.878833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:31.882755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:31.890403 INFO: === checking if optimization conditions were reached ===
2:56:31.890520 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:56:31.893492 INFO: Updating optimization_manager: rt_error            : 534.1748592976617 -> 565.9690857115036
2:56:31.893597 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 565.9691.
2:56:31.893661 INFO: ==============================================
2:56:31.893738 INFO: Starting optimization step 4.
2:56:31.893796 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:31.893854 INFO: Using rust extraction backend
2:56:31.893907 PROGRESS: Extracting batch of 5956 precursors
2:56:31.905244 INFO: === Search parameters used ===
2:56:31.905380 INFO: rt_error       : 565.9690857115036
2:56:31.905440 INFO: mobility_error : 0.1
2:56:31.905487 INFO: num_candidates : 3
2:56:31.905530 INFO: ms1_error      : 30
2:56:31.905572 INFO: ms2_error      : 10.0
2:56:31.905612 INFO: fwhm_rt        : 3.0
2:56:31.905651 INFO: quant_window   : 3
2:56:31.905691 INFO: ==============================================
2:56:32.011363 INFO: performing precursor FDR with 40 features
2:56:32.011492 INFO: Decoy channel: -1
2:56:32.011519 INFO: competitive: True
2:56:32.016548 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:32.020781 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:56:32.020920 INFO: Using random state 878889 for train-test-split
2:56:33.440480 INFO: Test AUC: 0.760
2:56:33.440593 INFO: Train AUC: 0.790
2:56:33.440622 INFO: AUC difference: 3.81%
2:56:33.694627 INFO: Resetting torch num_threads to 24
2:56:33.697212 PROGRESS: === Extracted 17857 precursors and 119625 fragments ===
2:56:33.697576 INFO: === FDR correction performed with classifier version 6 ===
2:56:33.698283 PROGRESS: ============================= Precursor FDR =============================
2:56:33.698364 PROGRESS: Total precursors accumulated: 2,673
2:56:33.698420 PROGRESS: Target precursors: 2,647 (99.03%)
2:56:33.698467 PROGRESS: Decoy precursors: 26 (0.97%)
2:56:33.698510 PROGRESS: 
2:56:33.698553 PROGRESS: Precursor Summary:
2:56:33.700168 PROGRESS: Channel   0:	 0.050 FDR: 2,647; 0.010 FDR: 2,647; 0.001 FDR: 1,716
2:56:33.700260 PROGRESS: 
2:56:33.700314 PROGRESS: Protein Summary:
2:56:33.702538 PROGRESS: Channel   0:	 0.050 FDR: 2,069; 0.010 FDR: 2,069; 0.001 FDR: 1,425
2:56:33.702627 PROGRESS: =========================================================================
2:56:33.703004 INFO: Target number of precursors reached.
2:56:33.729451 INFO: fragments_df: keeping 5000 of 119625 [sum(precursor_idx_mask)=59561 sum(mass_error_mask)=119625 stop_rank=5000
2:56:33.740465 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:34.115193 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:34.831884 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:34.832378 INFO: Using score_cutoff 9.593104833984375 (fac=0.99, q=1)
2:56:34.832691 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:34.832773 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:34.832826 INFO: Updating optimization_manager: score_cutoff        : 9.62012185935974 -> 9.593104833984375
2:56:34.832876 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:34.836856 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:34.844751 INFO: === checking if optimization conditions were reached ===
2:56:34.844868 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:56:34.847845 INFO: Updating optimization_manager: rt_error            : 565.9690857115036 -> 565.5314388052835
2:56:34.847953 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 565.5314.
2:56:34.848017 INFO: ==============================================
2:56:34.848087 INFO: Starting optimization step 5.
2:56:34.848145 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:56:34.848203 INFO: Using rust extraction backend
2:56:34.848256 PROGRESS: Extracting batch of 5956 precursors
2:56:34.859650 INFO: === Search parameters used ===
2:56:34.859769 INFO: rt_error       : 565.5314388052835
2:56:34.859821 INFO: mobility_error : 0.1
2:56:34.859866 INFO: num_candidates : 3
2:56:34.859908 INFO: ms1_error      : 30
2:56:34.859948 INFO: ms2_error      : 10.0
2:56:34.859990 INFO: fwhm_rt        : 3.0
2:56:34.860029 INFO: quant_window   : 3
2:56:34.860077 INFO: ==============================================
2:56:34.965083 INFO: performing precursor FDR with 40 features
2:56:34.965190 INFO: Decoy channel: -1
2:56:34.965216 INFO: competitive: True
2:56:34.970028 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:34.974305 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:56:34.974442 INFO: Using random state 878889 for train-test-split
2:56:36.422107 INFO: Test AUC: 0.760
2:56:36.422224 INFO: Train AUC: 0.791
2:56:36.422256 INFO: AUC difference: 3.93%
2:56:36.672768 INFO: Resetting torch num_threads to 24
2:56:36.675321 PROGRESS: === Extracted 17857 precursors and 119640 fragments ===
2:56:36.675725 INFO: === FDR correction performed with classifier version 6 ===
2:56:36.676457 PROGRESS: ============================= Precursor FDR =============================
2:56:36.676546 PROGRESS: Total precursors accumulated: 2,691
2:56:36.676607 PROGRESS: Target precursors: 2,665 (99.03%)
2:56:36.676658 PROGRESS: Decoy precursors: 26 (0.97%)
2:56:36.676707 PROGRESS: 
2:56:36.676755 PROGRESS: Precursor Summary:
2:56:36.678356 PROGRESS: Channel   0:	 0.050 FDR: 2,665; 0.010 FDR: 2,665; 0.001 FDR: 1,862
2:56:36.678451 PROGRESS: 
2:56:36.678508 PROGRESS: Protein Summary:
2:56:36.680796 PROGRESS: Channel   0:	 0.050 FDR: 2,079; 0.010 FDR: 2,079; 0.001 FDR: 1,518
2:56:36.680893 PROGRESS: =========================================================================
2:56:36.681279 INFO: Target number of precursors reached.
2:56:36.707627 INFO: fragments_df: keeping 5000 of 119640 [sum(precursor_idx_mask)=59989 sum(mass_error_mask)=119640 stop_rank=5000
2:56:36.718681 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:37.098880 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:37.816369 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:37.816823 INFO: Using score_cutoff 9.62160683670044 (fac=0.99, q=1)
2:56:37.817131 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:37.817208 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:37.817262 INFO: Updating optimization_manager: score_cutoff        : 9.593104833984375 -> 9.62160683670044
2:56:37.817315 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:37.821255 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:37.828954 INFO: === checking if optimization conditions were reached ===
2:56:37.829067 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:56:37.829804 INFO: Updating optimization_manager: rt_error            : 565.5314388052835 -> 497.0430232946943
2:56:37.829926 INFO: Updating optimization_manager: classifier_version  : 6 -> 9
2:56:37.830023 INFO: Updating optimization_manager: score_cutoff        : 9.62160683670044 -> 9.65221847705841
2:56:37.830112 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:37.830196 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:37.830290 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 497.0430 found after 6 searches.
2:56:37.830351 INFO: ==============================================
2:56:37.830420 PROGRESS: Optimization finished for rt_error.
2:56:37.840884 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:37.844682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:37.852543 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:56:37.852660 PROGRESS: ==============================================
2:56:37.852729 PROGRESS: ms2_error      : 10.0000
2:56:37.852785 PROGRESS: rt_error       : 497.0430
2:56:37.852831 PROGRESS: ==============================================
2:56:37.853396 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:37.986923 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:38.341940 INFO: Using rust extraction backend
2:56:38.342258 PROGRESS: Extracting batch of 262809 precursors
2:56:38.765667 INFO: === Search parameters used ===
2:56:38.765942 INFO: rt_error       : 497.0430232946943
2:56:38.765998 INFO: mobility_error : 0.1
2:56:38.766045 INFO: num_candidates : 3
2:56:38.766087 INFO: ms1_error      : 30
2:56:38.766128 INFO: ms2_error      : 10.0
2:56:38.766166 INFO: fwhm_rt        : 3.0
2:56:38.766216 INFO: quant_window   : 3
2:56:38.766257 INFO: ==============================================
2:56:39.816888 INFO: Removed 73507 precursors with score below cutoff 9.65221847705841
2:56:40.479308 INFO: performing precursor FDR with 40 features
2:56:40.479434 INFO: Decoy channel: -1
2:56:40.479475 INFO: competitive: True
2:56:40.536628 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:40.755869 INFO: Estimating optimal hyperparameters - samples: 571,936, batch_size: 2,342, learning_rate: 7.56e-04
2:56:40.756712 INFO: Using random state 951720 for train-test-split
2:56:52.644591 INFO: Test AUC: 0.775
2:56:52.644747 INFO: Train AUC: 0.778
2:56:52.644787 INFO: AUC difference: 0.45%
2:56:53.161430 INFO: Resetting torch num_threads to 24
2:56:53.476987 PROGRESS: ============================= Precursor FDR =============================
2:56:53.477285 PROGRESS: Total precursors accumulated: 122,331
2:56:53.477360 PROGRESS: Target precursors: 121,120 (99.01%)
2:56:53.477414 PROGRESS: Decoy precursors: 1,211 (0.99%)
2:56:53.477463 PROGRESS: 
2:56:53.477509 PROGRESS: Precursor Summary:
2:56:53.514978 PROGRESS: Channel   0:	 0.050 FDR: 121,120; 0.010 FDR: 121,120; 0.001 FDR: 107,442
2:56:53.515239 PROGRESS: 
2:56:53.515303 PROGRESS: Protein Summary:
2:56:53.575117 PROGRESS: Channel   0:	 0.050 FDR: 10,357; 0.010 FDR: 10,357; 0.001 FDR: 10,168
2:56:53.575376 PROGRESS: =========================================================================
2:56:53.578209 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
2:56:53.773773 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
2:56:54.067523 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:56:54.224877 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
2:56:54.225031 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:56:54.225117 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
2:56:54.225279 INFO: Initializing TimingManager
2:56:54.225708 INFO: Initializing RawFileManager
2:57:10.859088 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.
2:57:10.868826 INFO: Determining DIA cycle
2:57:10.885111 INFO: Found cycle with start 0.00 min and length 300.
2:57:12.546344 INFO: RT (min)            : 0.0 - 26.9
2:57:12.546448 INFO: RT duration (sec)   : 1611.2
2:57:12.546478 INFO: RT duration (min)   : 26.9
2:57:12.546504 INFO: Cycle len (scans)   : 300
2:57:12.546525 INFO: Cycle len (sec)     : 1.65
2:57:12.546545 INFO: Number of cycles    : 977
2:57:12.546565 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:57:12.546610 INFO: Creating DIA data object took: 18.320801258087158
2:57:15.913735 INFO: Creating DIA data NG object took: 3.3669843673706055
2:57:15.948257 INFO: Initializing CalibrationManager
2:57:15.948554 INFO: Setting up calibration estimators ..
2:57:15.948614 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:57:15.948703 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'}' ..
2:57:15.948805 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:57:15.948857 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:57:15.948912 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}}' ..
2:57:15.948966 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:57:15.949011 INFO: Done setting up calibration estimators.
2:57:15.949202 INFO: Initializing OptimizationManager
2:57:15.949326 INFO: initial parameter: ms1_error = 30
2:57:15.949378 INFO: initial parameter: ms2_error = 30
2:57:15.949424 INFO: initial parameter: rt_error = 805.5982666015625
2:57:15.949467 INFO: initial parameter: mobility_error = 0.1
2:57:15.949507 INFO: initial parameter: num_candidates = 1
2:57:15.949547 INFO: initial parameter: fwhm_rt = 5
2:57:15.949587 INFO: initial parameter: fwhm_mobility = 0.01
2:57:15.949627 INFO: initial parameter: score_cutoff = 0
2:57:15.949666 INFO: initial parameter: classifier_version = -1
2:57:15.949737 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:57:15.950014 INFO: FDRManager: loading saved state not requested, will be initialized.
2:57:15.950050 INFO: Initializing FDRManager
2:57:15.950082 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:57:15.989056 PROGRESS: Initializing spectral library: 132,778 target precursors potentially observable (0 removed)
2:57:16.014313 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:57:16.014693 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
2:57:16.014791 PROGRESS: Starting initial search for precursors.
2:57:16.014874 INFO: Starting optimization step 0.
2:57:16.014937 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:57:16.015000 INFO: Using rust extraction backend
2:57:16.015062 PROGRESS: Extracting batch of 1980 precursors
2:57:16.020001 INFO: === Search parameters used ===
2:57:16.020115 INFO: rt_error       : 805.5982666015625
2:57:16.020171 INFO: mobility_error : 0.1
2:57:16.020222 INFO: num_candidates : 1
2:57:16.020267 INFO: ms1_error      : 30
2:57:16.020309 INFO: ms2_error      : 30
2:57:16.020351 INFO: fwhm_rt        : 5
2:57:16.020393 INFO: quant_window   : 3
2:57:16.020434 INFO: ==============================================
2:57:16.063302 INFO: performing precursor FDR with 40 features
2:57:16.063381 INFO: Decoy channel: -1
2:57:16.063406 INFO: competitive: True
2:57:16.064746 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:16.066681 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
2:57:16.067559 INFO: Using random state 37656 for train-test-split
2:57:16.217405 INFO: Test AUC: 0.783
2:57:16.217491 INFO: Train AUC: 0.797
2:57:16.217520 INFO: AUC difference: 1.75%
2:57:16.461082 INFO: Resetting torch num_threads to 24
2:57:16.462750 PROGRESS: === Extracted 1975 precursors and 13651 fragments ===
2:57:16.463109 INFO: === FDR correction performed with classifier version -1 ===
2:57:16.463630 PROGRESS: ============================= Precursor FDR =============================
2:57:16.463718 PROGRESS: Total precursors accumulated: 340
2:57:16.463775 PROGRESS: Target precursors: 337 (99.12%)
2:57:16.463824 PROGRESS: Decoy precursors: 3 (0.88%)
2:57:16.463868 PROGRESS: 
2:57:16.463911 PROGRESS: Precursor Summary:
2:57:16.464950 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   337; 0.001 FDR:   210
2:57:16.465032 PROGRESS: 
2:57:16.465086 PROGRESS: Protein Summary:
2:57:16.466293 PROGRESS: Channel   0:	 0.050 FDR:   319; 0.010 FDR:   319; 0.001 FDR:   201
2:57:16.466376 PROGRESS: =========================================================================
2:57:16.466589 INFO: Target number of precursors not reached yet.
2:57:16.474303 INFO: Starting optimization step 1.
2:57:16.474428 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:57:16.474500 INFO: Using rust extraction backend
2:57:16.474555 PROGRESS: Extracting batch of 3976 precursors
2:57:16.482583 INFO: === Search parameters used ===
2:57:16.482682 INFO: rt_error       : 805.5982666015625
2:57:16.482738 INFO: mobility_error : 0.1
2:57:16.482784 INFO: num_candidates : 1
2:57:16.482826 INFO: ms1_error      : 30
2:57:16.482866 INFO: ms2_error      : 30
2:57:16.482906 INFO: fwhm_rt        : 5
2:57:16.482945 INFO: quant_window   : 3
2:57:16.482984 INFO: ==============================================
2:57:16.554459 INFO: performing precursor FDR with 40 features
2:57:16.554556 INFO: Decoy channel: -1
2:57:16.554580 INFO: competitive: True
2:57:16.558625 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:16.560935 INFO: Estimating optimal hyperparameters - samples: 4,757, batch_size: 128, learning_rate: 1.77e-04
2:57:16.561018 INFO: Using random state 328978 for train-test-split
2:57:17.026412 INFO: Test AUC: 0.834
2:57:17.026521 INFO: Train AUC: 0.831
2:57:17.026552 INFO: AUC difference: 0.35%
2:57:17.280890 INFO: Resetting torch num_threads to 24
2:57:17.284039 PROGRESS: === Extracted 5947 precursors and 40890 fragments ===
2:57:17.284429 INFO: === FDR correction performed with classifier version -1 ===
2:57:17.285051 PROGRESS: ============================= Precursor FDR =============================
2:57:17.285134 PROGRESS: Total precursors accumulated: 1,595
2:57:17.285190 PROGRESS: Target precursors: 1,580 (99.06%)
2:57:17.285238 PROGRESS: Decoy precursors: 15 (0.94%)
2:57:17.285283 PROGRESS: 
2:57:17.285325 PROGRESS: Precursor Summary:
2:57:17.286667 PROGRESS: Channel   0:	 0.050 FDR: 1,580; 0.010 FDR: 1,580; 0.001 FDR:   802
2:57:17.286752 PROGRESS: 
2:57:17.286806 PROGRESS: Protein Summary:
2:57:17.288556 PROGRESS: Channel   0:	 0.050 FDR: 1,307; 0.010 FDR: 1,307; 0.001 FDR:   714
2:57:17.288650 PROGRESS: =========================================================================
2:57:17.288929 INFO: Target number of precursors reached.
2:57:17.297861 INFO: fragments_df: keeping 5000 of 40890 [sum(precursor_idx_mask)=16248 sum(mass_error_mask)=40890 stop_rank=5000
2:57:17.308559 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:17.552931 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:18.269635 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:57:18.270097 INFO: Using score_cutoff 12.568509710025788 (fac=0.99, q=1)
2:57:18.270418 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:57:18.270497 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:57:18.270562 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.568509710025788
2:57:18.270620 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:18.274522 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:18.282624 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:57:18.282737 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:57:18.282816 INFO: Starting optimization step 2.
2:57:18.282885 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:18.282950 INFO: Using rust extraction backend
2:57:18.283006 PROGRESS: Extracting batch of 5956 precursors
2:57:18.294419 INFO: === Search parameters used ===
2:57:18.294548 INFO: rt_error       : 805.5982666015625
2:57:18.294600 INFO: mobility_error : 0.1
2:57:18.294645 INFO: num_candidates : 3
2:57:18.294688 INFO: ms1_error      : 30
2:57:18.294729 INFO: ms2_error      : 30
2:57:18.294770 INFO: fwhm_rt        : 3.0
2:57:18.294811 INFO: quant_window   : 3
2:57:18.294851 INFO: ==============================================
2:57:18.408300 INFO: performing precursor FDR with 40 features
2:57:18.408412 INFO: Decoy channel: -1
2:57:18.408437 INFO: competitive: True
2:57:18.413298 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:18.417458 INFO: Estimating optimal hyperparameters - samples: 14,264, batch_size: 128, learning_rate: 1.77e-04
2:57:18.417610 INFO: Using random state 462618 for train-test-split
2:57:19.840551 INFO: Test AUC: 0.698
2:57:19.840677 INFO: Train AUC: 0.706
2:57:19.840707 INFO: AUC difference: 1.14%
2:57:20.092146 INFO: Resetting torch num_threads to 24
2:57:20.094668 PROGRESS: === Extracted 17831 precursors and 106998 fragments ===
2:57:20.095046 INFO: === FDR correction performed with classifier version 1 ===
2:57:20.095712 PROGRESS: ============================= Precursor FDR =============================
2:57:20.095802 PROGRESS: Total precursors accumulated: 2,023
2:57:20.095859 PROGRESS: Target precursors: 2,003 (99.01%)
2:57:20.095907 PROGRESS: Decoy precursors: 20 (0.99%)
2:57:20.095949 PROGRESS: 
2:57:20.095990 PROGRESS: Precursor Summary:
2:57:20.097417 PROGRESS: Channel   0:	 0.050 FDR: 2,003; 0.010 FDR: 2,003; 0.001 FDR: 1,239
2:57:20.097503 PROGRESS: 
2:57:20.097569 PROGRESS: Protein Summary:
2:57:20.099514 PROGRESS: Channel   0:	 0.050 FDR: 1,605; 0.010 FDR: 1,605; 0.001 FDR: 1,031
2:57:20.099607 PROGRESS: =========================================================================
2:57:20.099984 INFO: Target number of precursors reached.
2:57:20.119518 INFO: fragments_df: keeping 5000 of 106998 [sum(precursor_idx_mask)=42745 sum(mass_error_mask)=106998 stop_rank=5000
2:57:20.130586 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:20.386088 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:21.036227 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:21.036703 INFO: Using score_cutoff 11.763629756927491 (fac=0.99, q=1)
2:57:21.037017 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:21.037090 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:21.037150 INFO: Updating optimization_manager: score_cutoff        : 12.568509710025788 -> 11.763629756927491
2:57:21.037201 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:21.041126 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:21.049054 INFO: === checking if optimization conditions were reached ===
2:57:21.050719 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:57:21.050813 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:57:21.050875 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:57:21.050929 INFO: ==============================================
2:57:21.050998 INFO: Starting optimization step 3.
2:57:21.051054 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:21.051115 INFO: Using rust extraction backend
2:57:21.051170 PROGRESS: Extracting batch of 5956 precursors
2:57:21.062469 INFO: === Search parameters used ===
2:57:21.062601 INFO: rt_error       : 805.5982666015625
2:57:21.062653 INFO: mobility_error : 0.1
2:57:21.062697 INFO: num_candidates : 3
2:57:21.062739 INFO: ms1_error      : 30
2:57:21.062780 INFO: ms2_error      : 10.0
2:57:21.062822 INFO: fwhm_rt        : 3.0
2:57:21.062862 INFO: quant_window   : 3
2:57:21.062902 INFO: ==============================================
2:57:21.166553 INFO: performing precursor FDR with 40 features
2:57:21.166666 INFO: Decoy channel: -1
2:57:21.166690 INFO: competitive: True
2:57:21.171503 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:21.175632 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:57:21.175768 INFO: Using random state 464936 for train-test-split
2:57:22.607111 INFO: Test AUC: 0.747
2:57:22.607214 INFO: Train AUC: 0.742
2:57:22.607242 INFO: AUC difference: 0.74%
2:57:22.862680 INFO: Resetting torch num_threads to 24
2:57:22.865251 PROGRESS: === Extracted 17855 precursors and 120551 fragments ===
2:57:22.865619 INFO: === FDR correction performed with classifier version 2 ===
2:57:22.866325 PROGRESS: ============================= Precursor FDR =============================
2:57:22.866408 PROGRESS: Total precursors accumulated: 2,617
2:57:22.866471 PROGRESS: Target precursors: 2,592 (99.04%)
2:57:22.866520 PROGRESS: Decoy precursors: 25 (0.96%)
2:57:22.866565 PROGRESS: 
2:57:22.866606 PROGRESS: Precursor Summary:
2:57:22.868190 PROGRESS: Channel   0:	 0.050 FDR: 2,592; 0.010 FDR: 2,592; 0.001 FDR: 1,601
2:57:22.868281 PROGRESS: 
2:57:22.868335 PROGRESS: Protein Summary:
2:57:22.870502 PROGRESS: Channel   0:	 0.050 FDR: 2,006; 0.010 FDR: 2,006; 0.001 FDR: 1,301
2:57:22.870590 PROGRESS: =========================================================================
2:57:22.870960 INFO: Target number of precursors reached.
2:57:22.897850 INFO: fragments_df: keeping 5000 of 120551 [sum(precursor_idx_mask)=58868 sum(mass_error_mask)=120551 stop_rank=5000
2:57:22.912362 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:23.228066 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:23.909216 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:23.909702 INFO: Using score_cutoff 10.234783214950562 (fac=0.99, q=1)
2:57:23.910018 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:23.910095 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:23.910152 INFO: Updating optimization_manager: score_cutoff        : 11.763629756927491 -> 10.234783214950562
2:57:23.910206 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:23.914136 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:23.922013 INFO: === checking if optimization conditions were reached ===
2:57:23.923666 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:57:23.923766 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:57:23.923830 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:57:23.923894 INFO: ==============================================
2:57:23.923961 INFO: Starting optimization step 4.
2:57:23.924018 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:23.924078 INFO: Using rust extraction backend
2:57:23.924132 PROGRESS: Extracting batch of 5956 precursors
2:57:23.935782 INFO: === Search parameters used ===
2:57:23.935899 INFO: rt_error       : 805.5982666015625
2:57:23.935951 INFO: mobility_error : 0.1
2:57:23.935996 INFO: num_candidates : 3
2:57:23.936039 INFO: ms1_error      : 30
2:57:23.936080 INFO: ms2_error      : 10.0
2:57:23.936120 INFO: fwhm_rt        : 3.0
2:57:23.936160 INFO: quant_window   : 3
2:57:23.936200 INFO: ==============================================
2:57:24.040576 INFO: performing precursor FDR with 40 features
2:57:24.040740 INFO: Decoy channel: -1
2:57:24.040767 INFO: competitive: True
2:57:24.046896 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:24.052705 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:57:24.052876 INFO: Using random state 837710 for train-test-split
2:57:25.496439 INFO: Test AUC: 0.739
2:57:25.496548 INFO: Train AUC: 0.759
2:57:25.496586 INFO: AUC difference: 2.58%
2:57:25.751105 INFO: Resetting torch num_threads to 24
2:57:25.753653 PROGRESS: === Extracted 17855 precursors and 120576 fragments ===
2:57:25.754013 INFO: === FDR correction performed with classifier version 3 ===
2:57:25.754718 PROGRESS: ============================= Precursor FDR =============================
2:57:25.754801 PROGRESS: Total precursors accumulated: 2,633
2:57:25.754860 PROGRESS: Target precursors: 2,607 (99.01%)
2:57:25.754910 PROGRESS: Decoy precursors: 26 (0.99%)
2:57:25.754956 PROGRESS: 
2:57:25.755007 PROGRESS: Precursor Summary:
2:57:25.756577 PROGRESS: Channel   0:	 0.050 FDR: 2,607; 0.010 FDR: 2,607; 0.001 FDR: 1,603
2:57:25.756670 PROGRESS: 
2:57:25.756726 PROGRESS: Protein Summary:
2:57:25.758891 PROGRESS: Channel   0:	 0.050 FDR: 2,026; 0.010 FDR: 2,026; 0.001 FDR: 1,301
2:57:25.758984 PROGRESS: =========================================================================
2:57:25.759388 INFO: Target number of precursors reached.
2:57:25.786242 INFO: fragments_df: keeping 5000 of 120576 [sum(precursor_idx_mask)=59190 sum(mass_error_mask)=120576 stop_rank=5000
2:57:25.804271 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:26.128271 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:26.775537 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:26.776023 INFO: Using score_cutoff 10.139950033950806 (fac=0.99, q=1)
2:57:26.776340 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:26.776414 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:26.776467 INFO: Updating optimization_manager: score_cutoff        : 10.234783214950562 -> 10.139950033950806
2:57:26.776518 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:26.780451 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:26.788245 INFO: === checking if optimization conditions were reached ===
2:57:26.789892 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:57:26.789996 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:57:26.790058 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:57:26.790113 INFO: ==============================================
2:57:26.790176 INFO: Starting optimization step 5.
2:57:26.790234 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:26.790293 INFO: Using rust extraction backend
2:57:26.790344 PROGRESS: Extracting batch of 5956 precursors
2:57:26.802438 INFO: === Search parameters used ===
2:57:26.802557 INFO: rt_error       : 805.5982666015625
2:57:26.802606 INFO: mobility_error : 0.1
2:57:26.802649 INFO: num_candidates : 3
2:57:26.802690 INFO: ms1_error      : 30
2:57:26.802734 INFO: ms2_error      : 10.0
2:57:26.802773 INFO: fwhm_rt        : 3.0
2:57:26.802812 INFO: quant_window   : 3
2:57:26.802850 INFO: ==============================================
2:57:26.919518 INFO: performing precursor FDR with 40 features
2:57:26.919626 INFO: Decoy channel: -1
2:57:26.919650 INFO: competitive: True
2:57:26.924457 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:26.928501 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:57:26.928637 INFO: Using random state 24394 for train-test-split
2:57:28.350071 INFO: Test AUC: 0.755
2:57:28.350189 INFO: Train AUC: 0.769
2:57:28.350219 INFO: AUC difference: 1.89%
2:57:28.605770 INFO: Resetting torch num_threads to 24
2:57:28.608247 PROGRESS: === Extracted 17855 precursors and 120585 fragments ===
2:57:28.608622 INFO: === FDR correction performed with classifier version 4 ===
2:57:28.609330 PROGRESS: ============================= Precursor FDR =============================
2:57:28.609411 PROGRESS: Total precursors accumulated: 2,670
2:57:28.609467 PROGRESS: Target precursors: 2,644 (99.03%)
2:57:28.609515 PROGRESS: Decoy precursors: 26 (0.97%)
2:57:28.609565 PROGRESS: 
2:57:28.609609 PROGRESS: Precursor Summary:
2:57:28.611203 PROGRESS: Channel   0:	 0.050 FDR: 2,644; 0.010 FDR: 2,644; 0.001 FDR: 1,935
2:57:28.611287 PROGRESS: 
2:57:28.611340 PROGRESS: Protein Summary:
2:57:28.613577 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,056; 0.001 FDR: 1,549
2:57:28.613671 PROGRESS: =========================================================================
2:57:28.614074 INFO: Target number of precursors reached.
2:57:28.640854 INFO: fragments_df: keeping 5000 of 120585 [sum(precursor_idx_mask)=59848 sum(mass_error_mask)=120585 stop_rank=5000
2:57:28.652463 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:28.976018 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:29.630055 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:29.630520 INFO: Using score_cutoff 9.99853697605133 (fac=0.99, q=1)
2:57:29.630840 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:29.630918 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:29.630974 INFO: Updating optimization_manager: score_cutoff        : 10.139950033950806 -> 9.99853697605133
2:57:29.631040 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:29.635006 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:29.642918 INFO: === checking if optimization conditions were reached ===
2:57:29.644599 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:57:29.644700 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:57:29.644763 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:57:29.644821 INFO: ==============================================
2:57:29.644886 INFO: Starting optimization step 6.
2:57:29.644945 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:29.645011 INFO: Using rust extraction backend
2:57:29.645074 PROGRESS: Extracting batch of 5956 precursors
2:57:29.656378 INFO: === Search parameters used ===
2:57:29.656510 INFO: rt_error       : 805.5982666015625
2:57:29.656562 INFO: mobility_error : 0.1
2:57:29.656608 INFO: num_candidates : 3
2:57:29.656653 INFO: ms1_error      : 30
2:57:29.656698 INFO: ms2_error      : 10.0
2:57:29.656738 INFO: fwhm_rt        : 3.0
2:57:29.656778 INFO: quant_window   : 3
2:57:29.656817 INFO: ==============================================
2:57:29.765550 INFO: performing precursor FDR with 40 features
2:57:29.765661 INFO: Decoy channel: -1
2:57:29.765686 INFO: competitive: True
2:57:29.770297 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:29.774433 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:57:29.774569 INFO: Using random state 791528 for train-test-split
2:57:31.215829 INFO: Test AUC: 0.759
2:57:31.215941 INFO: Train AUC: 0.781
2:57:31.215971 INFO: AUC difference: 2.81%
2:57:31.471489 INFO: Resetting torch num_threads to 24
2:57:31.474001 PROGRESS: === Extracted 17857 precursors and 120604 fragments ===
2:57:31.474365 INFO: === FDR correction performed with classifier version 5 ===
2:57:31.475070 PROGRESS: ============================= Precursor FDR =============================
2:57:31.475155 PROGRESS: Total precursors accumulated: 2,692
2:57:31.475219 PROGRESS: Target precursors: 2,666 (99.03%)
2:57:31.475272 PROGRESS: Decoy precursors: 26 (0.97%)
2:57:31.475319 PROGRESS: 
2:57:31.475363 PROGRESS: Precursor Summary:
2:57:31.477039 PROGRESS: Channel   0:	 0.050 FDR: 2,666; 0.010 FDR: 2,666; 0.001 FDR: 2,280
2:57:31.477131 PROGRESS: 
2:57:31.477194 PROGRESS: Protein Summary:
2:57:31.479503 PROGRESS: Channel   0:	 0.050 FDR: 2,070; 0.010 FDR: 2,070; 0.001 FDR: 1,786
2:57:31.479602 PROGRESS: =========================================================================
2:57:31.479978 INFO: Target number of precursors reached.
2:57:31.506876 INFO: fragments_df: keeping 5000 of 120604 [sum(precursor_idx_mask)=60304 sum(mass_error_mask)=120604 stop_rank=5000
2:57:31.517838 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:31.855961 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:32.509973 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:32.510441 INFO: Using score_cutoff 10.00589531993866 (fac=0.99, q=1)
2:57:32.510751 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:32.510825 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:32.510877 INFO: Updating optimization_manager: score_cutoff        : 9.99853697605133 -> 10.00589531993866
2:57:32.510928 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:32.514884 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:32.522843 INFO: === checking if optimization conditions were reached ===
2:57:32.524503 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:57:32.524605 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:57:32.524667 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:57:32.524721 INFO: ==============================================
2:57:32.524792 PROGRESS: Optimization finished for ms2_error.
2:57:32.535352 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:32.539167 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:32.547155 INFO: Starting optimization step 0.
2:57:32.547266 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:32.547339 INFO: Using rust extraction backend
2:57:32.547397 PROGRESS: Extracting batch of 5956 precursors
2:57:32.558759 INFO: === Search parameters used ===
2:57:32.558888 INFO: rt_error       : 805.5982666015625
2:57:32.558941 INFO: mobility_error : 0.1
2:57:32.558986 INFO: num_candidates : 3
2:57:32.559028 INFO: ms1_error      : 30
2:57:32.559069 INFO: ms2_error      : 10.0
2:57:32.559108 INFO: fwhm_rt        : 3.0
2:57:32.559147 INFO: quant_window   : 3
2:57:32.559185 INFO: ==============================================
2:57:32.666144 INFO: performing precursor FDR with 40 features
2:57:32.666253 INFO: Decoy channel: -1
2:57:32.666278 INFO: competitive: True
2:57:32.671007 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:32.675058 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:57:32.675179 INFO: Using random state 409307 for train-test-split
2:57:34.105311 INFO: Test AUC: 0.769
2:57:34.105425 INFO: Train AUC: 0.788
2:57:34.105457 INFO: AUC difference: 2.40%
2:57:34.352519 INFO: Resetting torch num_threads to 24
2:57:34.355006 PROGRESS: === Extracted 17856 precursors and 120591 fragments ===
2:57:34.355366 INFO: === FDR correction performed with classifier version 6 ===
2:57:34.356131 PROGRESS: ============================= Precursor FDR =============================
2:57:34.356224 PROGRESS: Total precursors accumulated: 2,769
2:57:34.356294 PROGRESS: Target precursors: 2,742 (99.02%)
2:57:34.356348 PROGRESS: Decoy precursors: 27 (0.98%)
2:57:34.356396 PROGRESS: 
2:57:34.356442 PROGRESS: Precursor Summary:
2:57:34.358092 PROGRESS: Channel   0:	 0.050 FDR: 2,742; 0.010 FDR: 2,742; 0.001 FDR: 2,079
2:57:34.358182 PROGRESS: 
2:57:34.358238 PROGRESS: Protein Summary:
2:57:34.360617 PROGRESS: Channel   0:	 0.050 FDR: 2,121; 0.010 FDR: 2,121; 0.001 FDR: 1,651
2:57:34.360713 PROGRESS: =========================================================================
2:57:34.361067 INFO: Target number of precursors reached.
2:57:34.388121 INFO: fragments_df: keeping 5000 of 120591 [sum(precursor_idx_mask)=61682 sum(mass_error_mask)=120591 stop_rank=5000
2:57:34.399053 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:34.735393 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:35.386098 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:35.386550 INFO: Using score_cutoff 9.630510913181304 (fac=0.99, q=1)
2:57:35.386871 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:35.386972 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:35.387029 INFO: Updating optimization_manager: score_cutoff        : 10.00589531993866 -> 9.630510913181304
2:57:35.387082 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:35.391049 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:35.398865 INFO: === checking if optimization conditions were reached ===
2:57:35.398993 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:57:35.401843 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 204.6066738725497
2:57:35.401948 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 204.6067.
2:57:35.402010 INFO: ==============================================
2:57:35.402075 INFO: Starting optimization step 1.
2:57:35.402132 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:35.402193 INFO: Using rust extraction backend
2:57:35.402248 PROGRESS: Extracting batch of 5956 precursors
2:57:35.413517 INFO: === Search parameters used ===
2:57:35.413634 INFO: rt_error       : 204.6066738725497
2:57:35.413684 INFO: mobility_error : 0.1
2:57:35.413729 INFO: num_candidates : 3
2:57:35.413785 INFO: ms1_error      : 30
2:57:35.413826 INFO: ms2_error      : 10.0
2:57:35.413865 INFO: fwhm_rt        : 3.0
2:57:35.413904 INFO: quant_window   : 3
2:57:35.413948 INFO: ==============================================
2:57:35.500388 INFO: performing precursor FDR with 40 features
2:57:35.500498 INFO: Decoy channel: -1
2:57:35.500524 INFO: competitive: True
2:57:35.505268 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:35.509465 INFO: Estimating optimal hyperparameters - samples: 14,280, batch_size: 128, learning_rate: 1.77e-04
2:57:35.509598 INFO: Using random state 409307 for train-test-split
2:57:36.930170 INFO: Test AUC: 0.777
2:57:36.930277 INFO: Train AUC: 0.788
2:57:36.930306 INFO: AUC difference: 1.32%
2:57:37.177048 INFO: Resetting torch num_threads to 24
2:57:37.179603 PROGRESS: === Extracted 17850 precursors and 115991 fragments ===
2:57:37.179971 INFO: === FDR correction performed with classifier version 6 ===
2:57:37.180676 PROGRESS: ============================= Precursor FDR =============================
2:57:37.180758 PROGRESS: Total precursors accumulated: 2,787
2:57:37.180814 PROGRESS: Target precursors: 2,760 (99.03%)
2:57:37.180861 PROGRESS: Decoy precursors: 27 (0.97%)
2:57:37.180905 PROGRESS: 
2:57:37.180948 PROGRESS: Precursor Summary:
2:57:37.182606 PROGRESS: Channel   0:	 0.050 FDR: 2,760; 0.010 FDR: 2,760; 0.001 FDR: 2,377
2:57:37.182691 PROGRESS: 
2:57:37.182742 PROGRESS: Protein Summary:
2:57:37.185127 PROGRESS: Channel   0:	 0.050 FDR: 2,129; 0.010 FDR: 2,129; 0.001 FDR: 1,851
2:57:37.185222 PROGRESS: =========================================================================
2:57:37.185588 INFO: Target number of precursors reached.
2:57:37.212002 INFO: fragments_df: keeping 5000 of 115991 [sum(precursor_idx_mask)=60968 sum(mass_error_mask)=115991 stop_rank=5000
2:57:37.222945 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:37.619009 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:38.333205 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:38.333669 INFO: Using score_cutoff 9.854156540966034 (fac=0.99, q=1)
2:57:38.333992 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:38.334067 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:38.334119 INFO: Updating optimization_manager: score_cutoff        : 9.630510913181304 -> 9.854156540966034
2:57:38.334169 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:38.338120 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:38.345848 INFO: === checking if optimization conditions were reached ===
2:57:38.345963 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:57:38.348880 INFO: Updating optimization_manager: rt_error            : 204.6066738725497 -> 94.27733237943411
2:57:38.348980 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 94.2773.
2:57:38.349041 INFO: ==============================================
2:57:38.349105 INFO: Starting optimization step 2.
2:57:38.349160 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:38.349218 INFO: Using rust extraction backend
2:57:38.349270 PROGRESS: Extracting batch of 5956 precursors
2:57:38.360581 INFO: === Search parameters used ===
2:57:38.360694 INFO: rt_error       : 94.27733237943411
2:57:38.360747 INFO: mobility_error : 0.1
2:57:38.360793 INFO: num_candidates : 3
2:57:38.360837 INFO: ms1_error      : 30
2:57:38.360877 INFO: ms2_error      : 10.0
2:57:38.360925 INFO: fwhm_rt        : 3.0
2:57:38.360966 INFO: quant_window   : 3
2:57:38.361006 INFO: ==============================================
2:57:38.441924 INFO: performing precursor FDR with 40 features
2:57:38.442034 INFO: Decoy channel: -1
2:57:38.442057 INFO: competitive: True
2:57:38.446692 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:38.450795 INFO: Estimating optimal hyperparameters - samples: 14,261, batch_size: 128, learning_rate: 1.77e-04
2:57:38.450941 INFO: Using random state 409307 for train-test-split
2:57:39.862615 INFO: Test AUC: 0.786
2:57:39.862728 INFO: Train AUC: 0.793
2:57:39.862758 INFO: AUC difference: 0.91%
2:57:40.113863 INFO: Resetting torch num_threads to 24
2:57:40.116397 PROGRESS: === Extracted 17827 precursors and 109207 fragments ===
2:57:40.116758 INFO: === FDR correction performed with classifier version 6 ===
2:57:40.117475 PROGRESS: ============================= Precursor FDR =============================
2:57:40.117560 PROGRESS: Total precursors accumulated: 2,834
2:57:40.117618 PROGRESS: Target precursors: 2,806 (99.01%)
2:57:40.117669 PROGRESS: Decoy precursors: 28 (0.99%)
2:57:40.117715 PROGRESS: 
2:57:40.117759 PROGRESS: Precursor Summary:
2:57:40.119417 PROGRESS: Channel   0:	 0.050 FDR: 2,806; 0.010 FDR: 2,806; 0.001 FDR: 2,341
2:57:40.119524 PROGRESS: 
2:57:40.119583 PROGRESS: Protein Summary:
2:57:40.121943 PROGRESS: Channel   0:	 0.050 FDR: 2,161; 0.010 FDR: 2,161; 0.001 FDR: 1,831
2:57:40.122034 PROGRESS: =========================================================================
2:57:40.122398 INFO: Target number of precursors reached.
2:57:40.147508 INFO: fragments_df: keeping 5000 of 109207 [sum(precursor_idx_mask)=59650 sum(mass_error_mask)=109207 stop_rank=5000
2:57:40.158368 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:40.562052 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:41.280071 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:41.280536 INFO: Using score_cutoff 9.267468282222747 (fac=0.99, q=1)
2:57:41.280856 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:41.280935 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:41.280989 INFO: Updating optimization_manager: score_cutoff        : 9.854156540966034 -> 9.267468282222747
2:57:41.281041 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:41.284992 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:41.293014 INFO: === checking if optimization conditions were reached ===
2:57:41.293126 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:57:41.296188 INFO: Updating optimization_manager: rt_error            : 94.27733237943411 -> 74.88124459646045
2:57:41.296290 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 74.8812.
2:57:41.296352 INFO: ==============================================
2:57:41.296418 INFO: Starting optimization step 3.
2:57:41.296476 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:41.296535 INFO: Using rust extraction backend
2:57:41.296588 PROGRESS: Extracting batch of 5956 precursors
2:57:41.308008 INFO: === Search parameters used ===
2:57:41.308131 INFO: rt_error       : 74.88124459646045
2:57:41.308184 INFO: mobility_error : 0.1
2:57:41.308233 INFO: num_candidates : 3
2:57:41.308286 INFO: ms1_error      : 30
2:57:41.308330 INFO: ms2_error      : 10.0
2:57:41.308372 INFO: fwhm_rt        : 3.0
2:57:41.308412 INFO: quant_window   : 3
2:57:41.308452 INFO: ==============================================
2:57:41.393353 INFO: performing precursor FDR with 40 features
2:57:41.393466 INFO: Decoy channel: -1
2:57:41.393490 INFO: competitive: True
2:57:41.398162 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:41.402171 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
2:57:41.402302 INFO: Using random state 409307 for train-test-split
2:57:42.832686 INFO: Test AUC: 0.778
2:57:42.832794 INFO: Train AUC: 0.805
2:57:42.832824 INFO: AUC difference: 3.26%
2:57:43.084512 INFO: Resetting torch num_threads to 24
2:57:43.086995 PROGRESS: === Extracted 17816 precursors and 106613 fragments ===
2:57:43.087347 INFO: === FDR correction performed with classifier version 6 ===
2:57:43.088084 PROGRESS: ============================= Precursor FDR =============================
2:57:43.088175 PROGRESS: Total precursors accumulated: 2,843
2:57:43.088240 PROGRESS: Target precursors: 2,815 (99.02%)
2:57:43.088291 PROGRESS: Decoy precursors: 28 (0.98%)
2:57:43.088336 PROGRESS: 
2:57:43.088379 PROGRESS: Precursor Summary:
2:57:43.090049 PROGRESS: Channel   0:	 0.050 FDR: 2,815; 0.010 FDR: 2,815; 0.001 FDR: 2,285
2:57:43.090133 PROGRESS: 
2:57:43.090188 PROGRESS: Protein Summary:
2:57:43.092551 PROGRESS: Channel   0:	 0.050 FDR: 2,166; 0.010 FDR: 2,166; 0.001 FDR: 1,792
2:57:43.092646 PROGRESS: =========================================================================
2:57:43.093014 INFO: Target number of precursors reached.
2:57:43.117331 INFO: fragments_df: keeping 5000 of 106613 [sum(precursor_idx_mask)=58988 sum(mass_error_mask)=106613 stop_rank=5000
2:57:43.128145 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:43.528211 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:44.177642 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:44.178110 INFO: Using score_cutoff 9.615174446296692 (fac=0.99, q=1)
2:57:44.178416 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:44.178492 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:44.178545 INFO: Updating optimization_manager: score_cutoff        : 9.267468282222747 -> 9.615174446296692
2:57:44.178595 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:44.182548 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:44.190471 INFO: === checking if optimization conditions were reached ===
2:57:44.190583 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:57:44.193637 INFO: Updating optimization_manager: rt_error            : 74.88124459646045 -> 66.88458177385961
2:57:44.193740 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 66.8846.
2:57:44.193800 INFO: ==============================================
2:57:44.193865 INFO: Starting optimization step 4.
2:57:44.193920 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:44.193978 INFO: Using rust extraction backend
2:57:44.194030 PROGRESS: Extracting batch of 5956 precursors
2:57:44.205407 INFO: === Search parameters used ===
2:57:44.205527 INFO: rt_error       : 66.88458177385961
2:57:44.205588 INFO: mobility_error : 0.1
2:57:44.205634 INFO: num_candidates : 3
2:57:44.205676 INFO: ms1_error      : 30
2:57:44.205718 INFO: ms2_error      : 10.0
2:57:44.205759 INFO: fwhm_rt        : 3.0
2:57:44.205799 INFO: quant_window   : 3
2:57:44.205839 INFO: ==============================================
2:57:44.289033 INFO: performing precursor FDR with 40 features
2:57:44.289154 INFO: Decoy channel: -1
2:57:44.289179 INFO: competitive: True
2:57:44.293877 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:44.297855 INFO: Estimating optimal hyperparameters - samples: 14,212, batch_size: 128, learning_rate: 1.77e-04
2:57:44.298001 INFO: Using random state 409307 for train-test-split
2:57:45.719516 INFO: Test AUC: 0.791
2:57:45.719625 INFO: Train AUC: 0.805
2:57:45.719655 INFO: AUC difference: 1.68%
2:57:45.966799 INFO: Resetting torch num_threads to 24
2:57:45.969304 PROGRESS: === Extracted 17765 precursors and 105015 fragments ===
2:57:45.969668 INFO: === FDR correction performed with classifier version 6 ===
2:57:45.970381 PROGRESS: ============================= Precursor FDR =============================
2:57:45.970468 PROGRESS: Total precursors accumulated: 2,816
2:57:45.970526 PROGRESS: Target precursors: 2,789 (99.04%)
2:57:45.970575 PROGRESS: Decoy precursors: 27 (0.96%)
2:57:45.970620 PROGRESS: 
2:57:45.970665 PROGRESS: Precursor Summary:
2:57:45.972329 PROGRESS: Channel   0:	 0.050 FDR: 2,789; 0.010 FDR: 2,789; 0.001 FDR: 2,243
2:57:45.972421 PROGRESS: 
2:57:45.972477 PROGRESS: Protein Summary:
2:57:45.974824 PROGRESS: Channel   0:	 0.050 FDR: 2,149; 0.010 FDR: 2,149; 0.001 FDR: 1,765
2:57:45.974921 PROGRESS: =========================================================================
2:57:45.975292 INFO: Target number of precursors reached.
2:57:45.999815 INFO: fragments_df: keeping 5000 of 105015 [sum(precursor_idx_mask)=57781 sum(mass_error_mask)=105015 stop_rank=5000
2:57:46.010664 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:46.432648 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:47.144439 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:47.144897 INFO: Using score_cutoff 9.765721355438233 (fac=0.99, q=1)
2:57:47.145205 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:47.145280 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:47.145332 INFO: Updating optimization_manager: score_cutoff        : 9.615174446296692 -> 9.765721355438233
2:57:47.145383 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:47.149309 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:47.157344 INFO: === checking if optimization conditions were reached ===
2:57:47.157455 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:57:47.160455 INFO: Updating optimization_manager: rt_error            : 66.88458177385961 -> 54.15008347077115
2:57:47.160557 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 54.1501.
2:57:47.160619 INFO: ==============================================
2:57:47.160684 INFO: Starting optimization step 5.
2:57:47.160740 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:47.160798 INFO: Using rust extraction backend
2:57:47.160852 PROGRESS: Extracting batch of 5956 precursors
2:57:47.172145 INFO: === Search parameters used ===
2:57:47.172266 INFO: rt_error       : 54.15008347077115
2:57:47.172318 INFO: mobility_error : 0.1
2:57:47.172370 INFO: num_candidates : 3
2:57:47.172414 INFO: ms1_error      : 30
2:57:47.172454 INFO: ms2_error      : 10.0
2:57:47.172493 INFO: fwhm_rt        : 3.0
2:57:47.172532 INFO: quant_window   : 3
2:57:47.172570 INFO: ==============================================
2:57:47.252282 INFO: performing precursor FDR with 40 features
2:57:47.252392 INFO: Decoy channel: -1
2:57:47.252416 INFO: competitive: True
2:57:47.256934 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:47.260828 INFO: Estimating optimal hyperparameters - samples: 13,712, batch_size: 128, learning_rate: 1.77e-04
2:57:47.260944 INFO: Using random state 409307 for train-test-split
2:57:48.622669 INFO: Test AUC: 0.828
2:57:48.622778 INFO: Train AUC: 0.823
2:57:48.622807 INFO: AUC difference: 0.65%
2:57:48.871529 INFO: Resetting torch num_threads to 24
2:57:48.873976 PROGRESS: === Extracted 17141 precursors and 99176 fragments ===
2:57:48.874333 INFO: === FDR correction performed with classifier version 6 ===
2:57:48.875038 PROGRESS: ============================= Precursor FDR =============================
2:57:48.875124 PROGRESS: Total precursors accumulated: 2,784
2:57:48.875180 PROGRESS: Target precursors: 2,757 (99.03%)
2:57:48.875228 PROGRESS: Decoy precursors: 27 (0.97%)
2:57:48.875273 PROGRESS: 
2:57:48.875316 PROGRESS: Precursor Summary:
2:57:48.876985 PROGRESS: Channel   0:	 0.050 FDR: 2,757; 0.010 FDR: 2,757; 0.001 FDR: 2,369
2:57:48.877075 PROGRESS: 
2:57:48.877128 PROGRESS: Protein Summary:
2:57:48.879447 PROGRESS: Channel   0:	 0.050 FDR: 2,126; 0.010 FDR: 2,126; 0.001 FDR: 1,851
2:57:48.879553 PROGRESS: =========================================================================
2:57:48.879916 INFO: Target number of precursors reached.
2:57:48.902652 INFO: fragments_df: keeping 5000 of 99176 [sum(precursor_idx_mask)=54029 sum(mass_error_mask)=99176 stop_rank=5000
2:57:48.913886 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:49.308983 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:50.020769 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:50.021234 INFO: Using score_cutoff 9.909849583053589 (fac=0.99, q=1)
2:57:50.021548 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:50.021632 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:50.021687 INFO: Updating optimization_manager: score_cutoff        : 9.765721355438233 -> 9.909849583053589
2:57:50.021740 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:50.025671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:50.033629 INFO: === checking if optimization conditions were reached ===
2:57:50.033740 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:57:50.036732 INFO: Updating optimization_manager: rt_error            : 54.15008347077115 -> 41.26163253730284
2:57:50.036834 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 41.2616.
2:57:50.036899 INFO: ==============================================
2:57:50.036966 INFO: Starting optimization step 6.
2:57:50.037025 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:50.037086 INFO: Using rust extraction backend
2:57:50.037148 PROGRESS: Extracting batch of 5956 precursors
2:57:50.048429 INFO: === Search parameters used ===
2:57:50.048541 INFO: rt_error       : 41.26163253730284
2:57:50.048603 INFO: mobility_error : 0.1
2:57:50.048647 INFO: num_candidates : 3
2:57:50.048689 INFO: ms1_error      : 30
2:57:50.048731 INFO: ms2_error      : 10.0
2:57:50.048771 INFO: fwhm_rt        : 3.0
2:57:50.048810 INFO: quant_window   : 3
2:57:50.048853 INFO: ==============================================
2:57:50.131112 INFO: performing precursor FDR with 40 features
2:57:50.131223 INFO: Decoy channel: -1
2:57:50.131247 INFO: competitive: True
2:57:50.135595 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:50.139304 INFO: Estimating optimal hyperparameters - samples: 13,047, batch_size: 128, learning_rate: 1.77e-04
2:57:50.139408 INFO: Using random state 409307 for train-test-split
2:57:51.445184 INFO: Test AUC: 0.834
2:57:51.445285 INFO: Train AUC: 0.841
2:57:51.445313 INFO: AUC difference: 0.82%
2:57:51.690940 INFO: Resetting torch num_threads to 24
2:57:51.693376 PROGRESS: === Extracted 16309 precursors and 94014 fragments ===
2:57:51.693734 INFO: === FDR correction performed with classifier version 6 ===
2:57:51.694438 PROGRESS: ============================= Precursor FDR =============================
2:57:51.694520 PROGRESS: Total precursors accumulated: 2,795
2:57:51.694575 PROGRESS: Target precursors: 2,768 (99.03%)
2:57:51.694623 PROGRESS: Decoy precursors: 27 (0.97%)
2:57:51.694666 PROGRESS: 
2:57:51.694710 PROGRESS: Precursor Summary:
2:57:51.696352 PROGRESS: Channel   0:	 0.050 FDR: 2,768; 0.010 FDR: 2,768; 0.001 FDR: 2,323
2:57:51.696442 PROGRESS: 
2:57:51.696494 PROGRESS: Protein Summary:
2:57:51.698810 PROGRESS: Channel   0:	 0.050 FDR: 2,133; 0.010 FDR: 2,133; 0.001 FDR: 1,816
2:57:51.698904 PROGRESS: =========================================================================
2:57:51.699245 INFO: Target number of precursors reached.
2:57:51.721026 INFO: fragments_df: keeping 5000 of 94014 [sum(precursor_idx_mask)=51267 sum(mass_error_mask)=94014 stop_rank=5000
2:57:51.731882 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:52.129782 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:52.842809 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:52.843276 INFO: Using score_cutoff 9.802517493438721 (fac=0.99, q=1)
2:57:52.843601 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:52.843682 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:52.843735 INFO: Updating optimization_manager: score_cutoff        : 9.909849583053589 -> 9.802517493438721
2:57:52.843787 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:52.847714 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:52.855621 INFO: === checking if optimization conditions were reached ===
2:57:52.855733 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:57:52.858713 INFO: Updating optimization_manager: rt_error            : 41.26163253730284 -> 33.63535833445299
2:57:52.858812 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 33.6354.
2:57:52.858873 INFO: ==============================================
2:57:52.858945 INFO: Starting optimization step 7.
2:57:52.859006 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:52.859065 INFO: Using rust extraction backend
2:57:52.859117 PROGRESS: Extracting batch of 5956 precursors
2:57:52.870352 INFO: === Search parameters used ===
2:57:52.870465 INFO: rt_error       : 33.63535833445299
2:57:52.870515 INFO: mobility_error : 0.1
2:57:52.870559 INFO: num_candidates : 3
2:57:52.870601 INFO: ms1_error      : 30
2:57:52.870642 INFO: ms2_error      : 10.0
2:57:52.870681 INFO: fwhm_rt        : 3.0
2:57:52.870720 INFO: quant_window   : 3
2:57:52.870759 INFO: ==============================================
2:57:52.949229 INFO: performing precursor FDR with 40 features
2:57:52.949342 INFO: Decoy channel: -1
2:57:52.949365 INFO: competitive: True
2:57:52.953660 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:52.957485 INFO: Estimating optimal hyperparameters - samples: 13,047, batch_size: 128, learning_rate: 1.77e-04
2:57:52.957605 INFO: Using random state 409307 for train-test-split
2:57:54.236589 INFO: Test AUC: 0.834
2:57:54.236695 INFO: Train AUC: 0.840
2:57:54.236724 INFO: AUC difference: 0.77%
2:57:54.481730 INFO: Resetting torch num_threads to 24
2:57:54.484197 PROGRESS: === Extracted 16309 precursors and 94030 fragments ===
2:57:54.484564 INFO: === FDR correction performed with classifier version 6 ===
2:57:54.485286 PROGRESS: ============================= Precursor FDR =============================
2:57:54.485369 PROGRESS: Total precursors accumulated: 2,804
2:57:54.485425 PROGRESS: Target precursors: 2,777 (99.04%)
2:57:54.485472 PROGRESS: Decoy precursors: 27 (0.96%)
2:57:54.485516 PROGRESS: 
2:57:54.485558 PROGRESS: Precursor Summary:
2:57:54.487235 PROGRESS: Channel   0:	 0.050 FDR: 2,777; 0.010 FDR: 2,777; 0.001 FDR: 2,388
2:57:54.487325 PROGRESS: 
2:57:54.487384 PROGRESS: Protein Summary:
2:57:54.489751 PROGRESS: Channel   0:	 0.050 FDR: 2,136; 0.010 FDR: 2,136; 0.001 FDR: 1,864
2:57:54.489846 PROGRESS: =========================================================================
2:57:54.490186 INFO: Target number of precursors reached.
2:57:54.511856 INFO: fragments_df: keeping 5000 of 94030 [sum(precursor_idx_mask)=51443 sum(mass_error_mask)=94030 stop_rank=5000
2:57:54.522686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:54.921029 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:55.633859 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:55.634332 INFO: Using score_cutoff 9.577164128494262 (fac=0.99, q=1)
2:57:55.634645 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:55.634724 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:55.634781 INFO: Updating optimization_manager: score_cutoff        : 9.802517493438721 -> 9.577164128494262
2:57:55.634837 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:55.638751 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:55.646701 INFO: === checking if optimization conditions were reached ===
2:57:55.646823 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:57:55.649837 INFO: Updating optimization_manager: rt_error            : 33.63535833445299 -> 36.12595638015287
2:57:55.649944 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 36.1260.
2:57:55.650015 INFO: ==============================================
2:57:55.650085 INFO: Starting optimization step 8.
2:57:55.650143 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:55.650202 INFO: Using rust extraction backend
2:57:55.650257 PROGRESS: Extracting batch of 5956 precursors
2:57:55.661543 INFO: === Search parameters used ===
2:57:55.661662 INFO: rt_error       : 36.12595638015287
2:57:55.661712 INFO: mobility_error : 0.1
2:57:55.661764 INFO: num_candidates : 3
2:57:55.661808 INFO: ms1_error      : 30
2:57:55.661849 INFO: ms2_error      : 10.0
2:57:55.661891 INFO: fwhm_rt        : 3.0
2:57:55.661931 INFO: quant_window   : 3
2:57:55.661970 INFO: ==============================================
2:57:55.739625 INFO: performing precursor FDR with 40 features
2:57:55.739736 INFO: Decoy channel: -1
2:57:55.739760 INFO: competitive: True
2:57:55.744172 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:55.747891 INFO: Estimating optimal hyperparameters - samples: 13,046, batch_size: 128, learning_rate: 1.77e-04
2:57:55.748004 INFO: Using random state 409307 for train-test-split
2:57:57.019225 INFO: Test AUC: 0.828
2:57:57.019331 INFO: Train AUC: 0.842
2:57:57.019359 INFO: AUC difference: 1.71%
2:57:57.261601 INFO: Resetting torch num_threads to 24
2:57:57.264003 PROGRESS: === Extracted 16308 precursors and 94062 fragments ===
2:57:57.264364 INFO: === FDR correction performed with classifier version 6 ===
2:57:57.265088 PROGRESS: ============================= Precursor FDR =============================
2:57:57.265170 PROGRESS: Total precursors accumulated: 2,776
2:57:57.265225 PROGRESS: Target precursors: 2,749 (99.03%)
2:57:57.265273 PROGRESS: Decoy precursors: 27 (0.97%)
2:57:57.265316 PROGRESS: 
2:57:57.265357 PROGRESS: Precursor Summary:
2:57:57.267044 PROGRESS: Channel   0:	 0.050 FDR: 2,749; 0.010 FDR: 2,749; 0.001 FDR: 2,434
2:57:57.267130 PROGRESS: 
2:57:57.267181 PROGRESS: Protein Summary:
2:57:57.269517 PROGRESS: Channel   0:	 0.050 FDR: 2,120; 0.010 FDR: 2,120; 0.001 FDR: 1,900
2:57:57.269612 PROGRESS: =========================================================================
2:57:57.269949 INFO: Target number of precursors reached.
2:57:57.291588 INFO: fragments_df: keeping 5000 of 94062 [sum(precursor_idx_mask)=50973 sum(mass_error_mask)=94062 stop_rank=5000
2:57:57.302375 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:57.696210 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:58.409805 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:58.410261 INFO: Using score_cutoff 9.792237950134277 (fac=0.99, q=1)
2:57:58.410564 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:58.410637 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:58.410689 INFO: Updating optimization_manager: score_cutoff        : 9.577164128494262 -> 9.792237950134277
2:57:58.410739 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:58.414685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:58.422803 INFO: === checking if optimization conditions were reached ===
2:57:58.422915 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:57:58.425883 INFO: Updating optimization_manager: rt_error            : 36.12595638015287 -> 33.17709507470291
2:57:58.425990 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 33.1771.
2:57:58.426054 INFO: ==============================================
2:57:58.426120 INFO: Starting optimization step 9.
2:57:58.426175 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:57:58.426234 INFO: Using rust extraction backend
2:57:58.426286 PROGRESS: Extracting batch of 5956 precursors
2:57:58.437563 INFO: === Search parameters used ===
2:57:58.437690 INFO: rt_error       : 33.17709507470291
2:57:58.437740 INFO: mobility_error : 0.1
2:57:58.437784 INFO: num_candidates : 3
2:57:58.437825 INFO: ms1_error      : 30
2:57:58.437865 INFO: ms2_error      : 10.0
2:57:58.437906 INFO: fwhm_rt        : 3.0
2:57:58.437948 INFO: quant_window   : 3
2:57:58.437988 INFO: ==============================================
2:57:58.515841 INFO: performing precursor FDR with 40 features
2:57:58.515950 INFO: Decoy channel: -1
2:57:58.515974 INFO: competitive: True
2:57:58.520369 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:58.524121 INFO: Estimating optimal hyperparameters - samples: 13,051, batch_size: 128, learning_rate: 1.77e-04
2:57:58.524242 INFO: Using random state 409307 for train-test-split
2:57:59.795597 INFO: Test AUC: 0.834
2:57:59.795705 INFO: Train AUC: 0.841
2:57:59.795734 INFO: AUC difference: 0.77%
2:58:00.039736 INFO: Resetting torch num_threads to 24
2:58:00.042173 PROGRESS: === Extracted 16314 precursors and 94076 fragments ===
2:58:00.042546 INFO: === FDR correction performed with classifier version 6 ===
2:58:00.043293 PROGRESS: ============================= Precursor FDR =============================
2:58:00.043381 PROGRESS: Total precursors accumulated: 2,784
2:58:00.043442 PROGRESS: Target precursors: 2,757 (99.03%)
2:58:00.043512 PROGRESS: Decoy precursors: 27 (0.97%)
2:58:00.043569 PROGRESS: 
2:58:00.043615 PROGRESS: Precursor Summary:
2:58:00.045277 PROGRESS: Channel   0:	 0.050 FDR: 2,757; 0.010 FDR: 2,757; 0.001 FDR: 2,431
2:58:00.045366 PROGRESS: 
2:58:00.045422 PROGRESS: Protein Summary:
2:58:00.047904 PROGRESS: Channel   0:	 0.050 FDR: 2,129; 0.010 FDR: 2,129; 0.001 FDR: 1,900
2:58:00.048000 PROGRESS: =========================================================================
2:58:00.048343 INFO: Target number of precursors reached.
2:58:00.069920 INFO: fragments_df: keeping 5000 of 94076 [sum(precursor_idx_mask)=51152 sum(mass_error_mask)=94076 stop_rank=5000
2:58:00.080732 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:00.477544 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:01.189206 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:01.189664 INFO: Using score_cutoff 9.796566178894043 (fac=0.99, q=1)
2:58:01.189971 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:01.190054 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:01.190107 INFO: Updating optimization_manager: score_cutoff        : 9.792237950134277 -> 9.796566178894043
2:58:01.190160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:01.194076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:01.202057 INFO: === checking if optimization conditions were reached ===
2:58:01.202173 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:58:01.205162 INFO: Updating optimization_manager: rt_error            : 33.17709507470291 -> 36.8173701427823
2:58:01.205265 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 36.8174.
2:58:01.205330 INFO: ==============================================
2:58:01.205396 INFO: Starting optimization step 10.
2:58:01.205463 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:01.205524 INFO: Using rust extraction backend
2:58:01.205582 PROGRESS: Extracting batch of 5956 precursors
2:58:01.216921 INFO: === Search parameters used ===
2:58:01.217048 INFO: rt_error       : 36.8173701427823
2:58:01.217100 INFO: mobility_error : 0.1
2:58:01.217147 INFO: num_candidates : 3
2:58:01.217191 INFO: ms1_error      : 30
2:58:01.217233 INFO: ms2_error      : 10.0
2:58:01.217274 INFO: fwhm_rt        : 3.0
2:58:01.217315 INFO: quant_window   : 3
2:58:01.217356 INFO: ==============================================
2:58:01.300104 INFO: performing precursor FDR with 40 features
2:58:01.300213 INFO: Decoy channel: -1
2:58:01.300238 INFO: competitive: True
2:58:01.304699 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:01.308407 INFO: Estimating optimal hyperparameters - samples: 13,054, batch_size: 128, learning_rate: 1.77e-04
2:58:01.308518 INFO: Using random state 409307 for train-test-split
2:58:02.604630 INFO: Test AUC: 0.832
2:58:02.604727 INFO: Train AUC: 0.842
2:58:02.604755 INFO: AUC difference: 1.14%
2:58:02.849444 INFO: Resetting torch num_threads to 24
2:58:02.851869 PROGRESS: === Extracted 16318 precursors and 94085 fragments ===
2:58:02.852229 INFO: === FDR correction performed with classifier version 6 ===
2:58:02.852957 PROGRESS: ============================= Precursor FDR =============================
2:58:02.853040 PROGRESS: Total precursors accumulated: 2,797
2:58:02.853099 PROGRESS: Target precursors: 2,770 (99.03%)
2:58:02.853154 PROGRESS: Decoy precursors: 27 (0.97%)
2:58:02.853201 PROGRESS: 
2:58:02.853243 PROGRESS: Precursor Summary:
2:58:02.854900 PROGRESS: Channel   0:	 0.050 FDR: 2,770; 0.010 FDR: 2,770; 0.001 FDR: 2,311
2:58:02.854984 PROGRESS: 
2:58:02.855038 PROGRESS: Protein Summary:
2:58:02.857371 PROGRESS: Channel   0:	 0.050 FDR: 2,137; 0.010 FDR: 2,137; 0.001 FDR: 1,810
2:58:02.857467 PROGRESS: =========================================================================
2:58:02.857817 INFO: Target number of precursors reached.
2:58:02.879557 INFO: fragments_df: keeping 5000 of 94085 [sum(precursor_idx_mask)=51352 sum(mass_error_mask)=94085 stop_rank=5000
2:58:02.890361 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:03.269419 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:03.949387 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:03.949863 INFO: Using score_cutoff 9.859882829761505 (fac=0.99, q=1)
2:58:03.950179 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:03.950255 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:03.950308 INFO: Updating optimization_manager: score_cutoff        : 9.796566178894043 -> 9.859882829761505
2:58:03.950360 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:03.954292 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:03.962338 INFO: === checking if optimization conditions were reached ===
2:58:03.962451 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:58:03.965447 INFO: Updating optimization_manager: rt_error            : 36.8173701427823 -> 37.11235954920143
2:58:03.965551 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 37.1124.
2:58:03.965614 INFO: ==============================================
2:58:03.965681 INFO: Starting optimization step 11.
2:58:03.965738 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:03.965795 INFO: Using rust extraction backend
2:58:03.965848 PROGRESS: Extracting batch of 5956 precursors
2:58:03.977153 INFO: === Search parameters used ===
2:58:03.977265 INFO: rt_error       : 37.11235954920143
2:58:03.977316 INFO: mobility_error : 0.1
2:58:03.977360 INFO: num_candidates : 3
2:58:03.977401 INFO: ms1_error      : 30
2:58:03.977442 INFO: ms2_error      : 10.0
2:58:03.977481 INFO: fwhm_rt        : 3.0
2:58:03.977520 INFO: quant_window   : 3
2:58:03.977557 INFO: ==============================================
2:58:04.052960 INFO: performing precursor FDR with 40 features
2:58:04.053071 INFO: Decoy channel: -1
2:58:04.053095 INFO: competitive: True
2:58:04.057364 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:04.061056 INFO: Estimating optimal hyperparameters - samples: 13,050, batch_size: 128, learning_rate: 1.77e-04
2:58:04.061167 INFO: Using random state 409307 for train-test-split
2:58:05.344034 INFO: Test AUC: 0.826
2:58:05.344143 INFO: Train AUC: 0.842
2:58:05.344174 INFO: AUC difference: 1.94%
2:58:05.588017 INFO: Resetting torch num_threads to 24
2:58:05.590432 PROGRESS: === Extracted 16313 precursors and 94088 fragments ===
2:58:05.590797 INFO: === FDR correction performed with classifier version 6 ===
2:58:05.591541 PROGRESS: ============================= Precursor FDR =============================
2:58:05.591642 PROGRESS: Total precursors accumulated: 2,787
2:58:05.591702 PROGRESS: Target precursors: 2,760 (99.03%)
2:58:05.591754 PROGRESS: Decoy precursors: 27 (0.97%)
2:58:05.591800 PROGRESS: 
2:58:05.591845 PROGRESS: Precursor Summary:
2:58:05.593490 PROGRESS: Channel   0:	 0.050 FDR: 2,760; 0.010 FDR: 2,760; 0.001 FDR: 2,399
2:58:05.593579 PROGRESS: 
2:58:05.593634 PROGRESS: Protein Summary:
2:58:05.595969 PROGRESS: Channel   0:	 0.050 FDR: 2,127; 0.010 FDR: 2,127; 0.001 FDR: 1,874
2:58:05.596079 PROGRESS: =========================================================================
2:58:05.596420 INFO: Target number of precursors reached.
2:58:05.618020 INFO: fragments_df: keeping 5000 of 94088 [sum(precursor_idx_mask)=51186 sum(mass_error_mask)=94088 stop_rank=5000
2:58:05.628802 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:08.034723 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:08.750955 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:08.751420 INFO: Using score_cutoff 9.798189264678955 (fac=0.99, q=1)
2:58:08.751760 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:08.751841 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:08.751897 INFO: Updating optimization_manager: score_cutoff        : 9.859882829761505 -> 9.798189264678955
2:58:08.751951 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:08.755951 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:08.764044 INFO: === checking if optimization conditions were reached ===
2:58:08.764161 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
2:58:08.764882 INFO: Updating optimization_manager: rt_error            : 37.11235954920143 -> 74.88124459646045
2:58:08.764999 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:58:08.765090 INFO: Updating optimization_manager: score_cutoff        : 9.798189264678955 -> 9.615174446296692
2:58:08.765174 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:08.765256 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:08.765338 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 74.8812 found after 12 searches.
2:58:08.765393 INFO: ==============================================
2:58:08.765456 PROGRESS: Optimization finished for rt_error.
2:58:08.776052 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:08.779875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:08.787950 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:58:08.788064 PROGRESS: ==============================================
2:58:08.788128 PROGRESS: ms2_error      : 10.0000
2:58:08.788179 PROGRESS: rt_error       : 74.8812
2:58:08.788224 PROGRESS: ==============================================
2:58:08.788749 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:08.922306 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:09.292079 INFO: Using rust extraction backend
2:58:09.292423 PROGRESS: Extracting batch of 262809 precursors
2:58:09.716097 INFO: === Search parameters used ===
2:58:09.716367 INFO: rt_error       : 74.88124459646045
2:58:09.716424 INFO: mobility_error : 0.1
2:58:09.716472 INFO: num_candidates : 3
2:58:09.716516 INFO: ms1_error      : 30
2:58:09.716557 INFO: ms2_error      : 10.0
2:58:09.716598 INFO: fwhm_rt        : 3.0
2:58:09.716635 INFO: quant_window   : 3
2:58:09.716673 INFO: ==============================================
2:58:10.134031 INFO: Removed 225040 precursors with score below cutoff 9.615174446296692
2:58:10.705414 INFO: performing precursor FDR with 40 features
2:58:10.705537 INFO: Decoy channel: -1
2:58:10.705564 INFO: competitive: True
2:58:10.752589 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:10.780463 WARNING: FDR calculation for 321955 target and 240430 decoy PSMs
2:58:10.780596 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:58:10.922124 INFO: Estimating optimal hyperparameters - samples: 449,908, batch_size: 1,842, learning_rate: 6.71e-04
2:58:10.922874 INFO: Using random state 41252 for train-test-split
2:58:21.130253 INFO: Test AUC: 0.830
2:58:21.130404 INFO: Train AUC: 0.834
2:58:21.130437 INFO: AUC difference: 0.45%
2:58:21.581318 INFO: Resetting torch num_threads to 24
2:58:21.900477 PROGRESS: ============================= Precursor FDR =============================
2:58:21.900761 PROGRESS: Total precursors accumulated: 125,568
2:58:21.900831 PROGRESS: Target precursors: 124,325 (99.01%)
2:58:21.900884 PROGRESS: Decoy precursors: 1,243 (0.99%)
2:58:21.900933 PROGRESS: 
2:58:21.900980 PROGRESS: Precursor Summary:
2:58:21.940283 PROGRESS: Channel   0:	 0.050 FDR: 124,325; 0.010 FDR: 124,325; 0.001 FDR: 115,283
2:58:21.940540 PROGRESS: 
2:58:21.940603 PROGRESS: Protein Summary:
2:58:22.009195 PROGRESS: Channel   0:	 0.050 FDR: 10,371; 0.010 FDR: 10,371; 0.001 FDR: 10,291
2:58:22.009459 PROGRESS: =========================================================================
2:58:22.011704 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
2:58:22.212017 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
2:58:22.524024 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:58:22.642742 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
2:58:22.642895 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:58:22.642975 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
2:58:22.643147 INFO: Initializing TimingManager
2:58:22.643752 INFO: Initializing RawFileManager
2:58:39.946963 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.
2:58:39.955972 INFO: Determining DIA cycle
2:58:39.973385 INFO: Found cycle with start 0.00 min and length 300.
2:58:41.666692 INFO: RT (min)            : 0.0 - 26.9
2:58:41.666790 INFO: RT duration (sec)   : 1611.2
2:58:41.666819 INFO: RT duration (min)   : 26.9
2:58:41.666842 INFO: Cycle len (scans)   : 300
2:58:41.666862 INFO: Cycle len (sec)     : 1.65
2:58:41.666880 INFO: Number of cycles    : 977
2:58:41.666899 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:58:41.666927 INFO: Creating DIA data object took: 19.02307152748108
2:58:45.022998 INFO: Creating DIA data NG object took: 3.3559350967407227
2:58:45.050125 INFO: Initializing CalibrationManager
2:58:45.050430 INFO: Setting up calibration estimators ..
2:58:45.050492 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:58:45.050561 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'}' ..
2:58:45.050632 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:58:45.050684 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:58:45.050738 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}}' ..
2:58:45.050792 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:58:45.050839 INFO: Done setting up calibration estimators.
2:58:45.051048 INFO: Initializing OptimizationManager
2:58:45.051179 INFO: initial parameter: ms1_error = 30
2:58:45.051232 INFO: initial parameter: ms2_error = 30
2:58:45.051279 INFO: initial parameter: rt_error = 805.6002197265625
2:58:45.051324 INFO: initial parameter: mobility_error = 0.1
2:58:45.051368 INFO: initial parameter: num_candidates = 1
2:58:45.051410 INFO: initial parameter: fwhm_rt = 5
2:58:45.051452 INFO: initial parameter: fwhm_mobility = 0.01
2:58:45.051527 INFO: initial parameter: score_cutoff = 0
2:58:45.051576 INFO: initial parameter: classifier_version = -1
2:58:45.051644 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:58:45.051866 INFO: FDRManager: loading saved state not requested, will be initialized.
2:58:45.051897 INFO: Initializing FDRManager
2:58:45.051928 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:58:45.090026 PROGRESS: Initializing spectral library: 132,778 target precursors potentially observable (0 removed)
2:58:45.115058 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:58:45.115422 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
2:58:45.115529 PROGRESS: Starting initial search for precursors.
2:58:45.115615 INFO: Starting optimization step 0.
2:58:45.115678 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:58:45.115733 INFO: Using rust extraction backend
2:58:45.115792 PROGRESS: Extracting batch of 1980 precursors
2:58:45.120409 INFO: === Search parameters used ===
2:58:45.120512 INFO: rt_error       : 805.6002197265625
2:58:45.120562 INFO: mobility_error : 0.1
2:58:45.120606 INFO: num_candidates : 1
2:58:45.120649 INFO: ms1_error      : 30
2:58:45.120690 INFO: ms2_error      : 30
2:58:45.120730 INFO: fwhm_rt        : 5
2:58:45.120770 INFO: quant_window   : 3
2:58:45.120808 INFO: ==============================================
2:58:45.152720 INFO: performing precursor FDR with 40 features
2:58:45.152798 INFO: Decoy channel: -1
2:58:45.152822 INFO: competitive: True
2:58:45.154056 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:45.155835 INFO: Estimating optimal hyperparameters - samples: 1,581, batch_size: 128, learning_rate: 1.77e-04
2:58:45.156656 INFO: Using random state 457697 for train-test-split
2:58:45.308117 INFO: Test AUC: 0.788
2:58:45.308196 INFO: Train AUC: 0.801
2:58:45.308224 INFO: AUC difference: 1.55%
2:58:45.551074 INFO: Resetting torch num_threads to 24
2:58:45.552719 PROGRESS: === Extracted 1977 precursors and 13523 fragments ===
2:58:45.553080 INFO: === FDR correction performed with classifier version -1 ===
2:58:45.553572 PROGRESS: ============================= Precursor FDR =============================
2:58:45.553653 PROGRESS: Total precursors accumulated: 256
2:58:45.553710 PROGRESS: Target precursors: 254 (99.22%)
2:58:45.553758 PROGRESS: Decoy precursors: 2 (0.78%)
2:58:45.553802 PROGRESS: 
2:58:45.553843 PROGRESS: Precursor Summary:
2:58:45.554863 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   254; 0.001 FDR:   235
2:58:45.554951 PROGRESS: 
2:58:45.555007 PROGRESS: Protein Summary:
2:58:45.556208 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   221
2:58:45.556305 PROGRESS: =========================================================================
2:58:45.556501 INFO: Target number of precursors not reached yet.
2:58:45.564284 INFO: Starting optimization step 1.
2:58:45.564397 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:58:45.564468 INFO: Using rust extraction backend
2:58:45.564523 PROGRESS: Extracting batch of 3976 precursors
2:58:45.572584 INFO: === Search parameters used ===
2:58:45.572691 INFO: rt_error       : 805.6002197265625
2:58:45.572746 INFO: mobility_error : 0.1
2:58:45.572790 INFO: num_candidates : 1
2:58:45.572831 INFO: ms1_error      : 30
2:58:45.572870 INFO: ms2_error      : 30
2:58:45.572910 INFO: fwhm_rt        : 5
2:58:45.572951 INFO: quant_window   : 3
2:58:45.572990 INFO: ==============================================
2:58:45.634562 INFO: performing precursor FDR with 40 features
2:58:45.634660 INFO: Decoy channel: -1
2:58:45.634684 INFO: competitive: True
2:58:45.638958 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:45.641284 INFO: Estimating optimal hyperparameters - samples: 4,757, batch_size: 128, learning_rate: 1.77e-04
2:58:45.641397 INFO: Using random state 650596 for train-test-split
2:58:46.120821 INFO: Test AUC: 0.828
2:58:46.120934 INFO: Train AUC: 0.828
2:58:46.120964 INFO: AUC difference: 0.02%
2:58:46.369931 INFO: Resetting torch num_threads to 24
2:58:46.373141 PROGRESS: === Extracted 5947 precursors and 40803 fragments ===
2:58:46.373528 INFO: === FDR correction performed with classifier version -1 ===
2:58:46.374163 PROGRESS: ============================= Precursor FDR =============================
2:58:46.374245 PROGRESS: Total precursors accumulated: 1,373
2:58:46.374306 PROGRESS: Target precursors: 1,360 (99.05%)
2:58:46.374354 PROGRESS: Decoy precursors: 13 (0.95%)
2:58:46.374397 PROGRESS: 
2:58:46.374438 PROGRESS: Precursor Summary:
2:58:46.375794 PROGRESS: Channel   0:	 0.050 FDR: 1,360; 0.010 FDR: 1,360; 0.001 FDR: 1,079
2:58:46.375892 PROGRESS: 
2:58:46.375947 PROGRESS: Protein Summary:
2:58:46.377716 PROGRESS: Channel   0:	 0.050 FDR: 1,132; 0.010 FDR: 1,132; 0.001 FDR:   918
2:58:46.377807 PROGRESS: =========================================================================
2:58:46.378055 INFO: Target number of precursors reached.
2:58:46.386814 INFO: fragments_df: keeping 5000 of 40803 [sum(precursor_idx_mask)=14167 sum(mass_error_mask)=40803 stop_rank=5000
2:58:46.397542 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:46.629761 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:47.353365 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:58:47.353828 INFO: Using score_cutoff 12.612875008392333 (fac=0.99, q=1)
2:58:47.354152 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:58:47.354232 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:58:47.354291 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.612875008392333
2:58:47.354350 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:47.358319 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:47.366425 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:58:47.366533 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:58:47.366616 INFO: Starting optimization step 2.
2:58:47.366686 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:47.366753 INFO: Using rust extraction backend
2:58:47.366812 PROGRESS: Extracting batch of 5956 precursors
2:58:47.378228 INFO: === Search parameters used ===
2:58:47.378368 INFO: rt_error       : 805.6002197265625
2:58:47.378421 INFO: mobility_error : 0.1
2:58:47.378467 INFO: num_candidates : 3
2:58:47.378510 INFO: ms1_error      : 30
2:58:47.378552 INFO: ms2_error      : 30
2:58:47.378593 INFO: fwhm_rt        : 3.0
2:58:47.378635 INFO: quant_window   : 3
2:58:47.378676 INFO: ==============================================
2:58:47.505949 INFO: performing precursor FDR with 40 features
2:58:47.506060 INFO: Decoy channel: -1
2:58:47.506089 INFO: competitive: True
2:58:47.511060 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:47.515027 INFO: Estimating optimal hyperparameters - samples: 14,260, batch_size: 128, learning_rate: 1.77e-04
2:58:47.515155 INFO: Using random state 932021 for train-test-split
2:58:48.864228 INFO: Test AUC: 0.689
2:58:48.864345 INFO: Train AUC: 0.707
2:58:48.864375 INFO: AUC difference: 2.59%
2:58:49.113192 INFO: Resetting torch num_threads to 24
2:58:49.115705 PROGRESS: === Extracted 17826 precursors and 106511 fragments ===
2:58:49.116076 INFO: === FDR correction performed with classifier version 1 ===
2:58:49.116795 PROGRESS: ============================= Precursor FDR =============================
2:58:49.116883 PROGRESS: Total precursors accumulated: 1,780
2:58:49.116942 PROGRESS: Target precursors: 1,763 (99.04%)
2:58:49.116994 PROGRESS: Decoy precursors: 17 (0.96%)
2:58:49.117041 PROGRESS: 
2:58:49.117087 PROGRESS: Precursor Summary:
2:58:49.118582 PROGRESS: Channel   0:	 0.050 FDR: 1,763; 0.010 FDR: 1,763; 0.001 FDR: 1,249
2:58:49.118679 PROGRESS: 
2:58:49.118741 PROGRESS: Protein Summary:
2:58:49.120662 PROGRESS: Channel   0:	 0.050 FDR: 1,429; 0.010 FDR: 1,429; 0.001 FDR: 1,045
2:58:49.120760 PROGRESS: =========================================================================
2:58:49.121166 INFO: Target number of precursors reached.
2:58:49.140096 INFO: fragments_df: keeping 5000 of 106511 [sum(precursor_idx_mask)=38062 sum(mass_error_mask)=106511 stop_rank=5000
2:58:49.151379 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:49.410400 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:50.131151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:50.131634 INFO: Using score_cutoff 12.122682122612 (fac=0.99, q=1)
2:58:50.131950 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:50.132026 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:50.132078 INFO: Updating optimization_manager: score_cutoff        : 12.612875008392333 -> 12.122682122612
2:58:50.132128 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:50.136090 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:50.144287 INFO: === checking if optimization conditions were reached ===
2:58:50.146030 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
2:58:50.146124 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:58:50.146186 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:58:50.146241 INFO: ==============================================
2:58:50.146311 INFO: Starting optimization step 3.
2:58:50.146369 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:50.146427 INFO: Using rust extraction backend
2:58:50.146479 PROGRESS: Extracting batch of 5956 precursors
2:58:50.157944 INFO: === Search parameters used ===
2:58:50.158072 INFO: rt_error       : 805.6002197265625
2:58:50.158124 INFO: mobility_error : 0.1
2:58:50.158168 INFO: num_candidates : 3
2:58:50.158211 INFO: ms1_error      : 30
2:58:50.158251 INFO: ms2_error      : 10.0
2:58:50.158292 INFO: fwhm_rt        : 3.0
2:58:50.158331 INFO: quant_window   : 3
2:58:50.158369 INFO: ==============================================
2:58:50.270231 INFO: performing precursor FDR with 40 features
2:58:50.270337 INFO: Decoy channel: -1
2:58:50.270360 INFO: competitive: True
2:58:50.275530 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:50.279583 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:58:50.279706 INFO: Using random state 813050 for train-test-split
2:58:51.696297 INFO: Test AUC: 0.733
2:58:51.696395 INFO: Train AUC: 0.748
2:58:51.696424 INFO: AUC difference: 2.03%
2:58:51.962070 INFO: Resetting torch num_threads to 24
2:58:51.965050 PROGRESS: === Extracted 17855 precursors and 120420 fragments ===
2:58:51.965441 INFO: === FDR correction performed with classifier version 2 ===
2:58:51.966227 PROGRESS: ============================= Precursor FDR =============================
2:58:51.966314 PROGRESS: Total precursors accumulated: 2,432
2:58:51.966373 PROGRESS: Target precursors: 2,408 (99.01%)
2:58:51.966420 PROGRESS: Decoy precursors: 24 (0.99%)
2:58:51.966466 PROGRESS: 
2:58:51.966511 PROGRESS: Precursor Summary:
2:58:51.968221 PROGRESS: Channel   0:	 0.050 FDR: 2,408; 0.010 FDR: 2,408; 0.001 FDR: 1,471
2:58:51.968337 PROGRESS: 
2:58:51.968398 PROGRESS: Protein Summary:
2:58:51.970680 PROGRESS: Channel   0:	 0.050 FDR: 1,878; 0.010 FDR: 1,878; 0.001 FDR: 1,220
2:58:51.970771 PROGRESS: =========================================================================
2:58:51.971169 INFO: Target number of precursors reached.
2:58:52.000386 INFO: fragments_df: keeping 5000 of 120420 [sum(precursor_idx_mask)=55459 sum(mass_error_mask)=120420 stop_rank=5000
2:58:52.018714 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:52.369797 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:53.089807 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:53.090267 INFO: Using score_cutoff 11.407648925685882 (fac=0.99, q=1)
2:58:53.090592 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:53.090672 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:53.090738 INFO: Updating optimization_manager: score_cutoff        : 12.122682122612 -> 11.407648925685882
2:58:53.090799 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:53.094755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:53.102556 INFO: === checking if optimization conditions were reached ===
2:58:53.104248 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:58:53.104349 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:58:53.104414 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:58:53.104480 INFO: ==============================================
2:58:53.104547 INFO: Starting optimization step 4.
2:58:53.104604 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:53.104664 INFO: Using rust extraction backend
2:58:53.104725 PROGRESS: Extracting batch of 5956 precursors
2:58:53.116121 INFO: === Search parameters used ===
2:58:53.116262 INFO: rt_error       : 805.6002197265625
2:58:53.116316 INFO: mobility_error : 0.1
2:58:53.116362 INFO: num_candidates : 3
2:58:53.116406 INFO: ms1_error      : 30
2:58:53.116448 INFO: ms2_error      : 10.0
2:58:53.116489 INFO: fwhm_rt        : 3.0
2:58:53.116530 INFO: quant_window   : 3
2:58:53.116569 INFO: ==============================================
2:58:53.231838 INFO: performing precursor FDR with 40 features
2:58:53.231946 INFO: Decoy channel: -1
2:58:53.231971 INFO: competitive: True
2:58:53.237031 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:53.241008 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:58:53.241139 INFO: Using random state 286379 for train-test-split
2:58:54.667434 INFO: Test AUC: 0.756
2:58:54.667554 INFO: Train AUC: 0.756
2:58:54.667584 INFO: AUC difference: 0.01%
2:58:54.923892 INFO: Resetting torch num_threads to 24
2:58:54.926407 PROGRESS: === Extracted 17857 precursors and 120368 fragments ===
2:58:54.926769 INFO: === FDR correction performed with classifier version 3 ===
2:58:54.927515 PROGRESS: ============================= Precursor FDR =============================
2:58:54.927603 PROGRESS: Total precursors accumulated: 2,474
2:58:54.927661 PROGRESS: Target precursors: 2,450 (99.03%)
2:58:54.927712 PROGRESS: Decoy precursors: 24 (0.97%)
2:58:54.927757 PROGRESS: 
2:58:54.927806 PROGRESS: Precursor Summary:
2:58:54.929378 PROGRESS: Channel   0:	 0.050 FDR: 2,450; 0.010 FDR: 2,450; 0.001 FDR: 1,328
2:58:54.929466 PROGRESS: 
2:58:54.929519 PROGRESS: Protein Summary:
2:58:54.931670 PROGRESS: Channel   0:	 0.050 FDR: 1,902; 0.010 FDR: 1,902; 0.001 FDR: 1,111
2:58:54.931767 PROGRESS: =========================================================================
2:58:54.932141 INFO: Target number of precursors reached.
2:58:54.957713 INFO: fragments_df: keeping 5000 of 120368 [sum(precursor_idx_mask)=56176 sum(mass_error_mask)=120368 stop_rank=5000
2:58:54.968756 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:55.321126 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:56.039808 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:56.040269 INFO: Using score_cutoff 10.983826428222656 (fac=0.99, q=1)
2:58:56.040595 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:56.040671 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:56.040723 INFO: Updating optimization_manager: score_cutoff        : 11.407648925685882 -> 10.983826428222656
2:58:56.040774 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:56.044762 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:56.052613 INFO: === checking if optimization conditions were reached ===
2:58:56.054286 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:58:56.054389 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:58:56.054453 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:58:56.054515 INFO: ==============================================
2:58:56.054578 INFO: Starting optimization step 5.
2:58:56.054634 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:56.054691 INFO: Using rust extraction backend
2:58:56.054744 PROGRESS: Extracting batch of 5956 precursors
2:58:56.066208 INFO: === Search parameters used ===
2:58:56.066336 INFO: rt_error       : 805.6002197265625
2:58:56.066388 INFO: mobility_error : 0.1
2:58:56.066432 INFO: num_candidates : 3
2:58:56.066473 INFO: ms1_error      : 30
2:58:56.066513 INFO: ms2_error      : 10.0
2:58:56.066553 INFO: fwhm_rt        : 3.0
2:58:56.066593 INFO: quant_window   : 3
2:58:56.066634 INFO: ==============================================
2:58:56.175837 INFO: performing precursor FDR with 40 features
2:58:56.175948 INFO: Decoy channel: -1
2:58:56.175972 INFO: competitive: True
2:58:56.181032 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:56.185005 INFO: Estimating optimal hyperparameters - samples: 14,285, batch_size: 128, learning_rate: 1.77e-04
2:58:56.185130 INFO: Using random state 441137 for train-test-split
2:58:57.595797 INFO: Test AUC: 0.772
2:58:57.595909 INFO: Train AUC: 0.762
2:58:57.595940 INFO: AUC difference: 1.31%
2:58:57.855295 INFO: Resetting torch num_threads to 24
2:58:57.857846 PROGRESS: === Extracted 17857 precursors and 120367 fragments ===
2:58:57.858217 INFO: === FDR correction performed with classifier version 4 ===
2:58:57.858945 PROGRESS: ============================= Precursor FDR =============================
2:58:57.859034 PROGRESS: Total precursors accumulated: 2,533
2:58:57.859103 PROGRESS: Target precursors: 2,508 (99.01%)
2:58:57.859154 PROGRESS: Decoy precursors: 25 (0.99%)
2:58:57.859205 PROGRESS: 
2:58:57.859251 PROGRESS: Precursor Summary:
2:58:57.860905 PROGRESS: Channel   0:	 0.050 FDR: 2,508; 0.010 FDR: 2,508; 0.001 FDR: 1,637
2:58:57.861006 PROGRESS: 
2:58:57.861061 PROGRESS: Protein Summary:
2:58:57.863254 PROGRESS: Channel   0:	 0.050 FDR: 1,949; 0.010 FDR: 1,949; 0.001 FDR: 1,333
2:58:57.863349 PROGRESS: =========================================================================
2:58:57.863735 INFO: Target number of precursors reached.
2:58:57.889521 INFO: fragments_df: keeping 5000 of 120367 [sum(precursor_idx_mask)=57249 sum(mass_error_mask)=120367 stop_rank=5000
2:58:57.900539 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:58.266062 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:58.983496 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:58.983969 INFO: Using score_cutoff 10.337187907218933 (fac=0.99, q=1)
2:58:58.984291 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:58.984368 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:58.984423 INFO: Updating optimization_manager: score_cutoff        : 10.983826428222656 -> 10.337187907218933
2:58:58.984476 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:58.988466 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:58.996279 INFO: === checking if optimization conditions were reached ===
2:58:58.997969 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:58:58.998066 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:58:58.998130 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:58:58.998188 INFO: ==============================================
2:58:58.998252 INFO: Starting optimization step 6.
2:58:58.998309 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:58:58.998367 INFO: Using rust extraction backend
2:58:58.998422 PROGRESS: Extracting batch of 5956 precursors
2:58:59.009773 INFO: === Search parameters used ===
2:58:59.009893 INFO: rt_error       : 805.6002197265625
2:58:59.009945 INFO: mobility_error : 0.1
2:58:59.009990 INFO: num_candidates : 3
2:58:59.010032 INFO: ms1_error      : 30
2:58:59.010072 INFO: ms2_error      : 10.0
2:58:59.010113 INFO: fwhm_rt        : 3.0
2:58:59.010165 INFO: quant_window   : 3
2:58:59.010207 INFO: ==============================================
2:58:59.118884 INFO: performing precursor FDR with 40 features
2:58:59.118997 INFO: Decoy channel: -1
2:58:59.119022 INFO: competitive: True
2:58:59.126311 INFO: Setting torch num_threads to 2 for FDR classification task
2:58:59.130338 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:58:59.130465 INFO: Using random state 180499 for train-test-split
2:59:00.570536 INFO: Test AUC: 0.766
2:59:00.570661 INFO: Train AUC: 0.773
2:59:00.570690 INFO: AUC difference: 1.02%
2:59:00.826120 INFO: Resetting torch num_threads to 24
2:59:00.828749 PROGRESS: === Extracted 17858 precursors and 120347 fragments ===
2:59:00.829121 INFO: === FDR correction performed with classifier version 5 ===
2:59:00.829845 PROGRESS: ============================= Precursor FDR =============================
2:59:00.829931 PROGRESS: Total precursors accumulated: 2,599
2:59:00.829993 PROGRESS: Target precursors: 2,574 (99.04%)
2:59:00.830045 PROGRESS: Decoy precursors: 25 (0.96%)
2:59:00.830090 PROGRESS: 
2:59:00.830133 PROGRESS: Precursor Summary:
2:59:00.831774 PROGRESS: Channel   0:	 0.050 FDR: 2,574; 0.010 FDR: 2,574; 0.001 FDR: 1,541
2:59:00.831867 PROGRESS: 
2:59:00.831921 PROGRESS: Protein Summary:
2:59:00.834124 PROGRESS: Channel   0:	 0.050 FDR: 2,002; 0.010 FDR: 2,002; 0.001 FDR: 1,269
2:59:00.834212 PROGRESS: =========================================================================
2:59:00.834597 INFO: Target number of precursors reached.
2:59:00.861416 INFO: fragments_df: keeping 5000 of 120347 [sum(precursor_idx_mask)=58521 sum(mass_error_mask)=120347 stop_rank=5000
2:59:00.872517 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:01.245365 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:01.964115 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:01.964562 INFO: Using score_cutoff 10.284072398471832 (fac=0.99, q=1)
2:59:01.964879 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:01.964954 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:01.965006 INFO: Updating optimization_manager: score_cutoff        : 10.337187907218933 -> 10.284072398471832
2:59:01.965056 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:01.969032 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:01.976791 INFO: === checking if optimization conditions were reached ===
2:59:01.978485 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:59:01.978578 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:59:01.978640 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:59:01.978695 INFO: ==============================================
2:59:01.978756 PROGRESS: Optimization finished for ms2_error.
2:59:01.989310 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:01.993088 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:02.000804 INFO: Starting optimization step 0.
2:59:02.000917 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:02.000991 INFO: Using rust extraction backend
2:59:02.001049 PROGRESS: Extracting batch of 5956 precursors
2:59:02.012486 INFO: === Search parameters used ===
2:59:02.012605 INFO: rt_error       : 805.6002197265625
2:59:02.012658 INFO: mobility_error : 0.1
2:59:02.012702 INFO: num_candidates : 3
2:59:02.012744 INFO: ms1_error      : 30
2:59:02.012784 INFO: ms2_error      : 10.0
2:59:02.012824 INFO: fwhm_rt        : 3.0
2:59:02.012863 INFO: quant_window   : 3
2:59:02.012901 INFO: ==============================================
2:59:02.122992 INFO: performing precursor FDR with 40 features
2:59:02.123105 INFO: Decoy channel: -1
2:59:02.123129 INFO: competitive: True
2:59:02.130517 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:02.134508 INFO: Estimating optimal hyperparameters - samples: 14,286, batch_size: 128, learning_rate: 1.77e-04
2:59:02.134649 INFO: Using random state 47425 for train-test-split
2:59:03.569041 INFO: Test AUC: 0.755
2:59:03.569155 INFO: Train AUC: 0.785
2:59:03.569186 INFO: AUC difference: 3.74%
2:59:03.825442 INFO: Resetting torch num_threads to 24
2:59:03.828015 PROGRESS: === Extracted 17858 precursors and 120359 fragments ===
2:59:03.828389 INFO: === FDR correction performed with classifier version 6 ===
2:59:03.829186 PROGRESS: ============================= Precursor FDR =============================
2:59:03.829277 PROGRESS: Total precursors accumulated: 2,613
2:59:03.829338 PROGRESS: Target precursors: 2,588 (99.04%)
2:59:03.829390 PROGRESS: Decoy precursors: 25 (0.96%)
2:59:03.829437 PROGRESS: 
2:59:03.829483 PROGRESS: Precursor Summary:
2:59:03.831105 PROGRESS: Channel   0:	 0.050 FDR: 2,588; 0.010 FDR: 2,588; 0.001 FDR: 1,869
2:59:03.831200 PROGRESS: 
2:59:03.831258 PROGRESS: Protein Summary:
2:59:03.833525 PROGRESS: Channel   0:	 0.050 FDR: 2,005; 0.010 FDR: 2,005; 0.001 FDR: 1,493
2:59:03.833622 PROGRESS: =========================================================================
2:59:03.834028 INFO: Target number of precursors reached.
2:59:03.860560 INFO: fragments_df: keeping 5000 of 120359 [sum(precursor_idx_mask)=58701 sum(mass_error_mask)=120359 stop_rank=5000
2:59:03.871686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:04.253537 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:04.969430 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:04.969903 INFO: Using score_cutoff 10.142761760616303 (fac=0.99, q=1)
2:59:04.970233 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:04.970310 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:04.970370 INFO: Updating optimization_manager: score_cutoff        : 10.284072398471832 -> 10.142761760616303
2:59:04.970425 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:04.974470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:04.982424 INFO: === checking if optimization conditions were reached ===
2:59:04.982538 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:59:04.985294 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 330.99861430216663
2:59:04.985400 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 330.9986.
2:59:04.985462 INFO: ==============================================
2:59:04.985527 INFO: Starting optimization step 1.
2:59:04.985583 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:04.985641 INFO: Using rust extraction backend
2:59:04.985695 PROGRESS: Extracting batch of 5956 precursors
2:59:04.996968 INFO: === Search parameters used ===
2:59:04.997091 INFO: rt_error       : 330.99861430216663
2:59:04.997141 INFO: mobility_error : 0.1
2:59:04.997190 INFO: num_candidates : 3
2:59:04.997234 INFO: ms1_error      : 30
2:59:04.997274 INFO: ms2_error      : 10.0
2:59:04.997314 INFO: fwhm_rt        : 3.0
2:59:04.997354 INFO: quant_window   : 3
2:59:04.997402 INFO: ==============================================
2:59:05.093545 INFO: performing precursor FDR with 40 features
2:59:05.093650 INFO: Decoy channel: -1
2:59:05.093675 INFO: competitive: True
2:59:05.100962 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:05.105028 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:59:05.105159 INFO: Using random state 47425 for train-test-split
2:59:06.535543 INFO: Test AUC: 0.756
2:59:06.535672 INFO: Train AUC: 0.784
2:59:06.535703 INFO: AUC difference: 3.65%
2:59:06.789741 INFO: Resetting torch num_threads to 24
2:59:06.792348 PROGRESS: === Extracted 17856 precursors and 119102 fragments ===
2:59:06.792728 INFO: === FDR correction performed with classifier version 6 ===
2:59:06.793478 PROGRESS: ============================= Precursor FDR =============================
2:59:06.793565 PROGRESS: Total precursors accumulated: 2,639
2:59:06.793633 PROGRESS: Target precursors: 2,613 (99.01%)
2:59:06.793681 PROGRESS: Decoy precursors: 26 (0.99%)
2:59:06.793725 PROGRESS: 
2:59:06.793766 PROGRESS: Precursor Summary:
2:59:06.795419 PROGRESS: Channel   0:	 0.050 FDR: 2,613; 0.010 FDR: 2,613; 0.001 FDR: 2,108
2:59:06.795521 PROGRESS: 
2:59:06.795579 PROGRESS: Protein Summary:
2:59:06.797868 PROGRESS: Channel   0:	 0.050 FDR: 2,025; 0.010 FDR: 2,025; 0.001 FDR: 1,659
2:59:06.797964 PROGRESS: =========================================================================
2:59:06.798357 INFO: Target number of precursors reached.
2:59:06.824548 INFO: fragments_df: keeping 5000 of 119102 [sum(precursor_idx_mask)=59073 sum(mass_error_mask)=119102 stop_rank=5000
2:59:06.836507 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:07.162791 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:07.806436 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:07.806912 INFO: Using score_cutoff 10.15192483291626 (fac=0.99, q=1)
2:59:07.807240 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:07.807321 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:07.807378 INFO: Updating optimization_manager: score_cutoff        : 10.142761760616303 -> 10.15192483291626
2:59:07.807433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:07.811389 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:07.819204 INFO: === checking if optimization conditions were reached ===
2:59:07.819325 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:59:07.822191 INFO: Updating optimization_manager: rt_error            : 330.99861430216663 -> 329.9087882545248
2:59:07.822299 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 329.9088.
2:59:07.822364 INFO: ==============================================
2:59:07.822436 INFO: Starting optimization step 2.
2:59:07.822497 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:07.822562 INFO: Using rust extraction backend
2:59:07.822620 PROGRESS: Extracting batch of 5956 precursors
2:59:07.833972 INFO: === Search parameters used ===
2:59:07.834095 INFO: rt_error       : 329.9087882545248
2:59:07.834151 INFO: mobility_error : 0.1
2:59:07.834200 INFO: num_candidates : 3
2:59:07.834245 INFO: ms1_error      : 30
2:59:07.834288 INFO: ms2_error      : 10.0
2:59:07.834341 INFO: fwhm_rt        : 3.0
2:59:07.834387 INFO: quant_window   : 3
2:59:07.834429 INFO: ==============================================
2:59:07.936848 INFO: performing precursor FDR with 40 features
2:59:07.936955 INFO: Decoy channel: -1
2:59:07.936981 INFO: competitive: True
2:59:07.944040 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:07.948122 INFO: Estimating optimal hyperparameters - samples: 14,284, batch_size: 128, learning_rate: 1.77e-04
2:59:07.948272 INFO: Using random state 47425 for train-test-split
2:59:09.382147 INFO: Test AUC: 0.757
2:59:09.382261 INFO: Train AUC: 0.783
2:59:09.382290 INFO: AUC difference: 3.38%
2:59:09.640520 INFO: Resetting torch num_threads to 24
2:59:09.643118 PROGRESS: === Extracted 17855 precursors and 119102 fragments ===
2:59:09.643494 INFO: === FDR correction performed with classifier version 6 ===
2:59:09.644216 PROGRESS: ============================= Precursor FDR =============================
2:59:09.644300 PROGRESS: Total precursors accumulated: 2,660
2:59:09.644359 PROGRESS: Target precursors: 2,634 (99.02%)
2:59:09.644409 PROGRESS: Decoy precursors: 26 (0.98%)
2:59:09.644455 PROGRESS: 
2:59:09.644499 PROGRESS: Precursor Summary:
2:59:09.646087 PROGRESS: Channel   0:	 0.050 FDR: 2,634; 0.010 FDR: 2,634; 0.001 FDR: 1,612
2:59:09.646175 PROGRESS: 
2:59:09.646230 PROGRESS: Protein Summary:
2:59:09.648425 PROGRESS: Channel   0:	 0.050 FDR: 2,038; 0.010 FDR: 2,038; 0.001 FDR: 1,317
2:59:09.648520 PROGRESS: =========================================================================
2:59:09.648933 INFO: Target number of precursors reached.
2:59:09.675497 INFO: fragments_df: keeping 5000 of 119102 [sum(precursor_idx_mask)=59419 sum(mass_error_mask)=119102 stop_rank=5000
2:59:09.686720 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:10.078311 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:10.829877 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:10.830341 INFO: Using score_cutoff 10.08150367898941 (fac=0.99, q=1)
2:59:10.830659 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:10.830733 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:10.830785 INFO: Updating optimization_manager: score_cutoff        : 10.15192483291626 -> 10.08150367898941
2:59:10.830835 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:10.834779 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:10.842554 INFO: === checking if optimization conditions were reached ===
2:59:10.842671 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:59:10.845633 INFO: Updating optimization_manager: rt_error            : 329.9087882545248 -> 303.8446123107882
2:59:10.845732 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 303.8446.
2:59:10.845793 INFO: ==============================================
2:59:10.845857 INFO: Starting optimization step 3.
2:59:10.845912 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:10.845970 INFO: Using rust extraction backend
2:59:10.846023 PROGRESS: Extracting batch of 5956 precursors
2:59:10.857296 INFO: === Search parameters used ===
2:59:10.857413 INFO: rt_error       : 303.8446123107882
2:59:10.857465 INFO: mobility_error : 0.1
2:59:10.857512 INFO: num_candidates : 3
2:59:10.857565 INFO: ms1_error      : 30
2:59:10.857608 INFO: ms2_error      : 10.0
2:59:10.857648 INFO: fwhm_rt        : 3.0
2:59:10.857687 INFO: quant_window   : 3
2:59:10.857725 INFO: ==============================================
2:59:10.965008 INFO: performing precursor FDR with 40 features
2:59:10.965124 INFO: Decoy channel: -1
2:59:10.965148 INFO: competitive: True
2:59:10.972299 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:10.976240 INFO: Estimating optimal hyperparameters - samples: 14,283, batch_size: 128, learning_rate: 1.77e-04
2:59:10.976372 INFO: Using random state 47425 for train-test-split
2:59:12.061601 INFO: Test AUC: 0.766
2:59:12.061713 INFO: Train AUC: 0.783
2:59:12.061742 INFO: AUC difference: 2.12%
2:59:12.315707 INFO: Resetting torch num_threads to 24
2:59:12.318215 PROGRESS: === Extracted 17854 precursors and 118646 fragments ===
2:59:12.318581 INFO: === FDR correction performed with classifier version 6 ===
2:59:12.319279 PROGRESS: ============================= Precursor FDR =============================
2:59:12.319361 PROGRESS: Total precursors accumulated: 2,639
2:59:12.319417 PROGRESS: Target precursors: 2,613 (99.01%)
2:59:12.319478 PROGRESS: Decoy precursors: 26 (0.99%)
2:59:12.319528 PROGRESS: 
2:59:12.319571 PROGRESS: Precursor Summary:
2:59:12.321196 PROGRESS: Channel   0:	 0.050 FDR: 2,613; 0.010 FDR: 2,613; 0.001 FDR: 2,150
2:59:12.321283 PROGRESS: 
2:59:12.321336 PROGRESS: Protein Summary:
2:59:12.323618 PROGRESS: Channel   0:	 0.050 FDR: 2,025; 0.010 FDR: 2,025; 0.001 FDR: 1,684
2:59:12.323713 PROGRESS: =========================================================================
2:59:12.324084 INFO: Target number of precursors reached.
2:59:12.350384 INFO: fragments_df: keeping 5000 of 118646 [sum(precursor_idx_mask)=58882 sum(mass_error_mask)=118646 stop_rank=5000
2:59:12.361406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:12.744968 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:13.493159 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:13.493641 INFO: Using score_cutoff 10.0738403881073 (fac=0.99, q=1)
2:59:13.493948 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:13.494035 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:13.494091 INFO: Updating optimization_manager: score_cutoff        : 10.08150367898941 -> 10.0738403881073
2:59:13.494145 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:13.498133 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:13.505877 INFO: === checking if optimization conditions were reached ===
2:59:13.505986 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:59:13.508915 INFO: Updating optimization_manager: rt_error            : 303.8446123107882 -> 285.54023671796483
2:59:13.509024 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 285.5402.
2:59:13.509088 INFO: ==============================================
2:59:13.509155 INFO: Starting optimization step 4.
2:59:13.509214 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:13.509273 INFO: Using rust extraction backend
2:59:13.509328 PROGRESS: Extracting batch of 5956 precursors
2:59:13.520644 INFO: === Search parameters used ===
2:59:13.520764 INFO: rt_error       : 285.54023671796483
2:59:13.520831 INFO: mobility_error : 0.1
2:59:13.520879 INFO: num_candidates : 3
2:59:13.520922 INFO: ms1_error      : 30
2:59:13.520964 INFO: ms2_error      : 10.0
2:59:13.521004 INFO: fwhm_rt        : 3.0
2:59:13.521045 INFO: quant_window   : 3
2:59:13.521084 INFO: ==============================================
2:59:13.629864 INFO: performing precursor FDR with 40 features
2:59:13.630002 INFO: Decoy channel: -1
2:59:13.630028 INFO: competitive: True
2:59:13.635080 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:13.639333 INFO: Estimating optimal hyperparameters - samples: 14,281, batch_size: 128, learning_rate: 1.77e-04
2:59:13.639481 INFO: Using random state 47425 for train-test-split
2:59:14.943134 INFO: Test AUC: 0.769
2:59:14.943244 INFO: Train AUC: 0.783
2:59:14.943272 INFO: AUC difference: 1.74%
2:59:15.196547 INFO: Resetting torch num_threads to 24
2:59:15.199092 PROGRESS: === Extracted 17852 precursors and 118314 fragments ===
2:59:15.199483 INFO: === FDR correction performed with classifier version 6 ===
2:59:15.200209 PROGRESS: ============================= Precursor FDR =============================
2:59:15.200293 PROGRESS: Total precursors accumulated: 2,654
2:59:15.200348 PROGRESS: Target precursors: 2,628 (99.02%)
2:59:15.200396 PROGRESS: Decoy precursors: 26 (0.98%)
2:59:15.200439 PROGRESS: 
2:59:15.200480 PROGRESS: Precursor Summary:
2:59:15.202113 PROGRESS: Channel   0:	 0.050 FDR: 2,628; 0.010 FDR: 2,628; 0.001 FDR: 2,168
2:59:15.202201 PROGRESS: 
2:59:15.202254 PROGRESS: Protein Summary:
2:59:15.204524 PROGRESS: Channel   0:	 0.050 FDR: 2,030; 0.010 FDR: 2,030; 0.001 FDR: 1,699
2:59:15.204622 PROGRESS: =========================================================================
2:59:15.205018 INFO: Target number of precursors reached.
2:59:15.230909 INFO: fragments_df: keeping 5000 of 118314 [sum(precursor_idx_mask)=59119 sum(mass_error_mask)=118314 stop_rank=5000
2:59:15.241911 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:15.671430 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:16.384730 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:16.385212 INFO: Using score_cutoff 10.079314167308807 (fac=0.99, q=1)
2:59:16.385538 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:16.385611 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:16.385663 INFO: Updating optimization_manager: score_cutoff        : 10.0738403881073 -> 10.079314167308807
2:59:16.385714 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:16.389678 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:16.397024 INFO: === checking if optimization conditions were reached ===
2:59:16.397144 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:59:16.400116 INFO: Updating optimization_manager: rt_error            : 285.54023671796483 -> 248.6515927518709
2:59:16.400223 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 248.6516.
2:59:16.400284 INFO: ==============================================
2:59:16.400359 INFO: Starting optimization step 5.
2:59:16.400415 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:16.400478 INFO: Using rust extraction backend
2:59:16.400534 PROGRESS: Extracting batch of 5956 precursors
2:59:16.411825 INFO: === Search parameters used ===
2:59:16.411945 INFO: rt_error       : 248.6515927518709
2:59:16.411997 INFO: mobility_error : 0.1
2:59:16.412042 INFO: num_candidates : 3
2:59:16.412083 INFO: ms1_error      : 30
2:59:16.412124 INFO: ms2_error      : 10.0
2:59:16.412164 INFO: fwhm_rt        : 3.0
2:59:16.412204 INFO: quant_window   : 3
2:59:16.412243 INFO: ==============================================
2:59:16.516740 INFO: performing precursor FDR with 40 features
2:59:16.516852 INFO: Decoy channel: -1
2:59:16.516875 INFO: competitive: True
2:59:16.523636 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:16.527617 INFO: Estimating optimal hyperparameters - samples: 14,280, batch_size: 128, learning_rate: 1.77e-04
2:59:16.527749 INFO: Using random state 47425 for train-test-split
2:59:17.931660 INFO: Test AUC: 0.759
2:59:17.931770 INFO: Train AUC: 0.785
2:59:17.931799 INFO: AUC difference: 3.25%
2:59:18.183996 INFO: Resetting torch num_threads to 24
2:59:18.186513 PROGRESS: === Extracted 17851 precursors and 117444 fragments ===
2:59:18.186875 INFO: === FDR correction performed with classifier version 6 ===
2:59:18.187633 PROGRESS: ============================= Precursor FDR =============================
2:59:18.187725 PROGRESS: Total precursors accumulated: 2,687
2:59:18.187782 PROGRESS: Target precursors: 2,661 (99.03%)
2:59:18.187831 PROGRESS: Decoy precursors: 26 (0.97%)
2:59:18.187874 PROGRESS: 
2:59:18.187915 PROGRESS: Precursor Summary:
2:59:18.189569 PROGRESS: Channel   0:	 0.050 FDR: 2,661; 0.010 FDR: 2,661; 0.001 FDR: 2,180
2:59:18.189659 PROGRESS: 
2:59:18.189717 PROGRESS: Protein Summary:
2:59:18.192025 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,056; 0.001 FDR: 1,700
2:59:18.192118 PROGRESS: =========================================================================
2:59:18.192492 INFO: Target number of precursors reached.
2:59:18.218546 INFO: fragments_df: keeping 5000 of 117444 [sum(precursor_idx_mask)=59460 sum(mass_error_mask)=117444 stop_rank=5000
2:59:18.229681 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:18.630118 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:19.343792 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:19.344255 INFO: Using score_cutoff 10.047032999038695 (fac=0.99, q=1)
2:59:19.344573 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:19.344654 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:19.344709 INFO: Updating optimization_manager: score_cutoff        : 10.079314167308807 -> 10.047032999038695
2:59:19.344762 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:19.348695 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:19.356241 INFO: === checking if optimization conditions were reached ===
2:59:19.356353 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:59:19.359301 INFO: Updating optimization_manager: rt_error            : 248.6515927518709 -> 280.74598719264657
2:59:19.359402 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 280.7460.
2:59:19.359476 INFO: ==============================================
2:59:19.359547 INFO: Starting optimization step 6.
2:59:19.359607 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:19.359669 INFO: Using rust extraction backend
2:59:19.359733 PROGRESS: Extracting batch of 5956 precursors
2:59:19.370995 INFO: === Search parameters used ===
2:59:19.371126 INFO: rt_error       : 280.74598719264657
2:59:19.371177 INFO: mobility_error : 0.1
2:59:19.371219 INFO: num_candidates : 3
2:59:19.371261 INFO: ms1_error      : 30
2:59:19.371301 INFO: ms2_error      : 10.0
2:59:19.371340 INFO: fwhm_rt        : 3.0
2:59:19.371378 INFO: quant_window   : 3
2:59:19.371417 INFO: ==============================================
2:59:19.473249 INFO: performing precursor FDR with 40 features
2:59:19.473363 INFO: Decoy channel: -1
2:59:19.473387 INFO: competitive: True
2:59:19.480195 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:19.484437 INFO: Estimating optimal hyperparameters - samples: 14,281, batch_size: 128, learning_rate: 1.77e-04
2:59:19.484579 INFO: Using random state 47425 for train-test-split
2:59:20.902623 INFO: Test AUC: 0.782
2:59:20.902731 INFO: Train AUC: 0.779
2:59:20.902760 INFO: AUC difference: 0.37%
2:59:21.154243 INFO: Resetting torch num_threads to 24
2:59:21.156811 PROGRESS: === Extracted 17852 precursors and 118253 fragments ===
2:59:21.157177 INFO: === FDR correction performed with classifier version 6 ===
2:59:21.157893 PROGRESS: ============================= Precursor FDR =============================
2:59:21.157975 PROGRESS: Total precursors accumulated: 2,665
2:59:21.158031 PROGRESS: Target precursors: 2,639 (99.02%)
2:59:21.158078 PROGRESS: Decoy precursors: 26 (0.98%)
2:59:21.158122 PROGRESS: 
2:59:21.158163 PROGRESS: Precursor Summary:
2:59:21.159811 PROGRESS: Channel   0:	 0.050 FDR: 2,639; 0.010 FDR: 2,639; 0.001 FDR: 2,159
2:59:21.159906 PROGRESS: 
2:59:21.159961 PROGRESS: Protein Summary:
2:59:21.162266 PROGRESS: Channel   0:	 0.050 FDR: 2,042; 0.010 FDR: 2,042; 0.001 FDR: 1,691
2:59:21.162363 PROGRESS: =========================================================================
2:59:21.162775 INFO: Target number of precursors reached.
2:59:21.188774 INFO: fragments_df: keeping 5000 of 118253 [sum(precursor_idx_mask)=59267 sum(mass_error_mask)=118253 stop_rank=5000
2:59:21.199949 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:21.580906 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:22.296497 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:22.296978 INFO: Using score_cutoff 10.138863369369506 (fac=0.99, q=1)
2:59:22.297291 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:22.297364 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:22.297415 INFO: Updating optimization_manager: score_cutoff        : 10.047032999038695 -> 10.138863369369506
2:59:22.297466 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:22.301464 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:22.309214 INFO: === checking if optimization conditions were reached ===
2:59:22.309319 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:59:22.312321 INFO: Updating optimization_manager: rt_error            : 280.74598719264657 -> 236.41800125184048
2:59:22.312421 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 236.4180.
2:59:22.312482 INFO: ==============================================
2:59:22.312547 INFO: Starting optimization step 7.
2:59:22.312611 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:22.312676 INFO: Using rust extraction backend
2:59:22.312730 PROGRESS: Extracting batch of 5956 precursors
2:59:22.324105 INFO: === Search parameters used ===
2:59:22.324224 INFO: rt_error       : 236.41800125184048
2:59:22.324276 INFO: mobility_error : 0.1
2:59:22.324321 INFO: num_candidates : 3
2:59:22.324363 INFO: ms1_error      : 30
2:59:22.324403 INFO: ms2_error      : 10.0
2:59:22.324443 INFO: fwhm_rt        : 3.0
2:59:22.324483 INFO: quant_window   : 3
2:59:22.324523 INFO: ==============================================
2:59:22.428548 INFO: performing precursor FDR with 40 features
2:59:22.428663 INFO: Decoy channel: -1
2:59:22.428685 INFO: competitive: True
2:59:22.435637 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:22.441561 INFO: Estimating optimal hyperparameters - samples: 14,280, batch_size: 128, learning_rate: 1.77e-04
2:59:22.441717 INFO: Using random state 47425 for train-test-split
2:59:23.849402 INFO: Test AUC: 0.756
2:59:23.849516 INFO: Train AUC: 0.785
2:59:23.849547 INFO: AUC difference: 3.70%
2:59:24.102004 INFO: Resetting torch num_threads to 24
2:59:24.104541 PROGRESS: === Extracted 17850 precursors and 117119 fragments ===
2:59:24.104921 INFO: === FDR correction performed with classifier version 6 ===
2:59:24.105635 PROGRESS: ============================= Precursor FDR =============================
2:59:24.105719 PROGRESS: Total precursors accumulated: 2,714
2:59:24.105779 PROGRESS: Target precursors: 2,688 (99.04%)
2:59:24.105830 PROGRESS: Decoy precursors: 26 (0.96%)
2:59:24.105882 PROGRESS: 
2:59:24.105929 PROGRESS: Precursor Summary:
2:59:24.107495 PROGRESS: Channel   0:	 0.050 FDR: 2,688; 0.010 FDR: 2,688; 0.001 FDR: 1,549
2:59:24.107589 PROGRESS: 
2:59:24.107651 PROGRESS: Protein Summary:
2:59:24.109875 PROGRESS: Channel   0:	 0.050 FDR: 2,075; 0.010 FDR: 2,075; 0.001 FDR: 1,274
2:59:24.109968 PROGRESS: =========================================================================
2:59:24.110363 INFO: Target number of precursors reached.
2:59:24.136340 INFO: fragments_df: keeping 5000 of 117119 [sum(precursor_idx_mask)=59864 sum(mass_error_mask)=117119 stop_rank=5000
2:59:24.148350 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:24.480264 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:25.125914 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:25.126390 INFO: Using score_cutoff 9.940198687076569 (fac=0.99, q=1)
2:59:25.126711 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:25.126786 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:25.126839 INFO: Updating optimization_manager: score_cutoff        : 10.138863369369506 -> 9.940198687076569
2:59:25.126890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:25.130847 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:25.138574 INFO: === checking if optimization conditions were reached ===
2:59:25.138689 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:59:25.141631 INFO: Updating optimization_manager: rt_error            : 236.41800125184048 -> 261.1110937847311
2:59:25.141731 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 261.1111.
2:59:25.141800 INFO: ==============================================
2:59:25.141868 INFO: Starting optimization step 8.
2:59:25.141925 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:25.141989 INFO: Using rust extraction backend
2:59:25.142045 PROGRESS: Extracting batch of 5956 precursors
2:59:25.153382 INFO: === Search parameters used ===
2:59:25.153517 INFO: rt_error       : 261.1110937847311
2:59:25.153569 INFO: mobility_error : 0.1
2:59:25.153615 INFO: num_candidates : 3
2:59:25.153659 INFO: ms1_error      : 30
2:59:25.153701 INFO: ms2_error      : 10.0
2:59:25.153742 INFO: fwhm_rt        : 3.0
2:59:25.153783 INFO: quant_window   : 3
2:59:25.153824 INFO: ==============================================
2:59:25.260134 INFO: performing precursor FDR with 40 features
2:59:25.260248 INFO: Decoy channel: -1
2:59:25.260273 INFO: competitive: True
2:59:25.265267 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:25.269163 INFO: Estimating optimal hyperparameters - samples: 14,282, batch_size: 128, learning_rate: 1.77e-04
2:59:25.269294 INFO: Using random state 47425 for train-test-split
2:59:26.689497 INFO: Test AUC: 0.765
2:59:26.689607 INFO: Train AUC: 0.783
2:59:26.689640 INFO: AUC difference: 2.27%
2:59:26.941245 INFO: Resetting torch num_threads to 24
2:59:26.943808 PROGRESS: === Extracted 17853 precursors and 117781 fragments ===
2:59:26.944179 INFO: === FDR correction performed with classifier version 6 ===
2:59:26.944903 PROGRESS: ============================= Precursor FDR =============================
2:59:26.944985 PROGRESS: Total precursors accumulated: 2,691
2:59:26.945041 PROGRESS: Target precursors: 2,665 (99.03%)
2:59:26.945088 PROGRESS: Decoy precursors: 26 (0.97%)
2:59:26.945131 PROGRESS: 
2:59:26.945173 PROGRESS: Precursor Summary:
2:59:26.946814 PROGRESS: Channel   0:	 0.050 FDR: 2,665; 0.010 FDR: 2,665; 0.001 FDR: 2,201
2:59:26.946902 PROGRESS: 
2:59:26.946954 PROGRESS: Protein Summary:
2:59:26.949296 PROGRESS: Channel   0:	 0.050 FDR: 2,057; 0.010 FDR: 2,057; 0.001 FDR: 1,717
2:59:26.949396 PROGRESS: =========================================================================
2:59:26.949779 INFO: Target number of precursors reached.
2:59:26.976272 INFO: fragments_df: keeping 5000 of 117781 [sum(precursor_idx_mask)=59585 sum(mass_error_mask)=117781 stop_rank=5000
2:59:26.987325 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:27.316281 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:27.963258 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:27.963744 INFO: Using score_cutoff 10.047757945632934 (fac=0.99, q=1)
2:59:27.964058 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:27.964133 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:27.964186 INFO: Updating optimization_manager: score_cutoff        : 9.940198687076569 -> 10.047757945632934
2:59:27.964237 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:27.968189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:27.976061 INFO: === checking if optimization conditions were reached ===
2:59:27.976176 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:59:27.979119 INFO: Updating optimization_manager: rt_error            : 261.1110937847311 -> 212.65814685904
2:59:27.979226 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 212.6581.
2:59:27.979290 INFO: ==============================================
2:59:27.979357 INFO: Starting optimization step 9.
2:59:27.979418 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:27.979500 INFO: Using rust extraction backend
2:59:27.979560 PROGRESS: Extracting batch of 5956 precursors
2:59:27.990924 INFO: === Search parameters used ===
2:59:27.991038 INFO: rt_error       : 212.65814685904
2:59:27.991090 INFO: mobility_error : 0.1
2:59:27.991135 INFO: num_candidates : 3
2:59:27.991178 INFO: ms1_error      : 30
2:59:27.991219 INFO: ms2_error      : 10.0
2:59:27.991258 INFO: fwhm_rt        : 3.0
2:59:27.991296 INFO: quant_window   : 3
2:59:27.991333 INFO: ==============================================
2:59:28.088574 INFO: performing precursor FDR with 40 features
2:59:28.088686 INFO: Decoy channel: -1
2:59:28.088710 INFO: competitive: True
2:59:28.093692 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:28.097697 INFO: Estimating optimal hyperparameters - samples: 14,276, batch_size: 128, learning_rate: 1.77e-04
2:59:28.097824 INFO: Using random state 47425 for train-test-split
2:59:29.517459 INFO: Test AUC: 0.744
2:59:29.517573 INFO: Train AUC: 0.789
2:59:29.517605 INFO: AUC difference: 5.72%
2:59:29.517627 WARNING: AUC difference > 5%. This may indicate overfitting.
2:59:29.769982 INFO: Resetting torch num_threads to 24
2:59:29.772497 PROGRESS: === Extracted 17846 precursors and 116296 fragments ===
2:59:29.772864 INFO: === FDR correction performed with classifier version 6 ===
2:59:29.773584 PROGRESS: ============================= Precursor FDR =============================
2:59:29.773671 PROGRESS: Total precursors accumulated: 2,711
2:59:29.773731 PROGRESS: Target precursors: 2,685 (99.04%)
2:59:29.773784 PROGRESS: Decoy precursors: 26 (0.96%)
2:59:29.773838 PROGRESS: 
2:59:29.773885 PROGRESS: Precursor Summary:
2:59:29.775546 PROGRESS: Channel   0:	 0.050 FDR: 2,685; 0.010 FDR: 2,685; 0.001 FDR: 2,198
2:59:29.775653 PROGRESS: 
2:59:29.775710 PROGRESS: Protein Summary:
2:59:29.778008 PROGRESS: Channel   0:	 0.050 FDR: 2,070; 0.010 FDR: 2,070; 0.001 FDR: 1,710
2:59:29.778094 PROGRESS: =========================================================================
2:59:29.778459 INFO: Target number of precursors reached.
2:59:29.804769 INFO: fragments_df: keeping 5000 of 116296 [sum(precursor_idx_mask)=59648 sum(mass_error_mask)=116296 stop_rank=5000
2:59:29.815754 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:30.144881 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:30.791661 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:30.792133 INFO: Using score_cutoff 10.051382678604126 (fac=0.99, q=1)
2:59:30.792441 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:30.792515 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:30.792567 INFO: Updating optimization_manager: score_cutoff        : 10.047757945632934 -> 10.051382678604126
2:59:30.792618 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:30.796550 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:30.804316 INFO: === checking if optimization conditions were reached ===
2:59:30.804430 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:59:30.807381 INFO: Updating optimization_manager: rt_error            : 212.65814685904 -> 206.480620035228
2:59:30.807498 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 206.4806.
2:59:30.807566 INFO: ==============================================
2:59:30.807634 INFO: Starting optimization step 10.
2:59:30.807693 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:59:30.807754 INFO: Using rust extraction backend
2:59:30.807807 PROGRESS: Extracting batch of 5956 precursors
2:59:30.819100 INFO: === Search parameters used ===
2:59:30.819212 INFO: rt_error       : 206.480620035228
2:59:30.819261 INFO: mobility_error : 0.1
2:59:30.819305 INFO: num_candidates : 3
2:59:30.819346 INFO: ms1_error      : 30
2:59:30.819386 INFO: ms2_error      : 10.0
2:59:30.819426 INFO: fwhm_rt        : 3.0
2:59:30.819475 INFO: quant_window   : 3
2:59:30.819519 INFO: ==============================================
2:59:30.915621 INFO: performing precursor FDR with 40 features
2:59:30.915732 INFO: Decoy channel: -1
2:59:30.915756 INFO: competitive: True
2:59:30.920626 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:30.924503 INFO: Estimating optimal hyperparameters - samples: 14,276, batch_size: 128, learning_rate: 1.77e-04
2:59:30.924632 INFO: Using random state 47425 for train-test-split
2:59:32.340876 INFO: Test AUC: 0.765
2:59:32.340982 INFO: Train AUC: 0.785
2:59:32.341011 INFO: AUC difference: 2.55%
2:59:32.593943 INFO: Resetting torch num_threads to 24
2:59:32.596407 PROGRESS: === Extracted 17846 precursors and 116016 fragments ===
2:59:32.596768 INFO: === FDR correction performed with classifier version 6 ===
2:59:32.597466 PROGRESS: ============================= Precursor FDR =============================
2:59:32.597547 PROGRESS: Total precursors accumulated: 2,707
2:59:32.597603 PROGRESS: Target precursors: 2,681 (99.04%)
2:59:32.597656 PROGRESS: Decoy precursors: 26 (0.96%)
2:59:32.597708 PROGRESS: 
2:59:32.597750 PROGRESS: Precursor Summary:
2:59:32.599382 PROGRESS: Channel   0:	 0.050 FDR: 2,681; 0.010 FDR: 2,681; 0.001 FDR: 2,399
2:59:32.599484 PROGRESS: 
2:59:32.599541 PROGRESS: Protein Summary:
2:59:32.601818 PROGRESS: Channel   0:	 0.050 FDR: 2,074; 0.010 FDR: 2,074; 0.001 FDR: 1,860
2:59:32.601903 PROGRESS: =========================================================================
2:59:32.602242 INFO: Target number of precursors reached.
2:59:32.628120 INFO: fragments_df: keeping 5000 of 116016 [sum(precursor_idx_mask)=59488 sum(mass_error_mask)=116016 stop_rank=5000
2:59:32.638979 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:59:32.967122 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:59:33.612897 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:59:33.613373 INFO: Using score_cutoff 10.066425584793091 (fac=0.99, q=1)
2:59:33.613688 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:33.613765 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:33.613821 INFO: Updating optimization_manager: score_cutoff        : 10.051382678604126 -> 10.066425584793091
2:59:33.613875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:33.617944 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:33.625906 INFO: === checking if optimization conditions were reached ===
2:59:33.626024 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:59:33.626749 INFO: Updating optimization_manager: rt_error            : 206.480620035228 -> 236.41800125184048
2:59:33.626870 INFO: Updating optimization_manager: classifier_version  : 6 -> 14
2:59:33.626965 INFO: Updating optimization_manager: score_cutoff        : 10.066425584793091 -> 9.940198687076569
2:59:33.627058 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:59:33.627145 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:59:33.627229 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 236.4180 found after 11 searches.
2:59:33.627289 INFO: ==============================================
2:59:33.627359 PROGRESS: Optimization finished for rt_error.
2:59:33.637857 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:33.641634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:33.649558 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:59:33.649666 PROGRESS: ==============================================
2:59:33.649735 PROGRESS: ms2_error      : 10.0000
2:59:33.649791 PROGRESS: rt_error       : 236.4180
2:59:33.649840 PROGRESS: ==============================================
2:59:33.650386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:59:33.786677 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:34.143123 INFO: Using rust extraction backend
2:59:34.143428 PROGRESS: Extracting batch of 262809 precursors
2:59:34.571185 INFO: === Search parameters used ===
2:59:34.571483 INFO: rt_error       : 236.41800125184048
2:59:34.571548 INFO: mobility_error : 0.1
2:59:34.571598 INFO: num_candidates : 3
2:59:34.571644 INFO: ms1_error      : 30
2:59:34.571687 INFO: ms2_error      : 10.0
2:59:34.571728 INFO: fwhm_rt        : 3.0
2:59:34.571769 INFO: quant_window   : 3
2:59:34.571810 INFO: ==============================================
2:59:35.265100 INFO: Removed 115178 precursors with score below cutoff 9.940198687076569
2:59:35.918701 INFO: performing precursor FDR with 40 features
2:59:35.918825 INFO: Decoy channel: -1
2:59:35.918852 INFO: competitive: True
2:59:35.973562 INFO: Setting torch num_threads to 2 for FDR classification task
2:59:36.012845 WARNING: FDR calculation for 359654 target and 313594 decoy PSMs
2:59:36.012996 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:59:36.179411 INFO: Estimating optimal hyperparameters - samples: 538,598, batch_size: 2,206, learning_rate: 7.34e-04
2:59:36.180324 INFO: Using random state 656663 for train-test-split
2:59:47.213989 INFO: Test AUC: 0.789
2:59:47.214128 INFO: Train AUC: 0.793
2:59:47.214164 INFO: AUC difference: 0.50%
2:59:47.719407 INFO: Resetting torch num_threads to 24
2:59:48.023130 PROGRESS: ============================= Precursor FDR =============================
2:59:48.023419 PROGRESS: Total precursors accumulated: 124,281
2:59:48.023511 PROGRESS: Target precursors: 123,051 (99.01%)
2:59:48.023569 PROGRESS: Decoy precursors: 1,230 (0.99%)
2:59:48.023618 PROGRESS: 
2:59:48.023666 PROGRESS: Precursor Summary:
2:59:48.062056 PROGRESS: Channel   0:	 0.050 FDR: 123,051; 0.010 FDR: 123,051; 0.001 FDR: 110,681
2:59:48.062329 PROGRESS: 
2:59:48.062393 PROGRESS: Protein Summary:
2:59:48.120518 PROGRESS: Channel   0:	 0.050 FDR: 10,378; 0.010 FDR: 10,378; 0.001 FDR: 10,224
2:59:48.120791 PROGRESS: =========================================================================
2:59:48.123174 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
2:59:48.345046 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
2:59:48.644378 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:59:48.900759 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:59:48.900914 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:59:48.901002 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
2:59:48.901175 INFO: Initializing TimingManager
2:59:48.901659 INFO: Initializing RawFileManager
3:00:02.053330 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.
3:00:02.062267 INFO: Determining DIA cycle
3:00:02.079681 INFO: Found cycle with start 0.00 min and length 300.
3:00:02.255270 INFO: RT (min)            : 0.0 - 26.9
3:00:02.255366 INFO: RT duration (sec)   : 1611.2
3:00:02.255395 INFO: RT duration (min)   : 26.9
3:00:02.255418 INFO: Cycle len (scans)   : 300
3:00:02.255438 INFO: Cycle len (sec)     : 1.65
3:00:02.255471 INFO: Number of cycles    : 978
3:00:02.255492 INFO: MS2 range (m/z)     : 380.4 - 980.7
3:00:02.255519 INFO: Creating DIA data object took: 13.353765964508057
3:00:04.082626 INFO: Creating DIA data NG object took: 1.826963186264038
3:00:04.117303 INFO: Initializing CalibrationManager
3:00:04.117609 INFO: Setting up calibration estimators ..
3:00:04.117674 INFO: Found 1 estimator(s) in calibration group 'fragment'
3:00:04.117746 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'}' ..
3:00:04.117825 INFO: Found 3 estimator(s) in calibration group 'precursor'
3:00:04.117878 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
3:00:04.117931 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}}' ..
3:00:04.117985 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
3:00:04.118032 INFO: Done setting up calibration estimators.
3:00:04.118238 INFO: Initializing OptimizationManager
3:00:04.118370 INFO: initial parameter: ms1_error = 30
3:00:04.118424 INFO: initial parameter: ms2_error = 30
3:00:04.118471 INFO: initial parameter: rt_error = 805.611083984375
3:00:04.118515 INFO: initial parameter: mobility_error = 0.1
3:00:04.118557 INFO: initial parameter: num_candidates = 1
3:00:04.118599 INFO: initial parameter: fwhm_rt = 5
3:00:04.118642 INFO: initial parameter: fwhm_mobility = 0.01
3:00:04.118684 INFO: initial parameter: score_cutoff = 0
3:00:04.118725 INFO: initial parameter: classifier_version = -1
3:00:04.118793 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:00:04.119025 INFO: FDRManager: loading saved state not requested, will be initialized.
3:00:04.119058 INFO: Initializing FDRManager
3:00:04.119089 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
3:00:04.157871 PROGRESS: Initializing spectral library: 132,778 target precursors potentially observable (0 removed)
3:00:04.183210 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
3:00:04.183600 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
3:00:04.183702 PROGRESS: Starting initial search for precursors.
3:00:04.183784 INFO: Starting optimization step 0.
3:00:04.183848 PROGRESS: === Extracting elution groups 0 to 1000 ===
3:00:04.183905 INFO: Using rust extraction backend
3:00:04.183968 PROGRESS: Extracting batch of 1980 precursors
3:00:04.188577 INFO: === Search parameters used ===
3:00:04.188678 INFO: rt_error       : 805.611083984375
3:00:04.188738 INFO: mobility_error : 0.1
3:00:04.188782 INFO: num_candidates : 1
3:00:04.188827 INFO: ms1_error      : 30
3:00:04.188868 INFO: ms2_error      : 30
3:00:04.188906 INFO: fwhm_rt        : 5
3:00:04.188945 INFO: quant_window   : 3
3:00:04.188984 INFO: ==============================================
3:00:04.220532 INFO: performing precursor FDR with 40 features
3:00:04.220622 INFO: Decoy channel: -1
3:00:04.220645 INFO: competitive: True
3:00:04.221919 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:04.223806 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
3:00:04.224652 INFO: Using random state 80745 for train-test-split
3:00:04.372412 INFO: Test AUC: 0.805
3:00:04.372496 INFO: Train AUC: 0.792
3:00:04.372524 INFO: AUC difference: 1.65%
3:00:04.611182 INFO: Resetting torch num_threads to 24
3:00:04.612825 PROGRESS: === Extracted 1976 precursors and 13481 fragments ===
3:00:04.613187 INFO: === FDR correction performed with classifier version -1 ===
3:00:04.613666 PROGRESS: ============================= Precursor FDR =============================
3:00:04.613748 PROGRESS: Total precursors accumulated: 239
3:00:04.613806 PROGRESS: Target precursors: 237 (99.16%)
3:00:04.613855 PROGRESS: Decoy precursors: 2 (0.84%)
3:00:04.613899 PROGRESS: 
3:00:04.613941 PROGRESS: Precursor Summary:
3:00:04.614954 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   232
3:00:04.615038 PROGRESS: 
3:00:04.615091 PROGRESS: Protein Summary:
3:00:04.616285 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:   221
3:00:04.616374 PROGRESS: =========================================================================
3:00:04.616588 INFO: Target number of precursors not reached yet.
3:00:04.624314 INFO: Starting optimization step 1.
3:00:04.624423 PROGRESS: === Extracting elution groups 1000 to 3000 ===
3:00:04.624499 INFO: Using rust extraction backend
3:00:04.624557 PROGRESS: Extracting batch of 3976 precursors
3:00:04.632557 INFO: === Search parameters used ===
3:00:04.632665 INFO: rt_error       : 805.611083984375
3:00:04.632715 INFO: mobility_error : 0.1
3:00:04.632759 INFO: num_candidates : 1
3:00:04.632801 INFO: ms1_error      : 30
3:00:04.632841 INFO: ms2_error      : 30
3:00:04.632880 INFO: fwhm_rt        : 5
3:00:04.632919 INFO: quant_window   : 3
3:00:04.632958 INFO: ==============================================
3:00:04.697975 INFO: performing precursor FDR with 40 features
3:00:04.698078 INFO: Decoy channel: -1
3:00:04.698102 INFO: competitive: True
3:00:04.702172 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:04.704415 INFO: Estimating optimal hyperparameters - samples: 4,758, batch_size: 128, learning_rate: 1.77e-04
3:00:04.704498 INFO: Using random state 861072 for train-test-split
3:00:05.172853 INFO: Test AUC: 0.806
3:00:05.172976 INFO: Train AUC: 0.832
3:00:05.173007 INFO: AUC difference: 3.14%
3:00:05.416308 INFO: Resetting torch num_threads to 24
3:00:05.419334 PROGRESS: === Extracted 5948 precursors and 40648 fragments ===
3:00:05.419721 INFO: === FDR correction performed with classifier version -1 ===
3:00:05.420323 PROGRESS: ============================= Precursor FDR =============================
3:00:05.420410 PROGRESS: Total precursors accumulated: 1,457
3:00:05.420470 PROGRESS: Target precursors: 1,443 (99.04%)
3:00:05.420535 PROGRESS: Decoy precursors: 14 (0.96%)
3:00:05.420588 PROGRESS: 
3:00:05.420634 PROGRESS: Precursor Summary:
3:00:05.421950 PROGRESS: Channel   0:	 0.050 FDR: 1,443; 0.010 FDR: 1,443; 0.001 FDR: 1,069
3:00:05.422035 PROGRESS: 
3:00:05.422089 PROGRESS: Protein Summary:
3:00:05.423854 PROGRESS: Channel   0:	 0.050 FDR: 1,198; 0.010 FDR: 1,198; 0.001 FDR:   907
3:00:05.423946 PROGRESS: =========================================================================
3:00:05.424212 INFO: Target number of precursors reached.
3:00:05.432823 INFO: fragments_df: keeping 5000 of 40648 [sum(precursor_idx_mask)=14918 sum(mass_error_mask)=40648 stop_rank=5000
3:00:05.443367 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:05.669211 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:06.383256 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
3:00:06.383723 INFO: Using score_cutoff 12.902193467330932 (fac=0.99, q=1)
3:00:06.384033 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
3:00:06.384107 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
3:00:06.384158 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.902193467330932
3:00:06.384212 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:06.388116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:06.396111 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
3:00:06.396224 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:00:06.396300 INFO: Starting optimization step 2.
3:00:06.396369 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:06.396431 INFO: Using rust extraction backend
3:00:06.396485 PROGRESS: Extracting batch of 5956 precursors
3:00:06.407772 INFO: === Search parameters used ===
3:00:06.407889 INFO: rt_error       : 805.611083984375
3:00:06.407939 INFO: mobility_error : 0.1
3:00:06.407983 INFO: num_candidates : 3
3:00:06.408024 INFO: ms1_error      : 30
3:00:06.408063 INFO: ms2_error      : 30
3:00:06.408104 INFO: fwhm_rt        : 3.0
3:00:06.408143 INFO: quant_window   : 3
3:00:06.408181 INFO: ==============================================
3:00:06.536430 INFO: performing precursor FDR with 40 features
3:00:06.536540 INFO: Decoy channel: -1
3:00:06.536564 INFO: competitive: True
3:00:06.541438 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:06.545412 INFO: Estimating optimal hyperparameters - samples: 14,261, batch_size: 128, learning_rate: 1.77e-04
3:00:06.545543 INFO: Using random state 342313 for train-test-split
3:00:07.969174 INFO: Test AUC: 0.689
3:00:07.969306 INFO: Train AUC: 0.708
3:00:07.969336 INFO: AUC difference: 2.69%
3:00:08.218376 INFO: Resetting torch num_threads to 24
3:00:08.220766 PROGRESS: === Extracted 17827 precursors and 106488 fragments ===
3:00:08.221142 INFO: === FDR correction performed with classifier version 1 ===
3:00:08.221775 PROGRESS: ============================= Precursor FDR =============================
3:00:08.221859 PROGRESS: Total precursors accumulated: 1,776
3:00:08.221915 PROGRESS: Target precursors: 1,759 (99.04%)
3:00:08.221963 PROGRESS: Decoy precursors: 17 (0.96%)
3:00:08.222014 PROGRESS: 
3:00:08.222056 PROGRESS: Precursor Summary:
3:00:08.223443 PROGRESS: Channel   0:	 0.050 FDR: 1,759; 0.010 FDR: 1,759; 0.001 FDR: 1,192
3:00:08.223553 PROGRESS: 
3:00:08.223612 PROGRESS: Protein Summary:
3:00:08.225438 PROGRESS: Channel   0:	 0.050 FDR: 1,426; 0.010 FDR: 1,426; 0.001 FDR:   999
3:00:08.225524 PROGRESS: =========================================================================
3:00:08.225903 INFO: Target number of precursors reached.
3:00:08.244372 INFO: fragments_df: keeping 5000 of 106488 [sum(precursor_idx_mask)=38079 sum(mass_error_mask)=106488 stop_rank=5000
3:00:08.255237 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:08.515441 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:09.162595 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:09.163065 INFO: Using score_cutoff 12.046280621910096 (fac=0.99, q=1)
3:00:09.163375 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:09.163450 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:09.163522 INFO: Updating optimization_manager: score_cutoff        : 12.902193467330932 -> 12.046280621910096
3:00:09.163576 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:09.167545 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:09.175715 INFO: === checking if optimization conditions were reached ===
3:00:09.177385 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
3:00:09.177478 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
3:00:09.177539 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
3:00:09.177594 INFO: ==============================================
3:00:09.177664 INFO: Starting optimization step 3.
3:00:09.177722 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:09.177783 INFO: Using rust extraction backend
3:00:09.177845 PROGRESS: Extracting batch of 5956 precursors
3:00:09.189099 INFO: === Search parameters used ===
3:00:09.189210 INFO: rt_error       : 805.611083984375
3:00:09.189260 INFO: mobility_error : 0.1
3:00:09.189303 INFO: num_candidates : 3
3:00:09.189343 INFO: ms1_error      : 30
3:00:09.189382 INFO: ms2_error      : 10.0
3:00:09.189421 INFO: fwhm_rt        : 3.0
3:00:09.189459 INFO: quant_window   : 3
3:00:09.189498 INFO: ==============================================
3:00:09.305315 INFO: performing precursor FDR with 40 features
3:00:09.305425 INFO: Decoy channel: -1
3:00:09.305448 INFO: competitive: True
3:00:09.310415 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:09.314576 INFO: Estimating optimal hyperparameters - samples: 14,289, batch_size: 128, learning_rate: 1.77e-04
3:00:09.314710 INFO: Using random state 710540 for train-test-split
3:00:10.747645 INFO: Test AUC: 0.740
3:00:10.747761 INFO: Train AUC: 0.749
3:00:10.747792 INFO: AUC difference: 1.21%
3:00:11.001320 INFO: Resetting torch num_threads to 24
3:00:11.003728 PROGRESS: === Extracted 17862 precursors and 120194 fragments ===
3:00:11.004099 INFO: === FDR correction performed with classifier version 2 ===
3:00:11.004787 PROGRESS: ============================= Precursor FDR =============================
3:00:11.004882 PROGRESS: Total precursors accumulated: 2,343
3:00:11.004941 PROGRESS: Target precursors: 2,320 (99.02%)
3:00:11.004993 PROGRESS: Decoy precursors: 23 (0.98%)
3:00:11.005041 PROGRESS: 
3:00:11.005086 PROGRESS: Precursor Summary:
3:00:11.006629 PROGRESS: Channel   0:	 0.050 FDR: 2,320; 0.010 FDR: 2,320; 0.001 FDR: 1,830
3:00:11.006718 PROGRESS: 
3:00:11.006773 PROGRESS: Protein Summary:
3:00:11.008887 PROGRESS: Channel   0:	 0.050 FDR: 1,829; 0.010 FDR: 1,829; 0.001 FDR: 1,484
3:00:11.008986 PROGRESS: =========================================================================
3:00:11.009339 INFO: Target number of precursors reached.
3:00:11.034405 INFO: fragments_df: keeping 5000 of 120194 [sum(precursor_idx_mask)=53599 sum(mass_error_mask)=120194 stop_rank=5000
3:00:11.045346 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:11.380517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:12.094762 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:12.095234 INFO: Using score_cutoff 11.159987119388582 (fac=0.99, q=1)
3:00:12.095565 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:12.095648 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:12.095703 INFO: Updating optimization_manager: score_cutoff        : 12.046280621910096 -> 11.159987119388582
3:00:12.095755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:12.099667 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:12.107212 INFO: === checking if optimization conditions were reached ===
3:00:12.108866 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
3:00:12.108976 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
3:00:12.109039 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
3:00:12.109100 INFO: ==============================================
3:00:12.109167 INFO: Starting optimization step 4.
3:00:12.109223 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:12.109280 INFO: Using rust extraction backend
3:00:12.109334 PROGRESS: Extracting batch of 5956 precursors
3:00:12.120571 INFO: === Search parameters used ===
3:00:12.120683 INFO: rt_error       : 805.611083984375
3:00:12.120735 INFO: mobility_error : 0.1
3:00:12.120778 INFO: num_candidates : 3
3:00:12.120819 INFO: ms1_error      : 30
3:00:12.120858 INFO: ms2_error      : 10.0
3:00:12.120897 INFO: fwhm_rt        : 3.0
3:00:12.120935 INFO: quant_window   : 3
3:00:12.120972 INFO: ==============================================
3:00:12.237246 INFO: performing precursor FDR with 40 features
3:00:12.237352 INFO: Decoy channel: -1
3:00:12.237377 INFO: competitive: True
3:00:12.242144 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:12.246316 INFO: Estimating optimal hyperparameters - samples: 14,289, batch_size: 128, learning_rate: 1.77e-04
3:00:12.246453 INFO: Using random state 103419 for train-test-split
3:00:13.605186 INFO: Test AUC: 0.759
3:00:13.605294 INFO: Train AUC: 0.760
3:00:13.605322 INFO: AUC difference: 0.14%
3:00:13.859974 INFO: Resetting torch num_threads to 24
3:00:13.862413 PROGRESS: === Extracted 17862 precursors and 120122 fragments ===
3:00:13.862774 INFO: === FDR correction performed with classifier version 3 ===
3:00:13.863480 PROGRESS: ============================= Precursor FDR =============================
3:00:13.863569 PROGRESS: Total precursors accumulated: 2,540
3:00:13.863626 PROGRESS: Target precursors: 2,515 (99.02%)
3:00:13.863674 PROGRESS: Decoy precursors: 25 (0.98%)
3:00:13.863718 PROGRESS: 
3:00:13.863765 PROGRESS: Precursor Summary:
3:00:13.865361 PROGRESS: Channel   0:	 0.050 FDR: 2,515; 0.010 FDR: 2,515; 0.001 FDR: 2,025
3:00:13.865447 PROGRESS: 
3:00:13.865501 PROGRESS: Protein Summary:
3:00:13.867703 PROGRESS: Channel   0:	 0.050 FDR: 1,966; 0.010 FDR: 1,966; 0.001 FDR: 1,624
3:00:13.867797 PROGRESS: =========================================================================
3:00:13.868155 INFO: Target number of precursors reached.
3:00:13.893955 INFO: fragments_df: keeping 5000 of 120122 [sum(precursor_idx_mask)=57314 sum(mass_error_mask)=120122 stop_rank=5000
3:00:13.904762 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:14.210604 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:14.870799 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:14.871261 INFO: Using score_cutoff 10.420594531059265 (fac=0.99, q=1)
3:00:14.871583 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:14.871664 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:14.871718 INFO: Updating optimization_manager: score_cutoff        : 11.159987119388582 -> 10.420594531059265
3:00:14.871768 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:14.875710 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:14.883327 INFO: === checking if optimization conditions were reached ===
3:00:14.884971 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
3:00:14.885078 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
3:00:14.885141 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
3:00:14.885197 INFO: ==============================================
3:00:14.885259 INFO: Starting optimization step 5.
3:00:14.885313 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:14.885367 INFO: Using rust extraction backend
3:00:14.885419 PROGRESS: Extracting batch of 5956 precursors
3:00:14.896699 INFO: === Search parameters used ===
3:00:14.896818 INFO: rt_error       : 805.611083984375
3:00:14.896881 INFO: mobility_error : 0.1
3:00:14.896926 INFO: num_candidates : 3
3:00:14.896967 INFO: ms1_error      : 30
3:00:14.897008 INFO: ms2_error      : 10.0
3:00:14.897048 INFO: fwhm_rt        : 3.0
3:00:14.897087 INFO: quant_window   : 3
3:00:14.897125 INFO: ==============================================
3:00:15.006242 INFO: performing precursor FDR with 40 features
3:00:15.006360 INFO: Decoy channel: -1
3:00:15.006383 INFO: competitive: True
3:00:15.011368 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:15.015485 INFO: Estimating optimal hyperparameters - samples: 14,289, batch_size: 128, learning_rate: 1.77e-04
3:00:15.015617 INFO: Using random state 834945 for train-test-split
3:00:16.448869 INFO: Test AUC: 0.758
3:00:16.448982 INFO: Train AUC: 0.772
3:00:16.449013 INFO: AUC difference: 1.81%
3:00:16.702734 INFO: Resetting torch num_threads to 24
3:00:16.705182 PROGRESS: === Extracted 17862 precursors and 120147 fragments ===
3:00:16.705549 INFO: === FDR correction performed with classifier version 4 ===
3:00:16.706249 PROGRESS: ============================= Precursor FDR =============================
3:00:16.706335 PROGRESS: Total precursors accumulated: 2,528
3:00:16.706394 PROGRESS: Target precursors: 2,503 (99.01%)
3:00:16.706452 PROGRESS: Decoy precursors: 25 (0.99%)
3:00:16.706501 PROGRESS: 
3:00:16.706547 PROGRESS: Precursor Summary:
3:00:16.708148 PROGRESS: Channel   0:	 0.050 FDR: 2,503; 0.010 FDR: 2,503; 0.001 FDR: 2,063
3:00:16.708243 PROGRESS: 
3:00:16.708298 PROGRESS: Protein Summary:
3:00:16.710482 PROGRESS: Channel   0:	 0.050 FDR: 1,954; 0.010 FDR: 1,954; 0.001 FDR: 1,651
3:00:16.710572 PROGRESS: =========================================================================
3:00:16.710921 INFO: Target number of precursors reached.
3:00:16.736783 INFO: fragments_df: keeping 5000 of 120147 [sum(precursor_idx_mask)=57036 sum(mass_error_mask)=120147 stop_rank=5000
3:00:16.747596 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:17.048186 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:17.729601 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:17.730061 INFO: Using score_cutoff 10.491547338294984 (fac=0.99, q=1)
3:00:17.730374 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:17.730450 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:17.730505 INFO: Updating optimization_manager: score_cutoff        : 10.420594531059265 -> 10.491547338294984
3:00:17.730557 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:17.734528 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:17.742368 INFO: === checking if optimization conditions were reached ===
3:00:17.744025 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
3:00:17.744124 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
3:00:17.744188 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
3:00:17.744245 INFO: ==============================================
3:00:17.744309 INFO: Starting optimization step 6.
3:00:17.744366 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:17.744422 INFO: Using rust extraction backend
3:00:17.744475 PROGRESS: Extracting batch of 5956 precursors
3:00:17.755701 INFO: === Search parameters used ===
3:00:17.755824 INFO: rt_error       : 805.611083984375
3:00:17.755875 INFO: mobility_error : 0.1
3:00:17.755921 INFO: num_candidates : 3
3:00:17.755963 INFO: ms1_error      : 30
3:00:17.756004 INFO: ms2_error      : 10.0
3:00:17.756046 INFO: fwhm_rt        : 3.0
3:00:17.756088 INFO: quant_window   : 3
3:00:17.756128 INFO: ==============================================
3:00:17.867181 INFO: performing precursor FDR with 40 features
3:00:17.867298 INFO: Decoy channel: -1
3:00:17.867324 INFO: competitive: True
3:00:17.872151 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:17.876214 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
3:00:17.876360 INFO: Using random state 306786 for train-test-split
3:00:19.313964 INFO: Test AUC: 0.764
3:00:19.314072 INFO: Train AUC: 0.780
3:00:19.314101 INFO: AUC difference: 2.10%
3:00:19.565896 INFO: Resetting torch num_threads to 24
3:00:19.568338 PROGRESS: === Extracted 17861 precursors and 120121 fragments ===
3:00:19.568696 INFO: === FDR correction performed with classifier version 5 ===
3:00:19.569391 PROGRESS: ============================= Precursor FDR =============================
3:00:19.569474 PROGRESS: Total precursors accumulated: 2,643
3:00:19.569538 PROGRESS: Target precursors: 2,617 (99.02%)
3:00:19.569588 PROGRESS: Decoy precursors: 26 (0.98%)
3:00:19.569631 PROGRESS: 
3:00:19.569673 PROGRESS: Precursor Summary:
3:00:19.571261 PROGRESS: Channel   0:	 0.050 FDR: 2,617; 0.010 FDR: 2,617; 0.001 FDR: 1,778
3:00:19.571350 PROGRESS: 
3:00:19.571403 PROGRESS: Protein Summary:
3:00:19.573567 PROGRESS: Channel   0:	 0.050 FDR: 2,038; 0.010 FDR: 2,038; 0.001 FDR: 1,447
3:00:19.573661 PROGRESS: =========================================================================
3:00:19.574012 INFO: Target number of precursors reached.
3:00:19.600149 INFO: fragments_df: keeping 5000 of 120121 [sum(precursor_idx_mask)=59013 sum(mass_error_mask)=120121 stop_rank=5000
3:00:19.610974 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:19.984392 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:20.665159 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:20.665638 INFO: Using score_cutoff 9.656256383514405 (fac=0.99, q=1)
3:00:20.665948 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:20.666029 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:20.666084 INFO: Updating optimization_manager: score_cutoff        : 10.491547338294984 -> 9.656256383514405
3:00:20.666139 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:20.670107 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:20.677919 INFO: === checking if optimization conditions were reached ===
3:00:20.679571 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
3:00:20.679671 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
3:00:20.679735 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
3:00:20.679793 INFO: ==============================================
3:00:20.679858 PROGRESS: Optimization finished for ms2_error.
3:00:20.690419 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:20.694214 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:20.701994 INFO: Starting optimization step 0.
3:00:20.702109 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:20.702185 INFO: Using rust extraction backend
3:00:20.702244 PROGRESS: Extracting batch of 5956 precursors
3:00:20.713547 INFO: === Search parameters used ===
3:00:20.713670 INFO: rt_error       : 805.611083984375
3:00:20.713729 INFO: mobility_error : 0.1
3:00:20.713779 INFO: num_candidates : 3
3:00:20.713823 INFO: ms1_error      : 30
3:00:20.713866 INFO: ms2_error      : 10.0
3:00:20.713907 INFO: fwhm_rt        : 3.0
3:00:20.713948 INFO: quant_window   : 3
3:00:20.713988 INFO: ==============================================
3:00:20.822690 INFO: performing precursor FDR with 40 features
3:00:20.822801 INFO: Decoy channel: -1
3:00:20.822828 INFO: competitive: True
3:00:20.827677 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:20.831901 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
3:00:20.832034 INFO: Using random state 515797 for train-test-split
3:00:22.277029 INFO: Test AUC: 0.776
3:00:22.277139 INFO: Train AUC: 0.786
3:00:22.277170 INFO: AUC difference: 1.24%
3:00:22.530593 INFO: Resetting torch num_threads to 24
3:00:22.533059 PROGRESS: === Extracted 17861 precursors and 120119 fragments ===
3:00:22.533418 INFO: === FDR correction performed with classifier version 6 ===
3:00:22.534117 PROGRESS: ============================= Precursor FDR =============================
3:00:22.534210 PROGRESS: Total precursors accumulated: 2,642
3:00:22.534267 PROGRESS: Target precursors: 2,616 (99.02%)
3:00:22.534315 PROGRESS: Decoy precursors: 26 (0.98%)
3:00:22.534359 PROGRESS: 
3:00:22.534400 PROGRESS: Precursor Summary:
3:00:22.536012 PROGRESS: Channel   0:	 0.050 FDR: 2,616; 0.010 FDR: 2,616; 0.001 FDR: 2,087
3:00:22.536104 PROGRESS: 
3:00:22.536157 PROGRESS: Protein Summary:
3:00:22.538385 PROGRESS: Channel   0:	 0.050 FDR: 2,036; 0.010 FDR: 2,036; 0.001 FDR: 1,669
3:00:22.538471 PROGRESS: =========================================================================
3:00:22.538824 INFO: Target number of precursors reached.
3:00:22.564835 INFO: fragments_df: keeping 5000 of 120119 [sum(precursor_idx_mask)=59013 sum(mass_error_mask)=120119 stop_rank=5000
3:00:22.575689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:22.948704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:23.663384 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:23.663856 INFO: Using score_cutoff 10.109591035366059 (fac=0.99, q=1)
3:00:23.664173 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:23.664262 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:23.664318 INFO: Updating optimization_manager: score_cutoff        : 9.656256383514405 -> 10.109591035366059
3:00:23.664369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:23.668299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:23.675991 INFO: === checking if optimization conditions were reached ===
3:00:23.676108 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
3:00:23.678823 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 493.3814871529938
3:00:23.678921 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 493.3815.
3:00:23.678982 INFO: ==============================================
3:00:23.679048 INFO: Starting optimization step 1.
3:00:23.679104 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:23.679161 INFO: Using rust extraction backend
3:00:23.679214 PROGRESS: Extracting batch of 5956 precursors
3:00:23.690427 INFO: === Search parameters used ===
3:00:23.690544 INFO: rt_error       : 493.3814871529938
3:00:23.690597 INFO: mobility_error : 0.1
3:00:23.690641 INFO: num_candidates : 3
3:00:23.690683 INFO: ms1_error      : 30
3:00:23.690723 INFO: ms2_error      : 10.0
3:00:23.690763 INFO: fwhm_rt        : 3.0
3:00:23.690812 INFO: quant_window   : 3
3:00:23.690853 INFO: ==============================================
3:00:23.795307 INFO: performing precursor FDR with 40 features
3:00:23.795435 INFO: Decoy channel: -1
3:00:23.795470 INFO: competitive: True
3:00:23.800023 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:23.804007 INFO: Estimating optimal hyperparameters - samples: 14,290, batch_size: 128, learning_rate: 1.77e-04
3:00:23.804129 INFO: Using random state 515797 for train-test-split
3:00:25.215131 INFO: Test AUC: 0.759
3:00:25.215239 INFO: Train AUC: 0.790
3:00:25.215267 INFO: AUC difference: 4.00%
3:00:25.468762 INFO: Resetting torch num_threads to 24
3:00:25.471225 PROGRESS: === Extracted 17863 precursors and 119997 fragments ===
3:00:25.471594 INFO: === FDR correction performed with classifier version 6 ===
3:00:25.472307 PROGRESS: ============================= Precursor FDR =============================
3:00:25.472391 PROGRESS: Total precursors accumulated: 2,652
3:00:25.472446 PROGRESS: Target precursors: 2,626 (99.02%)
3:00:25.472495 PROGRESS: Decoy precursors: 26 (0.98%)
3:00:25.472540 PROGRESS: 
3:00:25.472583 PROGRESS: Precursor Summary:
3:00:25.474195 PROGRESS: Channel   0:	 0.050 FDR: 2,626; 0.010 FDR: 2,626; 0.001 FDR: 2,132
3:00:25.474279 PROGRESS: 
3:00:25.474332 PROGRESS: Protein Summary:
3:00:25.476603 PROGRESS: Channel   0:	 0.050 FDR: 2,040; 0.010 FDR: 2,040; 0.001 FDR: 1,697
3:00:25.476707 PROGRESS: =========================================================================
3:00:25.477063 INFO: Target number of precursors reached.
3:00:25.502980 INFO: fragments_df: keeping 5000 of 119997 [sum(precursor_idx_mask)=59176 sum(mass_error_mask)=119997 stop_rank=5000
3:00:25.513834 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:25.829822 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:26.491470 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:26.491951 INFO: Using score_cutoff 9.656311955451965 (fac=0.99, q=1)
3:00:26.492289 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:26.492368 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:26.492423 INFO: Updating optimization_manager: score_cutoff        : 10.109591035366059 -> 9.656311955451965
3:00:26.492477 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:26.496416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:26.504218 INFO: === checking if optimization conditions were reached ===
3:00:26.504329 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
3:00:26.507152 INFO: Updating optimization_manager: rt_error            : 493.3814871529938 -> 494.37379198070795
3:00:26.507254 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 494.3738.
3:00:26.507319 INFO: ==============================================
3:00:26.507389 INFO: Starting optimization step 2.
3:00:26.507448 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:26.507528 INFO: Using rust extraction backend
3:00:26.507585 PROGRESS: Extracting batch of 5956 precursors
3:00:26.518827 INFO: === Search parameters used ===
3:00:26.518944 INFO: rt_error       : 494.37379198070795
3:00:26.518996 INFO: mobility_error : 0.1
3:00:26.519053 INFO: num_candidates : 3
3:00:26.519097 INFO: ms1_error      : 30
3:00:26.519139 INFO: ms2_error      : 10.0
3:00:26.519184 INFO: fwhm_rt        : 3.0
3:00:26.519226 INFO: quant_window   : 3
3:00:26.519268 INFO: ==============================================
3:00:26.626739 INFO: performing precursor FDR with 40 features
3:00:26.626843 INFO: Decoy channel: -1
3:00:26.626868 INFO: competitive: True
3:00:26.631827 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:26.635839 INFO: Estimating optimal hyperparameters - samples: 14,290, batch_size: 128, learning_rate: 1.77e-04
3:00:26.635963 INFO: Using random state 515797 for train-test-split
3:00:28.064753 INFO: Test AUC: 0.768
3:00:28.064862 INFO: Train AUC: 0.785
3:00:28.064892 INFO: AUC difference: 2.16%
3:00:28.316998 INFO: Resetting torch num_threads to 24
3:00:28.319452 PROGRESS: === Extracted 17863 precursors and 119999 fragments ===
3:00:28.319830 INFO: === FDR correction performed with classifier version 6 ===
3:00:28.320529 PROGRESS: ============================= Precursor FDR =============================
3:00:28.320616 PROGRESS: Total precursors accumulated: 2,689
3:00:28.320674 PROGRESS: Target precursors: 2,663 (99.03%)
3:00:28.320724 PROGRESS: Decoy precursors: 26 (0.97%)
3:00:28.320769 PROGRESS: 
3:00:28.320813 PROGRESS: Precursor Summary:
3:00:28.322414 PROGRESS: Channel   0:	 0.050 FDR: 2,663; 0.010 FDR: 2,663; 0.001 FDR: 2,163
3:00:28.322500 PROGRESS: 
3:00:28.322555 PROGRESS: Protein Summary:
3:00:28.324830 PROGRESS: Channel   0:	 0.050 FDR: 2,065; 0.010 FDR: 2,065; 0.001 FDR: 1,724
3:00:28.324925 PROGRESS: =========================================================================
3:00:28.325290 INFO: Target number of precursors reached.
3:00:28.351689 INFO: fragments_df: keeping 5000 of 119999 [sum(precursor_idx_mask)=59959 sum(mass_error_mask)=119999 stop_rank=5000
3:00:28.362519 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:28.781576 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:29.495667 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:29.496135 INFO: Using score_cutoff 9.651353269386291 (fac=0.99, q=1)
3:00:29.496449 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:29.496522 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:29.496575 INFO: Updating optimization_manager: score_cutoff        : 9.656311955451965 -> 9.651353269386291
3:00:29.496624 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:29.500588 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:29.508397 INFO: === checking if optimization conditions were reached ===
3:00:29.508505 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
3:00:29.511441 INFO: Updating optimization_manager: rt_error            : 494.37379198070795 -> 453.1798320381682
3:00:29.511559 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 453.1798.
3:00:29.511621 INFO: ==============================================
3:00:29.511687 INFO: Starting optimization step 3.
3:00:29.511742 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:29.511811 INFO: Using rust extraction backend
3:00:29.511864 PROGRESS: Extracting batch of 5956 precursors
3:00:29.523093 INFO: === Search parameters used ===
3:00:29.523206 INFO: rt_error       : 453.1798320381682
3:00:29.523257 INFO: mobility_error : 0.1
3:00:29.523302 INFO: num_candidates : 3
3:00:29.523351 INFO: ms1_error      : 30
3:00:29.523394 INFO: ms2_error      : 10.0
3:00:29.523434 INFO: fwhm_rt        : 3.0
3:00:29.523494 INFO: quant_window   : 3
3:00:29.523537 INFO: ==============================================
3:00:29.627849 INFO: performing precursor FDR with 40 features
3:00:29.627958 INFO: Decoy channel: -1
3:00:29.627983 INFO: competitive: True
3:00:29.632560 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:29.636634 INFO: Estimating optimal hyperparameters - samples: 14,289, batch_size: 128, learning_rate: 1.77e-04
3:00:29.636756 INFO: Using random state 515797 for train-test-split
3:00:31.066598 INFO: Test AUC: 0.768
3:00:31.066705 INFO: Train AUC: 0.788
3:00:31.066737 INFO: AUC difference: 2.54%
3:00:31.328112 INFO: Resetting torch num_threads to 24
3:00:31.330564 PROGRESS: === Extracted 17862 precursors and 119913 fragments ===
3:00:31.330924 INFO: === FDR correction performed with classifier version 6 ===
3:00:31.331641 PROGRESS: ============================= Precursor FDR =============================
3:00:31.331731 PROGRESS: Total precursors accumulated: 2,651
3:00:31.331801 PROGRESS: Target precursors: 2,625 (99.02%)
3:00:31.331852 PROGRESS: Decoy precursors: 26 (0.98%)
3:00:31.331899 PROGRESS: 
3:00:31.331943 PROGRESS: Precursor Summary:
3:00:31.333523 PROGRESS: Channel   0:	 0.050 FDR: 2,625; 0.010 FDR: 2,625; 0.001 FDR: 1,825
3:00:31.333612 PROGRESS: 
3:00:31.333668 PROGRESS: Protein Summary:
3:00:31.335879 PROGRESS: Channel   0:	 0.050 FDR: 2,041; 0.010 FDR: 2,041; 0.001 FDR: 1,480
3:00:31.335973 PROGRESS: =========================================================================
3:00:31.336327 INFO: Target number of precursors reached.
3:00:31.362727 INFO: fragments_df: keeping 5000 of 119913 [sum(precursor_idx_mask)=59150 sum(mass_error_mask)=119913 stop_rank=5000
3:00:31.374228 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:31.691436 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:32.339548 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:32.340005 INFO: Using score_cutoff 9.937318774795532 (fac=0.99, q=1)
3:00:32.340316 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:32.340392 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:32.340447 INFO: Updating optimization_manager: score_cutoff        : 9.651353269386291 -> 9.937318774795532
3:00:32.340501 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:32.344445 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:32.352171 INFO: === checking if optimization conditions were reached ===
3:00:32.352289 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
3:00:32.355212 INFO: Updating optimization_manager: rt_error            : 453.1798320381682 -> 436.14747641488964
3:00:32.355316 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 436.1475.
3:00:32.355380 INFO: ==============================================
3:00:32.355444 INFO: Starting optimization step 4.
3:00:32.355520 PROGRESS: === Extracting elution groups 0 to 3000 ===
3:00:32.355580 INFO: Using rust extraction backend
3:00:32.355632 PROGRESS: Extracting batch of 5956 precursors
3:00:32.366901 INFO: === Search parameters used ===
3:00:32.367017 INFO: rt_error       : 436.14747641488964
3:00:32.367086 INFO: mobility_error : 0.1
3:00:32.367132 INFO: num_candidates : 3
3:00:32.367174 INFO: ms1_error      : 30
3:00:32.367214 INFO: ms2_error      : 10.0
3:00:32.367254 INFO: fwhm_rt        : 3.0
3:00:32.367292 INFO: quant_window   : 3
3:00:32.367330 INFO: ==============================================
3:00:32.470776 INFO: performing precursor FDR with 40 features
3:00:32.470886 INFO: Decoy channel: -1
3:00:32.470909 INFO: competitive: True
3:00:32.475393 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:32.479343 INFO: Estimating optimal hyperparameters - samples: 14,288, batch_size: 128, learning_rate: 1.77e-04
3:00:32.479479 INFO: Using random state 515797 for train-test-split
3:00:33.897557 INFO: Test AUC: 0.766
3:00:33.897660 INFO: Train AUC: 0.786
3:00:33.897689 INFO: AUC difference: 2.61%
3:00:34.150003 INFO: Resetting torch num_threads to 24
3:00:34.152448 PROGRESS: === Extracted 17861 precursors and 119836 fragments ===
3:00:34.152807 INFO: === FDR correction performed with classifier version 6 ===
3:00:34.153503 PROGRESS: ============================= Precursor FDR =============================
3:00:34.153586 PROGRESS: Total precursors accumulated: 2,627
3:00:34.153643 PROGRESS: Target precursors: 2,601 (99.01%)
3:00:34.153692 PROGRESS: Decoy precursors: 26 (0.99%)
3:00:34.153735 PROGRESS: 
3:00:34.153778 PROGRESS: Precursor Summary:
3:00:34.155370 PROGRESS: Channel   0:	 0.050 FDR: 2,601; 0.010 FDR: 2,601; 0.001 FDR: 2,069
3:00:34.155469 PROGRESS: 
3:00:34.155532 PROGRESS: Protein Summary:
3:00:34.157714 PROGRESS: Channel   0:	 0.050 FDR: 2,023; 0.010 FDR: 2,023; 0.001 FDR: 1,653
3:00:34.157801 PROGRESS: =========================================================================
3:00:34.158147 INFO: Target number of precursors reached.
3:00:34.184296 INFO: fragments_df: keeping 5000 of 119836 [sum(precursor_idx_mask)=58641 sum(mass_error_mask)=119836 stop_rank=5000
3:00:34.195056 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:00:34.508319 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:00:35.154733 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:00:35.155185 INFO: Using score_cutoff 9.888416376113891 (fac=0.99, q=1)
3:00:35.155503 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:35.155583 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:35.155635 INFO: Updating optimization_manager: score_cutoff        : 9.937318774795532 -> 9.888416376113891
3:00:35.155685 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:35.159682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:35.167406 INFO: === checking if optimization conditions were reached ===
3:00:35.167581 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
3:00:35.168381 INFO: Updating optimization_manager: rt_error            : 436.14747641488964 -> 494.37379198070795
3:00:35.168504 INFO: Updating optimization_manager: classifier_version  : 6 -> 9
3:00:35.168597 INFO: Updating optimization_manager: score_cutoff        : 9.888416376113891 -> 9.651353269386291
3:00:35.168681 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
3:00:35.168761 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
3:00:35.168854 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 494.3738 found after 5 searches.
3:00:35.168917 INFO: ==============================================
3:00:35.168988 PROGRESS: Optimization finished for rt_error.
3:00:35.179829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:35.184007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:35.191948 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:00:35.192063 PROGRESS: ==============================================
3:00:35.192135 PROGRESS: ms2_error      : 10.0000
3:00:35.192189 PROGRESS: rt_error       : 494.3738
3:00:35.192233 PROGRESS: ==============================================
3:00:35.192826 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:00:35.334019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:00:35.694975 INFO: Using rust extraction backend
3:00:35.695271 PROGRESS: Extracting batch of 262809 precursors
3:00:36.118433 INFO: === Search parameters used ===
3:00:36.118703 INFO: rt_error       : 494.37379198070795
3:00:36.118763 INFO: mobility_error : 0.1
3:00:36.118813 INFO: num_candidates : 3
3:00:36.118855 INFO: ms1_error      : 30
3:00:36.118895 INFO: ms2_error      : 10.0
3:00:36.118933 INFO: fwhm_rt        : 3.0
3:00:36.118970 INFO: quant_window   : 3
3:00:36.119008 INFO: ==============================================
3:00:37.236914 INFO: Removed 71250 precursors with score below cutoff 9.651353269386291
3:00:37.883093 INFO: performing precursor FDR with 40 features
3:00:37.883211 INFO: Decoy channel: -1
3:00:37.883237 INFO: competitive: True
3:00:37.941877 INFO: Setting torch num_threads to 2 for FDR classification task
3:00:38.162810 INFO: Estimating optimal hyperparameters - samples: 573,741, batch_size: 2,350, learning_rate: 7.57e-04
3:00:38.163825 INFO: Using random state 748076 for train-test-split
3:00:50.113745 INFO: Test AUC: 0.776
3:00:50.113876 INFO: Train AUC: 0.779
3:00:50.113909 INFO: AUC difference: 0.42%
3:00:50.648386 INFO: Resetting torch num_threads to 24
3:00:50.954281 PROGRESS: ============================= Precursor FDR =============================
3:00:50.954554 PROGRESS: Total precursors accumulated: 123,276
3:00:50.954624 PROGRESS: Target precursors: 122,057 (99.01%)
3:00:50.954680 PROGRESS: Decoy precursors: 1,219 (0.99%)
3:00:50.954729 PROGRESS: 
3:00:50.954776 PROGRESS: Precursor Summary:
3:00:50.992422 PROGRESS: Channel   0:	 0.050 FDR: 122,057; 0.010 FDR: 122,057; 0.001 FDR: 109,297
3:00:50.992697 PROGRESS: 
3:00:50.992762 PROGRESS: Protein Summary:
3:00:51.050984 PROGRESS: Channel   0:	 0.050 FDR: 10,376; 0.010 FDR: 10,376; 0.001 FDR: 10,201
3:00:51.051217 PROGRESS: =========================================================================
3:00:51.053684 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
3:00:51.256777 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
3:00:51.551695 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:00:52.235582 PROGRESS: Processing search outputs
3:00:52.235708 PROGRESS: === Performing protein grouping and FDR ===
3:00:52.235745 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:00:52.325312 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:00:52.401390 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:00:52.480402 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:00:52.554953 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:00:52.627049 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:00:52.720339 INFO: Performing protein inference
3:00:53.746645 INFO: Inference strategy: library. Using library grouping for protein inference
3:00:53.751106 INFO: Performing protein FDR
3:00:59.861572 INFO: Normalizing q-values using 10,386 targets and 3,700 decoys
3:00:59.864344 INFO: Test AUC: 1.000
3:00:59.864394 INFO: Train AUC: 1.000
3:00:59.864425 INFO: AUC difference: 0.00%
3:01:00.666879 INFO: ================ Protein FDR =================
3:01:00.667025 INFO: Unique protein groups in output
3:01:00.667057 INFO:   1% protein FDR: 10,383
3:01:00.667078 INFO: 
3:01:00.667200 INFO: Unique precursor in output
3:01:00.667221 INFO:   1% protein FDR: 132,391
3:01:00.667239 INFO: ================================================
3:01:00.754212 PROGRESS: Building search statistics
3:01:00.888740 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
3:01:00.888940 INFO: Initializing OptimizationManager
3:01:00.889180 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
3:01:00.889253 INFO: Initializing CalibrationManager
3:01:00.889471 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
3:01:00.889545 INFO: Initializing RawFileManager
3:01:00.932476 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
3:01:00.932670 INFO: Initializing OptimizationManager
3:01:00.932889 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
3:01:00.932964 INFO: Initializing CalibrationManager
3:01:00.933191 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
3:01:00.933270 INFO: Initializing RawFileManager
3:01:00.976056 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
3:01:00.976258 INFO: Initializing OptimizationManager
3:01:00.976469 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
3:01:00.976547 INFO: Initializing CalibrationManager
3:01:00.976766 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
3:01:00.976839 INFO: Initializing RawFileManager
3:01:01.021029 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
3:01:01.021216 INFO: Initializing OptimizationManager
3:01:01.021428 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
3:01:01.021500 INFO: Initializing CalibrationManager
3:01:01.021722 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
3:01:01.021794 INFO: Initializing RawFileManager
3:01:01.065367 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
3:01:01.065556 INFO: Initializing OptimizationManager
3:01:01.065786 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
3:01:01.065871 INFO: Initializing CalibrationManager
3:01:01.066094 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
3:01:01.066166 INFO: Initializing RawFileManager
3:01:01.108733 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
3:01:01.108917 INFO: Initializing OptimizationManager
3:01:01.109140 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
3:01:01.109209 INFO: Initializing CalibrationManager
3:01:01.109426 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
3:01:01.109496 INFO: Initializing RawFileManager
3:01:01.113164 INFO: Writing stat output to disk
3:01:01.113226 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
3:01:01.124007 PROGRESS: Building internal statistics
3:01:01.124352 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
3:01:01.124394 INFO: Initializing TimingManager
3:01:01.124797 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
3:01:01.124833 INFO: Initializing TimingManager
3:01:01.125031 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
3:01:01.125066 INFO: Initializing TimingManager
3:01:01.125258 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
3:01:01.125291 INFO: Initializing TimingManager
3:01:01.125474 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
3:01:01.125506 INFO: Initializing TimingManager
3:01:01.125707 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
3:01:01.125740 INFO: Initializing TimingManager
3:01:01.126201 INFO: Writing internal output to disk
3:01:01.126247 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
3:01:01.222352 INFO: Performing label free quantification
3:01:01.222501 INFO: Accumulating fragment data
3:01:01.222560 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:01:01.306443 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:01:02.910727 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:01:04.546670 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:01:06.229259 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:01:07.966087 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:01:09.937320 INFO: Performing label free quantification on the precursor level
3:01:09.937477 INFO: Filtering fragments by quality
3:01:10.343556 INFO: Performing label-free quantification with directlfq normalization
3:01:10.984597 INFO: 132391 lfq-groups total
3:01:46.407094 INFO: using 24 processes
3:01:47.053762 INFO: lfq-object 0
3:01:47.898233 INFO: lfq-object 100
3:01:48.022897 INFO: lfq-object 200
3:01:48.150867 INFO: lfq-object 300
3:01:48.182473 INFO: lfq-object 1400
3:01:48.278714 INFO: lfq-object 400
3:01:48.314574 INFO: lfq-object 1500
3:01:48.410850 INFO: lfq-object 500
3:01:48.444271 INFO: lfq-object 1600
3:01:48.541417 INFO: lfq-object 600
3:01:48.574078 INFO: lfq-object 1700
3:01:48.598695 INFO: lfq-object 2800
3:01:48.671344 INFO: lfq-object 700
3:01:48.698148 INFO: lfq-object 1800
3:01:48.726368 INFO: lfq-object 2900
3:01:48.801535 INFO: lfq-object 800
3:01:48.825611 INFO: lfq-object 1900
3:01:48.855704 INFO: lfq-object 3000
3:01:48.933843 INFO: lfq-object 900
3:01:48.952611 INFO: lfq-object 2000
3:01:48.983332 INFO: lfq-object 3100
3:01:49.035124 INFO: lfq-object 6900
3:01:49.055005 INFO: lfq-object 4200
3:01:49.063798 INFO: lfq-object 1000
3:01:49.083050 INFO: lfq-object 2100
3:01:49.111384 INFO: lfq-object 3200
3:01:49.182171 INFO: lfq-object 4300
3:01:49.190944 INFO: lfq-object 1100
3:01:49.213262 INFO: lfq-object 2200
3:01:49.239602 INFO: lfq-object 3300
3:01:49.312503 INFO: lfq-object 4400
3:01:49.322243 INFO: lfq-object 1200
3:01:49.340358 INFO: lfq-object 2300
3:01:49.370078 INFO: lfq-object 3400
3:01:49.448312 INFO: lfq-object 4500
3:01:49.452853 INFO: lfq-object 1300
3:01:49.465503 INFO: lfq-object 5600
3:01:49.467474 INFO: lfq-object 2400
3:01:49.494259 INFO: lfq-object 3500
3:01:49.577787 INFO: lfq-object 4600
3:01:49.594613 INFO: lfq-object 2500
3:01:49.596303 INFO: lfq-object 5700
3:01:49.624316 INFO: lfq-object 3600
3:01:49.708411 INFO: lfq-object 4700
3:01:49.722475 INFO: lfq-object 2600
3:01:49.724132 INFO: lfq-object 5800
3:01:49.750696 INFO: lfq-object 3700
3:01:49.835943 INFO: lfq-object 4800
3:01:49.851509 INFO: lfq-object 5900
3:01:49.851974 INFO: lfq-object 2700
3:01:49.881940 INFO: lfq-object 7000
3:01:49.882350 INFO: lfq-object 3800
3:01:49.962928 INFO: lfq-object 4900
3:01:49.980105 INFO: lfq-object 6000
3:01:50.009607 INFO: lfq-object 3900
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3:05:27.396403 INFO: lfq-object 118300
3:05:27.434129 INFO: lfq-object 119000
3:05:27.494435 INFO: lfq-object 120000
3:05:27.525263 INFO: lfq-object 118400
3:05:27.567111 INFO: lfq-object 119100
3:05:27.626971 INFO: lfq-object 120100
3:05:27.651542 INFO: lfq-object 118500
3:05:27.701344 INFO: lfq-object 119200
3:05:27.760134 INFO: lfq-object 120200
3:05:27.797021 INFO: lfq-object 118600
3:05:27.836763 INFO: lfq-object 119300
3:05:27.892931 INFO: lfq-object 120300
3:05:27.927376 INFO: lfq-object 118700
3:05:27.972655 INFO: lfq-object 119400
3:05:28.022159 INFO: lfq-object 120400
3:05:28.108289 INFO: lfq-object 119500
3:05:28.157589 INFO: lfq-object 120500
3:05:28.239615 INFO: lfq-object 119600
3:05:28.291742 INFO: lfq-object 120600
3:05:28.371161 INFO: lfq-object 119700
3:05:28.424076 INFO: lfq-object 120700
3:05:28.498093 INFO: lfq-object 119800
3:05:28.556930 INFO: lfq-object 120800
3:05:28.625655 INFO: lfq-object 119900
3:05:28.688695 INFO: lfq-object 120900
3:05:28.819168 INFO: lfq-object 121000
3:05:28.951815 INFO: lfq-object 121100
3:05:35.174900 INFO: Performing label free quantification on the pg level
3:05:35.175287 INFO: Filtering fragments by quality
3:05:35.642128 INFO: Performing label-free quantification with directlfq normalization
3:05:35.858593 INFO: 10383 lfq-groups total
3:05:44.006810 INFO: using 24 processes
3:05:44.081171 INFO: lfq-object 0
3:05:45.273091 INFO: lfq-object 1100
3:05:45.273302 INFO: lfq-object 100
3:05:45.329879 INFO: lfq-object 1200
3:05:45.343148 INFO: lfq-object 800
3:05:45.365790 INFO: lfq-object 400
3:05:45.401284 INFO: lfq-object 900
3:05:45.407400 INFO: lfq-object 1000
3:05:45.430727 INFO: lfq-object 500
3:05:45.451723 INFO: lfq-object 700
3:05:45.485374 INFO: lfq-object 600
3:05:45.502755 INFO: lfq-object 300
3:05:45.587020 INFO: lfq-object 2000
3:05:45.628206 INFO: lfq-object 200
3:05:45.684915 INFO: lfq-object 1800
3:05:45.707066 INFO: lfq-object 1900
3:05:45.766439 INFO: lfq-object 2400
3:05:45.785851 INFO: lfq-object 2100
3:05:45.857270 INFO: lfq-object 1700
3:05:45.898429 INFO: lfq-object 2300
3:05:45.900047 INFO: lfq-object 2200
3:05:45.975045 INFO: lfq-object 2800
3:05:46.051895 INFO: lfq-object 3000
3:05:46.073361 INFO: lfq-object 1600
3:05:46.099147 INFO: lfq-object 3400
3:05:46.117750 INFO: lfq-object 1300
3:05:46.117888 INFO: lfq-object 2700
3:05:46.121955 INFO: lfq-object 3500
3:05:46.135516 INFO: lfq-object 1500
3:05:46.168967 INFO: lfq-object 3300
3:05:46.178449 INFO: lfq-object 3600
3:05:46.206279 INFO: lfq-object 3200
3:05:46.374071 INFO: lfq-object 1400
3:05:46.404575 INFO: lfq-object 2900
3:05:46.410209 INFO: lfq-object 3100
3:05:46.571295 INFO: lfq-object 2500
3:05:46.668424 INFO: lfq-object 3800
3:05:46.681980 INFO: lfq-object 2600
3:05:46.690038 INFO: lfq-object 4100
3:05:46.718873 INFO: lfq-object 4200
3:05:46.722573 INFO: lfq-object 4000
3:05:46.780457 INFO: lfq-object 4300
3:05:46.815828 INFO: lfq-object 3900
3:05:46.838558 INFO: lfq-object 4800
3:05:46.850802 INFO: lfq-object 4700
3:05:46.862670 INFO: lfq-object 4500
3:05:46.903404 INFO: lfq-object 4400
3:05:46.942744 INFO: lfq-object 3700
3:05:46.999713 INFO: lfq-object 4600
3:05:47.143581 INFO: lfq-object 5100
3:05:47.197598 INFO: lfq-object 5200
3:05:47.307012 INFO: lfq-object 5600
3:05:47.342367 INFO: lfq-object 5900
3:05:47.352997 INFO: lfq-object 5700
3:05:47.353675 INFO: lfq-object 6000
3:05:47.376625 INFO: lfq-object 5800
3:05:47.477944 INFO: lfq-object 5400
3:05:47.603562 INFO: lfq-object 5000
3:05:47.666214 INFO: lfq-object 5500
3:05:47.691669 INFO: lfq-object 5300
3:05:47.696762 INFO: lfq-object 6100
3:05:47.732586 INFO: lfq-object 4900
3:05:47.748775 INFO: lfq-object 6400
3:05:47.758592 INFO: lfq-object 6200
3:05:47.778800 INFO: lfq-object 6500
3:05:47.785790 INFO: lfq-object 6300
3:05:47.837242 INFO: lfq-object 7100
3:05:47.852083 INFO: lfq-object 7200
3:05:47.893770 INFO: lfq-object 6700
3:05:47.925321 INFO: lfq-object 7000
3:05:48.041923 INFO: lfq-object 6900
3:05:48.044752 INFO: lfq-object 6800
3:05:48.065462 INFO: lfq-object 6600
3:05:48.103105 INFO: lfq-object 7400
3:05:48.203196 INFO: lfq-object 7300
3:05:48.247078 INFO: lfq-object 7500
3:05:48.340799 INFO: lfq-object 7700
3:05:48.363201 INFO: lfq-object 7800
3:05:48.418401 INFO: lfq-object 7600
3:05:48.479361 INFO: lfq-object 7900
3:05:48.521044 INFO: lfq-object 8000
3:05:48.521916 INFO: lfq-object 8100
3:05:48.574519 INFO: lfq-object 8200
3:05:48.632527 INFO: lfq-object 8300
3:05:48.648349 INFO: lfq-object 8400
3:05:48.959900 INFO: lfq-object 8500
3:05:48.976748 INFO: lfq-object 8700
3:05:49.050241 INFO: lfq-object 9100
3:05:49.057404 INFO: lfq-object 8600
3:05:49.094450 INFO: lfq-object 9200
3:05:49.113286 INFO: lfq-object 9500
3:05:49.123277 INFO: lfq-object 9300
3:05:49.123600 INFO: lfq-object 9000
3:05:49.137144 INFO: lfq-object 9400
3:05:49.153276 INFO: lfq-object 9600
3:05:49.190325 INFO: lfq-object 8900
3:05:49.279701 INFO: lfq-object 8800
3:05:49.458745 INFO: lfq-object 9700
3:05:49.546917 INFO: lfq-object 9800
3:05:49.621830 INFO: lfq-object 9900
3:05:49.622060 INFO: lfq-object 10000
3:05:49.664186 INFO: lfq-object 10200
3:05:49.699955 INFO: lfq-object 10100
3:05:49.878672 INFO: lfq-object 10300
3:05:52.202841 INFO: Writing psm output to disk
3:05:52.329396 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
3:05:53.320538 INFO: Writing precursor output to disk
3:05:53.325669 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
3:05:53.443144 INFO: Writing peptide output to disk
3:05:53.448833 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
3:05:53.559884 INFO: Writing pg output to disk
3:05:53.563044 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
3:05:53.664119 PROGRESS: Building MBR spectral library
3:05:53.664315 INFO: Running MbrLibraryBuilder
3:05:54.109900 INFO: MBR spectral library contains 132,391 precursors, 10,383 proteins
3:05:54.110033 INFO: Writing MBR spectral library to disk
3:05:55.035610 PROGRESS: =================== Search step 'mbr' finished ===================
3:05:55.089166 INFO: =================== Search Finished ===================
