0:00:00.000054 INFO: Output directory: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output/work/68/3e5a78e26d0e1120e030fe3c55768e.
0:00:00.000183 INFO: User provided config file: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.013171 PROGRESS:           _      _         ___ ___   _   
0:00:00.013232 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.013264 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.013288 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.013309 PROGRESS:            |_|                           
0:00:00.013332 PROGRESS: 
0:00:00.013357 PROGRESS: version: 2.1.1
0:00:00.013377 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.013404 INFO: hostname: thestral
0:00:00.013436 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.013464 PROGRESS: python: 3.11.11 (CPython)
0:00:00.013516 INFO: date: 2026-07-10 10:15:51
0:00:00.013535 INFO: ================ AlphaX Environment ===============
0:00:00.013554 INFO: alphabase       : 1.8.1
0:00:00.013572 INFO: alpharaw        : 0.5.0
0:00:00.013589 INFO: alphatims       : 1.0.9
0:00:00.013606 INFO: alphapeptdeep   : 1.4.2
0:00:00.013623 INFO: directlfq       : 0.3.3
0:00:00.013638 INFO: ===================================================
0:00:00.013653 INFO: ================= Pip Environment =================
0:00:00.082253 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
0:00:00.082341 INFO: ===================================================
0:00:00.082385 INFO: =================== Running step 'library' ===================
0:00:00.082464 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
0:00:00.095115 INFO: loading additional config provided via CLI
0:00:00.095183 INFO: loading additional config provided via CLI parameters
0:00:00.095559 INFO: Updating config with 'user defined'
0:00:00.095631 INFO: Updating config with 'user defined (cli)'
0:00:00.095690 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/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 100, 'mbr_step_enabled': False, 'transfer_step_enabled': False}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [380.0, 980.0], 'fragment_mz': [150.0, 2000.0]}, 'search': {'target_ms1_tolerance': 3, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}, 'search_initial': {'ms1_tolerance': 3, 'ms2_tolerance': 10}}, {'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw']}]
0:00:00.095899 INFO: Updating config with 'user defined'
0:00:00.095946 INFO: Updating config with 'user defined (cli)'
0:00:00.095987 INFO: ├──version: None
0:00:00.096011 INFO: ├──workflow_name: None
0:00:00.096031 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1 [user defined, default: None][0m
0:00:00.096052 INFO: ├──library_path: None
0:00:00.096071 INFO: ├──raw_paths:
0:00:00.096091 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.096109 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.096126 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.096146 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.096163 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.096180 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.096198 INFO: ├──fasta_paths:
0:00:00.096215 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.096242 INFO: ├──quant_directory: None
0:00:00.096259 INFO: ├──general
0:00:00.096283 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.096302 INFO: │   ├──transfer_step_enabled: False
0:00:00.096319 INFO: │   ├──mbr_step_enabled: False
0:00:00.096337 INFO: │   ├──reuse_calibration: False
0:00:00.096354 INFO: │   ├──reuse_quant: False
0:00:00.096372 INFO: │   ├──log_level: INFO
0:00:00.096389 INFO: │   ├──use_gpu: True
0:00:00.096406 INFO: │   ├──save_figures: True
0:00:00.096423 INFO: │   ├──save_library: True
0:00:00.096442 INFO: │   ├──save_flat_library: False
0:00:00.096461 INFO: │   ├──input_library_type: base
0:00:00.096478 INFO: │   ├──save_mbr_library: True
0:00:00.096495 INFO: │   ├──random_state: None
0:00:00.096513 INFO: │   └──fail_fast: False
0:00:00.096530 INFO: ├──library_loading
0:00:00.096549 INFO: │   └──drop_decoys: False
0:00:00.096566 INFO: ├──library_prediction
0:00:00.096586 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.096604 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.096622 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.096640 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.096658 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.096675 INFO: │   ├──missed_cleavages: 1
0:00:00.096692 INFO: │   ├──precursor_len:
0:00:00.096710 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.096729 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.096747 INFO: │   ├──precursor_charge:
0:00:00.096764 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.096781 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.096797 INFO: │   ├──precursor_mz:
0:00:00.096815 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
0:00:00.096832 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
0:00:00.096848 INFO: │   ├──fragment_mz:
0:00:00.096865 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
0:00:00.096881 INFO: │   │   - 2000.0
0:00:00.096899 INFO: │   ├──nce: 25.0
0:00:00.096916 INFO: │   ├──fragment_types:
0:00:00.096933 INFO: │   │   - b
0:00:00.096949 INFO: │   │   - y
0:00:00.096966 INFO: │   ├──max_fragment_charge: 2
0:00:00.096983 INFO: │   ├──instrument: Lumos
0:00:00.097001 INFO: │   ├──peptdeep_model_path: None
0:00:00.097018 INFO: │   ├──peptdeep_model_type: generic
0:00:00.097035 INFO: │   ├──predict_charge: False
0:00:00.097053 INFO: │   └──min_charge_probability: 0.1
0:00:00.097070 INFO: ├──custom_modifications:
0:00:00.097089 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.097106 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.097124 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.097141 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.097158 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.097175 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.097193 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.097209 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.097226 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.097243 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.097261 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.097278 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.097295 INFO: │   ├──name: Label:13C(12)@K
0:00:00.097312 INFO: │   └──composition: C(12)
0:00:00.097329 INFO: ├──search
0:00:00.097346 INFO: │   ├──extraction_backend: rust
0:00:00.097363 INFO: │   [32;20m├──target_ms1_tolerance: 3 [user defined, default: 5][0m
0:00:00.097390 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.097410 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.097428 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.097445 INFO: │   ├──quant_window: 3
0:00:00.097462 INFO: │   ├──target_num_candidates: 3
0:00:00.097479 INFO: │   ├──channel_filter: 
0:00:00.097497 INFO: │   ├──compete_for_fragments: True
0:00:00.097513 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.097530 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.097548 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.097565 INFO: │   ├──optimized_peak_group_score: False
0:00:00.097582 INFO: │   ├──exclude_shared_ions: True
0:00:00.097599 INFO: │   ├──quant_all: True
0:00:00.097616 INFO: │   └──experimental_xic: True
0:00:00.097633 INFO: ├──calibration
0:00:00.097651 INFO: │   ├──batch_size: 1000
0:00:00.097669 INFO: │   ├──optimization_lock_target: 1000
0:00:00.097688 INFO: │   ├──max_steps: 20
0:00:00.097705 INFO: │   ├──min_steps: 5
0:00:00.097723 INFO: │   ├──max_skips: 1
0:00:00.097741 INFO: │   ├──max_fragments: 5000
0:00:00.097759 INFO: │   └──min_correlation: 0.7
0:00:00.097776 INFO: ├──search_initial
0:00:00.097794 INFO: │   ├──num_candidates: 1
0:00:00.097811 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
0:00:00.097829 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
0:00:00.097847 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.097865 INFO: │   └──rt_tolerance: 0.5
0:00:00.097882 INFO: ├──library_multiplexing
0:00:00.097912 INFO: │   ├──enabled: False
0:00:00.097934 INFO: │   ├──input_channel: 0
0:00:00.097952 INFO: │   └──multiplex_mapping:
0:00:00.097969 INFO: ├──multiplexing
0:00:00.097986 INFO: │   ├──enabled: False
0:00:00.098004 INFO: │   ├──target_channels: 4,8
0:00:00.098021 INFO: │   ├──decoy_channel: 12
0:00:00.098037 INFO: │   ├──reference_channel: 0
0:00:00.098054 INFO: │   └──competitive_scoring: True
0:00:00.098070 INFO: ├──fdr
0:00:00.098087 INFO: │   ├──fdr: 0.01
0:00:00.098104 INFO: │   ├──group_level: proteins
0:00:00.098121 INFO: │   ├──inference_strategy: heuristic
0:00:00.098139 INFO: │   ├──competitive_scoring: True
0:00:00.098155 INFO: │   ├──keep_decoys: False
0:00:00.098172 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.098190 INFO: │   ├──channel_wise_fdr: False
0:00:00.098207 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.098223 INFO: ├──search_output
0:00:00.098241 INFO: │   ├──file_format: parquet
0:00:00.098258 INFO: │   ├──precursor_level_lfq: True
0:00:00.098275 INFO: │   ├──peptide_level_lfq: True
0:00:00.098292 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.098309 INFO: │   ├──min_k_fragments: 12
0:00:00.098326 INFO: │   ├──min_correlation: 0.9
0:00:00.098344 INFO: │   ├──num_samples_quadratic: 50
0:00:00.098360 INFO: │   ├──min_nonnan: 3
0:00:00.098377 INFO: │   ├──normalization_method: directlfq
0:00:00.098395 INFO: │   └──normalize_directlfq: True
0:00:00.098412 INFO: ├──optimization
0:00:00.098429 INFO: │   ├──order_of_optimization: None
0:00:00.098446 INFO: │   ├──ms2_error
0:00:00.098464 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.098483 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.098500 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.098518 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.098536 INFO: │   │   ├──try_narrower_values: True
0:00:00.098554 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.098571 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.098592 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.098609 INFO: │   ├──ms1_error
0:00:00.098629 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.098646 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.098663 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.098680 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.098697 INFO: │   │   ├──try_narrower_values: False
0:00:00.098714 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.098731 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.098748 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.098765 INFO: │   ├──mobility_error
0:00:00.098782 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.098799 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.098816 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.098834 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.098851 INFO: │   │   ├──try_narrower_values: False
0:00:00.098869 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.098887 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.098904 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.098921 INFO: │   └──rt_error
0:00:00.098939 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.098957 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.098974 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.098993 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.099010 INFO: │       ├──try_narrower_values: True
0:00:00.099028 INFO: │       ├──maximal_decrease: 0.1
0:00:00.099045 INFO: │       ├──favour_narrower_optimum: False
0:00:00.099063 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.099080 INFO: ├──optimization_manager
0:00:00.099097 INFO: │   ├──fwhm_rt: 5
0:00:00.099115 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.099133 INFO: │   └──score_cutoff: 0
0:00:00.099150 INFO: ├──transfer_library
0:00:00.099168 INFO: │   ├──enabled: False
0:00:00.099185 INFO: │   ├──fragment_types:
0:00:00.099201 INFO: │   │   - b
0:00:00.099218 INFO: │   │   - y
0:00:00.099236 INFO: │   ├──max_charge: 2
0:00:00.099252 INFO: │   ├──top_k_samples: 3
0:00:00.099269 INFO: │   ├──norm_delta_max: True
0:00:00.099287 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.099304 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.099321 INFO: └──transfer_learning
0:00:00.099338 INFO:     ├──enabled: False
0:00:00.099355 INFO:     ├──batch_size: 2000
0:00:00.099373 INFO:     ├──max_lr: 0.0001
0:00:00.099390 INFO:     ├──train_fraction: 0.7
0:00:00.099408 INFO:     ├──validation_fraction: 0.2
0:00:00.099425 INFO:     ├──test_fraction: 0.1
0:00:00.099442 INFO:     ├──test_interval: 1
0:00:00.099458 INFO:     ├──lr_patience: 3
0:00:00.099476 INFO:     ├──epochs: 51
0:00:00.099493 INFO:     ├──warmup_epochs: 5
0:00:00.099509 INFO:     ├──nce: 25
0:00:00.099527 INFO:     └──instrument: Lumos
0:00:00.104837 INFO: Registering 7 custom modifications
0:00:00.139278 INFO: Searching 6 files:
0:00:00.139351 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.139374 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.139393 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.139410 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.139426 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.139443 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.139459 INFO: Using 1 fasta files:
0:00:00.139475 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.139495 INFO: Using library: None
0:00:00.139511 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1
0:00:00.139539 PROGRESS: Loading spectral library
0:00:00.139566 PROGRESS: No library provided. Building library from fasta files.
0:00:00.139603 INFO: Running FastaDigest
0:00:00.141242 INFO: Digesting fasta file
0:00:07.038294 INFO: Adding modifications
0:01:55.333295 INFO: Removing non-canonical amino acids
0:02:01.743774 INFO: Fasta library contains 6,091,314 precursors
0:02:01.743981 PROGRESS: Predicting library properties.
0:02:01.744075 INFO: Running PeptDeepPrediction
0:02:01.745151 INFO: Device set to cpu
0:02:03.541173 INFO: Loading PeptDeep models of type generic
0:02:04.556020 INFO: Predicting RT, MS2 and mobility
0:02:04.556250 INFO: Using multiprocessing with 100 processes ...
0:02:04.951787 INFO: Predicting rt,ms2,mobility ...
0:08:32.504354 INFO: Adding fragment mz information
0:08:32.806768 INFO: Adding fragment intensity information
0:08:33.109314 INFO: Adding precursor information
0:08:33.488528 INFO: Running PrecursorInitializer
0:08:33.513459 INFO: Running AnnotateFasta
0:09:03.603997 INFO: Running IsotopeGenerator
0:09:03.605190 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:13:32.731943 INFO: Running RTNormalization
0:13:32.732251 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:13:32.732353 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/speclib.hdf
0:14:08.231105 INFO: Running DecoyGenerator
0:16:07.285785 INFO: Running FlattenLibrary
0:16:36.213654 INFO: Running InitFlatColumns
0:16:36.432715 INFO: Running LogFlatLibraryStats
0:16:36.432852 INFO: ============ Library Stats ============
0:16:36.432887 INFO: Number of precursors: 12,150,378
0:16:38.034059 INFO: 	thereof targets:6,091,314
0:16:38.034294 INFO: 	thereof decoys: 6,059,064
0:16:38.113274 INFO: Number of elution groups: 6,091,314
0:16:38.113405 INFO: 	average size: 1.99
0:16:38.412377 INFO: Number of proteins: 117,993
0:16:38.445134 INFO: Number of channels: 1 ([0])
0:16:38.445353 INFO: Isotopes Distribution for 4 isotopes
0:16:38.445385 INFO: =======================================
0:16:38.445466 PROGRESS: =================== Starting Search Workflows for step library ===================
0:16:38.445595 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:16:38.445655 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant
0:16:38.445753 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:16:38.446037 INFO: Initializing TimingManager
0:16:38.446512 INFO: Initializing RawFileManager
0:16:48.468047 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:16:48.476605 INFO: Determining DIA cycle
0:16:48.798510 INFO: Found cycle with start 0.00 min and length 300.
0:16:48.961673 INFO: RT (min)            : 0.0 - 26.9
0:16:48.962537 INFO: RT duration (sec)   : 1611.2
0:16:48.962569 INFO: RT duration (min)   : 26.9
0:16:48.962593 INFO: Cycle len (scans)   : 300
0:16:48.962613 INFO: Cycle len (sec)     : 1.65
0:16:48.962633 INFO: Number of cycles    : 977
0:16:48.962654 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:16:48.962680 INFO: Creating DIA data object took: 10.516071319580078
0:16:49.731495 INFO: Creating DIA data NG object took: 0.7677464485168457
0:16:50.940512 INFO: Initializing CalibrationManager
0:16:50.940797 INFO: Setting up calibration estimators ..
0:16:50.940863 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:16:50.940945 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:16:50.941047 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:16:50.941104 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:16:50.941164 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:16:50.941219 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:16:50.941268 INFO: Done setting up calibration estimators.
0:16:50.941469 INFO: Initializing OptimizationManager
0:16:50.941597 INFO: initial parameter: ms1_error = 3
0:16:50.941651 INFO: initial parameter: ms2_error = 10
0:16:50.941697 INFO: initial parameter: rt_error = 805.5992431640625
0:16:50.941741 INFO: initial parameter: mobility_error = 0.1
0:16:50.941782 INFO: initial parameter: num_candidates = 1
0:16:50.941821 INFO: initial parameter: fwhm_rt = 5
0:16:50.941863 INFO: initial parameter: fwhm_mobility = 0.01
0:16:50.941920 INFO: initial parameter: score_cutoff = 0
0:16:50.941968 INFO: initial parameter: classifier_version = -1
0:16:50.942037 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:16:50.942279 INFO: FDRManager: loading saved state not requested, will be initialized.
0:16:50.942312 INFO: Initializing FDRManager
0:16:50.942350 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:16:52.304517 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:16:53.763328 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:16:53.763787 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:16:53.763907 PROGRESS: Starting initial search for precursors.
0:16:53.763993 INFO: Starting optimization step 0.
0:16:53.764056 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:16:53.764118 INFO: Using rust extraction backend
0:16:53.764183 PROGRESS: Extracting batch of 1965 precursors
0:16:53.769107 INFO: === Search parameters used ===
0:16:53.769217 INFO: rt_error       : 805.5992431640625
0:16:53.769267 INFO: mobility_error : 0.1
0:16:53.769311 INFO: num_candidates : 1
0:16:53.769352 INFO: ms1_error      : 3
0:16:53.769394 INFO: ms2_error      : 10
0:16:53.769436 INFO: fwhm_rt        : 5
0:16:53.769481 INFO: quant_window   : 3
0:16:53.769521 INFO: ==============================================
0:16:53.795072 INFO: performing precursor FDR with 40 features
0:16:53.795136 INFO: Decoy channel: -1
0:16:53.795159 INFO: competitive: True
0:16:53.796383 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:53.798455 INFO: Estimating optimal hyperparameters - samples: 1,570, batch_size: 128, learning_rate: 1.77e-04
0:16:53.799259 INFO: Using random state 706436 for train-test-split
0:16:53.961382 INFO: Test AUC: 0.464
0:16:53.961475 INFO: Train AUC: 0.611
0:16:53.961503 INFO: AUC difference: 24.14%
0:16:53.961524 WARNING: AUC difference > 5%. This may indicate overfitting.
0:16:54.251030 INFO: Resetting torch num_threads to 100
0:16:54.252525 PROGRESS: === Extracted 1963 precursors and 10957 fragments ===
0:16:54.252880 INFO: === FDR correction performed with classifier version -1 ===
0:16:54.253358 PROGRESS: ============================= Precursor FDR =============================
0:16:54.253437 PROGRESS: Total precursors accumulated: 11
0:16:54.253492 PROGRESS: Target precursors: 11 (100.00%)
0:16:54.253538 PROGRESS: Decoy precursors: 0 (0.00%)
0:16:54.253581 PROGRESS: 
0:16:54.253622 PROGRESS: Precursor Summary:
0:16:54.254705 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
0:16:54.254792 PROGRESS: 
0:16:54.254844 PROGRESS: Protein Summary:
0:16:54.256022 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
0:16:54.256105 PROGRESS: =========================================================================
0:16:54.256293 INFO: Target number of precursors not reached yet.
0:16:54.340078 INFO: Starting optimization step 1.
0:16:54.340303 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:16:54.340384 INFO: Using rust extraction backend
0:16:54.340443 PROGRESS: Extracting batch of 3948 precursors
0:16:54.348549 INFO: === Search parameters used ===
0:16:54.348665 INFO: rt_error       : 805.5992431640625
0:16:54.348715 INFO: mobility_error : 0.1
0:16:54.348759 INFO: num_candidates : 1
0:16:54.348800 INFO: ms1_error      : 3
0:16:54.348839 INFO: ms2_error      : 10
0:16:54.348877 INFO: fwhm_rt        : 5
0:16:54.348916 INFO: quant_window   : 3
0:16:54.348954 INFO: ==============================================
0:16:54.392118 INFO: performing precursor FDR with 40 features
0:16:54.392195 INFO: Decoy channel: -1
0:16:54.392220 INFO: competitive: True
0:16:54.396359 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:54.398679 INFO: Estimating optimal hyperparameters - samples: 4,722, batch_size: 128, learning_rate: 1.77e-04
0:16:54.398760 INFO: Using random state 915590 for train-test-split
0:16:54.857540 INFO: Test AUC: 0.537
0:16:54.857631 INFO: Train AUC: 0.581
0:16:54.857663 INFO: AUC difference: 7.62%
0:16:54.857687 WARNING: AUC difference > 5%. This may indicate overfitting.
0:16:55.099066 INFO: Resetting torch num_threads to 100
0:16:55.101854 PROGRESS: === Extracted 5903 precursors and 33156 fragments ===
0:16:55.102241 INFO: === FDR correction performed with classifier version -1 ===
0:16:55.102728 PROGRESS: ============================= Precursor FDR =============================
0:16:55.102814 PROGRESS: Total precursors accumulated: 25
0:16:55.102873 PROGRESS: Target precursors: 25 (100.00%)
0:16:55.102926 PROGRESS: Decoy precursors: 0 (0.00%)
0:16:55.102975 PROGRESS: 
0:16:55.103021 PROGRESS: Precursor Summary:
0:16:55.104084 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:    25; 0.001 FDR:    25
0:16:55.104170 PROGRESS: 
0:16:55.104225 PROGRESS: Protein Summary:
0:16:55.105394 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:    25; 0.001 FDR:    25
0:16:55.105479 PROGRESS: =========================================================================
0:16:55.105711 INFO: Target number of precursors not reached yet.
0:16:55.194385 INFO: Starting optimization step 2.
0:16:55.194617 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:16:55.194700 INFO: Using rust extraction backend
0:16:55.194763 PROGRESS: Extracting batch of 7900 precursors
0:16:55.209512 INFO: === Search parameters used ===
0:16:55.209655 INFO: rt_error       : 805.5992431640625
0:16:55.209708 INFO: mobility_error : 0.1
0:16:55.209757 INFO: num_candidates : 1
0:16:55.209802 INFO: ms1_error      : 3
0:16:55.209847 INFO: ms2_error      : 10
0:16:55.209893 INFO: fwhm_rt        : 5
0:16:55.209955 INFO: quant_window   : 3
0:16:55.210004 INFO: ==============================================
0:16:55.281539 INFO: performing precursor FDR with 40 features
0:16:55.281646 INFO: Decoy channel: -1
0:16:55.281671 INFO: competitive: True
0:16:55.288568 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:55.292100 INFO: Estimating optimal hyperparameters - samples: 11,028, batch_size: 128, learning_rate: 1.77e-04
0:16:55.292205 INFO: Using random state 844887 for train-test-split
0:16:56.417541 INFO: Test AUC: 0.563
0:16:56.417639 INFO: Train AUC: 0.591
0:16:56.417668 INFO: AUC difference: 4.72%
0:16:57.105444 INFO: Resetting torch num_threads to 100
0:16:57.109354 PROGRESS: === Extracted 13785 precursors and 77541 fragments ===
0:16:57.109738 INFO: === FDR correction performed with classifier version -1 ===
0:16:57.110259 PROGRESS: ============================= Precursor FDR =============================
0:16:57.110348 PROGRESS: Total precursors accumulated: 58
0:16:57.110407 PROGRESS: Target precursors: 58 (100.00%)
0:16:57.110458 PROGRESS: Decoy precursors: 0 (0.00%)
0:16:57.110504 PROGRESS: 
0:16:57.110549 PROGRESS: Precursor Summary:
0:16:57.111595 PROGRESS: Channel   0:	 0.050 FDR:    58; 0.010 FDR:    58; 0.001 FDR:    58
0:16:57.111688 PROGRESS: 
0:16:57.111748 PROGRESS: Protein Summary:
0:16:57.112905 PROGRESS: Channel   0:	 0.050 FDR:    57; 0.010 FDR:    57; 0.001 FDR:    57
0:16:57.112985 PROGRESS: =========================================================================
0:16:57.113286 INFO: Target number of precursors not reached yet.
0:16:57.211474 INFO: Starting optimization step 3.
0:16:57.211719 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:16:57.211800 INFO: Using rust extraction backend
0:16:57.211861 PROGRESS: Extracting batch of 15775 precursors
0:16:57.240036 INFO: === Search parameters used ===
0:16:57.240203 INFO: rt_error       : 805.5992431640625
0:16:57.240254 INFO: mobility_error : 0.1
0:16:57.240297 INFO: num_candidates : 1
0:16:57.240338 INFO: ms1_error      : 3
0:16:57.240379 INFO: ms2_error      : 10
0:16:57.240436 INFO: fwhm_rt        : 5
0:16:57.240478 INFO: quant_window   : 3
0:16:57.240516 INFO: ==============================================
0:16:57.370695 INFO: performing precursor FDR with 40 features
0:16:57.370806 INFO: Decoy channel: -1
0:16:57.370830 INFO: competitive: True
0:16:57.381516 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:57.388279 INFO: Estimating optimal hyperparameters - samples: 23,613, batch_size: 128, learning_rate: 1.77e-04
0:16:57.388440 INFO: Using random state 211370 for train-test-split
0:16:59.778856 INFO: Test AUC: 0.568
0:16:59.778970 INFO: Train AUC: 0.593
0:16:59.778999 INFO: AUC difference: 4.17%
0:17:00.041780 INFO: Resetting torch num_threads to 100
0:17:00.048132 PROGRESS: === Extracted 29517 precursors and 165549 fragments ===
0:17:00.048618 INFO: === FDR correction performed with classifier version -1 ===
0:17:00.049115 PROGRESS: ============================= Precursor FDR =============================
0:17:00.049205 PROGRESS: Total precursors accumulated: 141
0:17:00.049265 PROGRESS: Target precursors: 140 (99.29%)
0:17:00.049318 PROGRESS: Decoy precursors: 1 (0.71%)
0:17:00.049366 PROGRESS: 
0:17:00.049412 PROGRESS: Precursor Summary:
0:17:00.050400 PROGRESS: Channel   0:	 0.050 FDR:   140; 0.010 FDR:   140; 0.001 FDR:   114
0:17:00.050489 PROGRESS: 
0:17:00.050545 PROGRESS: Protein Summary:
0:17:00.051674 PROGRESS: Channel   0:	 0.050 FDR:   136; 0.010 FDR:   136; 0.001 FDR:   111
0:17:00.051761 PROGRESS: =========================================================================
0:17:00.052212 INFO: Target number of precursors not reached yet.
0:17:00.169362 INFO: Starting optimization step 4.
0:17:00.169616 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:17:00.169701 INFO: Using rust extraction backend
0:17:00.169766 PROGRESS: Extracting batch of 31568 precursors
0:17:00.224130 INFO: === Search parameters used ===
0:17:00.224355 INFO: rt_error       : 805.5992431640625
0:17:00.224409 INFO: mobility_error : 0.1
0:17:00.224458 INFO: num_candidates : 1
0:17:00.224504 INFO: ms1_error      : 3
0:17:00.224546 INFO: ms2_error      : 10
0:17:00.224588 INFO: fwhm_rt        : 5
0:17:00.224630 INFO: quant_window   : 3
0:17:00.224672 INFO: ==============================================
0:17:00.436153 INFO: performing precursor FDR with 40 features
0:17:00.436289 INFO: Decoy channel: -1
0:17:00.436314 INFO: competitive: True
0:17:00.457611 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:00.471524 INFO: Estimating optimal hyperparameters - samples: 48,809, batch_size: 199, learning_rate: 2.20e-04
0:17:00.471724 INFO: Using random state 732162 for train-test-split
0:17:04.230340 INFO: Test AUC: 0.582
0:17:04.230460 INFO: Train AUC: 0.610
0:17:04.230490 INFO: AUC difference: 4.58%
0:17:04.499951 INFO: Resetting torch num_threads to 100
0:17:04.525178 PROGRESS: === Extracted 61012 precursors and 342363 fragments ===
0:17:04.525782 INFO: === FDR correction performed with classifier version -1 ===
0:17:04.526359 PROGRESS: ============================= Precursor FDR =============================
0:17:04.526447 PROGRESS: Total precursors accumulated: 265
0:17:04.526505 PROGRESS: Target precursors: 263 (99.25%)
0:17:04.526555 PROGRESS: Decoy precursors: 2 (0.75%)
0:17:04.526623 PROGRESS: 
0:17:04.526667 PROGRESS: Precursor Summary:
0:17:04.527670 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   245
0:17:04.527754 PROGRESS: 
0:17:04.527807 PROGRESS: Protein Summary:
0:17:04.528970 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:   232
0:17:04.529051 PROGRESS: =========================================================================
0:17:04.530088 INFO: Target number of precursors not reached yet.
0:17:04.716973 INFO: Starting optimization step 5.
0:17:04.717225 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:17:04.717309 INFO: Using rust extraction backend
0:17:04.717371 PROGRESS: Extracting batch of 63098 precursors
0:17:04.824823 INFO: === Search parameters used ===
0:17:04.825078 INFO: rt_error       : 805.5992431640625
0:17:04.825131 INFO: mobility_error : 0.1
0:17:04.825177 INFO: num_candidates : 1
0:17:04.825220 INFO: ms1_error      : 3
0:17:04.825260 INFO: ms2_error      : 10
0:17:04.825299 INFO: fwhm_rt        : 5
0:17:04.825338 INFO: quant_window   : 3
0:17:04.825376 INFO: ==============================================
0:17:05.213296 INFO: performing precursor FDR with 40 features
0:17:05.213449 INFO: Decoy channel: -1
0:17:05.213475 INFO: competitive: True
0:17:05.259231 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:05.291995 INFO: Estimating optimal hyperparameters - samples: 99,151, batch_size: 406, learning_rate: 3.15e-04
0:17:05.292304 INFO: Using random state 382415 for train-test-split
0:17:09.974582 INFO: Test AUC: 0.588
0:17:09.974788 INFO: Train AUC: 0.613
0:17:09.974823 INFO: AUC difference: 4.10%
0:17:10.262889 INFO: Resetting torch num_threads to 100
0:17:10.289209 PROGRESS: === Extracted 123939 precursors and 695709 fragments ===
0:17:10.289896 INFO: === FDR correction performed with classifier version -1 ===
0:17:10.290614 PROGRESS: ============================= Precursor FDR =============================
0:17:10.290718 PROGRESS: Total precursors accumulated: 622
0:17:10.290778 PROGRESS: Target precursors: 616 (99.04%)
0:17:10.290830 PROGRESS: Decoy precursors: 6 (0.96%)
0:17:10.290877 PROGRESS: 
0:17:10.290938 PROGRESS: Precursor Summary:
0:17:10.292110 PROGRESS: Channel   0:	 0.050 FDR:   616; 0.010 FDR:   616; 0.001 FDR:   509
0:17:10.292204 PROGRESS: 
0:17:10.292259 PROGRESS: Protein Summary:
0:17:10.293653 PROGRESS: Channel   0:	 0.050 FDR:   567; 0.010 FDR:   567; 0.001 FDR:   475
0:17:10.293757 PROGRESS: =========================================================================
0:17:10.295501 INFO: Target number of precursors not reached yet.
0:17:10.572814 INFO: Starting optimization step 6.
0:17:10.573073 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:17:10.573187 INFO: Using rust extraction backend
0:17:10.573263 PROGRESS: Extracting batch of 126185 precursors
0:17:10.793539 INFO: === Search parameters used ===
0:17:10.793797 INFO: rt_error       : 805.5992431640625
0:17:10.793851 INFO: mobility_error : 0.1
0:17:10.793899 INFO: num_candidates : 1
0:17:10.793957 INFO: ms1_error      : 3
0:17:10.794000 INFO: ms2_error      : 10
0:17:10.794041 INFO: fwhm_rt        : 5
0:17:10.794082 INFO: quant_window   : 3
0:17:10.794123 INFO: ==============================================
0:17:11.492214 INFO: performing precursor FDR with 40 features
0:17:11.492330 INFO: Decoy channel: -1
0:17:11.492356 INFO: competitive: True
0:17:11.612249 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:11.694573 INFO: Estimating optimal hyperparameters - samples: 199,860, batch_size: 818, learning_rate: 4.47e-04
0:17:11.694940 INFO: Using random state 592637 for train-test-split
0:17:18.176967 INFO: Test AUC: 0.594
0:17:18.177087 INFO: Train AUC: 0.613
0:17:18.177119 INFO: AUC difference: 3.12%
0:17:18.506855 INFO: Resetting torch num_threads to 100
0:17:18.559293 PROGRESS: === Extracted 249825 precursors and 1401773 fragments ===
0:17:18.559923 INFO: === FDR correction performed with classifier version -1 ===
0:17:18.560744 PROGRESS: ============================= Precursor FDR =============================
0:17:18.560857 PROGRESS: Total precursors accumulated: 1,302
0:17:18.560917 PROGRESS: Target precursors: 1,290 (99.08%)
0:17:18.560967 PROGRESS: Decoy precursors: 12 (0.92%)
0:17:18.561013 PROGRESS: 
0:17:18.561058 PROGRESS: Precursor Summary:
0:17:18.562448 PROGRESS: Channel   0:	 0.050 FDR: 1,290; 0.010 FDR: 1,290; 0.001 FDR:   805
0:17:18.562546 PROGRESS: 
0:17:18.562600 PROGRESS: Protein Summary:
0:17:18.564263 PROGRESS: Channel   0:	 0.050 FDR: 1,106; 0.010 FDR: 1,106; 0.001 FDR:   706
0:17:18.564354 PROGRESS: =========================================================================
0:17:18.567844 INFO: Target number of precursors reached.
0:17:18.733728 INFO: fragments_df: keeping 5000 of 1401773 [sum(precursor_idx_mask)=13573 sum(mass_error_mask)=1401773 stop_rank=5000
0:17:19.181742 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:19.406922 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:20.126847 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:17:20.127274 INFO: Using score_cutoff 11.447691594028473 (fac=0.99, q=1)
0:17:20.127622 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:17:20.127697 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:17:20.127749 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.447691594028473
0:17:20.127814 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:20.282223 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:20.612151 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:17:20.612437 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:17:20.612553 INFO: Starting optimization step 7.
0:17:20.612633 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:17:20.612715 INFO: Using rust extraction backend
0:17:20.612800 PROGRESS: Extracting batch of 250439 precursors
0:17:21.035743 INFO: === Search parameters used ===
0:17:21.035995 INFO: rt_error       : 805.5992431640625
0:17:21.036053 INFO: mobility_error : 0.1
0:17:21.036103 INFO: num_candidates : 3
0:17:21.036149 INFO: ms1_error      : 3
0:17:21.036193 INFO: ms2_error      : 10
0:17:21.036237 INFO: fwhm_rt        : 3.0
0:17:21.036280 INFO: quant_window   : 3
0:17:21.036322 INFO: ==============================================
0:17:23.512703 INFO: performing precursor FDR with 40 features
0:17:23.512823 INFO: Decoy channel: -1
0:17:23.512849 INFO: competitive: True
0:17:23.700587 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:23.993000 INFO: Estimating optimal hyperparameters - samples: 599,615, batch_size: 2,456, learning_rate: 7.74e-04
0:17:23.994063 INFO: Using random state 940170 for train-test-split
0:17:36.549786 INFO: Test AUC: 0.594
0:17:36.550048 INFO: Train AUC: 0.605
0:17:36.550083 INFO: AUC difference: 1.89%
0:17:37.041916 INFO: Resetting torch num_threads to 100
0:17:37.074847 PROGRESS: === Extracted 749519 precursors and 4029512 fragments ===
0:17:37.075376 INFO: === FDR correction performed with classifier version 6 ===
0:17:37.076038 PROGRESS: ============================= Precursor FDR =============================
0:17:37.076146 PROGRESS: Total precursors accumulated: 1,393
0:17:37.076206 PROGRESS: Target precursors: 1,380 (99.07%)
0:17:37.076258 PROGRESS: Decoy precursors: 13 (0.93%)
0:17:37.076303 PROGRESS: 
0:17:37.076350 PROGRESS: Precursor Summary:
0:17:37.077689 PROGRESS: Channel   0:	 0.050 FDR: 1,380; 0.010 FDR: 1,380; 0.001 FDR: 1,123
0:17:37.077778 PROGRESS: 
0:17:37.077835 PROGRESS: Protein Summary:
0:17:37.079581 PROGRESS: Channel   0:	 0.050 FDR: 1,160; 0.010 FDR: 1,160; 0.001 FDR:   965
0:17:37.079681 PROGRESS: =========================================================================
0:17:37.092945 INFO: Target number of precursors reached.
0:17:37.533836 INFO: fragments_df: keeping 5000 of 4029512 [sum(precursor_idx_mask)=32916 sum(mass_error_mask)=4029512 stop_rank=5000
0:17:38.020394 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:38.242335 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:38.960422 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:38.960853 INFO: Using score_cutoff 12.215870719814301 (fac=0.99, q=1)
0:17:38.961200 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:38.961274 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:38.961324 INFO: Updating optimization_manager: score_cutoff        : 11.447691594028473 -> 12.215870719814301
0:17:38.961386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:39.113964 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:39.444052 INFO: === checking if optimization conditions were reached ===
0:17:39.446567 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:17:39.446691 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:17:39.446770 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:17:39.446837 INFO: ==============================================
0:17:39.446917 INFO: Starting optimization step 8.
0:17:39.446983 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:17:39.447068 INFO: Using rust extraction backend
0:17:39.447149 PROGRESS: Extracting batch of 250439 precursors
0:17:39.870194 INFO: === Search parameters used ===
0:17:39.870453 INFO: rt_error       : 805.5992431640625
0:17:39.870509 INFO: mobility_error : 0.1
0:17:39.870556 INFO: num_candidates : 3
0:17:39.870599 INFO: ms1_error      : 3
0:17:39.870640 INFO: ms2_error      : 10.0
0:17:39.870678 INFO: fwhm_rt        : 3.0
0:17:39.870716 INFO: quant_window   : 3
0:17:39.870754 INFO: ==============================================
0:17:42.326952 INFO: performing precursor FDR with 40 features
0:17:42.327073 INFO: Decoy channel: -1
0:17:42.327099 INFO: competitive: True
0:17:42.512978 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:42.808852 INFO: Estimating optimal hyperparameters - samples: 599,612, batch_size: 2,456, learning_rate: 7.74e-04
0:17:42.809830 INFO: Using random state 945809 for train-test-split
0:17:54.991262 INFO: Test AUC: 0.602
0:17:54.991395 INFO: Train AUC: 0.615
0:17:54.991427 INFO: AUC difference: 2.06%
0:17:55.473815 INFO: Resetting torch num_threads to 100
0:17:55.501805 PROGRESS: === Extracted 749516 precursors and 4029579 fragments ===
0:17:55.502286 INFO: === FDR correction performed with classifier version 7 ===
0:17:55.502974 PROGRESS: ============================= Precursor FDR =============================
0:17:55.503064 PROGRESS: Total precursors accumulated: 1,489
0:17:55.503123 PROGRESS: Target precursors: 1,475 (99.06%)
0:17:55.503174 PROGRESS: Decoy precursors: 14 (0.94%)
0:17:55.503220 PROGRESS: 
0:17:55.503264 PROGRESS: Precursor Summary:
0:17:55.504580 PROGRESS: Channel   0:	 0.050 FDR: 1,475; 0.010 FDR: 1,475; 0.001 FDR: 1,016
0:17:55.504679 PROGRESS: 
0:17:55.504734 PROGRESS: Protein Summary:
0:17:55.506495 PROGRESS: Channel   0:	 0.050 FDR: 1,230; 0.010 FDR: 1,230; 0.001 FDR:   877
0:17:55.506588 PROGRESS: =========================================================================
0:17:55.519847 INFO: Target number of precursors reached.
0:17:55.976429 INFO: fragments_df: keeping 5000 of 4029579 [sum(precursor_idx_mask)=35139 sum(mass_error_mask)=4029579 stop_rank=5000
0:17:56.388872 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:56.674482 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:57.412242 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:57.412665 INFO: Using score_cutoff 12.011374798393248 (fac=0.99, q=1)
0:17:57.412965 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:57.413040 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:57.413093 INFO: Updating optimization_manager: score_cutoff        : 12.215870719814301 -> 12.011374798393248
0:17:57.413157 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:57.563461 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:57.896332 INFO: === checking if optimization conditions were reached ===
0:17:57.898870 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:17:57.898993 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:17:57.899076 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:17:57.899149 INFO: ==============================================
0:17:57.899231 INFO: Starting optimization step 9.
0:17:57.899304 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:17:57.899381 INFO: Using rust extraction backend
0:17:57.899455 PROGRESS: Extracting batch of 250439 precursors
0:17:58.321588 INFO: === Search parameters used ===
0:17:58.321859 INFO: rt_error       : 805.5992431640625
0:17:58.321930 INFO: mobility_error : 0.1
0:17:58.321985 INFO: num_candidates : 3
0:17:58.322035 INFO: ms1_error      : 3
0:17:58.322080 INFO: ms2_error      : 10.0
0:17:58.322124 INFO: fwhm_rt        : 3.0
0:17:58.322167 INFO: quant_window   : 3
0:17:58.322210 INFO: ==============================================
0:18:00.796051 INFO: performing precursor FDR with 40 features
0:18:00.796175 INFO: Decoy channel: -1
0:18:00.796202 INFO: competitive: True
0:18:00.977950 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:01.266107 INFO: Estimating optimal hyperparameters - samples: 599,621, batch_size: 2,456, learning_rate: 7.74e-04
0:18:01.267091 INFO: Using random state 117775 for train-test-split
0:18:13.811472 INFO: Test AUC: 0.604
0:18:13.811704 INFO: Train AUC: 0.618
0:18:13.811741 INFO: AUC difference: 2.34%
0:18:14.296368 INFO: Resetting torch num_threads to 100
0:18:14.328614 PROGRESS: === Extracted 749527 precursors and 4030281 fragments ===
0:18:14.329156 INFO: === FDR correction performed with classifier version 8 ===
0:18:14.329833 PROGRESS: ============================= Precursor FDR =============================
0:18:14.329940 PROGRESS: Total precursors accumulated: 1,455
0:18:14.330004 PROGRESS: Target precursors: 1,441 (99.04%)
0:18:14.330055 PROGRESS: Decoy precursors: 14 (0.96%)
0:18:14.330110 PROGRESS: 
0:18:14.330156 PROGRESS: Precursor Summary:
0:18:14.331477 PROGRESS: Channel   0:	 0.050 FDR: 1,441; 0.010 FDR: 1,441; 0.001 FDR:   689
0:18:14.331565 PROGRESS: 
0:18:14.331623 PROGRESS: Protein Summary:
0:18:14.333330 PROGRESS: Channel   0:	 0.050 FDR: 1,206; 0.010 FDR: 1,206; 0.001 FDR:   608
0:18:14.333421 PROGRESS: =========================================================================
0:18:14.346654 INFO: Target number of precursors reached.
0:18:14.789368 INFO: fragments_df: keeping 5000 of 4030281 [sum(precursor_idx_mask)=34367 sum(mass_error_mask)=4030281 stop_rank=5000
0:18:15.272041 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:15.513470 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:16.230766 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:16.231206 INFO: Using score_cutoff 12.302643184661864 (fac=0.99, q=1)
0:18:16.231562 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:16.231646 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:16.231712 INFO: Updating optimization_manager: score_cutoff        : 12.011374798393248 -> 12.302643184661864
0:18:16.231778 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:16.382414 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:16.727215 INFO: === checking if optimization conditions were reached ===
0:18:16.729741 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:16.729867 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:18:16.729962 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:18:16.730038 INFO: ==============================================
0:18:16.730125 INFO: Starting optimization step 10.
0:18:16.730198 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:16.730332 INFO: Using rust extraction backend
0:18:16.730417 PROGRESS: Extracting batch of 250439 precursors
0:18:17.154550 INFO: === Search parameters used ===
0:18:17.154815 INFO: rt_error       : 805.5992431640625
0:18:17.154870 INFO: mobility_error : 0.1
0:18:17.154914 INFO: num_candidates : 3
0:18:17.154957 INFO: ms1_error      : 3
0:18:17.155009 INFO: ms2_error      : 10.0
0:18:17.155049 INFO: fwhm_rt        : 3.0
0:18:17.155087 INFO: quant_window   : 3
0:18:17.155125 INFO: ==============================================
0:18:19.617445 INFO: performing precursor FDR with 40 features
0:18:19.617565 INFO: Decoy channel: -1
0:18:19.617593 INFO: competitive: True
0:18:19.810082 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:20.110198 INFO: Estimating optimal hyperparameters - samples: 599,614, batch_size: 2,456, learning_rate: 7.74e-04
0:18:20.111321 INFO: Using random state 676219 for train-test-split
0:18:32.643602 INFO: Test AUC: 0.611
0:18:32.643739 INFO: Train AUC: 0.622
0:18:32.643772 INFO: AUC difference: 1.79%
0:18:33.533424 INFO: Resetting torch num_threads to 100
0:18:33.562761 PROGRESS: === Extracted 749518 precursors and 4029673 fragments ===
0:18:33.563229 INFO: === FDR correction performed with classifier version 9 ===
0:18:33.563894 PROGRESS: ============================= Precursor FDR =============================
0:18:33.563997 PROGRESS: Total precursors accumulated: 1,547
0:18:33.564056 PROGRESS: Target precursors: 1,532 (99.03%)
0:18:33.564106 PROGRESS: Decoy precursors: 15 (0.97%)
0:18:33.564153 PROGRESS: 
0:18:33.564198 PROGRESS: Precursor Summary:
0:18:33.565530 PROGRESS: Channel   0:	 0.050 FDR: 1,532; 0.010 FDR: 1,532; 0.001 FDR: 1,144
0:18:33.565620 PROGRESS: 
0:18:33.565676 PROGRESS: Protein Summary:
0:18:33.567448 PROGRESS: Channel   0:	 0.050 FDR: 1,279; 0.010 FDR: 1,279; 0.001 FDR:   981
0:18:33.567541 PROGRESS: =========================================================================
0:18:33.581139 INFO: Target number of precursors reached.
0:18:34.029603 INFO: fragments_df: keeping 5000 of 4029673 [sum(precursor_idx_mask)=36375 sum(mass_error_mask)=4029673 stop_rank=5000
0:18:34.443319 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:34.682331 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:35.402585 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:35.403020 INFO: Using score_cutoff 12.070450458812713 (fac=0.99, q=1)
0:18:35.403323 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:35.403409 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:35.403465 INFO: Updating optimization_manager: score_cutoff        : 12.302643184661864 -> 12.070450458812713
0:18:35.403522 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:35.552676 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:35.876929 INFO: === checking if optimization conditions were reached ===
0:18:35.879522 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:35.879693 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:18:35.879774 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:18:35.879853 INFO: ==============================================
0:18:35.879935 INFO: Starting optimization step 11.
0:18:35.880009 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:35.880084 INFO: Using rust extraction backend
0:18:35.880153 PROGRESS: Extracting batch of 250439 precursors
0:18:36.305392 INFO: === Search parameters used ===
0:18:36.305658 INFO: rt_error       : 805.5992431640625
0:18:36.305716 INFO: mobility_error : 0.1
0:18:36.305765 INFO: num_candidates : 3
0:18:36.305811 INFO: ms1_error      : 3
0:18:36.305853 INFO: ms2_error      : 10.0
0:18:36.305896 INFO: fwhm_rt        : 3.0
0:18:36.305952 INFO: quant_window   : 3
0:18:36.306056 INFO: ==============================================
0:18:38.748336 INFO: performing precursor FDR with 40 features
0:18:38.748455 INFO: Decoy channel: -1
0:18:38.748501 INFO: competitive: True
0:18:38.943990 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:39.251359 INFO: Estimating optimal hyperparameters - samples: 599,619, batch_size: 2,456, learning_rate: 7.74e-04
0:18:39.252510 INFO: Using random state 928619 for train-test-split
0:18:51.646196 INFO: Test AUC: 0.611
0:18:51.646431 INFO: Train AUC: 0.624
0:18:51.646466 INFO: AUC difference: 2.15%
0:18:52.123032 INFO: Resetting torch num_threads to 100
0:18:52.153267 PROGRESS: === Extracted 749524 precursors and 4030008 fragments ===
0:18:52.153798 INFO: === FDR correction performed with classifier version 10 ===
0:18:52.154508 PROGRESS: ============================= Precursor FDR =============================
0:18:52.154603 PROGRESS: Total precursors accumulated: 1,559
0:18:52.154664 PROGRESS: Target precursors: 1,544 (99.04%)
0:18:52.154715 PROGRESS: Decoy precursors: 15 (0.96%)
0:18:52.154761 PROGRESS: 
0:18:52.154809 PROGRESS: Precursor Summary:
0:18:52.156190 PROGRESS: Channel   0:	 0.050 FDR: 1,544; 0.010 FDR: 1,544; 0.001 FDR: 1,259
0:18:52.156276 PROGRESS: 
0:18:52.156332 PROGRESS: Protein Summary:
0:18:52.158175 PROGRESS: Channel   0:	 0.050 FDR: 1,288; 0.010 FDR: 1,288; 0.001 FDR: 1,070
0:18:52.158274 PROGRESS: =========================================================================
0:18:52.172662 INFO: Target number of precursors reached.
0:18:52.623406 INFO: fragments_df: keeping 5000 of 4030008 [sum(precursor_idx_mask)=36766 sum(mass_error_mask)=4030008 stop_rank=5000
0:18:53.111743 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:53.359185 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:54.080044 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:54.080491 INFO: Using score_cutoff 12.20670084028244 (fac=0.99, q=1)
0:18:54.080844 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:54.080923 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:54.080977 INFO: Updating optimization_manager: score_cutoff        : 12.070450458812713 -> 12.20670084028244
0:18:54.081038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:54.230948 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:54.576299 INFO: === checking if optimization conditions were reached ===
0:18:54.578855 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:54.578983 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:18:54.579063 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:18:54.579132 INFO: ==============================================
0:18:54.579221 PROGRESS: Optimization finished for ms2_error.
0:18:54.973306 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:55.121998 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:55.462281 INFO: Starting optimization step 0.
0:18:55.462578 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:55.462689 INFO: Using rust extraction backend
0:18:55.462782 PROGRESS: Extracting batch of 250439 precursors
0:18:55.887911 INFO: === Search parameters used ===
0:18:55.888172 INFO: rt_error       : 805.5992431640625
0:18:55.888229 INFO: mobility_error : 0.1
0:18:55.888294 INFO: num_candidates : 3
0:18:55.888341 INFO: ms1_error      : 3
0:18:55.888389 INFO: ms2_error      : 10.0
0:18:55.888432 INFO: fwhm_rt        : 3.0
0:18:55.888473 INFO: quant_window   : 3
0:18:55.888513 INFO: ==============================================
0:18:58.332837 INFO: performing precursor FDR with 40 features
0:18:58.332960 INFO: Decoy channel: -1
0:18:58.332987 INFO: competitive: True
0:18:58.510268 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:58.808949 INFO: Estimating optimal hyperparameters - samples: 599,624, batch_size: 2,456, learning_rate: 7.74e-04
0:18:58.810147 INFO: Using random state 143539 for train-test-split
0:19:10.844209 INFO: Test AUC: 0.612
0:19:10.844343 INFO: Train AUC: 0.625
0:19:10.844376 INFO: AUC difference: 2.16%
0:19:11.323112 INFO: Resetting torch num_threads to 100
0:19:11.347224 PROGRESS: === Extracted 749530 precursors and 4029765 fragments ===
0:19:11.347693 INFO: === FDR correction performed with classifier version 11 ===
0:19:11.348351 PROGRESS: ============================= Precursor FDR =============================
0:19:11.348439 PROGRESS: Total precursors accumulated: 1,674
0:19:11.348500 PROGRESS: Target precursors: 1,658 (99.04%)
0:19:11.348554 PROGRESS: Decoy precursors: 16 (0.96%)
0:19:11.348603 PROGRESS: 
0:19:11.348652 PROGRESS: Precursor Summary:
0:19:11.350075 PROGRESS: Channel   0:	 0.050 FDR: 1,658; 0.010 FDR: 1,658; 0.001 FDR: 1,275
0:19:11.350167 PROGRESS: 
0:19:11.350223 PROGRESS: Protein Summary:
0:19:11.352099 PROGRESS: Channel   0:	 0.050 FDR: 1,392; 0.010 FDR: 1,392; 0.001 FDR: 1,089
0:19:11.352191 PROGRESS: =========================================================================
0:19:11.364777 INFO: Target number of precursors reached.
0:19:11.805954 INFO: fragments_df: keeping 5000 of 4029765 [sum(precursor_idx_mask)=38212 sum(mass_error_mask)=4029765 stop_rank=5000
0:19:12.217663 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:12.485076 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:13.205499 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:13.205944 INFO: Using score_cutoff 8.4208014421463 (fac=0.99, q=1)
0:19:13.206255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:13.206335 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:13.206390 INFO: Updating optimization_manager: score_cutoff        : 12.20670084028244 -> 8.4208014421463
0:19:13.206449 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:13.354932 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:13.686805 INFO: === checking if optimization conditions were reached ===
0:19:13.687136 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:19:13.690356 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 911.9836616887239
0:19:13.690509 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 911.9837.
0:19:13.690588 INFO: ==============================================
0:19:13.690674 INFO: Starting optimization step 1.
0:19:13.690746 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:13.690820 INFO: Using rust extraction backend
0:19:13.690891 PROGRESS: Extracting batch of 250439 precursors
0:19:14.112262 INFO: === Search parameters used ===
0:19:14.112545 INFO: rt_error       : 911.9836616887239
0:19:14.112606 INFO: mobility_error : 0.1
0:19:14.112656 INFO: num_candidates : 3
0:19:14.112702 INFO: ms1_error      : 3
0:19:14.112746 INFO: ms2_error      : 10.0
0:19:14.112790 INFO: fwhm_rt        : 3.0
0:19:14.112835 INFO: quant_window   : 3
0:19:14.112878 INFO: ==============================================
0:19:16.616872 INFO: performing precursor FDR with 40 features
0:19:16.616991 INFO: Decoy channel: -1
0:19:16.617020 INFO: competitive: True
0:19:16.810884 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:17.120194 INFO: Estimating optimal hyperparameters - samples: 599,580, batch_size: 2,455, learning_rate: 7.74e-04
0:19:17.121113 INFO: Using random state 143539 for train-test-split
0:19:30.145034 INFO: Test AUC: 0.612
0:19:30.145264 INFO: Train AUC: 0.626
0:19:30.145301 INFO: AUC difference: 2.31%
0:19:30.632684 INFO: Resetting torch num_threads to 100
0:19:30.659813 PROGRESS: === Extracted 749475 precursors and 4030069 fragments ===
0:19:30.660353 INFO: === FDR correction performed with classifier version 11 ===
0:19:30.661027 PROGRESS: ============================= Precursor FDR =============================
0:19:30.661115 PROGRESS: Total precursors accumulated: 1,703
0:19:30.661177 PROGRESS: Target precursors: 1,687 (99.06%)
0:19:30.661229 PROGRESS: Decoy precursors: 16 (0.94%)
0:19:30.661278 PROGRESS: 
0:19:30.661330 PROGRESS: Precursor Summary:
0:19:30.662773 PROGRESS: Channel   0:	 0.050 FDR: 1,687; 0.010 FDR: 1,687; 0.001 FDR: 1,199
0:19:30.662863 PROGRESS: 
0:19:30.662919 PROGRESS: Protein Summary:
0:19:30.664766 PROGRESS: Channel   0:	 0.050 FDR: 1,430; 0.010 FDR: 1,430; 0.001 FDR: 1,030
0:19:30.664861 PROGRESS: =========================================================================
0:19:30.679114 INFO: Target number of precursors reached.
0:19:31.110075 INFO: fragments_df: keeping 5000 of 4030069 [sum(precursor_idx_mask)=38531 sum(mass_error_mask)=4030069 stop_rank=5000
0:19:31.596484 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:31.852292 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:32.570119 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:32.570568 INFO: Using score_cutoff 8.205502009391784 (fac=0.99, q=1)
0:19:32.570913 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:32.570992 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:32.571048 INFO: Updating optimization_manager: score_cutoff        : 8.4208014421463 -> 8.205502009391784
0:19:32.571112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:32.718015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:33.049221 INFO: === checking if optimization conditions were reached ===
0:19:33.049548 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:19:33.053066 INFO: Updating optimization_manager: rt_error            : 911.9836616887239 -> 1060.3428934075932
0:19:33.053237 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1060.3429.
0:19:33.053318 INFO: ==============================================
0:19:33.053413 INFO: Starting optimization step 2.
0:19:33.053489 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:33.053588 INFO: Using rust extraction backend
0:19:33.053697 PROGRESS: Extracting batch of 250439 precursors
0:19:33.481520 INFO: === Search parameters used ===
0:19:33.481787 INFO: rt_error       : 1060.3428934075932
0:19:33.481845 INFO: mobility_error : 0.1
0:19:33.481894 INFO: num_candidates : 3
0:19:33.481957 INFO: ms1_error      : 3
0:19:33.482003 INFO: ms2_error      : 10.0
0:19:33.482046 INFO: fwhm_rt        : 3.0
0:19:33.482087 INFO: quant_window   : 3
0:19:33.482128 INFO: ==============================================
0:19:36.002705 INFO: performing precursor FDR with 40 features
0:19:36.002822 INFO: Decoy channel: -1
0:19:36.002848 INFO: competitive: True
0:19:36.185592 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:36.470135 INFO: Estimating optimal hyperparameters - samples: 599,525, batch_size: 2,455, learning_rate: 7.74e-04
0:19:36.471125 INFO: Using random state 143539 for train-test-split
0:19:49.465074 INFO: Test AUC: 0.610
0:19:49.465206 INFO: Train AUC: 0.625
0:19:49.465238 INFO: AUC difference: 2.39%
0:19:49.947064 INFO: Resetting torch num_threads to 100
0:19:49.971575 PROGRESS: === Extracted 749407 precursors and 4028861 fragments ===
0:19:49.972031 INFO: === FDR correction performed with classifier version 11 ===
0:19:49.972668 PROGRESS: ============================= Precursor FDR =============================
0:19:49.972757 PROGRESS: Total precursors accumulated: 1,603
0:19:49.972817 PROGRESS: Target precursors: 1,588 (99.06%)
0:19:49.972868 PROGRESS: Decoy precursors: 15 (0.94%)
0:19:49.972914 PROGRESS: 
0:19:49.972959 PROGRESS: Precursor Summary:
0:19:49.974322 PROGRESS: Channel   0:	 0.050 FDR: 1,588; 0.010 FDR: 1,588; 0.001 FDR: 1,272
0:19:49.974414 PROGRESS: 
0:19:49.974471 PROGRESS: Protein Summary:
0:19:49.976266 PROGRESS: Channel   0:	 0.050 FDR: 1,321; 0.010 FDR: 1,321; 0.001 FDR: 1,081
0:19:49.976370 PROGRESS: =========================================================================
0:19:49.989781 INFO: Target number of precursors reached.
0:19:50.427005 INFO: fragments_df: keeping 5000 of 4028861 [sum(precursor_idx_mask)=37553 sum(mass_error_mask)=4028861 stop_rank=5000
0:19:50.837287 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:51.078028 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:51.801254 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:51.801688 INFO: Using score_cutoff 11.857271917819977 (fac=0.99, q=1)
0:19:51.802000 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:51.802081 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:51.802135 INFO: Updating optimization_manager: score_cutoff        : 8.205502009391784 -> 11.857271917819977
0:19:51.802187 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:51.949742 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:52.281671 INFO: === checking if optimization conditions were reached ===
0:19:52.281976 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:19:52.285311 INFO: Updating optimization_manager: rt_error            : 1060.3428934075932 -> 661.2167907588437
0:19:52.285455 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 661.2168.
0:19:52.285530 INFO: ==============================================
0:19:52.285611 INFO: Starting optimization step 3.
0:19:52.285699 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:52.285770 INFO: Using rust extraction backend
0:19:52.285836 PROGRESS: Extracting batch of 250439 precursors
0:19:52.707183 INFO: === Search parameters used ===
0:19:52.707445 INFO: rt_error       : 661.2167907588437
0:19:52.707501 INFO: mobility_error : 0.1
0:19:52.707548 INFO: num_candidates : 3
0:19:52.707592 INFO: ms1_error      : 3
0:19:52.707699 INFO: ms2_error      : 10.0
0:19:52.707739 INFO: fwhm_rt        : 3.0
0:19:52.707780 INFO: quant_window   : 3
0:19:52.707820 INFO: ==============================================
0:19:55.125793 INFO: performing precursor FDR with 40 features
0:19:55.125942 INFO: Decoy channel: -1
0:19:55.125970 INFO: competitive: True
0:19:55.312021 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:55.605414 INFO: Estimating optimal hyperparameters - samples: 599,503, batch_size: 2,455, learning_rate: 7.74e-04
0:19:55.606422 INFO: Using random state 143539 for train-test-split
0:20:08.803474 INFO: Test AUC: 0.611
0:20:08.803708 INFO: Train AUC: 0.625
0:20:08.803743 INFO: AUC difference: 2.28%
0:20:09.289518 INFO: Resetting torch num_threads to 100
0:20:09.319273 PROGRESS: === Extracted 749379 precursors and 4021782 fragments ===
0:20:09.319802 INFO: === FDR correction performed with classifier version 11 ===
0:20:09.320467 PROGRESS: ============================= Precursor FDR =============================
0:20:09.320555 PROGRESS: Total precursors accumulated: 1,616
0:20:09.320615 PROGRESS: Target precursors: 1,600 (99.01%)
0:20:09.320666 PROGRESS: Decoy precursors: 16 (0.99%)
0:20:09.320714 PROGRESS: 
0:20:09.320762 PROGRESS: Precursor Summary:
0:20:09.322171 PROGRESS: Channel   0:	 0.050 FDR: 1,600; 0.010 FDR: 1,596; 0.001 FDR: 1,332
0:20:09.322265 PROGRESS: 
0:20:09.322338 PROGRESS: Protein Summary:
0:20:09.324174 PROGRESS: Channel   0:	 0.050 FDR: 1,328; 0.010 FDR: 1,324; 0.001 FDR: 1,124
0:20:09.324266 PROGRESS: =========================================================================
0:20:09.338167 INFO: Target number of precursors reached.
0:20:09.772636 INFO: fragments_df: keeping 5000 of 4021782 [sum(precursor_idx_mask)=37973 sum(mass_error_mask)=4021782 stop_rank=5000
0:20:10.257923 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:10.502010 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:11.222383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:11.222817 INFO: Using score_cutoff 11.988987606525422 (fac=0.99, q=1)
0:20:11.223158 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:11.223239 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:11.223295 INFO: Updating optimization_manager: score_cutoff        : 11.857271917819977 -> 11.988987606525422
0:20:11.223365 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:11.372441 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:11.703985 INFO: === checking if optimization conditions were reached ===
0:20:11.704296 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:20:11.707737 INFO: Updating optimization_manager: rt_error            : 661.2167907588437 -> 514.4856423358369
0:20:11.707885 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 514.4856.
0:20:11.707999 INFO: ==============================================
0:20:11.708092 INFO: Starting optimization step 4.
0:20:11.708167 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:11.708258 INFO: Using rust extraction backend
0:20:11.708349 PROGRESS: Extracting batch of 250439 precursors
0:20:12.133817 INFO: === Search parameters used ===
0:20:12.134082 INFO: rt_error       : 514.4856423358369
0:20:12.134139 INFO: mobility_error : 0.1
0:20:12.134185 INFO: num_candidates : 3
0:20:12.134227 INFO: ms1_error      : 3
0:20:12.134266 INFO: ms2_error      : 10.0
0:20:12.134306 INFO: fwhm_rt        : 3.0
0:20:12.134346 INFO: quant_window   : 3
0:20:12.134388 INFO: ==============================================
0:20:14.546988 INFO: performing precursor FDR with 40 features
0:20:14.547103 INFO: Decoy channel: -1
0:20:14.547127 INFO: competitive: True
0:20:14.738405 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:15.042544 INFO: Estimating optimal hyperparameters - samples: 599,008, batch_size: 2,453, learning_rate: 7.74e-04
0:20:15.043666 INFO: Using random state 143539 for train-test-split
0:20:27.760688 INFO: Test AUC: 0.610
0:20:27.760818 INFO: Train AUC: 0.623
0:20:27.760850 INFO: AUC difference: 2.00%
0:20:28.240245 INFO: Resetting torch num_threads to 100
0:20:28.268112 PROGRESS: === Extracted 748761 precursors and 3981168 fragments ===
0:20:28.268580 INFO: === FDR correction performed with classifier version 11 ===
0:20:28.269226 PROGRESS: ============================= Precursor FDR =============================
0:20:28.269330 PROGRESS: Total precursors accumulated: 1,610
0:20:28.269392 PROGRESS: Target precursors: 1,595 (99.07%)
0:20:28.269445 PROGRESS: Decoy precursors: 15 (0.93%)
0:20:28.269492 PROGRESS: 
0:20:28.269538 PROGRESS: Precursor Summary:
0:20:28.270948 PROGRESS: Channel   0:	 0.050 FDR: 1,595; 0.010 FDR: 1,595; 0.001 FDR: 1,349
0:20:28.271050 PROGRESS: 
0:20:28.271108 PROGRESS: Protein Summary:
0:20:28.272954 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR: 1,135
0:20:28.273062 PROGRESS: =========================================================================
0:20:28.285506 INFO: Target number of precursors reached.
0:20:28.716768 INFO: fragments_df: keeping 5000 of 3981168 [sum(precursor_idx_mask)=37922 sum(mass_error_mask)=3981168 stop_rank=5000
0:20:29.123909 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:29.366197 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:30.086252 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:30.086680 INFO: Using score_cutoff 12.016403463935852 (fac=0.99, q=1)
0:20:30.086977 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:30.087054 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:30.087108 INFO: Updating optimization_manager: score_cutoff        : 11.988987606525422 -> 12.016403463935852
0:20:30.087160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:30.238287 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:30.566024 INFO: === checking if optimization conditions were reached ===
0:20:30.566329 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:20:30.569629 INFO: Updating optimization_manager: rt_error            : 514.4856423358369 -> 542.826796645432
0:20:30.569767 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 542.8268.
0:20:30.569853 INFO: ==============================================
0:20:30.569946 INFO: Starting optimization step 5.
0:20:30.570018 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:30.570088 INFO: Using rust extraction backend
0:20:30.570152 PROGRESS: Extracting batch of 250439 precursors
0:20:30.993443 INFO: === Search parameters used ===
0:20:30.993700 INFO: rt_error       : 542.826796645432
0:20:30.993756 INFO: mobility_error : 0.1
0:20:30.993800 INFO: num_candidates : 3
0:20:30.993844 INFO: ms1_error      : 3
0:20:30.993884 INFO: ms2_error      : 10.0
0:20:30.993934 INFO: fwhm_rt        : 3.0
0:20:30.993976 INFO: quant_window   : 3
0:20:30.994015 INFO: ==============================================
0:20:33.359329 INFO: performing precursor FDR with 40 features
0:20:33.359442 INFO: Decoy channel: -1
0:20:33.359466 INFO: competitive: True
0:20:33.546902 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:33.842171 INFO: Estimating optimal hyperparameters - samples: 599,092, batch_size: 2,453, learning_rate: 7.74e-04
0:20:33.843168 INFO: Using random state 143539 for train-test-split
0:20:46.876707 INFO: Test AUC: 0.608
0:20:46.876944 INFO: Train AUC: 0.624
0:20:46.876983 INFO: AUC difference: 2.57%
0:20:47.364469 INFO: Resetting torch num_threads to 100
0:20:47.393324 PROGRESS: === Extracted 748866 precursors and 3992732 fragments ===
0:20:47.393839 INFO: === FDR correction performed with classifier version 11 ===
0:20:47.394583 PROGRESS: ============================= Precursor FDR =============================
0:20:47.394675 PROGRESS: Total precursors accumulated: 1,542
0:20:47.394737 PROGRESS: Target precursors: 1,527 (99.03%)
0:20:47.394792 PROGRESS: Decoy precursors: 15 (0.97%)
0:20:47.394855 PROGRESS: 
0:20:47.394904 PROGRESS: Precursor Summary:
0:20:47.396307 PROGRESS: Channel   0:	 0.050 FDR: 1,527; 0.010 FDR: 1,527; 0.001 FDR: 1,266
0:20:47.396398 PROGRESS: 
0:20:47.396453 PROGRESS: Protein Summary:
0:20:47.398296 PROGRESS: Channel   0:	 0.050 FDR: 1,275; 0.010 FDR: 1,275; 0.001 FDR: 1,073
0:20:47.398407 PROGRESS: =========================================================================
0:20:47.412672 INFO: Target number of precursors reached.
0:20:47.855071 INFO: fragments_df: keeping 5000 of 3992732 [sum(precursor_idx_mask)=36341 sum(mass_error_mask)=3992732 stop_rank=5000
0:20:48.318696 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:48.559852 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:49.279367 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:49.279808 INFO: Using score_cutoff 12.06532440547943 (fac=0.99, q=1)
0:20:49.280141 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:49.280221 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:49.280278 INFO: Updating optimization_manager: score_cutoff        : 12.016403463935852 -> 12.06532440547943
0:20:49.280338 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:49.430535 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:49.761675 INFO: === checking if optimization conditions were reached ===
0:20:49.762032 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:20:49.765466 INFO: Updating optimization_manager: rt_error            : 542.826796645432 -> 448.78108229397117
0:20:49.765590 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 448.7811.
0:20:49.765666 INFO: ==============================================
0:20:49.765757 INFO: Starting optimization step 6.
0:20:49.765831 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:49.765935 INFO: Using rust extraction backend
0:20:49.766029 PROGRESS: Extracting batch of 250439 precursors
0:20:50.188474 INFO: === Search parameters used ===
0:20:50.188749 INFO: rt_error       : 448.78108229397117
0:20:50.188807 INFO: mobility_error : 0.1
0:20:50.188873 INFO: num_candidates : 3
0:20:50.188918 INFO: ms1_error      : 3
0:20:50.188959 INFO: ms2_error      : 10.0
0:20:50.188998 INFO: fwhm_rt        : 3.0
0:20:50.189036 INFO: quant_window   : 3
0:20:50.189074 INFO: ==============================================
0:20:52.547808 INFO: performing precursor FDR with 40 features
0:20:52.547928 INFO: Decoy channel: -1
0:20:52.547955 INFO: competitive: True
0:20:52.734468 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:53.023283 INFO: Estimating optimal hyperparameters - samples: 598,512, batch_size: 2,451, learning_rate: 7.74e-04
0:20:53.024378 INFO: Using random state 143539 for train-test-split
0:21:05.840687 INFO: Test AUC: 0.607
0:21:05.840818 INFO: Train AUC: 0.623
0:21:05.840851 INFO: AUC difference: 2.52%
0:21:06.825424 INFO: Resetting torch num_threads to 100
0:21:06.850929 PROGRESS: === Extracted 748140 precursors and 3933518 fragments ===
0:21:06.851379 INFO: === FDR correction performed with classifier version 11 ===
0:21:06.852041 PROGRESS: ============================= Precursor FDR =============================
0:21:06.852131 PROGRESS: Total precursors accumulated: 1,653
0:21:06.852206 PROGRESS: Target precursors: 1,637 (99.03%)
0:21:06.852258 PROGRESS: Decoy precursors: 16 (0.97%)
0:21:06.852304 PROGRESS: 
0:21:06.852349 PROGRESS: Precursor Summary:
0:21:06.853638 PROGRESS: Channel   0:	 0.050 FDR: 1,637; 0.010 FDR: 1,637; 0.001 FDR:    39
0:21:06.853727 PROGRESS: 
0:21:06.853783 PROGRESS: Protein Summary:
0:21:06.855423 PROGRESS: Channel   0:	 0.050 FDR: 1,365; 0.010 FDR: 1,365; 0.001 FDR:    39
0:21:06.855515 PROGRESS: =========================================================================
0:21:06.870697 INFO: Target number of precursors reached.
0:21:07.302083 INFO: fragments_df: keeping 5000 of 3933518 [sum(precursor_idx_mask)=38581 sum(mass_error_mask)=3933518 stop_rank=5000
0:21:07.726892 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:07.985437 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:08.706186 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:08.706619 INFO: Using score_cutoff 11.481445503616332 (fac=0.99, q=1)
0:21:08.706925 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:08.707011 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:08.707078 INFO: Updating optimization_manager: score_cutoff        : 12.06532440547943 -> 11.481445503616332
0:21:08.707134 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:08.856030 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:09.203837 INFO: === checking if optimization conditions were reached ===
0:21:09.204151 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:21:09.207618 INFO: Updating optimization_manager: rt_error            : 448.78108229397117 -> 533.3094172908723
0:21:09.207785 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 533.3094.
0:21:09.207874 INFO: ==============================================
0:21:09.207957 INFO: Starting optimization step 7.
0:21:09.208028 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:09.208101 INFO: Using rust extraction backend
0:21:09.208169 PROGRESS: Extracting batch of 250439 precursors
0:21:09.629205 INFO: === Search parameters used ===
0:21:09.629470 INFO: rt_error       : 533.3094172908723
0:21:09.629527 INFO: mobility_error : 0.1
0:21:09.629576 INFO: num_candidates : 3
0:21:09.629622 INFO: ms1_error      : 3
0:21:09.629665 INFO: ms2_error      : 10.0
0:21:09.629709 INFO: fwhm_rt        : 3.0
0:21:09.629758 INFO: quant_window   : 3
0:21:09.629798 INFO: ==============================================
0:21:12.050510 INFO: performing precursor FDR with 40 features
0:21:12.050628 INFO: Decoy channel: -1
0:21:12.050655 INFO: competitive: True
0:21:12.242273 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:12.549853 INFO: Estimating optimal hyperparameters - samples: 599,110, batch_size: 2,453, learning_rate: 7.74e-04
0:21:12.551014 INFO: Using random state 143539 for train-test-split
0:21:25.737045 INFO: Test AUC: 0.608
0:21:25.737289 INFO: Train AUC: 0.624
0:21:25.737323 INFO: AUC difference: 2.41%
0:21:26.229327 INFO: Resetting torch num_threads to 100
0:21:26.254202 PROGRESS: === Extracted 748888 precursors and 3991188 fragments ===
0:21:26.254743 INFO: === FDR correction performed with classifier version 11 ===
0:21:26.255434 PROGRESS: ============================= Precursor FDR =============================
0:21:26.255526 PROGRESS: Total precursors accumulated: 1,665
0:21:26.255586 PROGRESS: Target precursors: 1,649 (99.04%)
0:21:26.255636 PROGRESS: Decoy precursors: 16 (0.96%)
0:21:26.255683 PROGRESS: 
0:21:26.255731 PROGRESS: Precursor Summary:
0:21:26.257151 PROGRESS: Channel   0:	 0.050 FDR: 1,649; 0.010 FDR: 1,649; 0.001 FDR: 1,271
0:21:26.257242 PROGRESS: 
0:21:26.257297 PROGRESS: Protein Summary:
0:21:26.259206 PROGRESS: Channel   0:	 0.050 FDR: 1,372; 0.010 FDR: 1,372; 0.001 FDR: 1,081
0:21:26.259304 PROGRESS: =========================================================================
0:21:26.272831 INFO: Target number of precursors reached.
0:21:26.707899 INFO: fragments_df: keeping 5000 of 3991188 [sum(precursor_idx_mask)=38758 sum(mass_error_mask)=3991188 stop_rank=5000
0:21:27.184209 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:27.434680 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:28.155434 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:28.155878 INFO: Using score_cutoff 11.493756415557861 (fac=0.99, q=1)
0:21:28.156219 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:28.156294 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:28.156351 INFO: Updating optimization_manager: score_cutoff        : 11.481445503616332 -> 11.493756415557861
0:21:28.156416 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:28.304295 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:28.627828 INFO: === checking if optimization conditions were reached ===
0:21:28.628121 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:21:28.631640 INFO: Updating optimization_manager: rt_error            : 533.3094172908723 -> 642.5816998243749
0:21:28.631795 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 642.5817.
0:21:28.631876 INFO: ==============================================
0:21:28.631968 INFO: Starting optimization step 8.
0:21:28.632042 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:28.632134 INFO: Using rust extraction backend
0:21:28.632219 PROGRESS: Extracting batch of 250439 precursors
0:21:29.061811 INFO: === Search parameters used ===
0:21:29.062063 INFO: rt_error       : 642.5816998243749
0:21:29.062124 INFO: mobility_error : 0.1
0:21:29.062175 INFO: num_candidates : 3
0:21:29.062223 INFO: ms1_error      : 3
0:21:29.062272 INFO: ms2_error      : 10.0
0:21:29.062317 INFO: fwhm_rt        : 3.0
0:21:29.062359 INFO: quant_window   : 3
0:21:29.062401 INFO: ==============================================
0:21:31.499916 INFO: performing precursor FDR with 40 features
0:21:31.500031 INFO: Decoy channel: -1
0:21:31.500057 INFO: competitive: True
0:21:31.683489 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:31.972331 INFO: Estimating optimal hyperparameters - samples: 599,459, batch_size: 2,455, learning_rate: 7.74e-04
0:21:31.973467 INFO: Using random state 143539 for train-test-split
0:21:45.171370 INFO: Test AUC: 0.610
0:21:45.171502 INFO: Train AUC: 0.624
0:21:45.171534 INFO: AUC difference: 2.25%
0:21:45.655787 INFO: Resetting torch num_threads to 100
0:21:45.684511 PROGRESS: === Extracted 749324 precursors and 4019662 fragments ===
0:21:45.685004 INFO: === FDR correction performed with classifier version 11 ===
0:21:45.685694 PROGRESS: ============================= Precursor FDR =============================
0:21:45.685790 PROGRESS: Total precursors accumulated: 1,555
0:21:45.685855 PROGRESS: Target precursors: 1,540 (99.04%)
0:21:45.685914 PROGRESS: Decoy precursors: 15 (0.96%)
0:21:45.685965 PROGRESS: 
0:21:45.686008 PROGRESS: Precursor Summary:
0:21:45.687361 PROGRESS: Channel   0:	 0.050 FDR: 1,540; 0.010 FDR: 1,540; 0.001 FDR: 1,243
0:21:45.687445 PROGRESS: 
0:21:45.687498 PROGRESS: Protein Summary:
0:21:45.689278 PROGRESS: Channel   0:	 0.050 FDR: 1,288; 0.010 FDR: 1,288; 0.001 FDR: 1,064
0:21:45.689364 PROGRESS: =========================================================================
0:21:45.703114 INFO: Target number of precursors reached.
0:21:46.140571 INFO: fragments_df: keeping 5000 of 4019662 [sum(precursor_idx_mask)=36527 sum(mass_error_mask)=4019662 stop_rank=5000
0:21:46.551216 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:46.791615 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:47.513148 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:47.513563 INFO: Using score_cutoff 11.562048756408691 (fac=0.99, q=1)
0:21:47.513864 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:47.513950 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:47.514016 INFO: Updating optimization_manager: score_cutoff        : 11.493756415557861 -> 11.562048756408691
0:21:47.514070 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:47.661631 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:47.981865 INFO: === checking if optimization conditions were reached ===
0:21:47.982174 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:21:47.985479 INFO: Updating optimization_manager: rt_error            : 642.5816998243749 -> 634.1864787494001
0:21:47.985621 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 634.1865.
0:21:47.985696 INFO: ==============================================
0:21:47.985775 INFO: Starting optimization step 9.
0:21:47.985842 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:47.985921 INFO: Using rust extraction backend
0:21:47.985999 PROGRESS: Extracting batch of 250439 precursors
0:21:48.411678 INFO: === Search parameters used ===
0:21:48.411938 INFO: rt_error       : 634.1864787494001
0:21:48.411994 INFO: mobility_error : 0.1
0:21:48.412041 INFO: num_candidates : 3
0:21:48.412083 INFO: ms1_error      : 3
0:21:48.412124 INFO: ms2_error      : 10.0
0:21:48.412163 INFO: fwhm_rt        : 3.0
0:21:48.412202 INFO: quant_window   : 3
0:21:48.412258 INFO: ==============================================
0:21:50.874530 INFO: performing precursor FDR with 40 features
0:21:50.874653 INFO: Decoy channel: -1
0:21:50.874680 INFO: competitive: True
0:21:51.060715 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:51.357980 INFO: Estimating optimal hyperparameters - samples: 599,535, batch_size: 2,455, learning_rate: 7.74e-04
0:21:51.359023 INFO: Using random state 143539 for train-test-split
0:22:04.542427 INFO: Test AUC: 0.611
0:22:04.542559 INFO: Train AUC: 0.626
0:22:04.542592 INFO: AUC difference: 2.38%
0:22:05.030631 INFO: Resetting torch num_threads to 100
0:22:05.089361 PROGRESS: === Extracted 749419 precursors and 4022065 fragments ===
0:22:05.089844 INFO: === FDR correction performed with classifier version 11 ===
0:22:05.090503 PROGRESS: ============================= Precursor FDR =============================
0:22:05.090599 PROGRESS: Total precursors accumulated: 1,621
0:22:05.090660 PROGRESS: Target precursors: 1,605 (99.01%)
0:22:05.090712 PROGRESS: Decoy precursors: 16 (0.99%)
0:22:05.090765 PROGRESS: 
0:22:05.090812 PROGRESS: Precursor Summary:
0:22:05.092198 PROGRESS: Channel   0:	 0.050 FDR: 1,605; 0.010 FDR: 1,605; 0.001 FDR: 1,359
0:22:05.092288 PROGRESS: 
0:22:05.092346 PROGRESS: Protein Summary:
0:22:05.094201 PROGRESS: Channel   0:	 0.050 FDR: 1,327; 0.010 FDR: 1,327; 0.001 FDR: 1,143
0:22:05.094319 PROGRESS: =========================================================================
0:22:05.107977 INFO: Target number of precursors reached.
0:22:05.542436 INFO: fragments_df: keeping 5000 of 4022065 [sum(precursor_idx_mask)=37990 sum(mass_error_mask)=4022065 stop_rank=5000
0:22:06.037895 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:06.283204 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:07.004746 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:07.005228 INFO: Using score_cutoff 11.99460474357605 (fac=0.99, q=1)
0:22:07.005549 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:07.005627 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:07.005683 INFO: Updating optimization_manager: score_cutoff        : 11.562048756408691 -> 11.99460474357605
0:22:07.005745 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:07.152849 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:07.477554 INFO: === checking if optimization conditions were reached ===
0:22:07.477879 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
0:22:07.479099 INFO: Updating optimization_manager: rt_error            : 634.1864787494001 -> 911.9836616887239
0:22:07.479249 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
0:22:07.479367 INFO: Updating optimization_manager: score_cutoff        : 11.99460474357605 -> 8.205502009391784
0:22:07.479482 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:07.479589 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:07.479706 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 911.9837 found after 10 searches.
0:22:07.479778 INFO: ==============================================
0:22:07.479874 PROGRESS: Optimization finished for rt_error.
0:22:07.902719 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:08.050236 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:08.374948 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:22:08.375267 PROGRESS: ==============================================
0:22:08.375370 PROGRESS: ms2_error      : 10.0000
0:22:08.375441 PROGRESS: rt_error       : 911.9837
0:22:08.375502 PROGRESS: ==============================================
0:22:08.382836 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:15.854903 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:31.652733 INFO: Using rust extraction backend
0:22:31.653165 PROGRESS: Extracting batch of 11997144 precursors
0:22:47.679203 INFO: === Search parameters used ===
0:22:47.679723 INFO: rt_error       : 911.9836616887239
0:22:47.679791 INFO: mobility_error : 0.1
0:22:47.679847 INFO: num_candidates : 3
0:22:47.679914 INFO: ms1_error      : 3
0:22:47.679963 INFO: ms2_error      : 10.0
0:22:47.680009 INFO: fwhm_rt        : 3.0
0:22:47.680052 INFO: quant_window   : 3
0:22:47.680095 INFO: ==============================================
0:23:23.944863 INFO: Removed 3671968 precursors with score below cutoff 8.205502009391784
0:23:49.146347 INFO: performing precursor FDR with 40 features
0:23:49.146578 INFO: Decoy channel: -1
0:23:49.146610 INFO: competitive: True
0:23:52.526959 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:06.085150 INFO: Estimating optimal hyperparameters - samples: 25,855,334, batch_size: 4,096, learning_rate: 1.00e-03
0:24:06.162093 INFO: Using random state 929608 for train-test-split
0:32:17.798041 INFO: Test AUC: 0.622
0:32:17.798316 INFO: Train AUC: 0.623
0:32:17.798358 INFO: AUC difference: 0.06%
0:32:24.919872 INFO: Resetting torch num_threads to 100
0:32:27.073841 PROGRESS: ============================= Precursor FDR =============================
0:32:27.074277 PROGRESS: Total precursors accumulated: 91,777
0:32:27.074352 PROGRESS: Target precursors: 90,869 (99.01%)
0:32:27.074426 PROGRESS: Decoy precursors: 908 (0.99%)
0:32:27.074484 PROGRESS: 
0:32:27.074535 PROGRESS: Precursor Summary:
0:32:27.098974 PROGRESS: Channel   0:	 0.050 FDR: 90,869; 0.010 FDR: 90,869; 0.001 FDR: 57,008
0:32:27.099226 PROGRESS: 
0:32:27.099285 PROGRESS: Protein Summary:
0:32:27.130939 PROGRESS: Channel   0:	 0.050 FDR: 13,589; 0.010 FDR: 13,589; 0.001 FDR: 9,298
0:32:27.131189 PROGRESS: =========================================================================
0:32:27.300541 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:32:27.463324 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:32:27.682219 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:32:28.150370 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
0:32:28.150519 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant
0:32:28.150618 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:32:28.150806 INFO: Initializing TimingManager
0:32:28.151197 INFO: Initializing RawFileManager
0:32:38.209894 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.
0:32:38.218473 INFO: Determining DIA cycle
0:32:38.235894 INFO: Found cycle with start 0.00 min and length 300.
0:32:38.405545 INFO: RT (min)            : 0.0 - 26.9
0:32:38.405635 INFO: RT duration (sec)   : 1611.2
0:32:38.405665 INFO: RT duration (min)   : 26.9
0:32:38.405689 INFO: Cycle len (scans)   : 300
0:32:38.405710 INFO: Cycle len (sec)     : 1.65
0:32:38.405729 INFO: Number of cycles    : 978
0:32:38.405749 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:32:38.405774 INFO: Creating DIA data object took: 10.254488229751587
0:32:39.071736 INFO: Creating DIA data NG object took: 0.6658453941345215
0:32:40.371908 INFO: Initializing CalibrationManager
0:32:40.372190 INFO: Setting up calibration estimators ..
0:32:40.372258 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:32:40.372339 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'}' ..
0:32:40.372444 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:32:40.372498 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:32:40.372554 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}}' ..
0:32:40.372606 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:32:40.372652 INFO: Done setting up calibration estimators.
0:32:40.372846 INFO: Initializing OptimizationManager
0:32:40.372981 INFO: initial parameter: ms1_error = 3
0:32:40.373033 INFO: initial parameter: ms2_error = 10
0:32:40.373080 INFO: initial parameter: rt_error = 805.6019897460938
0:32:40.373122 INFO: initial parameter: mobility_error = 0.1
0:32:40.373163 INFO: initial parameter: num_candidates = 1
0:32:40.373204 INFO: initial parameter: fwhm_rt = 5
0:32:40.373244 INFO: initial parameter: fwhm_mobility = 0.01
0:32:40.373283 INFO: initial parameter: score_cutoff = 0
0:32:40.373323 INFO: initial parameter: classifier_version = -1
0:32:40.373389 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:32:40.373622 INFO: FDRManager: loading saved state not requested, will be initialized.
0:32:40.373661 INFO: Initializing FDRManager
0:32:40.373700 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:32:41.761753 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:32:42.642666 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:32:42.643083 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:32:42.643179 PROGRESS: Starting initial search for precursors.
0:32:42.643262 INFO: Starting optimization step 0.
0:32:42.643325 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:32:42.643382 INFO: Using rust extraction backend
0:32:42.643437 PROGRESS: Extracting batch of 1965 precursors
0:32:42.648266 INFO: === Search parameters used ===
0:32:42.648364 INFO: rt_error       : 805.6019897460938
0:32:42.648414 INFO: mobility_error : 0.1
0:32:42.648458 INFO: num_candidates : 1
0:32:42.648498 INFO: ms1_error      : 3
0:32:42.648538 INFO: ms2_error      : 10
0:32:42.648576 INFO: fwhm_rt        : 5
0:32:42.648614 INFO: quant_window   : 3
0:32:42.648652 INFO: ==============================================
0:32:42.674375 INFO: performing precursor FDR with 40 features
0:32:42.674437 INFO: Decoy channel: -1
0:32:42.674461 INFO: competitive: True
0:32:42.675697 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:42.677598 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
0:32:42.678414 INFO: Using random state 333997 for train-test-split
0:32:42.796397 INFO: Test AUC: 0.491
0:32:42.796484 INFO: Train AUC: 0.567
0:32:42.796512 INFO: AUC difference: 13.37%
0:32:42.796534 WARNING: AUC difference > 5%. This may indicate overfitting.
0:32:43.042887 INFO: Resetting torch num_threads to 100
0:32:43.044381 PROGRESS: === Extracted 1957 precursors and 10822 fragments ===
0:32:43.044738 INFO: === FDR correction performed with classifier version -1 ===
0:32:43.045223 PROGRESS: ============================= Precursor FDR =============================
0:32:43.045305 PROGRESS: Total precursors accumulated: 19
0:32:43.045360 PROGRESS: Target precursors: 19 (100.00%)
0:32:43.045408 PROGRESS: Decoy precursors: 0 (0.00%)
0:32:43.045452 PROGRESS: 
0:32:43.045493 PROGRESS: Precursor Summary:
0:32:43.046550 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:32:43.046643 PROGRESS: 
0:32:43.046696 PROGRESS: Protein Summary:
0:32:43.047861 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:32:43.047942 PROGRESS: =========================================================================
0:32:43.048143 INFO: Target number of precursors not reached yet.
0:32:43.131871 INFO: Starting optimization step 1.
0:32:43.132100 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:32:43.132176 INFO: Using rust extraction backend
0:32:43.132232 PROGRESS: Extracting batch of 3948 precursors
0:32:43.140456 INFO: === Search parameters used ===
0:32:43.140586 INFO: rt_error       : 805.6019897460938
0:32:43.140635 INFO: mobility_error : 0.1
0:32:43.140678 INFO: num_candidates : 1
0:32:43.140718 INFO: ms1_error      : 3
0:32:43.140756 INFO: ms2_error      : 10
0:32:43.140795 INFO: fwhm_rt        : 5
0:32:43.140833 INFO: quant_window   : 3
0:32:43.140871 INFO: ==============================================
0:32:43.185046 INFO: performing precursor FDR with 40 features
0:32:43.185128 INFO: Decoy channel: -1
0:32:43.185152 INFO: competitive: True
0:32:43.189512 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:43.191837 INFO: Estimating optimal hyperparameters - samples: 4,712, batch_size: 128, learning_rate: 1.77e-04
0:32:43.191919 INFO: Using random state 180899 for train-test-split
0:32:43.589299 INFO: Test AUC: 0.526
0:32:43.589384 INFO: Train AUC: 0.572
0:32:43.589412 INFO: AUC difference: 7.96%
0:32:43.589434 WARNING: AUC difference > 5%. This may indicate overfitting.
0:32:43.835127 INFO: Resetting torch num_threads to 100
0:32:43.837946 PROGRESS: === Extracted 5891 precursors and 32662 fragments ===
0:32:43.838310 INFO: === FDR correction performed with classifier version -1 ===
0:32:43.838804 PROGRESS: ============================= Precursor FDR =============================
0:32:43.838890 PROGRESS: Total precursors accumulated: 20
0:32:43.838950 PROGRESS: Target precursors: 20 (100.00%)
0:32:43.839000 PROGRESS: Decoy precursors: 0 (0.00%)
0:32:43.839049 PROGRESS: 
0:32:43.839095 PROGRESS: Precursor Summary:
0:32:43.840154 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
0:32:43.840237 PROGRESS: 
0:32:43.840292 PROGRESS: Protein Summary:
0:32:43.841453 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
0:32:43.841536 PROGRESS: =========================================================================
0:32:43.841781 INFO: Target number of precursors not reached yet.
0:32:43.930608 INFO: Starting optimization step 2.
0:32:43.930844 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:32:43.930923 INFO: Using rust extraction backend
0:32:43.930982 PROGRESS: Extracting batch of 7900 precursors
0:32:43.945940 INFO: === Search parameters used ===
0:32:43.946087 INFO: rt_error       : 805.6019897460938
0:32:43.946140 INFO: mobility_error : 0.1
0:32:43.946186 INFO: num_candidates : 1
0:32:43.946232 INFO: ms1_error      : 3
0:32:43.946278 INFO: ms2_error      : 10
0:32:43.946321 INFO: fwhm_rt        : 5
0:32:43.946363 INFO: quant_window   : 3
0:32:43.946404 INFO: ==============================================
0:32:44.018557 INFO: performing precursor FDR with 40 features
0:32:44.018659 INFO: Decoy channel: -1
0:32:44.018684 INFO: competitive: True
0:32:44.024728 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:44.028197 INFO: Estimating optimal hyperparameters - samples: 11,017, batch_size: 128, learning_rate: 1.77e-04
0:32:44.028327 INFO: Using random state 372980 for train-test-split
0:32:45.138105 INFO: Test AUC: 0.553
0:32:45.138217 INFO: Train AUC: 0.589
0:32:45.138246 INFO: AUC difference: 6.12%
0:32:45.138266 WARNING: AUC difference > 5%. This may indicate overfitting.
0:32:45.389532 INFO: Resetting torch num_threads to 100
0:32:45.393682 PROGRESS: === Extracted 13772 precursors and 76365 fragments ===
0:32:45.394090 INFO: === FDR correction performed with classifier version -1 ===
0:32:45.394602 PROGRESS: ============================= Precursor FDR =============================
0:32:45.394685 PROGRESS: Total precursors accumulated: 55
0:32:45.394741 PROGRESS: Target precursors: 55 (100.00%)
0:32:45.394789 PROGRESS: Decoy precursors: 0 (0.00%)
0:32:45.394834 PROGRESS: 
0:32:45.394876 PROGRESS: Precursor Summary:
0:32:45.395925 PROGRESS: Channel   0:	 0.050 FDR:    55; 0.010 FDR:    55; 0.001 FDR:    55
0:32:45.396006 PROGRESS: 
0:32:45.396058 PROGRESS: Protein Summary:
0:32:45.397233 PROGRESS: Channel   0:	 0.050 FDR:    54; 0.010 FDR:    54; 0.001 FDR:    54
0:32:45.397313 PROGRESS: =========================================================================
0:32:45.397647 INFO: Target number of precursors not reached yet.
0:32:45.500604 INFO: Starting optimization step 3.
0:32:45.500846 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:32:45.500923 INFO: Using rust extraction backend
0:32:45.500982 PROGRESS: Extracting batch of 15775 precursors
0:32:45.534063 INFO: === Search parameters used ===
0:32:45.534240 INFO: rt_error       : 805.6019897460938
0:32:45.534296 INFO: mobility_error : 0.1
0:32:45.534343 INFO: num_candidates : 1
0:32:45.534387 INFO: ms1_error      : 3
0:32:45.534427 INFO: ms2_error      : 10
0:32:45.534483 INFO: fwhm_rt        : 5
0:32:45.534525 INFO: quant_window   : 3
0:32:45.534565 INFO: ==============================================
0:32:45.668069 INFO: performing precursor FDR with 40 features
0:32:45.668180 INFO: Decoy channel: -1
0:32:45.668203 INFO: competitive: True
0:32:45.678929 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:45.686052 INFO: Estimating optimal hyperparameters - samples: 23,607, batch_size: 128, learning_rate: 1.77e-04
0:32:45.686246 INFO: Using random state 969411 for train-test-split
0:32:48.056581 INFO: Test AUC: 0.576
0:32:48.056694 INFO: Train AUC: 0.606
0:32:48.056723 INFO: AUC difference: 4.90%
0:32:48.317152 INFO: Resetting torch num_threads to 100
0:32:48.325348 PROGRESS: === Extracted 29509 precursors and 163964 fragments ===
0:32:48.325867 INFO: === FDR correction performed with classifier version -1 ===
0:32:48.326409 PROGRESS: ============================= Precursor FDR =============================
0:32:48.326497 PROGRESS: Total precursors accumulated: 118
0:32:48.326552 PROGRESS: Target precursors: 117 (99.15%)
0:32:48.326601 PROGRESS: Decoy precursors: 1 (0.85%)
0:32:48.326644 PROGRESS: 
0:32:48.326685 PROGRESS: Precursor Summary:
0:32:48.327645 PROGRESS: Channel   0:	 0.050 FDR:   117; 0.010 FDR:   117; 0.001 FDR:    96
0:32:48.327727 PROGRESS: 
0:32:48.327778 PROGRESS: Protein Summary:
0:32:48.328875 PROGRESS: Channel   0:	 0.050 FDR:   115; 0.010 FDR:   115; 0.001 FDR:    94
0:32:48.328957 PROGRESS: =========================================================================
0:32:48.329483 INFO: Target number of precursors not reached yet.
0:32:48.462450 INFO: Starting optimization step 4.
0:32:48.462709 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:32:48.462788 INFO: Using rust extraction backend
0:32:48.462849 PROGRESS: Extracting batch of 31568 precursors
0:32:48.519953 INFO: === Search parameters used ===
0:32:48.520197 INFO: rt_error       : 805.6019897460938
0:32:48.520248 INFO: mobility_error : 0.1
0:32:48.520293 INFO: num_candidates : 1
0:32:48.520335 INFO: ms1_error      : 3
0:32:48.520374 INFO: ms2_error      : 10
0:32:48.520412 INFO: fwhm_rt        : 5
0:32:48.520451 INFO: quant_window   : 3
0:32:48.520489 INFO: ==============================================
0:32:48.740952 INFO: performing precursor FDR with 40 features
0:32:48.741062 INFO: Decoy channel: -1
0:32:48.741086 INFO: competitive: True
0:32:48.764601 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:48.784589 INFO: Estimating optimal hyperparameters - samples: 48,793, batch_size: 199, learning_rate: 2.20e-04
0:32:48.784788 INFO: Using random state 978651 for train-test-split
0:32:52.464734 INFO: Test AUC: 0.579
0:32:52.464852 INFO: Train AUC: 0.612
0:32:52.464884 INFO: AUC difference: 5.41%
0:32:52.464907 WARNING: AUC difference > 5%. This may indicate overfitting.
0:32:52.727672 INFO: Resetting torch num_threads to 100
0:32:52.738350 PROGRESS: === Extracted 60992 precursors and 339066 fragments ===
0:32:52.738968 INFO: === FDR correction performed with classifier version -1 ===
0:32:52.739531 PROGRESS: ============================= Precursor FDR =============================
0:32:52.739620 PROGRESS: Total precursors accumulated: 290
0:32:52.739682 PROGRESS: Target precursors: 288 (99.31%)
0:32:52.739736 PROGRESS: Decoy precursors: 2 (0.69%)
0:32:52.739784 PROGRESS: 
0:32:52.739832 PROGRESS: Precursor Summary:
0:32:52.740865 PROGRESS: Channel   0:	 0.050 FDR:   288; 0.010 FDR:   288; 0.001 FDR:   277
0:32:52.740951 PROGRESS: 
0:32:52.741008 PROGRESS: Protein Summary:
0:32:52.742224 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   263
0:32:52.742331 PROGRESS: =========================================================================
0:32:52.743197 INFO: Target number of precursors not reached yet.
0:32:52.907166 INFO: Starting optimization step 5.
0:32:52.907421 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:32:52.907499 INFO: Using rust extraction backend
0:32:52.907560 PROGRESS: Extracting batch of 63098 precursors
0:32:53.015077 INFO: === Search parameters used ===
0:32:53.015332 INFO: rt_error       : 805.6019897460938
0:32:53.015385 INFO: mobility_error : 0.1
0:32:53.015430 INFO: num_candidates : 1
0:32:53.015473 INFO: ms1_error      : 3
0:32:53.015514 INFO: ms2_error      : 10
0:32:53.015555 INFO: fwhm_rt        : 5
0:32:53.015595 INFO: quant_window   : 3
0:32:53.015635 INFO: ==============================================
0:32:53.401612 INFO: performing precursor FDR with 40 features
0:32:53.401727 INFO: Decoy channel: -1
0:32:53.401751 INFO: competitive: True
0:32:53.448591 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:53.479196 INFO: Estimating optimal hyperparameters - samples: 99,136, batch_size: 406, learning_rate: 3.15e-04
0:32:53.479460 INFO: Using random state 527974 for train-test-split
0:32:58.066288 INFO: Test AUC: 0.583
0:32:58.066413 INFO: Train AUC: 0.608
0:32:58.066444 INFO: AUC difference: 4.24%
0:32:58.345807 INFO: Resetting torch num_threads to 100
0:32:58.367060 PROGRESS: === Extracted 123921 precursors and 689937 fragments ===
0:32:58.367686 INFO: === FDR correction performed with classifier version -1 ===
0:32:58.368309 PROGRESS: ============================= Precursor FDR =============================
0:32:58.368400 PROGRESS: Total precursors accumulated: 581
0:32:58.368462 PROGRESS: Target precursors: 576 (99.14%)
0:32:58.368516 PROGRESS: Decoy precursors: 5 (0.86%)
0:32:58.368564 PROGRESS: 
0:32:58.368625 PROGRESS: Precursor Summary:
0:32:58.369735 PROGRESS: Channel   0:	 0.050 FDR:   576; 0.010 FDR:   576; 0.001 FDR:   357
0:32:58.369835 PROGRESS: 
0:32:58.369895 PROGRESS: Protein Summary:
0:32:58.371243 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   535; 0.001 FDR:   334
0:32:58.371335 PROGRESS: =========================================================================
0:32:58.373204 INFO: Target number of precursors not reached yet.
0:32:58.614517 INFO: Starting optimization step 6.
0:32:58.614783 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:32:58.614861 INFO: Using rust extraction backend
0:32:58.614923 PROGRESS: Extracting batch of 126185 precursors
0:32:58.828534 INFO: === Search parameters used ===
0:32:58.828797 INFO: rt_error       : 805.6019897460938
0:32:58.828853 INFO: mobility_error : 0.1
0:32:58.828901 INFO: num_candidates : 1
0:32:58.828946 INFO: ms1_error      : 3
0:32:58.828989 INFO: ms2_error      : 10
0:32:58.829031 INFO: fwhm_rt        : 5
0:32:58.829072 INFO: quant_window   : 3
0:32:58.829117 INFO: ==============================================
0:32:59.528428 INFO: performing precursor FDR with 40 features
0:32:59.528549 INFO: Decoy channel: -1
0:32:59.528575 INFO: competitive: True
0:32:59.626803 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:59.703270 INFO: Estimating optimal hyperparameters - samples: 199,835, batch_size: 818, learning_rate: 4.47e-04
0:32:59.703756 INFO: Using random state 943784 for train-test-split
0:33:06.236293 INFO: Test AUC: 0.591
0:33:06.236523 INFO: Train AUC: 0.611
0:33:06.236557 INFO: AUC difference: 3.30%
0:33:06.569736 INFO: Resetting torch num_threads to 100
0:33:06.629297 PROGRESS: === Extracted 249794 precursors and 1390143 fragments ===
0:33:06.630049 INFO: === FDR correction performed with classifier version -1 ===
0:33:06.630885 PROGRESS: ============================= Precursor FDR =============================
0:33:06.630976 PROGRESS: Total precursors accumulated: 1,212
0:33:06.631038 PROGRESS: Target precursors: 1,200 (99.01%)
0:33:06.631090 PROGRESS: Decoy precursors: 12 (0.99%)
0:33:06.631138 PROGRESS: 
0:33:06.631186 PROGRESS: Precursor Summary:
0:33:06.632436 PROGRESS: Channel   0:	 0.050 FDR: 1,200; 0.010 FDR: 1,198; 0.001 FDR:   549
0:33:06.632525 PROGRESS: 
0:33:06.632580 PROGRESS: Protein Summary:
0:33:06.634182 PROGRESS: Channel   0:	 0.050 FDR: 1,024; 0.010 FDR: 1,022; 0.001 FDR:   486
0:33:06.634275 PROGRESS: =========================================================================
0:33:06.638427 INFO: Target number of precursors reached.
0:33:06.801477 INFO: fragments_df: keeping 5000 of 1390143 [sum(precursor_idx_mask)=12709 sum(mass_error_mask)=1390143 stop_rank=5000
0:33:07.245395 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:07.448052 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:08.167404 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:33:08.167845 INFO: Using score_cutoff 11.833174439620972 (fac=0.99, q=1)
0:33:08.168188 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:33:08.168264 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:33:08.168322 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.833174439620972
0:33:08.168381 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:08.318551 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:08.663961 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:33:08.664242 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:33:08.664361 INFO: Starting optimization step 7.
0:33:08.664436 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:33:08.664531 INFO: Using rust extraction backend
0:33:08.664618 PROGRESS: Extracting batch of 250439 precursors
0:33:09.093308 INFO: === Search parameters used ===
0:33:09.093578 INFO: rt_error       : 805.6019897460938
0:33:09.093635 INFO: mobility_error : 0.1
0:33:09.093682 INFO: num_candidates : 3
0:33:09.093731 INFO: ms1_error      : 3
0:33:09.093774 INFO: ms2_error      : 10
0:33:09.093815 INFO: fwhm_rt        : 3.0
0:33:09.093856 INFO: quant_window   : 3
0:33:09.093897 INFO: ==============================================
0:33:11.703304 INFO: performing precursor FDR with 40 features
0:33:11.703426 INFO: Decoy channel: -1
0:33:11.703456 INFO: competitive: True
0:33:11.892193 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:12.200863 INFO: Estimating optimal hyperparameters - samples: 599,616, batch_size: 2,456, learning_rate: 7.74e-04
0:33:12.202148 INFO: Using random state 928283 for train-test-split
0:33:24.424673 INFO: Test AUC: 0.597
0:33:24.424811 INFO: Train AUC: 0.609
0:33:24.424843 INFO: AUC difference: 1.96%
0:33:25.498301 INFO: Resetting torch num_threads to 100
0:33:25.527478 PROGRESS: === Extracted 749520 precursors and 4008179 fragments ===
0:33:25.527946 INFO: === FDR correction performed with classifier version 6 ===
0:33:25.528590 PROGRESS: ============================= Precursor FDR =============================
0:33:25.528692 PROGRESS: Total precursors accumulated: 1,419
0:33:25.528753 PROGRESS: Target precursors: 1,405 (99.01%)
0:33:25.528805 PROGRESS: Decoy precursors: 14 (0.99%)
0:33:25.528851 PROGRESS: 
0:33:25.528896 PROGRESS: Precursor Summary:
0:33:25.530216 PROGRESS: Channel   0:	 0.050 FDR: 1,405; 0.010 FDR: 1,405; 0.001 FDR:   713
0:33:25.530310 PROGRESS: 
0:33:25.530367 PROGRESS: Protein Summary:
0:33:25.532036 PROGRESS: Channel   0:	 0.050 FDR: 1,172; 0.010 FDR: 1,172; 0.001 FDR:   627
0:33:25.532123 PROGRESS: =========================================================================
0:33:25.545504 INFO: Target number of precursors reached.
0:33:25.978777 INFO: fragments_df: keeping 5000 of 4008179 [sum(precursor_idx_mask)=33744 sum(mass_error_mask)=4008179 stop_rank=5000
0:33:26.385268 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:26.612846 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:27.337703 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:33:27.338160 INFO: Using score_cutoff 12.023513140869142 (fac=0.99, q=1)
0:33:27.338460 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:27.338537 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:27.338592 INFO: Updating optimization_manager: score_cutoff        : 11.833174439620972 -> 12.023513140869142
0:33:27.338647 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:27.488635 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:27.815727 INFO: === checking if optimization conditions were reached ===
0:33:27.818259 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:33:27.818383 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:33:27.818462 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:33:27.818533 INFO: ==============================================
0:33:27.818634 INFO: Starting optimization step 8.
0:33:27.818703 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:33:27.818776 INFO: Using rust extraction backend
0:33:27.818843 PROGRESS: Extracting batch of 250439 precursors
0:33:28.240357 INFO: === Search parameters used ===
0:33:28.240624 INFO: rt_error       : 805.6019897460938
0:33:28.240682 INFO: mobility_error : 0.1
0:33:28.240730 INFO: num_candidates : 3
0:33:28.240773 INFO: ms1_error      : 3
0:33:28.240813 INFO: ms2_error      : 10.0
0:33:28.240854 INFO: fwhm_rt        : 3.0
0:33:28.240894 INFO: quant_window   : 3
0:33:28.240934 INFO: ==============================================
0:33:30.779657 INFO: performing precursor FDR with 40 features
0:33:30.779779 INFO: Decoy channel: -1
0:33:30.779806 INFO: competitive: True
0:33:30.967871 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:31.260050 INFO: Estimating optimal hyperparameters - samples: 599,615, batch_size: 2,456, learning_rate: 7.74e-04
0:33:31.261180 INFO: Using random state 85569 for train-test-split
0:33:43.523153 INFO: Test AUC: 0.604
0:33:43.523394 INFO: Train AUC: 0.616
0:33:43.523429 INFO: AUC difference: 1.86%
0:33:44.017506 INFO: Resetting torch num_threads to 100
0:33:44.049253 PROGRESS: === Extracted 749519 precursors and 4008432 fragments ===
0:33:44.049782 INFO: === FDR correction performed with classifier version 7 ===
0:33:44.050565 PROGRESS: ============================= Precursor FDR =============================
0:33:44.050659 PROGRESS: Total precursors accumulated: 1,523
0:33:44.050718 PROGRESS: Target precursors: 1,508 (99.02%)
0:33:44.050768 PROGRESS: Decoy precursors: 15 (0.98%)
0:33:44.050814 PROGRESS: 
0:33:44.050861 PROGRESS: Precursor Summary:
0:33:44.052192 PROGRESS: Channel   0:	 0.050 FDR: 1,508; 0.010 FDR: 1,508; 0.001 FDR:   741
0:33:44.052282 PROGRESS: 
0:33:44.052339 PROGRESS: Protein Summary:
0:33:44.054089 PROGRESS: Channel   0:	 0.050 FDR: 1,265; 0.010 FDR: 1,265; 0.001 FDR:   651
0:33:44.054189 PROGRESS: =========================================================================
0:33:44.068473 INFO: Target number of precursors reached.
0:33:44.511281 INFO: fragments_df: keeping 5000 of 4008432 [sum(precursor_idx_mask)=35596 sum(mass_error_mask)=4008432 stop_rank=5000
0:33:45.065104 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:45.307692 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:46.027331 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:33:46.027776 INFO: Using score_cutoff 10.319670067119599 (fac=0.99, q=1)
0:33:46.028114 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:46.028192 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:46.028246 INFO: Updating optimization_manager: score_cutoff        : 12.023513140869142 -> 10.319670067119599
0:33:46.028311 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:46.178220 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:46.508732 INFO: === checking if optimization conditions were reached ===
0:33:46.511274 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:33:46.511401 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:33:46.511487 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:33:46.511559 INFO: ==============================================
0:33:46.511649 INFO: Starting optimization step 9.
0:33:46.511722 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:33:46.511812 INFO: Using rust extraction backend
0:33:46.511898 PROGRESS: Extracting batch of 250439 precursors
0:33:46.944240 INFO: === Search parameters used ===
0:33:46.944510 INFO: rt_error       : 805.6019897460938
0:33:46.944569 INFO: mobility_error : 0.1
0:33:46.944620 INFO: num_candidates : 3
0:33:46.944667 INFO: ms1_error      : 3
0:33:46.944711 INFO: ms2_error      : 10.0
0:33:46.944753 INFO: fwhm_rt        : 3.0
0:33:46.944818 INFO: quant_window   : 3
0:33:46.944859 INFO: ==============================================
0:33:49.394356 INFO: performing precursor FDR with 40 features
0:33:49.394470 INFO: Decoy channel: -1
0:33:49.394494 INFO: competitive: True
0:33:49.573152 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:49.861869 INFO: Estimating optimal hyperparameters - samples: 599,628, batch_size: 2,456, learning_rate: 7.74e-04
0:33:49.862785 INFO: Using random state 33436 for train-test-split
0:34:02.004820 INFO: Test AUC: 0.606
0:34:02.004945 INFO: Train AUC: 0.619
0:34:02.004978 INFO: AUC difference: 2.09%
0:34:02.484049 INFO: Resetting torch num_threads to 100
0:34:02.511556 PROGRESS: === Extracted 749535 precursors and 4008821 fragments ===
0:34:02.512021 INFO: === FDR correction performed with classifier version 8 ===
0:34:02.512678 PROGRESS: ============================= Precursor FDR =============================
0:34:02.512764 PROGRESS: Total precursors accumulated: 1,527
0:34:02.512821 PROGRESS: Target precursors: 1,512 (99.02%)
0:34:02.512871 PROGRESS: Decoy precursors: 15 (0.98%)
0:34:02.512916 PROGRESS: 
0:34:02.512959 PROGRESS: Precursor Summary:
0:34:02.514289 PROGRESS: Channel   0:	 0.050 FDR: 1,512; 0.010 FDR: 1,512; 0.001 FDR:   710
0:34:02.514388 PROGRESS: 
0:34:02.514443 PROGRESS: Protein Summary:
0:34:02.516184 PROGRESS: Channel   0:	 0.050 FDR: 1,263; 0.010 FDR: 1,263; 0.001 FDR:   629
0:34:02.516273 PROGRESS: =========================================================================
0:34:02.529194 INFO: Target number of precursors reached.
0:34:02.968235 INFO: fragments_df: keeping 5000 of 4008821 [sum(precursor_idx_mask)=35763 sum(mass_error_mask)=4008821 stop_rank=5000
0:34:03.377643 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:34:03.620291 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:34:04.342093 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:34:04.342525 INFO: Using score_cutoff 10.783702524662019 (fac=0.99, q=1)
0:34:04.342826 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:34:04.342902 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:34:04.342963 INFO: Updating optimization_manager: score_cutoff        : 10.319670067119599 -> 10.783702524662019
0:34:04.343019 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:04.493129 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:04.821321 INFO: === checking if optimization conditions were reached ===
0:34:04.823883 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:34:04.824049 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:34:04.824128 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:34:04.824199 INFO: ==============================================
0:34:04.824279 INFO: Starting optimization step 10.
0:34:04.824347 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:34:04.824418 INFO: Using rust extraction backend
0:34:04.824487 PROGRESS: Extracting batch of 250439 precursors
0:34:05.246454 INFO: === Search parameters used ===
0:34:05.246726 INFO: rt_error       : 805.6019897460938
0:34:05.246819 INFO: mobility_error : 0.1
0:34:05.246868 INFO: num_candidates : 3
0:34:05.246912 INFO: ms1_error      : 3
0:34:05.246955 INFO: ms2_error      : 10.0
0:34:05.246995 INFO: fwhm_rt        : 3.0
0:34:05.247036 INFO: quant_window   : 3
0:34:05.247078 INFO: ==============================================
0:34:07.735973 INFO: performing precursor FDR with 40 features
0:34:07.736097 INFO: Decoy channel: -1
0:34:07.736123 INFO: competitive: True
0:34:07.923189 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:08.216239 INFO: Estimating optimal hyperparameters - samples: 599,636, batch_size: 2,456, learning_rate: 7.74e-04
0:34:08.217248 INFO: Using random state 672540 for train-test-split
0:34:20.627353 INFO: Test AUC: 0.607
0:34:20.627589 INFO: Train AUC: 0.622
0:34:20.627624 INFO: AUC difference: 2.37%
0:34:21.111535 INFO: Resetting torch num_threads to 100
0:34:21.138119 PROGRESS: === Extracted 749545 precursors and 4008629 fragments ===
0:34:21.138659 INFO: === FDR correction performed with classifier version 9 ===
0:34:21.139316 PROGRESS: ============================= Precursor FDR =============================
0:34:21.139403 PROGRESS: Total precursors accumulated: 1,579
0:34:21.139461 PROGRESS: Target precursors: 1,564 (99.05%)
0:34:21.139512 PROGRESS: Decoy precursors: 15 (0.95%)
0:34:21.139558 PROGRESS: 
0:34:21.139605 PROGRESS: Precursor Summary:
0:34:21.140915 PROGRESS: Channel   0:	 0.050 FDR: 1,564; 0.010 FDR: 1,564; 0.001 FDR:   723
0:34:21.141003 PROGRESS: 
0:34:21.141057 PROGRESS: Protein Summary:
0:34:21.142831 PROGRESS: Channel   0:	 0.050 FDR: 1,302; 0.010 FDR: 1,302; 0.001 FDR:   633
0:34:21.142928 PROGRESS: =========================================================================
0:34:21.159022 INFO: Target number of precursors reached.
0:34:21.603692 INFO: fragments_df: keeping 5000 of 4008629 [sum(precursor_idx_mask)=36958 sum(mass_error_mask)=4008629 stop_rank=5000
0:34:22.160254 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:34:22.407908 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:34:23.127164 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:34:23.127603 INFO: Using score_cutoff 11.060924947929381 (fac=0.99, q=1)
0:34:23.127939 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:34:23.128024 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:34:23.128080 INFO: Updating optimization_manager: score_cutoff        : 10.783702524662019 -> 11.060924947929381
0:34:23.128143 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:23.278814 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:23.624381 INFO: === checking if optimization conditions were reached ===
0:34:23.626915 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:34:23.627041 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:34:23.627122 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:34:23.627194 INFO: ==============================================
0:34:23.627282 INFO: Starting optimization step 11.
0:34:23.627353 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:34:23.627465 INFO: Using rust extraction backend
0:34:23.627551 PROGRESS: Extracting batch of 250439 precursors
0:34:24.054254 INFO: === Search parameters used ===
0:34:24.054521 INFO: rt_error       : 805.6019897460938
0:34:24.054576 INFO: mobility_error : 0.1
0:34:24.054623 INFO: num_candidates : 3
0:34:24.054666 INFO: ms1_error      : 3
0:34:24.054707 INFO: ms2_error      : 10.0
0:34:24.054748 INFO: fwhm_rt        : 3.0
0:34:24.054804 INFO: quant_window   : 3
0:34:24.054849 INFO: ==============================================
0:34:26.572631 INFO: performing precursor FDR with 40 features
0:34:26.572749 INFO: Decoy channel: -1
0:34:26.572774 INFO: competitive: True
0:34:26.754409 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:27.043247 INFO: Estimating optimal hyperparameters - samples: 599,620, batch_size: 2,456, learning_rate: 7.74e-04
0:34:27.044419 INFO: Using random state 915521 for train-test-split
0:34:39.022013 INFO: Test AUC: 0.612
0:34:39.022145 INFO: Train AUC: 0.624
0:34:39.022177 INFO: AUC difference: 1.97%
0:34:39.490279 INFO: Resetting torch num_threads to 100
0:34:39.515231 PROGRESS: === Extracted 749526 precursors and 4008129 fragments ===
0:34:39.515699 INFO: === FDR correction performed with classifier version 10 ===
0:34:39.516411 PROGRESS: ============================= Precursor FDR =============================
0:34:39.516499 PROGRESS: Total precursors accumulated: 1,585
0:34:39.516558 PROGRESS: Target precursors: 1,570 (99.05%)
0:34:39.516611 PROGRESS: Decoy precursors: 15 (0.95%)
0:34:39.516662 PROGRESS: 
0:34:39.516708 PROGRESS: Precursor Summary:
0:34:39.518047 PROGRESS: Channel   0:	 0.050 FDR: 1,570; 0.010 FDR: 1,570; 0.001 FDR:   882
0:34:39.518135 PROGRESS: 
0:34:39.518193 PROGRESS: Protein Summary:
0:34:39.519926 PROGRESS: Channel   0:	 0.050 FDR: 1,318; 0.010 FDR: 1,318; 0.001 FDR:   767
0:34:39.520014 PROGRESS: =========================================================================
0:34:39.533691 INFO: Target number of precursors reached.
0:34:39.994900 INFO: fragments_df: keeping 5000 of 4008129 [sum(precursor_idx_mask)=37082 sum(mass_error_mask)=4008129 stop_rank=5000
0:34:40.429572 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:34:40.676948 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:34:41.403598 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:34:41.404029 INFO: Using score_cutoff 11.125757524967193 (fac=0.99, q=1)
0:34:41.404339 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:34:41.404416 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:34:41.404470 INFO: Updating optimization_manager: score_cutoff        : 11.060924947929381 -> 11.125757524967193
0:34:41.404524 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:41.553952 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:41.883687 INFO: === checking if optimization conditions were reached ===
0:34:41.886163 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:34:41.886284 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:34:41.886394 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:34:41.886488 INFO: ==============================================
0:34:41.886569 PROGRESS: Optimization finished for ms2_error.
0:34:42.350433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:42.499859 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:42.829608 INFO: Starting optimization step 0.
0:34:42.829895 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:34:42.829998 INFO: Using rust extraction backend
0:34:42.830072 PROGRESS: Extracting batch of 250439 precursors
0:34:43.252427 INFO: === Search parameters used ===
0:34:43.252692 INFO: rt_error       : 805.6019897460938
0:34:43.252766 INFO: mobility_error : 0.1
0:34:43.252814 INFO: num_candidates : 3
0:34:43.252857 INFO: ms1_error      : 3
0:34:43.252896 INFO: ms2_error      : 10.0
0:34:43.252943 INFO: fwhm_rt        : 3.0
0:34:43.252982 INFO: quant_window   : 3
0:34:43.253019 INFO: ==============================================
0:34:45.759144 INFO: performing precursor FDR with 40 features
0:34:45.759269 INFO: Decoy channel: -1
0:34:45.759296 INFO: competitive: True
0:34:45.973262 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:46.281475 INFO: Estimating optimal hyperparameters - samples: 599,624, batch_size: 2,456, learning_rate: 7.74e-04
0:34:46.282602 INFO: Using random state 577530 for train-test-split
0:34:58.568079 INFO: Test AUC: 0.612
0:34:58.568299 INFO: Train AUC: 0.627
0:34:58.568336 INFO: AUC difference: 2.36%
0:34:59.047441 INFO: Resetting torch num_threads to 100
0:34:59.074925 PROGRESS: === Extracted 749531 precursors and 4008368 fragments ===
0:34:59.075433 INFO: === FDR correction performed with classifier version 11 ===
0:34:59.076140 PROGRESS: ============================= Precursor FDR =============================
0:34:59.076230 PROGRESS: Total precursors accumulated: 1,648
0:34:59.076293 PROGRESS: Target precursors: 1,632 (99.03%)
0:34:59.076346 PROGRESS: Decoy precursors: 16 (0.97%)
0:34:59.076394 PROGRESS: 
0:34:59.076442 PROGRESS: Precursor Summary:
0:34:59.077816 PROGRESS: Channel   0:	 0.050 FDR: 1,632; 0.010 FDR: 1,632; 0.001 FDR:   716
0:34:59.077915 PROGRESS: 
0:34:59.077978 PROGRESS: Protein Summary:
0:34:59.079743 PROGRESS: Channel   0:	 0.050 FDR: 1,372; 0.010 FDR: 1,372; 0.001 FDR:   634
0:34:59.079839 PROGRESS: =========================================================================
0:34:59.095004 INFO: Target number of precursors reached.
0:34:59.533486 INFO: fragments_df: keeping 5000 of 4008368 [sum(precursor_idx_mask)=37857 sum(mass_error_mask)=4008368 stop_rank=5000
0:34:59.998640 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:00.220603 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:00.874066 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:00.874513 INFO: Using score_cutoff 10.27609035730362 (fac=0.99, q=1)
0:35:00.874851 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:00.874927 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:00.874980 INFO: Updating optimization_manager: score_cutoff        : 11.125757524967193 -> 10.27609035730362
0:35:00.875047 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:01.025149 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:01.360581 INFO: === checking if optimization conditions were reached ===
0:35:01.360886 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:35:01.364017 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 701.3851271339582
0:35:01.364136 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 701.3851.
0:35:01.364209 INFO: ==============================================
0:35:01.364302 INFO: Starting optimization step 1.
0:35:01.364372 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:35:01.364459 INFO: Using rust extraction backend
0:35:01.364540 PROGRESS: Extracting batch of 250439 precursors
0:35:01.795930 INFO: === Search parameters used ===
0:35:01.796211 INFO: rt_error       : 701.3851271339582
0:35:01.796267 INFO: mobility_error : 0.1
0:35:01.796314 INFO: num_candidates : 3
0:35:01.796362 INFO: ms1_error      : 3
0:35:01.796403 INFO: ms2_error      : 10.0
0:35:01.796442 INFO: fwhm_rt        : 3.0
0:35:01.796480 INFO: quant_window   : 3
0:35:01.796517 INFO: ==============================================
0:35:04.284995 INFO: performing precursor FDR with 40 features
0:35:04.285120 INFO: Decoy channel: -1
0:35:04.285144 INFO: competitive: True
0:35:04.472618 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:04.765922 INFO: Estimating optimal hyperparameters - samples: 599,633, batch_size: 2,456, learning_rate: 7.74e-04
0:35:04.766860 INFO: Using random state 577530 for train-test-split
0:35:16.813011 INFO: Test AUC: 0.612
0:35:16.813145 INFO: Train AUC: 0.627
0:35:16.813177 INFO: AUC difference: 2.35%
0:35:17.290408 INFO: Resetting torch num_threads to 100
0:35:17.324169 PROGRESS: === Extracted 749542 precursors and 4008170 fragments ===
0:35:17.324639 INFO: === FDR correction performed with classifier version 11 ===
0:35:17.325367 PROGRESS: ============================= Precursor FDR =============================
0:35:17.325459 PROGRESS: Total precursors accumulated: 1,519
0:35:17.325519 PROGRESS: Target precursors: 1,504 (99.01%)
0:35:17.325572 PROGRESS: Decoy precursors: 15 (0.99%)
0:35:17.325623 PROGRESS: 
0:35:17.325670 PROGRESS: Precursor Summary:
0:35:17.327015 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR: 1,037
0:35:17.327109 PROGRESS: 
0:35:17.327165 PROGRESS: Protein Summary:
0:35:17.328911 PROGRESS: Channel   0:	 0.050 FDR: 1,260; 0.010 FDR: 1,260; 0.001 FDR:   888
0:35:17.329003 PROGRESS: =========================================================================
0:35:17.342685 INFO: Target number of precursors reached.
0:35:17.783097 INFO: fragments_df: keeping 5000 of 4008170 [sum(precursor_idx_mask)=35500 sum(mass_error_mask)=4008170 stop_rank=5000
0:35:18.229054 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:18.440323 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:19.094871 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:19.095298 INFO: Using score_cutoff 11.164834321689606 (fac=0.99, q=1)
0:35:19.095604 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:19.095685 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:19.095738 INFO: Updating optimization_manager: score_cutoff        : 10.27609035730362 -> 11.164834321689606
0:35:19.095800 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:19.244432 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:19.573745 INFO: === checking if optimization conditions were reached ===
0:35:19.574054 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:35:19.577203 INFO: Updating optimization_manager: rt_error            : 701.3851271339582 -> 732.794114397991
0:35:19.577333 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 732.7941.
0:35:19.577407 INFO: ==============================================
0:35:19.577486 INFO: Starting optimization step 2.
0:35:19.577553 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:35:19.577622 INFO: Using rust extraction backend
0:35:19.577720 PROGRESS: Extracting batch of 250439 precursors
0:35:19.999543 INFO: === Search parameters used ===
0:35:19.999815 INFO: rt_error       : 732.794114397991
0:35:19.999873 INFO: mobility_error : 0.1
0:35:19.999920 INFO: num_candidates : 3
0:35:19.999965 INFO: ms1_error      : 3
0:35:20.000008 INFO: ms2_error      : 10.0
0:35:20.000051 INFO: fwhm_rt        : 3.0
0:35:20.000093 INFO: quant_window   : 3
0:35:20.000133 INFO: ==============================================
0:35:22.465715 INFO: performing precursor FDR with 40 features
0:35:22.465836 INFO: Decoy channel: -1
0:35:22.465863 INFO: competitive: True
0:35:22.644093 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:22.931005 INFO: Estimating optimal hyperparameters - samples: 599,601, batch_size: 2,455, learning_rate: 7.74e-04
0:35:22.932171 INFO: Using random state 577530 for train-test-split
0:35:35.727848 INFO: Test AUC: 0.609
0:35:35.728085 INFO: Train AUC: 0.626
0:35:35.728119 INFO: AUC difference: 2.70%
0:35:36.211280 INFO: Resetting torch num_threads to 100
0:35:36.237226 PROGRESS: === Extracted 749502 precursors and 4007557 fragments ===
0:35:36.237752 INFO: === FDR correction performed with classifier version 11 ===
0:35:36.238580 PROGRESS: ============================= Precursor FDR =============================
0:35:36.238674 PROGRESS: Total precursors accumulated: 1,642
0:35:36.238734 PROGRESS: Target precursors: 1,626 (99.03%)
0:35:36.238786 PROGRESS: Decoy precursors: 16 (0.97%)
0:35:36.238832 PROGRESS: 
0:35:36.238879 PROGRESS: Precursor Summary:
0:35:36.240230 PROGRESS: Channel   0:	 0.050 FDR: 1,626; 0.010 FDR: 1,626; 0.001 FDR:   682
0:35:36.240318 PROGRESS: 
0:35:36.240373 PROGRESS: Protein Summary:
0:35:36.242157 PROGRESS: Channel   0:	 0.050 FDR: 1,366; 0.010 FDR: 1,366; 0.001 FDR:   600
0:35:36.242267 PROGRESS: =========================================================================
0:35:36.258357 INFO: Target number of precursors reached.
0:35:36.701640 INFO: fragments_df: keeping 5000 of 4007557 [sum(precursor_idx_mask)=38006 sum(mass_error_mask)=4007557 stop_rank=5000
0:35:37.259840 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:37.481762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:38.139508 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:38.139960 INFO: Using score_cutoff 10.82840304851532 (fac=0.99, q=1)
0:35:38.140305 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:38.140384 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:38.140440 INFO: Updating optimization_manager: score_cutoff        : 11.164834321689606 -> 10.82840304851532
0:35:38.140499 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:38.297864 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:38.635636 INFO: === checking if optimization conditions were reached ===
0:35:38.635978 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:35:38.639584 INFO: Updating optimization_manager: rt_error            : 732.794114397991 -> 650.8019014237902
0:35:38.639706 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 650.8019.
0:35:38.639809 INFO: ==============================================
0:35:38.639905 INFO: Starting optimization step 3.
0:35:38.639988 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:35:38.640090 INFO: Using rust extraction backend
0:35:38.640175 PROGRESS: Extracting batch of 250439 precursors
0:35:39.068083 INFO: === Search parameters used ===
0:35:39.068350 INFO: rt_error       : 650.8019014237902
0:35:39.068408 INFO: mobility_error : 0.1
0:35:39.068463 INFO: num_candidates : 3
0:35:39.068516 INFO: ms1_error      : 3
0:35:39.068559 INFO: ms2_error      : 10.0
0:35:39.068601 INFO: fwhm_rt        : 3.0
0:35:39.068642 INFO: quant_window   : 3
0:35:39.068683 INFO: ==============================================
0:35:41.629508 INFO: performing precursor FDR with 40 features
0:35:41.629627 INFO: Decoy channel: -1
0:35:41.629655 INFO: competitive: True
0:35:41.813836 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:42.105335 INFO: Estimating optimal hyperparameters - samples: 599,549, batch_size: 2,455, learning_rate: 7.74e-04
0:35:42.106504 INFO: Using random state 577530 for train-test-split
0:35:54.921938 INFO: Test AUC: 0.612
0:35:54.922076 INFO: Train AUC: 0.627
0:35:54.922108 INFO: AUC difference: 2.37%
0:35:55.404641 INFO: Resetting torch num_threads to 100
0:35:55.432392 PROGRESS: === Extracted 749437 precursors and 4004474 fragments ===
0:35:55.432851 INFO: === FDR correction performed with classifier version 11 ===
0:35:55.433492 PROGRESS: ============================= Precursor FDR =============================
0:35:55.433580 PROGRESS: Total precursors accumulated: 1,495
0:35:55.433639 PROGRESS: Target precursors: 1,481 (99.06%)
0:35:55.433690 PROGRESS: Decoy precursors: 14 (0.94%)
0:35:55.433738 PROGRESS: 
0:35:55.433784 PROGRESS: Precursor Summary:
0:35:55.435091 PROGRESS: Channel   0:	 0.050 FDR: 1,481; 0.010 FDR: 1,481; 0.001 FDR:   804
0:35:55.435194 PROGRESS: 
0:35:55.435250 PROGRESS: Protein Summary:
0:35:55.436943 PROGRESS: Channel   0:	 0.050 FDR: 1,253; 0.010 FDR: 1,253; 0.001 FDR:   708
0:35:55.437030 PROGRESS: =========================================================================
0:35:55.450930 INFO: Target number of precursors reached.
0:35:55.891209 INFO: fragments_df: keeping 5000 of 4004474 [sum(precursor_idx_mask)=35062 sum(mass_error_mask)=4004474 stop_rank=5000
0:35:56.311466 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:56.546240 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:57.268435 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:57.268862 INFO: Using score_cutoff 10.670221200942994 (fac=0.99, q=1)
0:35:57.269160 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:57.269238 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:57.269291 INFO: Updating optimization_manager: score_cutoff        : 10.82840304851532 -> 10.670221200942994
0:35:57.269344 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:57.419104 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:57.746235 INFO: === checking if optimization conditions were reached ===
0:35:57.746535 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:35:57.749760 INFO: Updating optimization_manager: rt_error            : 650.8019014237902 -> 759.6730907967393
0:35:57.749878 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 759.6731.
0:35:57.750006 INFO: ==============================================
0:35:57.750094 INFO: Starting optimization step 4.
0:35:57.750163 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:35:57.750234 INFO: Using rust extraction backend
0:35:57.750300 PROGRESS: Extracting batch of 250439 precursors
0:35:58.171800 INFO: === Search parameters used ===
0:35:58.172070 INFO: rt_error       : 759.6730907967393
0:35:58.172126 INFO: mobility_error : 0.1
0:35:58.172174 INFO: num_candidates : 3
0:35:58.172237 INFO: ms1_error      : 3
0:35:58.172278 INFO: ms2_error      : 10.0
0:35:58.172317 INFO: fwhm_rt        : 3.0
0:35:58.172354 INFO: quant_window   : 3
0:35:58.172394 INFO: ==============================================
0:36:00.638556 INFO: performing precursor FDR with 40 features
0:36:00.638680 INFO: Decoy channel: -1
0:36:00.638706 INFO: competitive: True
0:36:00.814996 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:01.101811 INFO: Estimating optimal hyperparameters - samples: 599,632, batch_size: 2,456, learning_rate: 7.74e-04
0:36:01.103173 INFO: Using random state 577530 for train-test-split
0:36:13.359807 INFO: Test AUC: 0.613
0:36:13.359957 INFO: Train AUC: 0.627
0:36:13.359993 INFO: AUC difference: 2.21%
0:36:13.835949 INFO: Resetting torch num_threads to 100
0:36:13.862823 PROGRESS: === Extracted 749541 precursors and 4008428 fragments ===
0:36:13.863372 INFO: === FDR correction performed with classifier version 11 ===
0:36:13.864046 PROGRESS: ============================= Precursor FDR =============================
0:36:13.864135 PROGRESS: Total precursors accumulated: 1,692
0:36:13.864196 PROGRESS: Target precursors: 1,676 (99.05%)
0:36:13.864249 PROGRESS: Decoy precursors: 16 (0.95%)
0:36:13.864315 PROGRESS: 
0:36:13.864363 PROGRESS: Precursor Summary:
0:36:13.865747 PROGRESS: Channel   0:	 0.050 FDR: 1,676; 0.010 FDR: 1,676; 0.001 FDR: 1,081
0:36:13.865834 PROGRESS: 
0:36:13.865889 PROGRESS: Protein Summary:
0:36:13.867738 PROGRESS: Channel   0:	 0.050 FDR: 1,405; 0.010 FDR: 1,405; 0.001 FDR:   920
0:36:13.867838 PROGRESS: =========================================================================
0:36:13.882617 INFO: Target number of precursors reached.
0:36:14.323998 INFO: fragments_df: keeping 5000 of 4008428 [sum(precursor_idx_mask)=38774 sum(mass_error_mask)=4008428 stop_rank=5000
0:36:14.768966 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:15.027420 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:15.750571 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:15.751017 INFO: Using score_cutoff 9.55014793395996 (fac=0.99, q=1)
0:36:15.751356 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:15.751435 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:15.751490 INFO: Updating optimization_manager: score_cutoff        : 10.670221200942994 -> 9.55014793395996
0:36:15.751549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:15.900473 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:16.238756 INFO: === checking if optimization conditions were reached ===
0:36:16.239625 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:36:16.243071 INFO: Updating optimization_manager: rt_error            : 759.6730907967393 -> 780.2004906256982
0:36:16.243210 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 780.2005.
0:36:16.243286 INFO: ==============================================
0:36:16.243384 INFO: Starting optimization step 5.
0:36:16.243458 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:36:16.243547 INFO: Using rust extraction backend
0:36:16.243633 PROGRESS: Extracting batch of 250439 precursors
0:36:16.667815 INFO: === Search parameters used ===
0:36:16.668080 INFO: rt_error       : 780.2004906256982
0:36:16.668138 INFO: mobility_error : 0.1
0:36:16.668187 INFO: num_candidates : 3
0:36:16.668231 INFO: ms1_error      : 3
0:36:16.668274 INFO: ms2_error      : 10.0
0:36:16.668318 INFO: fwhm_rt        : 3.0
0:36:16.668360 INFO: quant_window   : 3
0:36:16.668401 INFO: ==============================================
0:36:19.153531 INFO: performing precursor FDR with 40 features
0:36:19.153646 INFO: Decoy channel: -1
0:36:19.153672 INFO: competitive: True
0:36:19.337185 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:19.632042 INFO: Estimating optimal hyperparameters - samples: 599,649, batch_size: 2,456, learning_rate: 7.74e-04
0:36:19.633209 INFO: Using random state 577530 for train-test-split
0:36:31.845619 INFO: Test AUC: 0.614
0:36:31.845751 INFO: Train AUC: 0.626
0:36:31.845784 INFO: AUC difference: 1.92%
0:36:32.316643 INFO: Resetting torch num_threads to 100
0:36:32.341488 PROGRESS: === Extracted 749562 precursors and 4008847 fragments ===
0:36:32.341959 INFO: === FDR correction performed with classifier version 11 ===
0:36:32.342618 PROGRESS: ============================= Precursor FDR =============================
0:36:32.342706 PROGRESS: Total precursors accumulated: 1,649
0:36:32.342776 PROGRESS: Target precursors: 1,633 (99.03%)
0:36:32.342828 PROGRESS: Decoy precursors: 16 (0.97%)
0:36:32.342880 PROGRESS: 
0:36:32.342927 PROGRESS: Precursor Summary:
0:36:32.344232 PROGRESS: Channel   0:	 0.050 FDR: 1,633; 0.010 FDR: 1,633; 0.001 FDR:   798
0:36:32.344317 PROGRESS: 
0:36:32.344372 PROGRESS: Protein Summary:
0:36:32.346107 PROGRESS: Channel   0:	 0.050 FDR: 1,361; 0.010 FDR: 1,361; 0.001 FDR:   699
0:36:32.346196 PROGRESS: =========================================================================
0:36:32.359502 INFO: Target number of precursors reached.
0:36:32.772246 INFO: fragments_df: keeping 5000 of 4008847 [sum(precursor_idx_mask)=38567 sum(mass_error_mask)=4008847 stop_rank=5000
0:36:33.255837 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:33.508577 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:34.228650 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:34.229087 INFO: Using score_cutoff 11.417945151901245 (fac=0.99, q=1)
0:36:34.229383 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:34.229461 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:34.229516 INFO: Updating optimization_manager: score_cutoff        : 9.55014793395996 -> 11.417945151901245
0:36:34.229571 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:34.380172 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:34.710468 INFO: === checking if optimization conditions were reached ===
0:36:34.710785 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:36:34.711883 INFO: Updating optimization_manager: rt_error            : 780.2004906256982 -> 759.6730907967393
0:36:34.712034 INFO: Updating optimization_manager: classifier_version  : 11 -> 16
0:36:34.712158 INFO: Updating optimization_manager: score_cutoff        : 11.417945151901245 -> 9.55014793395996
0:36:34.712265 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:34.712366 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:34.712478 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 759.6731 found after 6 searches.
0:36:34.712552 INFO: ==============================================
0:36:34.712640 PROGRESS: Optimization finished for rt_error.
0:36:35.110930 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:35.261253 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:35.590390 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:36:35.590673 PROGRESS: ==============================================
0:36:35.590757 PROGRESS: ms2_error      : 10.0000
0:36:35.590826 PROGRESS: rt_error       : 759.6731
0:36:35.590885 PROGRESS: ==============================================
0:36:35.591767 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:43.230921 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:59.817255 INFO: Using rust extraction backend
0:36:59.817916 PROGRESS: Extracting batch of 11997144 precursors
0:37:15.889848 INFO: === Search parameters used ===
0:37:15.890457 INFO: rt_error       : 759.6730907967393
0:37:15.890525 INFO: mobility_error : 0.1
0:37:15.890579 INFO: num_candidates : 3
0:37:15.890631 INFO: ms1_error      : 3
0:37:15.890677 INFO: ms2_error      : 10.0
0:37:15.890722 INFO: fwhm_rt        : 3.0
0:37:15.890777 INFO: quant_window   : 3
0:37:15.890821 INFO: ==============================================
0:37:46.028368 INFO: Removed 6161500 precursors with score below cutoff 9.55014793395996
0:38:09.438024 INFO: performing precursor FDR with 40 features
0:38:09.438267 INFO: Decoy channel: -1
0:38:09.438298 INFO: competitive: True
0:38:12.518222 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:24.523235 INFO: Estimating optimal hyperparameters - samples: 23,863,623, batch_size: 4,096, learning_rate: 1.00e-03
0:38:24.594912 INFO: Using random state 748307 for train-test-split
0:46:10.405294 INFO: Test AUC: 0.622
0:46:10.405579 INFO: Train AUC: 0.622
0:46:10.405620 INFO: AUC difference: 0.11%
0:46:17.999991 INFO: Resetting torch num_threads to 100
0:46:20.142207 PROGRESS: ============================= Precursor FDR =============================
0:46:20.142520 PROGRESS: Total precursors accumulated: 88,394
0:46:20.142591 PROGRESS: Target precursors: 87,519 (99.01%)
0:46:20.142646 PROGRESS: Decoy precursors: 875 (0.99%)
0:46:20.142695 PROGRESS: 
0:46:20.142744 PROGRESS: Precursor Summary:
0:46:20.166332 PROGRESS: Channel   0:	 0.050 FDR: 87,519; 0.010 FDR: 87,519; 0.001 FDR: 54,493
0:46:20.166578 PROGRESS: 
0:46:20.166642 PROGRESS: Protein Summary:
0:46:20.198585 PROGRESS: Channel   0:	 0.050 FDR: 14,557; 0.010 FDR: 14,557; 0.001 FDR: 9,322
0:46:20.198839 PROGRESS: =========================================================================
0:46:20.354402 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:46:20.506037 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:46:20.730553 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:46:21.203098 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
0:46:21.203244 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant
0:46:21.203343 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:46:21.203523 INFO: Initializing TimingManager
0:46:21.203941 INFO: Initializing RawFileManager
0:46:31.887376 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.
0:46:31.896207 INFO: Determining DIA cycle
0:46:31.913639 INFO: Found cycle with start 0.00 min and length 300.
0:46:32.077555 INFO: RT (min)            : 0.0 - 26.9
0:46:32.077648 INFO: RT duration (sec)   : 1611.2
0:46:32.077677 INFO: RT duration (min)   : 26.9
0:46:32.077700 INFO: Cycle len (scans)   : 300
0:46:32.077722 INFO: Cycle len (sec)     : 1.65
0:46:32.077741 INFO: Number of cycles    : 977
0:46:32.077761 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:46:32.077796 INFO: Creating DIA data object took: 10.873764276504517
0:46:32.726957 INFO: Creating DIA data NG object took: 0.6490285396575928
0:46:34.125275 INFO: Initializing CalibrationManager
0:46:34.125576 INFO: Setting up calibration estimators ..
0:46:34.125638 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:46:34.125727 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'}' ..
0:46:34.125830 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:46:34.125884 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:46:34.125960 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}}' ..
0:46:34.126031 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:46:34.126085 INFO: Done setting up calibration estimators.
0:46:34.126284 INFO: Initializing OptimizationManager
0:46:34.126423 INFO: initial parameter: ms1_error = 3
0:46:34.126478 INFO: initial parameter: ms2_error = 10
0:46:34.126523 INFO: initial parameter: rt_error = 805.6004638671875
0:46:34.126565 INFO: initial parameter: mobility_error = 0.1
0:46:34.126605 INFO: initial parameter: num_candidates = 1
0:46:34.126643 INFO: initial parameter: fwhm_rt = 5
0:46:34.126683 INFO: initial parameter: fwhm_mobility = 0.01
0:46:34.126721 INFO: initial parameter: score_cutoff = 0
0:46:34.126763 INFO: initial parameter: classifier_version = -1
0:46:34.126831 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:46:34.127098 INFO: FDRManager: loading saved state not requested, will be initialized.
0:46:34.127130 INFO: Initializing FDRManager
0:46:34.127168 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:46:35.536568 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:46:36.419385 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:46:36.419823 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:46:36.419931 PROGRESS: Starting initial search for precursors.
0:46:36.420021 INFO: Starting optimization step 0.
0:46:36.420087 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:46:36.420149 INFO: Using rust extraction backend
0:46:36.420210 PROGRESS: Extracting batch of 1965 precursors
0:46:36.427863 INFO: === Search parameters used ===
0:46:36.427963 INFO: rt_error       : 805.6004638671875
0:46:36.428016 INFO: mobility_error : 0.1
0:46:36.428062 INFO: num_candidates : 1
0:46:36.428105 INFO: ms1_error      : 3
0:46:36.428147 INFO: ms2_error      : 10
0:46:36.428188 INFO: fwhm_rt        : 5
0:46:36.428229 INFO: quant_window   : 3
0:46:36.428269 INFO: ==============================================
0:46:36.454842 INFO: performing precursor FDR with 40 features
0:46:36.454907 INFO: Decoy channel: -1
0:46:36.454934 INFO: competitive: True
0:46:36.456316 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:36.458273 INFO: Estimating optimal hyperparameters - samples: 1,567, batch_size: 128, learning_rate: 1.77e-04
0:46:36.459129 INFO: Using random state 310115 for train-test-split
0:46:36.578590 INFO: Test AUC: 0.468
0:46:36.578668 INFO: Train AUC: 0.582
0:46:36.578698 INFO: AUC difference: 19.58%
0:46:36.578720 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:36.825874 INFO: Resetting torch num_threads to 100
0:46:36.827379 PROGRESS: === Extracted 1959 precursors and 10940 fragments ===
0:46:36.827744 INFO: === FDR correction performed with classifier version -1 ===
0:46:36.828219 PROGRESS: ============================= Precursor FDR =============================
0:46:36.828304 PROGRESS: Total precursors accumulated: 3
0:46:36.828362 PROGRESS: Target precursors: 3 (100.00%)
0:46:36.828413 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:36.828459 PROGRESS: 
0:46:36.828504 PROGRESS: Precursor Summary:
0:46:36.829533 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:46:36.829617 PROGRESS: 
0:46:36.829672 PROGRESS: Protein Summary:
0:46:36.830812 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:46:36.830899 PROGRESS: =========================================================================
0:46:36.831104 INFO: Target number of precursors not reached yet.
0:46:36.914990 INFO: Starting optimization step 1.
0:46:36.915219 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:46:36.915314 INFO: Using rust extraction backend
0:46:36.915374 PROGRESS: Extracting batch of 3948 precursors
0:46:36.923729 INFO: === Search parameters used ===
0:46:36.923865 INFO: rt_error       : 805.6004638671875
0:46:36.923918 INFO: mobility_error : 0.1
0:46:36.923969 INFO: num_candidates : 1
0:46:36.924013 INFO: ms1_error      : 3
0:46:36.924055 INFO: ms2_error      : 10
0:46:36.924096 INFO: fwhm_rt        : 5
0:46:36.924137 INFO: quant_window   : 3
0:46:36.924176 INFO: ==============================================
0:46:36.970731 INFO: performing precursor FDR with 40 features
0:46:36.970825 INFO: Decoy channel: -1
0:46:36.970849 INFO: competitive: True
0:46:36.975299 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:36.977528 INFO: Estimating optimal hyperparameters - samples: 4,717, batch_size: 128, learning_rate: 1.77e-04
0:46:36.977606 INFO: Using random state 693696 for train-test-split
0:46:37.392005 INFO: Test AUC: 0.558
0:46:37.392102 INFO: Train AUC: 0.597
0:46:37.392130 INFO: AUC difference: 6.45%
0:46:37.392151 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:37.638746 INFO: Resetting torch num_threads to 100
0:46:37.641574 PROGRESS: === Extracted 5897 precursors and 32855 fragments ===
0:46:37.641952 INFO: === FDR correction performed with classifier version -1 ===
0:46:37.642449 PROGRESS: ============================= Precursor FDR =============================
0:46:37.642531 PROGRESS: Total precursors accumulated: 1
0:46:37.642588 PROGRESS: Target precursors: 1 (100.00%)
0:46:37.642637 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:37.642680 PROGRESS: 
0:46:37.642722 PROGRESS: Precursor Summary:
0:46:37.643769 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:46:37.643850 PROGRESS: 
0:46:37.643902 PROGRESS: Protein Summary:
0:46:37.645047 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:46:37.645127 PROGRESS: =========================================================================
0:46:37.645371 INFO: Target number of precursors not reached yet.
0:46:37.734086 INFO: Starting optimization step 2.
0:46:37.734323 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:46:37.734397 INFO: Using rust extraction backend
0:46:37.734455 PROGRESS: Extracting batch of 7900 precursors
0:46:37.749537 INFO: === Search parameters used ===
0:46:37.749678 INFO: rt_error       : 805.6004638671875
0:46:37.749727 INFO: mobility_error : 0.1
0:46:37.749772 INFO: num_candidates : 1
0:46:37.749813 INFO: ms1_error      : 3
0:46:37.749852 INFO: ms2_error      : 10
0:46:37.749893 INFO: fwhm_rt        : 5
0:46:37.749952 INFO: quant_window   : 3
0:46:37.749994 INFO: ==============================================
0:46:37.823828 INFO: performing precursor FDR with 40 features
0:46:37.823936 INFO: Decoy channel: -1
0:46:37.823960 INFO: competitive: True
0:46:37.830106 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:37.833566 INFO: Estimating optimal hyperparameters - samples: 11,017, batch_size: 128, learning_rate: 1.77e-04
0:46:37.833669 INFO: Using random state 637327 for train-test-split
0:46:38.946249 INFO: Test AUC: 0.573
0:46:38.946357 INFO: Train AUC: 0.589
0:46:38.946387 INFO: AUC difference: 2.82%
0:46:39.195086 INFO: Resetting torch num_threads to 100
0:46:39.199122 PROGRESS: === Extracted 13772 precursors and 76906 fragments ===
0:46:39.199525 INFO: === FDR correction performed with classifier version -1 ===
0:46:39.200039 PROGRESS: ============================= Precursor FDR =============================
0:46:39.200123 PROGRESS: Total precursors accumulated: 37
0:46:39.200179 PROGRESS: Target precursors: 37 (100.00%)
0:46:39.200228 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:39.200272 PROGRESS: 
0:46:39.200315 PROGRESS: Precursor Summary:
0:46:39.201363 PROGRESS: Channel   0:	 0.050 FDR:    37; 0.010 FDR:    37; 0.001 FDR:    37
0:46:39.201444 PROGRESS: 
0:46:39.201496 PROGRESS: Protein Summary:
0:46:39.202663 PROGRESS: Channel   0:	 0.050 FDR:    37; 0.010 FDR:    37; 0.001 FDR:    37
0:46:39.202752 PROGRESS: =========================================================================
0:46:39.203062 INFO: Target number of precursors not reached yet.
0:46:39.301512 INFO: Starting optimization step 3.
0:46:39.301757 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:46:39.301833 INFO: Using rust extraction backend
0:46:39.301891 PROGRESS: Extracting batch of 15775 precursors
0:46:39.330049 INFO: === Search parameters used ===
0:46:39.330248 INFO: rt_error       : 805.6004638671875
0:46:39.330299 INFO: mobility_error : 0.1
0:46:39.330343 INFO: num_candidates : 1
0:46:39.330384 INFO: ms1_error      : 3
0:46:39.330423 INFO: ms2_error      : 10
0:46:39.330500 INFO: fwhm_rt        : 5
0:46:39.330542 INFO: quant_window   : 3
0:46:39.330582 INFO: ==============================================
0:46:39.463553 INFO: performing precursor FDR with 40 features
0:46:39.463665 INFO: Decoy channel: -1
0:46:39.463689 INFO: competitive: True
0:46:39.474590 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:39.481248 INFO: Estimating optimal hyperparameters - samples: 23,601, batch_size: 128, learning_rate: 1.77e-04
0:46:39.481419 INFO: Using random state 201514 for train-test-split
0:46:41.881095 INFO: Test AUC: 0.570
0:46:41.881212 INFO: Train AUC: 0.602
0:46:41.881243 INFO: AUC difference: 5.30%
0:46:41.881266 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:42.151996 INFO: Resetting torch num_threads to 100
0:46:42.160012 PROGRESS: === Extracted 29502 precursors and 164907 fragments ===
0:46:42.160508 INFO: === FDR correction performed with classifier version -1 ===
0:46:42.160998 PROGRESS: ============================= Precursor FDR =============================
0:46:42.161087 PROGRESS: Total precursors accumulated: 122
0:46:42.161145 PROGRESS: Target precursors: 121 (99.18%)
0:46:42.161197 PROGRESS: Decoy precursors: 1 (0.82%)
0:46:42.161244 PROGRESS: 
0:46:42.161291 PROGRESS: Precursor Summary:
0:46:42.162304 PROGRESS: Channel   0:	 0.050 FDR:   121; 0.010 FDR:   121; 0.001 FDR:   112
0:46:42.162399 PROGRESS: 
0:46:42.162454 PROGRESS: Protein Summary:
0:46:42.163561 PROGRESS: Channel   0:	 0.050 FDR:   119; 0.010 FDR:   119; 0.001 FDR:   111
0:46:42.163656 PROGRESS: =========================================================================
0:46:42.164200 INFO: Target number of precursors not reached yet.
0:46:42.292277 INFO: Starting optimization step 4.
0:46:42.292542 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:46:42.292622 INFO: Using rust extraction backend
0:46:42.292684 PROGRESS: Extracting batch of 31568 precursors
0:46:42.347646 INFO: === Search parameters used ===
0:46:42.347888 INFO: rt_error       : 805.6004638671875
0:46:42.347941 INFO: mobility_error : 0.1
0:46:42.347988 INFO: num_candidates : 1
0:46:42.348032 INFO: ms1_error      : 3
0:46:42.348075 INFO: ms2_error      : 10
0:46:42.348116 INFO: fwhm_rt        : 5
0:46:42.348158 INFO: quant_window   : 3
0:46:42.348198 INFO: ==============================================
0:46:42.571321 INFO: performing precursor FDR with 40 features
0:46:42.571433 INFO: Decoy channel: -1
0:46:42.571458 INFO: competitive: True
0:46:42.594089 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:42.609592 INFO: Estimating optimal hyperparameters - samples: 48,791, batch_size: 199, learning_rate: 2.20e-04
0:46:42.609820 INFO: Using random state 397885 for train-test-split
0:46:46.310853 INFO: Test AUC: 0.589
0:46:46.310943 INFO: Train AUC: 0.605
0:46:46.310976 INFO: AUC difference: 2.74%
0:46:46.599145 INFO: Resetting torch num_threads to 100
0:46:46.611426 PROGRESS: === Extracted 60989 precursors and 341243 fragments ===
0:46:46.612038 INFO: === FDR correction performed with classifier version -1 ===
0:46:46.612607 PROGRESS: ============================= Precursor FDR =============================
0:46:46.612696 PROGRESS: Total precursors accumulated: 118
0:46:46.612756 PROGRESS: Target precursors: 117 (99.15%)
0:46:46.612809 PROGRESS: Decoy precursors: 1 (0.85%)
0:46:46.612857 PROGRESS: 
0:46:46.612903 PROGRESS: Precursor Summary:
0:46:46.613862 PROGRESS: Channel   0:	 0.050 FDR:   117; 0.010 FDR:   117; 0.001 FDR:     0
0:46:46.613971 PROGRESS: 
0:46:46.614047 PROGRESS: Protein Summary:
0:46:46.615125 PROGRESS: Channel   0:	 0.050 FDR:   113; 0.010 FDR:   113; 0.001 FDR:     0
0:46:46.615219 PROGRESS: =========================================================================
0:46:46.616155 INFO: Target number of precursors not reached yet.
0:46:46.789604 INFO: Starting optimization step 5.
0:46:46.789869 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:46:46.789965 INFO: Using rust extraction backend
0:46:46.790028 PROGRESS: Extracting batch of 63098 precursors
0:46:46.898537 INFO: === Search parameters used ===
0:46:46.898809 INFO: rt_error       : 805.6004638671875
0:46:46.898885 INFO: mobility_error : 0.1
0:46:46.898931 INFO: num_candidates : 1
0:46:46.898972 INFO: ms1_error      : 3
0:46:46.899013 INFO: ms2_error      : 10
0:46:46.899051 INFO: fwhm_rt        : 5
0:46:46.899088 INFO: quant_window   : 3
0:46:46.899125 INFO: ==============================================
0:46:47.284045 INFO: performing precursor FDR with 40 features
0:46:47.284162 INFO: Decoy channel: -1
0:46:47.284186 INFO: competitive: True
0:46:47.329845 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:47.360661 INFO: Estimating optimal hyperparameters - samples: 99,136, batch_size: 406, learning_rate: 3.15e-04
0:46:47.360938 INFO: Using random state 881805 for train-test-split
0:46:52.062832 INFO: Test AUC: 0.593
0:46:52.062956 INFO: Train AUC: 0.609
0:46:52.062987 INFO: AUC difference: 2.63%
0:46:52.345968 INFO: Resetting torch num_threads to 100
0:46:52.367124 PROGRESS: === Extracted 123920 precursors and 694422 fragments ===
0:46:52.367754 INFO: === FDR correction performed with classifier version -1 ===
0:46:52.368401 PROGRESS: ============================= Precursor FDR =============================
0:46:52.368490 PROGRESS: Total precursors accumulated: 615
0:46:52.368550 PROGRESS: Target precursors: 609 (99.02%)
0:46:52.368601 PROGRESS: Decoy precursors: 6 (0.98%)
0:46:52.368647 PROGRESS: 
0:46:52.368709 PROGRESS: Precursor Summary:
0:46:52.369837 PROGRESS: Channel   0:	 0.050 FDR:   609; 0.010 FDR:   609; 0.001 FDR:   248
0:46:52.369936 PROGRESS: 
0:46:52.369994 PROGRESS: Protein Summary:
0:46:52.371353 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   552; 0.001 FDR:   238
0:46:52.371443 PROGRESS: =========================================================================
0:46:52.373300 INFO: Target number of precursors not reached yet.
0:46:52.614865 INFO: Starting optimization step 6.
0:46:52.615137 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:46:52.615216 INFO: Using rust extraction backend
0:46:52.615279 PROGRESS: Extracting batch of 126185 precursors
0:46:52.828783 INFO: === Search parameters used ===
0:46:52.829051 INFO: rt_error       : 805.6004638671875
0:46:52.829106 INFO: mobility_error : 0.1
0:46:52.829153 INFO: num_candidates : 1
0:46:52.829197 INFO: ms1_error      : 3
0:46:52.829241 INFO: ms2_error      : 10
0:46:52.829284 INFO: fwhm_rt        : 5
0:46:52.829328 INFO: quant_window   : 3
0:46:52.829376 INFO: ==============================================
0:46:53.516488 INFO: performing precursor FDR with 40 features
0:46:53.516613 INFO: Decoy channel: -1
0:46:53.516641 INFO: competitive: True
0:46:53.614455 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:53.691291 INFO: Estimating optimal hyperparameters - samples: 199,883, batch_size: 818, learning_rate: 4.47e-04
0:46:53.691693 INFO: Using random state 604442 for train-test-split
0:47:00.170415 INFO: Test AUC: 0.587
0:47:00.170545 INFO: Train AUC: 0.611
0:47:00.170576 INFO: AUC difference: 3.92%
0:47:00.497348 INFO: Resetting torch num_threads to 100
0:47:00.539127 PROGRESS: === Extracted 249854 precursors and 1399847 fragments ===
0:47:00.539800 INFO: === FDR correction performed with classifier version -1 ===
0:47:00.540583 PROGRESS: ============================= Precursor FDR =============================
0:47:00.540675 PROGRESS: Total precursors accumulated: 1,238
0:47:00.540735 PROGRESS: Target precursors: 1,226 (99.03%)
0:47:00.540788 PROGRESS: Decoy precursors: 12 (0.97%)
0:47:00.540843 PROGRESS: 
0:47:00.540887 PROGRESS: Precursor Summary:
0:47:00.542310 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR: 1,121
0:47:00.542405 PROGRESS: 
0:47:00.542459 PROGRESS: Protein Summary:
0:47:00.544146 PROGRESS: Channel   0:	 0.050 FDR: 1,036; 0.010 FDR: 1,036; 0.001 FDR:   952
0:47:00.544234 PROGRESS: =========================================================================
0:47:00.548197 INFO: Target number of precursors reached.
0:47:00.713516 INFO: fragments_df: keeping 5000 of 1399847 [sum(precursor_idx_mask)=13024 sum(mass_error_mask)=1399847 stop_rank=5000
0:47:01.111954 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:01.324611 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:02.045990 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:47:02.046440 INFO: Using score_cutoff 11.913464012145996 (fac=0.99, q=1)
0:47:02.046765 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:47:02.046848 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:47:02.046921 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.913464012145996
0:47:02.046986 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:02.198937 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:02.551071 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:47:02.551376 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:47:02.551509 INFO: Starting optimization step 7.
0:47:02.551616 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:47:02.551708 INFO: Using rust extraction backend
0:47:02.551801 PROGRESS: Extracting batch of 250439 precursors
0:47:02.980614 INFO: === Search parameters used ===
0:47:02.980903 INFO: rt_error       : 805.6004638671875
0:47:02.980963 INFO: mobility_error : 0.1
0:47:02.981018 INFO: num_candidates : 3
0:47:02.981064 INFO: ms1_error      : 3
0:47:02.981109 INFO: ms2_error      : 10
0:47:02.981150 INFO: fwhm_rt        : 3.0
0:47:02.981191 INFO: quant_window   : 3
0:47:02.981230 INFO: ==============================================
0:47:05.692459 INFO: performing precursor FDR with 40 features
0:47:05.692690 INFO: Decoy channel: -1
0:47:05.692720 INFO: competitive: True
0:47:05.877997 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:06.176669 INFO: Estimating optimal hyperparameters - samples: 599,592, batch_size: 2,455, learning_rate: 7.74e-04
0:47:06.177813 INFO: Using random state 304020 for train-test-split
0:47:19.182621 INFO: Test AUC: 0.593
0:47:19.182776 INFO: Train AUC: 0.604
0:47:19.182809 INFO: AUC difference: 1.83%
0:47:19.673118 INFO: Resetting torch num_threads to 100
0:47:19.700707 PROGRESS: === Extracted 749491 precursors and 4023036 fragments ===
0:47:19.701268 INFO: === FDR correction performed with classifier version 6 ===
0:47:19.701914 PROGRESS: ============================= Precursor FDR =============================
0:47:19.702020 PROGRESS: Total precursors accumulated: 1,320
0:47:19.702080 PROGRESS: Target precursors: 1,307 (99.02%)
0:47:19.702130 PROGRESS: Decoy precursors: 13 (0.98%)
0:47:19.702176 PROGRESS: 
0:47:19.702223 PROGRESS: Precursor Summary:
0:47:19.703495 PROGRESS: Channel   0:	 0.050 FDR: 1,307; 0.010 FDR: 1,307; 0.001 FDR:   705
0:47:19.703585 PROGRESS: 
0:47:19.703642 PROGRESS: Protein Summary:
0:47:19.705298 PROGRESS: Channel   0:	 0.050 FDR: 1,102; 0.010 FDR: 1,102; 0.001 FDR:   620
0:47:19.705390 PROGRESS: =========================================================================
0:47:19.719107 INFO: Target number of precursors reached.
0:47:20.156810 INFO: fragments_df: keeping 5000 of 4023036 [sum(precursor_idx_mask)=31708 sum(mass_error_mask)=4023036 stop_rank=5000
0:47:20.600964 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:20.819012 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:21.535867 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:21.536313 INFO: Using score_cutoff 12.149785668754577 (fac=0.99, q=1)
0:47:21.536641 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:21.536723 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:21.536779 INFO: Updating optimization_manager: score_cutoff        : 11.913464012145996 -> 12.149785668754577
0:47:21.536838 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:21.689123 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:22.027715 INFO: === checking if optimization conditions were reached ===
0:47:22.030363 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:47:22.030538 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:47:22.030618 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:47:22.030687 INFO: ==============================================
0:47:22.030772 INFO: Starting optimization step 8.
0:47:22.030844 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:47:22.030934 INFO: Using rust extraction backend
0:47:22.031016 PROGRESS: Extracting batch of 250439 precursors
0:47:22.458889 INFO: === Search parameters used ===
0:47:22.459164 INFO: rt_error       : 805.6004638671875
0:47:22.459224 INFO: mobility_error : 0.1
0:47:22.459273 INFO: num_candidates : 3
0:47:22.459319 INFO: ms1_error      : 3
0:47:22.459366 INFO: ms2_error      : 10.0
0:47:22.459412 INFO: fwhm_rt        : 3.0
0:47:22.459458 INFO: quant_window   : 3
0:47:22.459502 INFO: ==============================================
0:47:24.977469 INFO: performing precursor FDR with 40 features
0:47:24.977591 INFO: Decoy channel: -1
0:47:24.977617 INFO: competitive: True
0:47:25.172038 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:25.479632 INFO: Estimating optimal hyperparameters - samples: 599,590, batch_size: 2,455, learning_rate: 7.74e-04
0:47:25.480761 INFO: Using random state 902696 for train-test-split
0:47:38.513679 INFO: Test AUC: 0.605
0:47:38.513813 INFO: Train AUC: 0.614
0:47:38.513846 INFO: AUC difference: 1.42%
0:47:38.998549 INFO: Resetting torch num_threads to 100
0:47:39.027423 PROGRESS: === Extracted 749488 precursors and 4022528 fragments ===
0:47:39.027866 INFO: === FDR correction performed with classifier version 7 ===
0:47:39.028571 PROGRESS: ============================= Precursor FDR =============================
0:47:39.028665 PROGRESS: Total precursors accumulated: 1,454
0:47:39.028724 PROGRESS: Target precursors: 1,440 (99.04%)
0:47:39.028774 PROGRESS: Decoy precursors: 14 (0.96%)
0:47:39.028820 PROGRESS: 
0:47:39.028864 PROGRESS: Precursor Summary:
0:47:39.030257 PROGRESS: Channel   0:	 0.050 FDR: 1,440; 0.010 FDR: 1,440; 0.001 FDR: 1,015
0:47:39.030350 PROGRESS: 
0:47:39.030406 PROGRESS: Protein Summary:
0:47:39.032139 PROGRESS: Channel   0:	 0.050 FDR: 1,201; 0.010 FDR: 1,201; 0.001 FDR:   868
0:47:39.032229 PROGRESS: =========================================================================
0:47:39.045663 INFO: Target number of precursors reached.
0:47:39.487160 INFO: fragments_df: keeping 5000 of 4022528 [sum(precursor_idx_mask)=34648 sum(mass_error_mask)=4022528 stop_rank=5000
0:47:39.902241 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:40.135520 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:40.853738 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:40.854181 INFO: Using score_cutoff 12.123997230720521 (fac=0.99, q=1)
0:47:40.854487 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:40.854563 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:40.854616 INFO: Updating optimization_manager: score_cutoff        : 12.149785668754577 -> 12.123997230720521
0:47:40.854676 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:41.005222 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:41.334812 INFO: === checking if optimization conditions were reached ===
0:47:41.337378 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:47:41.337568 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:47:41.337647 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:47:41.337717 INFO: ==============================================
0:47:41.337796 INFO: Starting optimization step 9.
0:47:41.337864 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:47:41.337951 INFO: Using rust extraction backend
0:47:41.338023 PROGRESS: Extracting batch of 250439 precursors
0:47:41.761518 INFO: === Search parameters used ===
0:47:41.761789 INFO: rt_error       : 805.6004638671875
0:47:41.761845 INFO: mobility_error : 0.1
0:47:41.761892 INFO: num_candidates : 3
0:47:41.761966 INFO: ms1_error      : 3
0:47:41.762009 INFO: ms2_error      : 10.0
0:47:41.762050 INFO: fwhm_rt        : 3.0
0:47:41.762091 INFO: quant_window   : 3
0:47:41.762133 INFO: ==============================================
0:47:44.280284 INFO: performing precursor FDR with 40 features
0:47:44.280407 INFO: Decoy channel: -1
0:47:44.280434 INFO: competitive: True
0:47:44.474438 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:44.777647 INFO: Estimating optimal hyperparameters - samples: 599,597, batch_size: 2,455, learning_rate: 7.74e-04
0:47:44.778554 INFO: Using random state 902429 for train-test-split
0:47:57.969677 INFO: Test AUC: 0.610
0:47:57.969929 INFO: Train AUC: 0.617
0:47:57.969966 INFO: AUC difference: 1.15%
0:47:58.458311 INFO: Resetting torch num_threads to 100
0:47:58.487875 PROGRESS: === Extracted 749497 precursors and 4022513 fragments ===
0:47:58.488394 INFO: === FDR correction performed with classifier version 8 ===
0:47:58.489048 PROGRESS: ============================= Precursor FDR =============================
0:47:58.489133 PROGRESS: Total precursors accumulated: 1,448
0:47:58.489193 PROGRESS: Target precursors: 1,434 (99.03%)
0:47:58.489244 PROGRESS: Decoy precursors: 14 (0.97%)
0:47:58.489295 PROGRESS: 
0:47:58.489347 PROGRESS: Precursor Summary:
0:47:58.490655 PROGRESS: Channel   0:	 0.050 FDR: 1,434; 0.010 FDR: 1,434; 0.001 FDR:   883
0:47:58.490744 PROGRESS: 
0:47:58.490802 PROGRESS: Protein Summary:
0:47:58.492486 PROGRESS: Channel   0:	 0.050 FDR: 1,211; 0.010 FDR: 1,211; 0.001 FDR:   758
0:47:58.492578 PROGRESS: =========================================================================
0:47:58.506560 INFO: Target number of precursors reached.
0:47:58.950984 INFO: fragments_df: keeping 5000 of 4022513 [sum(precursor_idx_mask)=34279 sum(mass_error_mask)=4022513 stop_rank=5000
0:47:59.498030 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:59.731420 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:48:00.451391 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:48:00.451827 INFO: Using score_cutoff 11.80623609867096 (fac=0.99, q=1)
0:48:00.452162 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:48:00.452241 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:48:00.452304 INFO: Updating optimization_manager: score_cutoff        : 12.123997230720521 -> 11.80623609867096
0:48:00.452364 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:48:00.603431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:00.938718 INFO: === checking if optimization conditions were reached ===
0:48:00.941254 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:48:00.941415 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:48:00.941497 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:48:00.941567 INFO: ==============================================
0:48:00.941656 INFO: Starting optimization step 10.
0:48:00.941729 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:48:00.941820 INFO: Using rust extraction backend
0:48:00.941921 PROGRESS: Extracting batch of 250439 precursors
0:48:01.369576 INFO: === Search parameters used ===
0:48:01.369846 INFO: rt_error       : 805.6004638671875
0:48:01.369933 INFO: mobility_error : 0.1
0:48:01.369987 INFO: num_candidates : 3
0:48:01.370033 INFO: ms1_error      : 3
0:48:01.370075 INFO: ms2_error      : 10.0
0:48:01.370116 INFO: fwhm_rt        : 3.0
0:48:01.370158 INFO: quant_window   : 3
0:48:01.370201 INFO: ==============================================
0:48:03.843996 INFO: performing precursor FDR with 40 features
0:48:03.844136 INFO: Decoy channel: -1
0:48:03.844161 INFO: competitive: True
0:48:04.036485 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:04.341493 INFO: Estimating optimal hyperparameters - samples: 599,600, batch_size: 2,455, learning_rate: 7.74e-04
0:48:04.342450 INFO: Using random state 552981 for train-test-split
0:48:17.307154 INFO: Test AUC: 0.611
0:48:17.307295 INFO: Train AUC: 0.620
0:48:17.307327 INFO: AUC difference: 1.35%
0:48:17.789988 INFO: Resetting torch num_threads to 100
0:48:17.818334 PROGRESS: === Extracted 749500 precursors and 4022786 fragments ===
0:48:17.818790 INFO: === FDR correction performed with classifier version 9 ===
0:48:17.819422 PROGRESS: ============================= Precursor FDR =============================
0:48:17.819515 PROGRESS: Total precursors accumulated: 1,463
0:48:17.819576 PROGRESS: Target precursors: 1,449 (99.04%)
0:48:17.819629 PROGRESS: Decoy precursors: 14 (0.96%)
0:48:17.819681 PROGRESS: 
0:48:17.819728 PROGRESS: Precursor Summary:
0:48:17.821037 PROGRESS: Channel   0:	 0.050 FDR: 1,449; 0.010 FDR: 1,449; 0.001 FDR: 1,073
0:48:17.821123 PROGRESS: 
0:48:17.821186 PROGRESS: Protein Summary:
0:48:17.822946 PROGRESS: Channel   0:	 0.050 FDR: 1,223; 0.010 FDR: 1,223; 0.001 FDR:   913
0:48:17.823041 PROGRESS: =========================================================================
0:48:17.836588 INFO: Target number of precursors reached.
0:48:18.291392 INFO: fragments_df: keeping 5000 of 4022786 [sum(precursor_idx_mask)=34714 sum(mass_error_mask)=4022786 stop_rank=5000
0:48:18.751905 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:48:18.985844 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:48:19.707814 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:48:19.708245 INFO: Using score_cutoff 11.7466568069458 (fac=0.99, q=1)
0:48:19.708546 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:48:19.708634 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:48:19.708688 INFO: Updating optimization_manager: score_cutoff        : 11.80623609867096 -> 11.7466568069458
0:48:19.708741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:48:19.859097 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:20.191260 INFO: === checking if optimization conditions were reached ===
0:48:20.193758 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:48:20.193873 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:48:20.193967 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:48:20.194042 INFO: ==============================================
0:48:20.194123 INFO: Starting optimization step 11.
0:48:20.194199 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:48:20.194273 INFO: Using rust extraction backend
0:48:20.194346 PROGRESS: Extracting batch of 250439 precursors
0:48:20.621542 INFO: === Search parameters used ===
0:48:20.621833 INFO: rt_error       : 805.6004638671875
0:48:20.621891 INFO: mobility_error : 0.1
0:48:20.621998 INFO: num_candidates : 3
0:48:20.622046 INFO: ms1_error      : 3
0:48:20.622108 INFO: ms2_error      : 10.0
0:48:20.622152 INFO: fwhm_rt        : 3.0
0:48:20.622200 INFO: quant_window   : 3
0:48:20.622241 INFO: ==============================================
0:48:23.263011 INFO: performing precursor FDR with 40 features
0:48:23.263237 INFO: Decoy channel: -1
0:48:23.263264 INFO: competitive: True
0:48:23.456251 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:23.764077 INFO: Estimating optimal hyperparameters - samples: 599,593, batch_size: 2,455, learning_rate: 7.74e-04
0:48:23.765250 INFO: Using random state 359956 for train-test-split
0:48:36.924643 INFO: Test AUC: 0.610
0:48:36.924905 INFO: Train AUC: 0.622
0:48:36.924941 INFO: AUC difference: 1.85%
0:48:37.409975 INFO: Resetting torch num_threads to 100
0:48:37.440273 PROGRESS: === Extracted 749492 precursors and 4022591 fragments ===
0:48:37.440855 INFO: === FDR correction performed with classifier version 10 ===
0:48:37.441582 PROGRESS: ============================= Precursor FDR =============================
0:48:37.441671 PROGRESS: Total precursors accumulated: 1,501
0:48:37.441731 PROGRESS: Target precursors: 1,487 (99.07%)
0:48:37.441784 PROGRESS: Decoy precursors: 14 (0.93%)
0:48:37.441835 PROGRESS: 
0:48:37.441885 PROGRESS: Precursor Summary:
0:48:37.443234 PROGRESS: Channel   0:	 0.050 FDR: 1,487; 0.010 FDR: 1,487; 0.001 FDR: 1,055
0:48:37.443332 PROGRESS: 
0:48:37.443387 PROGRESS: Protein Summary:
0:48:37.445134 PROGRESS: Channel   0:	 0.050 FDR: 1,249; 0.010 FDR: 1,249; 0.001 FDR:   900
0:48:37.445233 PROGRESS: =========================================================================
0:48:37.458249 INFO: Target number of precursors reached.
0:48:37.910101 INFO: fragments_df: keeping 5000 of 4022591 [sum(precursor_idx_mask)=35772 sum(mass_error_mask)=4022591 stop_rank=5000
0:48:38.455822 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:48:38.695521 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:48:39.413808 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:48:39.414290 INFO: Using score_cutoff 12.213684427642821 (fac=0.99, q=1)
0:48:39.414639 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:48:39.414717 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:48:39.414772 INFO: Updating optimization_manager: score_cutoff        : 11.7466568069458 -> 12.213684427642821
0:48:39.414834 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:48:39.567777 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:39.901386 INFO: === checking if optimization conditions were reached ===
0:48:39.903887 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:48:39.904009 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:48:39.904089 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:48:39.904157 INFO: ==============================================
0:48:39.904261 PROGRESS: Optimization finished for ms2_error.
0:48:40.320109 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:48:40.471495 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:40.801859 INFO: Starting optimization step 0.
0:48:40.802176 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:48:40.802286 INFO: Using rust extraction backend
0:48:40.802383 PROGRESS: Extracting batch of 250439 precursors
0:48:41.231101 INFO: === Search parameters used ===
0:48:41.231379 INFO: rt_error       : 805.6004638671875
0:48:41.231453 INFO: mobility_error : 0.1
0:48:41.231503 INFO: num_candidates : 3
0:48:41.231547 INFO: ms1_error      : 3
0:48:41.231592 INFO: ms2_error      : 10.0
0:48:41.231635 INFO: fwhm_rt        : 3.0
0:48:41.231677 INFO: quant_window   : 3
0:48:41.231718 INFO: ==============================================
0:48:43.793945 INFO: performing precursor FDR with 40 features
0:48:43.794067 INFO: Decoy channel: -1
0:48:43.794093 INFO: competitive: True
0:48:43.978915 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:44.268090 INFO: Estimating optimal hyperparameters - samples: 599,575, batch_size: 2,455, learning_rate: 7.74e-04
0:48:44.269185 INFO: Using random state 498079 for train-test-split
0:48:57.212717 INFO: Test AUC: 0.611
0:48:57.212851 INFO: Train AUC: 0.623
0:48:57.212886 INFO: AUC difference: 1.99%
0:48:57.686940 INFO: Resetting torch num_threads to 100
0:48:57.715353 PROGRESS: === Extracted 749469 precursors and 4022110 fragments ===
0:48:57.715778 INFO: === FDR correction performed with classifier version 11 ===
0:48:57.716489 PROGRESS: ============================= Precursor FDR =============================
0:48:57.716582 PROGRESS: Total precursors accumulated: 1,453
0:48:57.716642 PROGRESS: Target precursors: 1,439 (99.04%)
0:48:57.716692 PROGRESS: Decoy precursors: 14 (0.96%)
0:48:57.716746 PROGRESS: 
0:48:57.716792 PROGRESS: Precursor Summary:
0:48:57.718143 PROGRESS: Channel   0:	 0.050 FDR: 1,439; 0.010 FDR: 1,439; 0.001 FDR:   883
0:48:57.718238 PROGRESS: 
0:48:57.718300 PROGRESS: Protein Summary:
0:48:57.720023 PROGRESS: Channel   0:	 0.050 FDR: 1,208; 0.010 FDR: 1,208; 0.001 FDR:   759
0:48:57.720112 PROGRESS: =========================================================================
0:48:57.733463 INFO: Target number of precursors reached.
0:48:58.179541 INFO: fragments_df: keeping 5000 of 4022110 [sum(precursor_idx_mask)=34604 sum(mass_error_mask)=4022110 stop_rank=5000
0:48:58.585501 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:48:58.818651 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:48:59.536239 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:48:59.536663 INFO: Using score_cutoff 12.123708494567872 (fac=0.99, q=1)
0:48:59.536959 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:48:59.537037 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:48:59.537090 INFO: Updating optimization_manager: score_cutoff        : 12.213684427642821 -> 12.123708494567872
0:48:59.537143 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:48:59.688015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:00.018869 INFO: === checking if optimization conditions were reached ===
0:49:00.019210 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:49:00.022252 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 697.423356516567
0:49:00.022388 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 697.4234.
0:49:00.022463 INFO: ==============================================
0:49:00.022544 INFO: Starting optimization step 1.
0:49:00.022611 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:49:00.022683 INFO: Using rust extraction backend
0:49:00.022749 PROGRESS: Extracting batch of 250439 precursors
0:49:00.449093 INFO: === Search parameters used ===
0:49:00.449394 INFO: rt_error       : 697.423356516567
0:49:00.449455 INFO: mobility_error : 0.1
0:49:00.449503 INFO: num_candidates : 3
0:49:00.449546 INFO: ms1_error      : 3
0:49:00.449588 INFO: ms2_error      : 10.0
0:49:00.449627 INFO: fwhm_rt        : 3.0
0:49:00.449666 INFO: quant_window   : 3
0:49:00.449704 INFO: ==============================================
0:49:02.929530 INFO: performing precursor FDR with 40 features
0:49:02.929703 INFO: Decoy channel: -1
0:49:02.929731 INFO: competitive: True
0:49:03.116293 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:03.412932 INFO: Estimating optimal hyperparameters - samples: 599,552, batch_size: 2,455, learning_rate: 7.74e-04
0:49:03.413980 INFO: Using random state 498079 for train-test-split
0:49:16.259747 INFO: Test AUC: 0.615
0:49:16.259904 INFO: Train AUC: 0.624
0:49:16.259937 INFO: AUC difference: 1.43%
0:49:16.748768 INFO: Resetting torch num_threads to 100
0:49:16.780490 PROGRESS: === Extracted 749440 precursors and 4019793 fragments ===
0:49:16.780974 INFO: === FDR correction performed with classifier version 11 ===
0:49:16.781658 PROGRESS: ============================= Precursor FDR =============================
0:49:16.781746 PROGRESS: Total precursors accumulated: 1,550
0:49:16.781807 PROGRESS: Target precursors: 1,535 (99.03%)
0:49:16.781859 PROGRESS: Decoy precursors: 15 (0.97%)
0:49:16.781919 PROGRESS: 
0:49:16.781975 PROGRESS: Precursor Summary:
0:49:16.783342 PROGRESS: Channel   0:	 0.050 FDR: 1,535; 0.010 FDR: 1,535; 0.001 FDR: 1,206
0:49:16.783431 PROGRESS: 
0:49:16.783487 PROGRESS: Protein Summary:
0:49:16.785289 PROGRESS: Channel   0:	 0.050 FDR: 1,307; 0.010 FDR: 1,307; 0.001 FDR: 1,018
0:49:16.785396 PROGRESS: =========================================================================
0:49:16.799604 INFO: Target number of precursors reached.
0:49:17.252564 INFO: fragments_df: keeping 5000 of 4019793 [sum(precursor_idx_mask)=35789 sum(mass_error_mask)=4019793 stop_rank=5000
0:49:17.731274 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:49:18.829357 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:49:19.549094 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:49:19.549602 INFO: Using score_cutoff 9.185090494537354 (fac=0.99, q=1)
0:49:19.549919 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:49:19.550001 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:49:19.550057 INFO: Updating optimization_manager: score_cutoff        : 12.123708494567872 -> 9.185090494537354
0:49:19.550112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:49:19.700135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:20.034534 INFO: === checking if optimization conditions were reached ===
0:49:20.034866 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:49:20.038122 INFO: Updating optimization_manager: rt_error            : 697.423356516567 -> 742.8189489780304
0:49:20.038246 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 742.8189.
0:49:20.038324 INFO: ==============================================
0:49:20.038409 INFO: Starting optimization step 2.
0:49:20.038482 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:49:20.038561 INFO: Using rust extraction backend
0:49:20.038652 PROGRESS: Extracting batch of 250439 precursors
0:49:20.466145 INFO: === Search parameters used ===
0:49:20.466412 INFO: rt_error       : 742.8189489780304
0:49:20.466471 INFO: mobility_error : 0.1
0:49:20.466523 INFO: num_candidates : 3
0:49:20.466568 INFO: ms1_error      : 3
0:49:20.466612 INFO: ms2_error      : 10.0
0:49:20.466654 INFO: fwhm_rt        : 3.0
0:49:20.466695 INFO: quant_window   : 3
0:49:20.466735 INFO: ==============================================
0:49:22.990337 INFO: performing precursor FDR with 40 features
0:49:22.990456 INFO: Decoy channel: -1
0:49:22.990480 INFO: competitive: True
0:49:23.183149 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:23.487200 INFO: Estimating optimal hyperparameters - samples: 599,623, batch_size: 2,456, learning_rate: 7.74e-04
0:49:23.488235 INFO: Using random state 498079 for train-test-split
0:49:35.848957 INFO: Test AUC: 0.614
0:49:35.849094 INFO: Train AUC: 0.624
0:49:35.849127 INFO: AUC difference: 1.68%
0:49:36.328380 INFO: Resetting torch num_threads to 100
0:49:36.359055 PROGRESS: === Extracted 749529 precursors and 4023051 fragments ===
0:49:36.359515 INFO: === FDR correction performed with classifier version 11 ===
0:49:36.360245 PROGRESS: ============================= Precursor FDR =============================
0:49:36.360340 PROGRESS: Total precursors accumulated: 1,430
0:49:36.360400 PROGRESS: Target precursors: 1,416 (99.02%)
0:49:36.360451 PROGRESS: Decoy precursors: 14 (0.98%)
0:49:36.360498 PROGRESS: 
0:49:36.360544 PROGRESS: Precursor Summary:
0:49:36.361946 PROGRESS: Channel   0:	 0.050 FDR: 1,416; 0.010 FDR: 1,416; 0.001 FDR: 1,254
0:49:36.362046 PROGRESS: 
0:49:36.362104 PROGRESS: Protein Summary:
0:49:36.363917 PROGRESS: Channel   0:	 0.050 FDR: 1,195; 0.010 FDR: 1,195; 0.001 FDR: 1,055
0:49:36.364021 PROGRESS: =========================================================================
0:49:36.376972 INFO: Target number of precursors reached.
0:49:36.819341 INFO: fragments_df: keeping 5000 of 4023051 [sum(precursor_idx_mask)=33867 sum(mass_error_mask)=4023051 stop_rank=5000
0:49:37.240197 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:49:37.471399 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:49:38.191670 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:49:38.192121 INFO: Using score_cutoff 11.674579786777496 (fac=0.99, q=1)
0:49:38.192430 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:49:38.192504 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:49:38.192556 INFO: Updating optimization_manager: score_cutoff        : 9.185090494537354 -> 11.674579786777496
0:49:38.192606 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:49:38.343431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:38.672586 INFO: === checking if optimization conditions were reached ===
0:49:38.672887 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:49:38.676120 INFO: Updating optimization_manager: rt_error            : 742.8189489780304 -> 677.3385992724732
0:49:38.676242 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 677.3386.
0:49:38.676316 INFO: ==============================================
0:49:38.676397 INFO: Starting optimization step 3.
0:49:38.676484 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:49:38.676555 INFO: Using rust extraction backend
0:49:38.676621 PROGRESS: Extracting batch of 250439 precursors
0:49:39.098029 INFO: === Search parameters used ===
0:49:39.098303 INFO: rt_error       : 677.3385992724732
0:49:39.098361 INFO: mobility_error : 0.1
0:49:39.098412 INFO: num_candidates : 3
0:49:39.098460 INFO: ms1_error      : 3
0:49:39.098506 INFO: ms2_error      : 10.0
0:49:39.098551 INFO: fwhm_rt        : 3.0
0:49:39.098594 INFO: quant_window   : 3
0:49:39.098637 INFO: ==============================================
0:49:41.502775 INFO: performing precursor FDR with 40 features
0:49:41.502893 INFO: Decoy channel: -1
0:49:41.502920 INFO: competitive: True
0:49:41.681808 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:41.975796 INFO: Estimating optimal hyperparameters - samples: 599,471, batch_size: 2,455, learning_rate: 7.74e-04
0:49:41.976814 INFO: Using random state 498079 for train-test-split
0:49:55.106132 INFO: Test AUC: 0.613
0:49:55.106289 INFO: Train AUC: 0.625
0:49:55.106323 INFO: AUC difference: 1.93%
0:49:55.598208 INFO: Resetting torch num_threads to 100
0:49:55.662946 PROGRESS: === Extracted 749339 precursors and 4015826 fragments ===
0:49:55.663422 INFO: === FDR correction performed with classifier version 11 ===
0:49:55.664161 PROGRESS: ============================= Precursor FDR =============================
0:49:55.664251 PROGRESS: Total precursors accumulated: 1,556
0:49:55.664312 PROGRESS: Target precursors: 1,541 (99.04%)
0:49:55.664364 PROGRESS: Decoy precursors: 15 (0.96%)
0:49:55.664411 PROGRESS: 
0:49:55.664457 PROGRESS: Precursor Summary:
0:49:55.665796 PROGRESS: Channel   0:	 0.050 FDR: 1,541; 0.010 FDR: 1,541; 0.001 FDR:   930
0:49:55.665897 PROGRESS: 
0:49:55.665968 PROGRESS: Protein Summary:
0:49:55.667731 PROGRESS: Channel   0:	 0.050 FDR: 1,302; 0.010 FDR: 1,302; 0.001 FDR:   797
0:49:55.667825 PROGRESS: =========================================================================
0:49:55.685282 INFO: Target number of precursors reached.
0:49:56.134841 INFO: fragments_df: keeping 5000 of 4015826 [sum(precursor_idx_mask)=36205 sum(mass_error_mask)=4015826 stop_rank=5000
0:49:56.607440 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:49:56.860940 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:49:57.577417 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:49:57.577857 INFO: Using score_cutoff 9.604751564025879 (fac=0.99, q=1)
0:49:57.578181 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:49:57.578259 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:49:57.578311 INFO: Updating optimization_manager: score_cutoff        : 11.674579786777496 -> 9.604751564025879
0:49:57.578364 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:49:57.731117 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:58.067463 INFO: === checking if optimization conditions were reached ===
0:49:58.067786 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:49:58.071094 INFO: Updating optimization_manager: rt_error            : 677.3385992724732 -> 722.7038985403344
0:49:58.071214 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 722.7039.
0:49:58.071310 INFO: ==============================================
0:49:58.071399 INFO: Starting optimization step 4.
0:49:58.071469 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:49:58.071544 INFO: Using rust extraction backend
0:49:58.071611 PROGRESS: Extracting batch of 250439 precursors
0:49:58.497457 INFO: === Search parameters used ===
0:49:58.497738 INFO: rt_error       : 722.7038985403344
0:49:58.497794 INFO: mobility_error : 0.1
0:49:58.497842 INFO: num_candidates : 3
0:49:58.497885 INFO: ms1_error      : 3
0:49:58.497941 INFO: ms2_error      : 10.0
0:49:58.497983 INFO: fwhm_rt        : 3.0
0:49:58.498021 INFO: quant_window   : 3
0:49:58.498059 INFO: ==============================================
0:50:00.970416 INFO: performing precursor FDR with 40 features
0:50:00.970520 INFO: Decoy channel: -1
0:50:00.970547 INFO: competitive: True
0:50:01.164000 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:01.466980 INFO: Estimating optimal hyperparameters - samples: 599,578, batch_size: 2,455, learning_rate: 7.74e-04
0:50:01.467994 INFO: Using random state 498079 for train-test-split
0:50:14.448829 INFO: Test AUC: 0.611
0:50:14.448961 INFO: Train AUC: 0.623
0:50:14.448993 INFO: AUC difference: 1.94%
0:50:14.930329 INFO: Resetting torch num_threads to 100
0:50:14.959047 PROGRESS: === Extracted 749473 precursors and 4021233 fragments ===
0:50:14.959467 INFO: === FDR correction performed with classifier version 11 ===
0:50:14.960147 PROGRESS: ============================= Precursor FDR =============================
0:50:14.960238 PROGRESS: Total precursors accumulated: 1,459
0:50:14.960298 PROGRESS: Target precursors: 1,445 (99.04%)
0:50:14.960350 PROGRESS: Decoy precursors: 14 (0.96%)
0:50:14.960398 PROGRESS: 
0:50:14.960444 PROGRESS: Precursor Summary:
0:50:14.961827 PROGRESS: Channel   0:	 0.050 FDR: 1,445; 0.010 FDR: 1,445; 0.001 FDR: 1,274
0:50:14.961932 PROGRESS: 
0:50:14.961992 PROGRESS: Protein Summary:
0:50:14.963765 PROGRESS: Channel   0:	 0.050 FDR: 1,220; 0.010 FDR: 1,220; 0.001 FDR: 1,083
0:50:14.963866 PROGRESS: =========================================================================
0:50:14.977391 INFO: Target number of precursors reached.
0:50:15.434166 INFO: fragments_df: keeping 5000 of 4021233 [sum(precursor_idx_mask)=34555 sum(mass_error_mask)=4021233 stop_rank=5000
0:50:15.839712 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:50:16.070302 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:50:16.785821 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:50:16.786269 INFO: Using score_cutoff 11.679321179580688 (fac=0.99, q=1)
0:50:16.786569 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:50:16.786647 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:50:16.786703 INFO: Updating optimization_manager: score_cutoff        : 9.604751564025879 -> 11.679321179580688
0:50:16.786758 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:50:16.937667 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:50:17.279391 INFO: === checking if optimization conditions were reached ===
0:50:17.279699 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:50:17.282985 INFO: Updating optimization_manager: rt_error            : 722.7038985403344 -> 623.3464049843167
0:50:17.283172 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 623.3464.
0:50:17.283252 INFO: ==============================================
0:50:17.283337 INFO: Starting optimization step 5.
0:50:17.283415 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:50:17.283490 INFO: Using rust extraction backend
0:50:17.283558 PROGRESS: Extracting batch of 250439 precursors
0:50:17.704145 INFO: === Search parameters used ===
0:50:17.704411 INFO: rt_error       : 623.3464049843167
0:50:17.704466 INFO: mobility_error : 0.1
0:50:17.704512 INFO: num_candidates : 3
0:50:17.704555 INFO: ms1_error      : 3
0:50:17.704597 INFO: ms2_error      : 10.0
0:50:17.704637 INFO: fwhm_rt        : 3.0
0:50:17.704677 INFO: quant_window   : 3
0:50:17.704716 INFO: ==============================================
0:50:20.103761 INFO: performing precursor FDR with 40 features
0:50:20.103876 INFO: Decoy channel: -1
0:50:20.103902 INFO: competitive: True
0:50:20.282997 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:20.587238 INFO: Estimating optimal hyperparameters - samples: 599,392, batch_size: 2,455, learning_rate: 7.74e-04
0:50:20.589242 INFO: Using random state 498079 for train-test-split
0:50:33.670066 INFO: Test AUC: 0.610
0:50:33.670235 INFO: Train AUC: 0.625
0:50:33.670268 INFO: AUC difference: 2.31%
0:50:34.165827 INFO: Resetting torch num_threads to 100
0:50:34.191980 PROGRESS: === Extracted 749241 precursors and 4009194 fragments ===
0:50:34.192466 INFO: === FDR correction performed with classifier version 11 ===
0:50:34.193126 PROGRESS: ============================= Precursor FDR =============================
0:50:34.193217 PROGRESS: Total precursors accumulated: 1,578
0:50:34.193278 PROGRESS: Target precursors: 1,563 (99.05%)
0:50:34.193330 PROGRESS: Decoy precursors: 15 (0.95%)
0:50:34.193401 PROGRESS: 
0:50:34.193447 PROGRESS: Precursor Summary:
0:50:34.194845 PROGRESS: Channel   0:	 0.050 FDR: 1,563; 0.010 FDR: 1,563; 0.001 FDR: 1,226
0:50:34.194938 PROGRESS: 
0:50:34.194993 PROGRESS: Protein Summary:
0:50:34.196806 PROGRESS: Channel   0:	 0.050 FDR: 1,331; 0.010 FDR: 1,331; 0.001 FDR: 1,043
0:50:34.196896 PROGRESS: =========================================================================
0:50:34.209190 INFO: Target number of precursors reached.
0:50:34.660621 INFO: fragments_df: keeping 5000 of 4009194 [sum(precursor_idx_mask)=36424 sum(mass_error_mask)=4009194 stop_rank=5000
0:50:35.115898 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:50:35.355954 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:50:36.075560 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:50:36.075997 INFO: Using score_cutoff 9.503807433700562 (fac=0.99, q=1)
0:50:36.076311 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:50:36.076390 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:50:36.076444 INFO: Updating optimization_manager: score_cutoff        : 11.679321179580688 -> 9.503807433700562
0:50:36.076499 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:50:36.232133 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:50:36.576974 INFO: === checking if optimization conditions were reached ===
0:50:36.577301 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:50:36.580748 INFO: Updating optimization_manager: rt_error            : 623.3464049843167 -> 673.3887780943631
0:50:36.580869 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 673.3888.
0:50:36.580946 INFO: ==============================================
0:50:36.581035 INFO: Starting optimization step 6.
0:50:36.581113 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:50:36.581192 INFO: Using rust extraction backend
0:50:36.581264 PROGRESS: Extracting batch of 250439 precursors
0:50:37.006473 INFO: === Search parameters used ===
0:50:37.006727 INFO: rt_error       : 673.3887780943631
0:50:37.006789 INFO: mobility_error : 0.1
0:50:37.006839 INFO: num_candidates : 3
0:50:37.006888 INFO: ms1_error      : 3
0:50:37.006939 INFO: ms2_error      : 10.0
0:50:37.006983 INFO: fwhm_rt        : 3.0
0:50:37.007025 INFO: quant_window   : 3
0:50:37.007084 INFO: ==============================================
0:50:39.487896 INFO: performing precursor FDR with 40 features
0:50:39.488015 INFO: Decoy channel: -1
0:50:39.488040 INFO: competitive: True
0:50:39.665718 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:39.953224 INFO: Estimating optimal hyperparameters - samples: 599,553, batch_size: 2,455, learning_rate: 7.74e-04
0:50:39.954273 INFO: Using random state 498079 for train-test-split
0:50:52.735786 INFO: Test AUC: 0.610
0:50:52.735917 INFO: Train AUC: 0.625
0:50:52.735950 INFO: AUC difference: 2.34%
0:50:53.214719 INFO: Resetting torch num_threads to 100
0:50:53.247514 PROGRESS: === Extracted 749442 precursors and 4020367 fragments ===
0:50:53.247989 INFO: === FDR correction performed with classifier version 11 ===
0:50:53.248666 PROGRESS: ============================= Precursor FDR =============================
0:50:53.248754 PROGRESS: Total precursors accumulated: 1,488
0:50:53.248820 PROGRESS: Target precursors: 1,474 (99.06%)
0:50:53.248871 PROGRESS: Decoy precursors: 14 (0.94%)
0:50:53.248915 PROGRESS: 
0:50:53.248957 PROGRESS: Precursor Summary:
0:50:53.250292 PROGRESS: Channel   0:	 0.050 FDR: 1,474; 0.010 FDR: 1,474; 0.001 FDR:   868
0:50:53.250382 PROGRESS: 
0:50:53.250439 PROGRESS: Protein Summary:
0:50:53.252154 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR: 1,240; 0.001 FDR:   749
0:50:53.252241 PROGRESS: =========================================================================
0:50:53.264960 INFO: Target number of precursors reached.
0:50:53.701375 INFO: fragments_df: keeping 5000 of 4020367 [sum(precursor_idx_mask)=35291 sum(mass_error_mask)=4020367 stop_rank=5000
0:50:54.109088 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:50:54.315724 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:50:55.006190 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:50:55.006638 INFO: Using score_cutoff 12.24107911748886 (fac=0.99, q=1)
0:50:55.006941 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:50:55.007017 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:50:55.007071 INFO: Updating optimization_manager: score_cutoff        : 9.503807433700562 -> 12.24107911748886
0:50:55.007124 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:50:55.157899 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:50:55.489013 INFO: === checking if optimization conditions were reached ===
0:50:55.489316 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:50:55.492539 INFO: Updating optimization_manager: rt_error            : 673.3887780943631 -> 530.9360246797944
0:50:55.492662 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 530.9360.
0:50:55.492737 INFO: ==============================================
0:50:55.492821 INFO: Starting optimization step 7.
0:50:55.492890 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:50:55.492961 INFO: Using rust extraction backend
0:50:55.493029 PROGRESS: Extracting batch of 250439 precursors
0:50:55.915288 INFO: === Search parameters used ===
0:50:55.915556 INFO: rt_error       : 530.9360246797944
0:50:55.915613 INFO: mobility_error : 0.1
0:50:55.915660 INFO: num_candidates : 3
0:50:55.915705 INFO: ms1_error      : 3
0:50:55.915747 INFO: ms2_error      : 10.0
0:50:55.915788 INFO: fwhm_rt        : 3.0
0:50:55.915828 INFO: quant_window   : 3
0:50:55.915867 INFO: ==============================================
0:50:58.340747 INFO: performing precursor FDR with 40 features
0:50:58.340867 INFO: Decoy channel: -1
0:50:58.340894 INFO: competitive: True
0:50:58.567244 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:58.874477 INFO: Estimating optimal hyperparameters - samples: 599,002, batch_size: 2,453, learning_rate: 7.74e-04
0:50:58.875469 INFO: Using random state 498079 for train-test-split
0:51:11.641442 INFO: Test AUC: 0.609
0:51:11.641626 INFO: Train AUC: 0.622
0:51:11.641682 INFO: AUC difference: 2.13%
0:51:12.130450 INFO: Resetting torch num_threads to 100
0:51:12.160819 PROGRESS: === Extracted 748753 precursors and 3978209 fragments ===
0:51:12.161338 INFO: === FDR correction performed with classifier version 11 ===
0:51:12.161997 PROGRESS: ============================= Precursor FDR =============================
0:51:12.162087 PROGRESS: Total precursors accumulated: 1,345
0:51:12.162143 PROGRESS: Target precursors: 1,332 (99.03%)
0:51:12.162190 PROGRESS: Decoy precursors: 13 (0.97%)
0:51:12.162232 PROGRESS: 
0:51:12.162273 PROGRESS: Precursor Summary:
0:51:12.163562 PROGRESS: Channel   0:	 0.050 FDR: 1,332; 0.010 FDR: 1,332; 0.001 FDR: 1,107
0:51:12.163645 PROGRESS: 
0:51:12.163697 PROGRESS: Protein Summary:
0:51:12.165379 PROGRESS: Channel   0:	 0.050 FDR: 1,137; 0.010 FDR: 1,137; 0.001 FDR:   947
0:51:12.165464 PROGRESS: =========================================================================
0:51:12.185908 INFO: Target number of precursors reached.
0:51:12.623316 INFO: fragments_df: keeping 5000 of 3978209 [sum(precursor_idx_mask)=30882 sum(mass_error_mask)=3978209 stop_rank=5000
0:51:13.081314 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:13.302227 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:14.022573 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:14.023008 INFO: Using score_cutoff 7.7820813557624815 (fac=0.99, q=1)
0:51:14.023325 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:14.023404 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:14.023459 INFO: Updating optimization_manager: score_cutoff        : 12.24107911748886 -> 7.7820813557624815
0:51:14.023523 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:14.173685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:14.512244 INFO: === checking if optimization conditions were reached ===
0:51:14.512551 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:51:14.515743 INFO: Updating optimization_manager: rt_error            : 530.9360246797944 -> 634.1806348321281
0:51:14.515863 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 634.1806.
0:51:14.515940 INFO: ==============================================
0:51:14.516032 INFO: Starting optimization step 8.
0:51:14.516103 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:14.516183 INFO: Using rust extraction backend
0:51:14.516253 PROGRESS: Extracting batch of 250439 precursors
0:51:14.944002 INFO: === Search parameters used ===
0:51:14.944269 INFO: rt_error       : 634.1806348321281
0:51:14.944328 INFO: mobility_error : 0.1
0:51:14.944378 INFO: num_candidates : 3
0:51:14.944422 INFO: ms1_error      : 3
0:51:14.944464 INFO: ms2_error      : 10.0
0:51:14.944506 INFO: fwhm_rt        : 3.0
0:51:14.944546 INFO: quant_window   : 3
0:51:14.944588 INFO: ==============================================
0:51:17.400424 INFO: performing precursor FDR with 40 features
0:51:17.400554 INFO: Decoy channel: -1
0:51:17.400581 INFO: competitive: True
0:51:17.585313 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:17.893065 INFO: Estimating optimal hyperparameters - samples: 599,488, batch_size: 2,455, learning_rate: 7.74e-04
0:51:17.894241 INFO: Using random state 498079 for train-test-split
0:51:31.244188 INFO: Test AUC: 0.611
0:51:31.244324 INFO: Train AUC: 0.625
0:51:31.244356 INFO: AUC difference: 2.31%
0:51:31.718497 INFO: Resetting torch num_threads to 100
0:51:31.747074 PROGRESS: === Extracted 749360 precursors and 4015675 fragments ===
0:51:31.747546 INFO: === FDR correction performed with classifier version 11 ===
0:51:31.748262 PROGRESS: ============================= Precursor FDR =============================
0:51:31.748358 PROGRESS: Total precursors accumulated: 1,486
0:51:31.748417 PROGRESS: Target precursors: 1,472 (99.06%)
0:51:31.748467 PROGRESS: Decoy precursors: 14 (0.94%)
0:51:31.748523 PROGRESS: 
0:51:31.748570 PROGRESS: Precursor Summary:
0:51:31.749979 PROGRESS: Channel   0:	 0.050 FDR: 1,472; 0.010 FDR: 1,472; 0.001 FDR: 1,141
0:51:31.750084 PROGRESS: 
0:51:31.750139 PROGRESS: Protein Summary:
0:51:31.751898 PROGRESS: Channel   0:	 0.050 FDR: 1,250; 0.010 FDR: 1,250; 0.001 FDR:   964
0:51:31.751991 PROGRESS: =========================================================================
0:51:31.764986 INFO: Target number of precursors reached.
0:51:32.205707 INFO: fragments_df: keeping 5000 of 4015675 [sum(precursor_idx_mask)=34767 sum(mass_error_mask)=4015675 stop_rank=5000
0:51:32.626099 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:32.892489 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:33.613779 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:33.614488 INFO: Using score_cutoff 9.394081067848205 (fac=0.99, q=1)
0:51:33.614795 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:33.614875 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:33.614939 INFO: Updating optimization_manager: score_cutoff        : 7.7820813557624815 -> 9.394081067848205
0:51:33.614996 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:33.765950 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:34.099174 INFO: === checking if optimization conditions were reached ===
0:51:34.099475 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:51:34.102701 INFO: Updating optimization_manager: rt_error            : 634.1806348321281 -> 716.4898371331291
0:51:34.102823 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 716.4898.
0:51:34.102899 INFO: ==============================================
0:51:34.102982 INFO: Starting optimization step 9.
0:51:34.103054 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:34.103128 INFO: Using rust extraction backend
0:51:34.103195 PROGRESS: Extracting batch of 250439 precursors
0:51:34.525208 INFO: === Search parameters used ===
0:51:34.525480 INFO: rt_error       : 716.4898371331291
0:51:34.525540 INFO: mobility_error : 0.1
0:51:34.525589 INFO: num_candidates : 3
0:51:34.525634 INFO: ms1_error      : 3
0:51:34.525677 INFO: ms2_error      : 10.0
0:51:34.525719 INFO: fwhm_rt        : 3.0
0:51:34.525762 INFO: quant_window   : 3
0:51:34.525822 INFO: ==============================================
0:51:36.948898 INFO: performing precursor FDR with 40 features
0:51:36.949018 INFO: Decoy channel: -1
0:51:36.949044 INFO: competitive: True
0:51:37.132612 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:37.438134 INFO: Estimating optimal hyperparameters - samples: 599,546, batch_size: 2,455, learning_rate: 7.74e-04
0:51:37.439066 INFO: Using random state 498079 for train-test-split
0:51:50.541710 INFO: Test AUC: 0.612
0:51:50.541848 INFO: Train AUC: 0.624
0:51:50.541884 INFO: AUC difference: 2.00%
0:51:51.027116 INFO: Resetting torch num_threads to 100
0:51:51.112665 PROGRESS: === Extracted 749433 precursors and 4019230 fragments ===
0:51:51.113161 INFO: === FDR correction performed with classifier version 11 ===
0:51:51.114088 PROGRESS: ============================= Precursor FDR =============================
0:51:51.114188 PROGRESS: Total precursors accumulated: 1,538
0:51:51.114250 PROGRESS: Target precursors: 1,523 (99.02%)
0:51:51.114308 PROGRESS: Decoy precursors: 15 (0.98%)
0:51:51.114356 PROGRESS: 
0:51:51.114403 PROGRESS: Precursor Summary:
0:51:51.115742 PROGRESS: Channel   0:	 0.050 FDR: 1,523; 0.010 FDR: 1,523; 0.001 FDR:   788
0:51:51.115833 PROGRESS: 
0:51:51.115894 PROGRESS: Protein Summary:
0:51:51.117616 PROGRESS: Channel   0:	 0.050 FDR: 1,275; 0.010 FDR: 1,275; 0.001 FDR:   686
0:51:51.117707 PROGRESS: =========================================================================
0:51:51.151533 INFO: Target number of precursors reached.
0:51:51.602199 INFO: fragments_df: keeping 5000 of 4019230 [sum(precursor_idx_mask)=36354 sum(mass_error_mask)=4019230 stop_rank=5000
0:51:52.047470 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:52.290190 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:53.011951 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:53.012496 INFO: Using score_cutoff 11.722872376441956 (fac=0.99, q=1)
0:51:53.012848 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:53.012926 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:53.012980 INFO: Updating optimization_manager: score_cutoff        : 9.394081067848205 -> 11.722872376441956
0:51:53.013041 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:53.162486 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:53.496191 INFO: === checking if optimization conditions were reached ===
0:51:53.496504 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
0:51:53.499895 INFO: Updating optimization_manager: rt_error            : 716.4898371331291 -> 723.9631354740652
0:51:53.500019 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 723.9631.
0:51:53.500097 INFO: ==============================================
0:51:53.500186 INFO: Starting optimization step 10.
0:51:53.500260 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:53.500345 INFO: Using rust extraction backend
0:51:53.500420 PROGRESS: Extracting batch of 250439 precursors
0:51:53.927732 INFO: === Search parameters used ===
0:51:53.928007 INFO: rt_error       : 723.9631354740652
0:51:53.928065 INFO: mobility_error : 0.1
0:51:53.928113 INFO: num_candidates : 3
0:51:53.928157 INFO: ms1_error      : 3
0:51:53.928198 INFO: ms2_error      : 10.0
0:51:53.928283 INFO: fwhm_rt        : 3.0
0:51:53.928325 INFO: quant_window   : 3
0:51:53.928365 INFO: ==============================================
0:51:56.457405 INFO: performing precursor FDR with 40 features
0:51:56.457525 INFO: Decoy channel: -1
0:51:56.457568 INFO: competitive: True
0:51:56.648312 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:56.953961 INFO: Estimating optimal hyperparameters - samples: 599,576, batch_size: 2,455, learning_rate: 7.74e-04
0:51:56.955083 INFO: Using random state 498079 for train-test-split
0:52:09.951966 INFO: Test AUC: 0.611
0:52:09.952102 INFO: Train AUC: 0.624
0:52:09.952135 INFO: AUC difference: 2.17%
0:52:10.425798 INFO: Resetting torch num_threads to 100
0:52:10.454647 PROGRESS: === Extracted 749471 precursors and 4021317 fragments ===
0:52:10.455121 INFO: === FDR correction performed with classifier version 11 ===
0:52:10.455770 PROGRESS: ============================= Precursor FDR =============================
0:52:10.455864 PROGRESS: Total precursors accumulated: 1,482
0:52:10.455925 PROGRESS: Target precursors: 1,468 (99.06%)
0:52:10.455978 PROGRESS: Decoy precursors: 14 (0.94%)
0:52:10.456025 PROGRESS: 
0:52:10.456071 PROGRESS: Precursor Summary:
0:52:10.457381 PROGRESS: Channel   0:	 0.050 FDR: 1,468; 0.010 FDR: 1,468; 0.001 FDR:   659
0:52:10.457471 PROGRESS: 
0:52:10.457527 PROGRESS: Protein Summary:
0:52:10.459223 PROGRESS: Channel   0:	 0.050 FDR: 1,229; 0.010 FDR: 1,229; 0.001 FDR:   578
0:52:10.459317 PROGRESS: =========================================================================
0:52:10.472565 INFO: Target number of precursors reached.
0:52:10.920023 INFO: fragments_df: keeping 5000 of 4021317 [sum(precursor_idx_mask)=35359 sum(mass_error_mask)=4021317 stop_rank=5000
0:52:11.328286 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:11.563478 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:12.284239 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:12.284671 INFO: Using score_cutoff 12.260559998989105 (fac=0.99, q=1)
0:52:12.284972 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:12.285050 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:12.285113 INFO: Updating optimization_manager: score_cutoff        : 11.722872376441956 -> 12.260559998989105
0:52:12.285167 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:12.435637 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:12.767128 INFO: === checking if optimization conditions were reached ===
0:52:12.767414 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
0:52:12.768469 INFO: Updating optimization_manager: rt_error            : 723.9631354740652 -> 623.3464049843167
0:52:12.768625 INFO: Updating optimization_manager: classifier_version  : 11 -> 17
0:52:12.768744 INFO: Updating optimization_manager: score_cutoff        : 12.260559998989105 -> 9.503807433700562
0:52:12.768851 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:12.768958 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:12.769064 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 623.3464 found after 11 searches.
0:52:12.769137 INFO: ==============================================
0:52:12.769223 PROGRESS: Optimization finished for rt_error.
0:52:13.168263 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:13.319176 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:13.649920 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:52:13.650206 PROGRESS: ==============================================
0:52:13.650291 PROGRESS: ms2_error      : 10.0000
0:52:13.650357 PROGRESS: rt_error       : 623.3464
0:52:13.650414 PROGRESS: ==============================================
0:52:13.651262 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:21.225522 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:37.464714 INFO: Using rust extraction backend
0:52:37.465264 PROGRESS: Extracting batch of 11997144 precursors
0:52:53.498412 INFO: === Search parameters used ===
0:52:53.498868 INFO: rt_error       : 623.3464049843167
0:52:53.498938 INFO: mobility_error : 0.1
0:52:53.499000 INFO: num_candidates : 3
0:52:53.499050 INFO: ms1_error      : 3
0:52:53.499098 INFO: ms2_error      : 10.0
0:52:53.499146 INFO: fwhm_rt        : 3.0
0:52:53.499192 INFO: quant_window   : 3
0:52:53.499237 INFO: ==============================================
0:53:21.826517 INFO: Removed 6198979 precursors with score below cutoff 9.503807433700562
0:53:45.861423 INFO: performing precursor FDR with 40 features
0:53:45.861602 INFO: Decoy channel: -1
0:53:45.861632 INFO: competitive: True
0:53:48.995376 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:01.170534 INFO: Estimating optimal hyperparameters - samples: 23,833,262, batch_size: 4,096, learning_rate: 1.00e-03
0:54:01.244140 INFO: Using random state 236485 for train-test-split
1:03:54.851923 INFO: Test AUC: 0.622
1:03:54.852267 INFO: Train AUC: 0.622
1:03:54.852311 INFO: AUC difference: 0.06%
1:04:04.472619 INFO: Resetting torch num_threads to 100
1:04:06.537075 PROGRESS: ============================= Precursor FDR =============================
1:04:06.537380 PROGRESS: Total precursors accumulated: 89,260
1:04:06.537465 PROGRESS: Target precursors: 88,377 (99.01%)
1:04:06.537521 PROGRESS: Decoy precursors: 883 (0.99%)
1:04:06.537569 PROGRESS: 
1:04:06.537620 PROGRESS: Precursor Summary:
1:04:06.559972 PROGRESS: Channel   0:	 0.050 FDR: 88,377; 0.010 FDR: 88,377; 0.001 FDR: 51,543
1:04:06.560217 PROGRESS: 
1:04:06.560276 PROGRESS: Protein Summary:
1:04:06.593227 PROGRESS: Channel   0:	 0.050 FDR: 12,907; 0.010 FDR: 12,907; 0.001 FDR: 8,642
1:04:06.593468 PROGRESS: =========================================================================
1:04:06.751822 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
1:04:06.907867 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
1:04:07.132446 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:04:07.645189 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
1:04:07.645333 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant
1:04:07.645431 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:04:07.645609 INFO: Initializing TimingManager
1:04:07.646025 INFO: Initializing RawFileManager
1:04:18.373340 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.
1:04:18.385151 INFO: Determining DIA cycle
1:04:18.402718 INFO: Found cycle with start 0.00 min and length 300.
1:04:18.580040 INFO: RT (min)            : 0.0 - 26.9
1:04:18.580799 INFO: RT duration (sec)   : 1611.2
1:04:18.580831 INFO: RT duration (min)   : 26.9
1:04:18.580854 INFO: Cycle len (scans)   : 300
1:04:18.580875 INFO: Cycle len (sec)     : 1.65
1:04:18.580894 INFO: Number of cycles    : 977
1:04:18.580914 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:04:18.580944 INFO: Creating DIA data object took: 10.934825897216797
1:04:19.320716 INFO: Creating DIA data NG object took: 0.7387604713439941
1:04:20.601467 INFO: Initializing CalibrationManager
1:04:20.601757 INFO: Setting up calibration estimators ..
1:04:20.601819 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:04:20.601894 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'}' ..
1:04:20.602005 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:04:20.602058 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:04:20.602113 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}}' ..
1:04:20.602165 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:04:20.602212 INFO: Done setting up calibration estimators.
1:04:20.602402 INFO: Initializing OptimizationManager
1:04:20.602541 INFO: initial parameter: ms1_error = 3
1:04:20.602594 INFO: initial parameter: ms2_error = 10
1:04:20.602641 INFO: initial parameter: rt_error = 805.5982666015625
1:04:20.602685 INFO: initial parameter: mobility_error = 0.1
1:04:20.602727 INFO: initial parameter: num_candidates = 1
1:04:20.602768 INFO: initial parameter: fwhm_rt = 5
1:04:20.602809 INFO: initial parameter: fwhm_mobility = 0.01
1:04:20.602851 INFO: initial parameter: score_cutoff = 0
1:04:20.602894 INFO: initial parameter: classifier_version = -1
1:04:20.602964 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:04:20.603445 INFO: FDRManager: loading saved state not requested, will be initialized.
1:04:20.603482 INFO: Initializing FDRManager
1:04:20.603517 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:04:21.909583 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:04:22.783368 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:04:22.783782 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
1:04:22.783883 PROGRESS: Starting initial search for precursors.
1:04:22.783969 INFO: Starting optimization step 0.
1:04:22.784034 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:04:22.784093 INFO: Using rust extraction backend
1:04:22.784169 PROGRESS: Extracting batch of 1965 precursors
1:04:22.789058 INFO: === Search parameters used ===
1:04:22.789159 INFO: rt_error       : 805.5982666015625
1:04:22.789210 INFO: mobility_error : 0.1
1:04:22.789256 INFO: num_candidates : 1
1:04:22.789300 INFO: ms1_error      : 3
1:04:22.789352 INFO: ms2_error      : 10
1:04:22.789392 INFO: fwhm_rt        : 5
1:04:22.789432 INFO: quant_window   : 3
1:04:22.789470 INFO: ==============================================
1:04:22.820903 INFO: performing precursor FDR with 40 features
1:04:22.820973 INFO: Decoy channel: -1
1:04:22.820998 INFO: competitive: True
1:04:22.822302 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:22.824201 INFO: Estimating optimal hyperparameters - samples: 1,568, batch_size: 128, learning_rate: 1.77e-04
1:04:22.825053 INFO: Using random state 221872 for train-test-split
1:04:22.982049 INFO: Test AUC: 0.521
1:04:22.982130 INFO: Train AUC: 0.513
1:04:22.982157 INFO: AUC difference: 1.65%
1:04:23.230608 INFO: Resetting torch num_threads to 100
1:04:23.232121 PROGRESS: === Extracted 1961 precursors and 10911 fragments ===
1:04:23.232483 INFO: === FDR correction performed with classifier version -1 ===
1:04:23.232971 PROGRESS: ============================= Precursor FDR =============================
1:04:23.233055 PROGRESS: Total precursors accumulated: 2
1:04:23.233111 PROGRESS: Target precursors: 2 (100.00%)
1:04:23.233158 PROGRESS: Decoy precursors: 0 (0.00%)
1:04:23.233201 PROGRESS: 
1:04:23.233244 PROGRESS: Precursor Summary:
1:04:23.234320 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:04:23.234408 PROGRESS: 
1:04:23.234463 PROGRESS: Protein Summary:
1:04:23.235630 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:04:23.235727 PROGRESS: =========================================================================
1:04:23.235963 INFO: Target number of precursors not reached yet.
1:04:23.322113 INFO: Starting optimization step 1.
1:04:23.322347 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:04:23.322423 INFO: Using rust extraction backend
1:04:23.322481 PROGRESS: Extracting batch of 3948 precursors
1:04:23.334804 INFO: === Search parameters used ===
1:04:23.334943 INFO: rt_error       : 805.5982666015625
1:04:23.334996 INFO: mobility_error : 0.1
1:04:23.335042 INFO: num_candidates : 1
1:04:23.335088 INFO: ms1_error      : 3
1:04:23.335129 INFO: ms2_error      : 10
1:04:23.335169 INFO: fwhm_rt        : 5
1:04:23.335207 INFO: quant_window   : 3
1:04:23.335245 INFO: ==============================================
1:04:23.384918 INFO: performing precursor FDR with 40 features
1:04:23.385007 INFO: Decoy channel: -1
1:04:23.385031 INFO: competitive: True
1:04:23.389562 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:23.392355 INFO: Estimating optimal hyperparameters - samples: 4,719, batch_size: 128, learning_rate: 1.77e-04
1:04:23.392437 INFO: Using random state 96988 for train-test-split
1:04:23.883212 INFO: Test AUC: 0.540
1:04:23.883308 INFO: Train AUC: 0.555
1:04:23.883336 INFO: AUC difference: 2.73%
1:04:24.130039 INFO: Resetting torch num_threads to 100
1:04:24.132879 PROGRESS: === Extracted 5899 precursors and 32981 fragments ===
1:04:24.133250 INFO: === FDR correction performed with classifier version -1 ===
1:04:24.133746 PROGRESS: ============================= Precursor FDR =============================
1:04:24.133830 PROGRESS: Total precursors accumulated: 1
1:04:24.133888 PROGRESS: Target precursors: 1 (100.00%)
1:04:24.133954 PROGRESS: Decoy precursors: 0 (0.00%)
1:04:24.134002 PROGRESS: 
1:04:24.134047 PROGRESS: Precursor Summary:
1:04:24.135112 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:04:24.135196 PROGRESS: 
1:04:24.135250 PROGRESS: Protein Summary:
1:04:24.136398 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:04:24.136481 PROGRESS: =========================================================================
1:04:24.136737 INFO: Target number of precursors not reached yet.
1:04:24.234000 INFO: Starting optimization step 2.
1:04:24.234245 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:04:24.234322 INFO: Using rust extraction backend
1:04:24.234382 PROGRESS: Extracting batch of 7900 precursors
1:04:24.249273 INFO: === Search parameters used ===
1:04:24.249428 INFO: rt_error       : 805.5982666015625
1:04:24.249482 INFO: mobility_error : 0.1
1:04:24.249527 INFO: num_candidates : 1
1:04:24.249570 INFO: ms1_error      : 3
1:04:24.249612 INFO: ms2_error      : 10
1:04:24.249652 INFO: fwhm_rt        : 5
1:04:24.249692 INFO: quant_window   : 3
1:04:24.249732 INFO: ==============================================
1:04:24.331268 INFO: performing precursor FDR with 40 features
1:04:24.331375 INFO: Decoy channel: -1
1:04:24.331400 INFO: competitive: True
1:04:24.338057 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:24.341821 INFO: Estimating optimal hyperparameters - samples: 11,025, batch_size: 128, learning_rate: 1.77e-04
1:04:24.341936 INFO: Using random state 867991 for train-test-split
1:04:25.512095 INFO: Test AUC: 0.539
1:04:25.512206 INFO: Train AUC: 0.578
1:04:25.512235 INFO: AUC difference: 6.83%
1:04:25.512256 WARNING: AUC difference > 5%. This may indicate overfitting.
1:04:25.762730 INFO: Resetting torch num_threads to 100
1:04:25.766715 PROGRESS: === Extracted 13782 precursors and 77336 fragments ===
1:04:25.767115 INFO: === FDR correction performed with classifier version -1 ===
1:04:25.767620 PROGRESS: ============================= Precursor FDR =============================
1:04:25.767702 PROGRESS: Total precursors accumulated: 38
1:04:25.767757 PROGRESS: Target precursors: 38 (100.00%)
1:04:25.767804 PROGRESS: Decoy precursors: 0 (0.00%)
1:04:25.767854 PROGRESS: 
1:04:25.767897 PROGRESS: Precursor Summary:
1:04:25.768944 PROGRESS: Channel   0:	 0.050 FDR:    38; 0.010 FDR:    38; 0.001 FDR:    38
1:04:25.769023 PROGRESS: 
1:04:25.769074 PROGRESS: Protein Summary:
1:04:25.770231 PROGRESS: Channel   0:	 0.050 FDR:    38; 0.010 FDR:    38; 0.001 FDR:    38
1:04:25.770318 PROGRESS: =========================================================================
1:04:25.770636 INFO: Target number of precursors not reached yet.
1:04:25.872755 INFO: Starting optimization step 3.
1:04:25.873004 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:04:25.873080 INFO: Using rust extraction backend
1:04:25.873137 PROGRESS: Extracting batch of 15775 precursors
1:04:25.901617 INFO: === Search parameters used ===
1:04:25.901795 INFO: rt_error       : 805.5982666015625
1:04:25.901846 INFO: mobility_error : 0.1
1:04:25.901890 INFO: num_candidates : 1
1:04:25.901945 INFO: ms1_error      : 3
1:04:25.901987 INFO: ms2_error      : 10
1:04:25.902052 INFO: fwhm_rt        : 5
1:04:25.902094 INFO: quant_window   : 3
1:04:25.902133 INFO: ==============================================
1:04:26.038756 INFO: performing precursor FDR with 40 features
1:04:26.038872 INFO: Decoy channel: -1
1:04:26.038896 INFO: competitive: True
1:04:26.050779 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:26.057869 INFO: Estimating optimal hyperparameters - samples: 23,613, batch_size: 128, learning_rate: 1.77e-04
1:04:26.058157 INFO: Using random state 486094 for train-test-split
1:04:28.482112 INFO: Test AUC: 0.569
1:04:28.482234 INFO: Train AUC: 0.589
1:04:28.482264 INFO: AUC difference: 3.41%
1:04:28.736037 INFO: Resetting torch num_threads to 100
1:04:28.742614 PROGRESS: === Extracted 29517 precursors and 165655 fragments ===
1:04:28.743123 INFO: === FDR correction performed with classifier version -1 ===
1:04:28.743626 PROGRESS: ============================= Precursor FDR =============================
1:04:28.743714 PROGRESS: Total precursors accumulated: 136
1:04:28.743775 PROGRESS: Target precursors: 135 (99.26%)
1:04:28.743828 PROGRESS: Decoy precursors: 1 (0.74%)
1:04:28.743878 PROGRESS: 
1:04:28.743927 PROGRESS: Precursor Summary:
1:04:28.744901 PROGRESS: Channel   0:	 0.050 FDR:   135; 0.010 FDR:   135; 0.001 FDR:   128
1:04:28.744991 PROGRESS: 
1:04:28.745063 PROGRESS: Protein Summary:
1:04:28.746186 PROGRESS: Channel   0:	 0.050 FDR:   130; 0.010 FDR:   130; 0.001 FDR:   124
1:04:28.746276 PROGRESS: =========================================================================
1:04:28.746741 INFO: Target number of precursors not reached yet.
1:04:28.868279 INFO: Starting optimization step 4.
1:04:28.868550 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:04:28.868631 INFO: Using rust extraction backend
1:04:28.868695 PROGRESS: Extracting batch of 31568 precursors
1:04:28.923402 INFO: === Search parameters used ===
1:04:28.923653 INFO: rt_error       : 805.5982666015625
1:04:28.923705 INFO: mobility_error : 0.1
1:04:28.923752 INFO: num_candidates : 1
1:04:28.923795 INFO: ms1_error      : 3
1:04:28.923836 INFO: ms2_error      : 10
1:04:28.923877 INFO: fwhm_rt        : 5
1:04:28.923918 INFO: quant_window   : 3
1:04:28.923957 INFO: ==============================================
1:04:29.145792 INFO: performing precursor FDR with 40 features
1:04:29.145929 INFO: Decoy channel: -1
1:04:29.145957 INFO: competitive: True
1:04:29.169742 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:29.184413 INFO: Estimating optimal hyperparameters - samples: 48,804, batch_size: 199, learning_rate: 2.20e-04
1:04:29.184617 INFO: Using random state 475250 for train-test-split
1:04:32.937406 INFO: Test AUC: 0.580
1:04:32.937528 INFO: Train AUC: 0.605
1:04:32.937557 INFO: AUC difference: 4.00%
1:04:33.200351 INFO: Resetting torch num_threads to 100
1:04:33.220124 PROGRESS: === Extracted 61005 precursors and 342592 fragments ===
1:04:33.220742 INFO: === FDR correction performed with classifier version -1 ===
1:04:33.221313 PROGRESS: ============================= Precursor FDR =============================
1:04:33.221402 PROGRESS: Total precursors accumulated: 286
1:04:33.221461 PROGRESS: Target precursors: 284 (99.30%)
1:04:33.221512 PROGRESS: Decoy precursors: 2 (0.70%)
1:04:33.221559 PROGRESS: 
1:04:33.221604 PROGRESS: Precursor Summary:
1:04:33.222671 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   284; 0.001 FDR:   220
1:04:33.222760 PROGRESS: 
1:04:33.222816 PROGRESS: Protein Summary:
1:04:33.223999 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   265; 0.001 FDR:   211
1:04:33.224098 PROGRESS: =========================================================================
1:04:33.225198 INFO: Target number of precursors not reached yet.
1:04:33.395895 INFO: Starting optimization step 5.
1:04:33.396155 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:04:33.396234 INFO: Using rust extraction backend
1:04:33.396294 PROGRESS: Extracting batch of 63098 precursors
1:04:33.507141 INFO: === Search parameters used ===
1:04:33.507744 INFO: rt_error       : 805.5982666015625
1:04:33.507804 INFO: mobility_error : 0.1
1:04:33.507853 INFO: num_candidates : 1
1:04:33.507899 INFO: ms1_error      : 3
1:04:33.507941 INFO: ms2_error      : 10
1:04:33.507983 INFO: fwhm_rt        : 5
1:04:33.508031 INFO: quant_window   : 3
1:04:33.508074 INFO: ==============================================
1:04:33.897040 INFO: performing precursor FDR with 40 features
1:04:33.897160 INFO: Decoy channel: -1
1:04:33.897185 INFO: competitive: True
1:04:33.950301 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:33.982484 INFO: Estimating optimal hyperparameters - samples: 99,164, batch_size: 406, learning_rate: 3.15e-04
1:04:33.982763 INFO: Using random state 595362 for train-test-split
1:04:38.717882 INFO: Test AUC: 0.584
1:04:38.718033 INFO: Train AUC: 0.610
1:04:38.718065 INFO: AUC difference: 4.22%
1:04:39.005219 INFO: Resetting torch num_threads to 100
1:04:39.054089 PROGRESS: === Extracted 123956 precursors and 697093 fragments ===
1:04:39.054724 INFO: === FDR correction performed with classifier version -1 ===
1:04:39.055352 PROGRESS: ============================= Precursor FDR =============================
1:04:39.055444 PROGRESS: Total precursors accumulated: 665
1:04:39.055513 PROGRESS: Target precursors: 659 (99.10%)
1:04:39.055570 PROGRESS: Decoy precursors: 6 (0.90%)
1:04:39.055641 PROGRESS: 
1:04:39.055696 PROGRESS: Precursor Summary:
1:04:39.056808 PROGRESS: Channel   0:	 0.050 FDR:   659; 0.010 FDR:   659; 0.001 FDR:   182
1:04:39.056894 PROGRESS: 
1:04:39.056966 PROGRESS: Protein Summary:
1:04:39.058304 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   593; 0.001 FDR:   174
1:04:39.058394 PROGRESS: =========================================================================
1:04:39.060349 INFO: Target number of precursors not reached yet.
1:04:39.369263 INFO: Starting optimization step 6.
1:04:39.369539 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:04:39.369624 INFO: Using rust extraction backend
1:04:39.369684 PROGRESS: Extracting batch of 126185 precursors
1:04:39.588508 INFO: === Search parameters used ===
1:04:39.589073 INFO: rt_error       : 805.5982666015625
1:04:39.589143 INFO: mobility_error : 0.1
1:04:39.589195 INFO: num_candidates : 1
1:04:39.589243 INFO: ms1_error      : 3
1:04:39.589290 INFO: ms2_error      : 10
1:04:39.589339 INFO: fwhm_rt        : 5
1:04:39.589383 INFO: quant_window   : 3
1:04:39.589425 INFO: ==============================================
1:04:40.323481 INFO: performing precursor FDR with 40 features
1:04:40.323604 INFO: Decoy channel: -1
1:04:40.323632 INFO: competitive: True
1:04:40.424057 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:40.506703 INFO: Estimating optimal hyperparameters - samples: 199,888, batch_size: 818, learning_rate: 4.47e-04
1:04:40.507190 INFO: Using random state 973807 for train-test-split
1:04:46.844202 INFO: Test AUC: 0.593
1:04:46.844353 INFO: Train AUC: 0.612
1:04:46.844383 INFO: AUC difference: 3.16%
1:04:48.121719 INFO: Resetting torch num_threads to 100
1:04:48.165915 PROGRESS: === Extracted 249860 precursors and 1405142 fragments ===
1:04:48.166586 INFO: === FDR correction performed with classifier version -1 ===
1:04:48.167442 PROGRESS: ============================= Precursor FDR =============================
1:04:48.167531 PROGRESS: Total precursors accumulated: 1,283
1:04:48.167590 PROGRESS: Target precursors: 1,271 (99.06%)
1:04:48.167641 PROGRESS: Decoy precursors: 12 (0.94%)
1:04:48.167688 PROGRESS: 
1:04:48.167732 PROGRESS: Precursor Summary:
1:04:48.169040 PROGRESS: Channel   0:	 0.050 FDR: 1,271; 0.010 FDR: 1,271; 0.001 FDR:   460
1:04:48.169136 PROGRESS: 
1:04:48.169191 PROGRESS: Protein Summary:
1:04:48.170840 PROGRESS: Channel   0:	 0.050 FDR: 1,071; 0.010 FDR: 1,071; 0.001 FDR:   407
1:04:48.170947 PROGRESS: =========================================================================
1:04:48.174666 INFO: Target number of precursors reached.
1:04:48.338350 INFO: fragments_df: keeping 5000 of 1405142 [sum(precursor_idx_mask)=13534 sum(mass_error_mask)=1405142 stop_rank=5000
1:04:48.754948 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:04:48.970161 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:04:49.691229 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:04:49.691669 INFO: Using score_cutoff 11.897697575569152 (fac=0.99, q=1)
1:04:49.691964 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:04:49.692041 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:04:49.692105 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.897697575569152
1:04:49.692163 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:04:49.844302 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:04:50.189457 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:04:50.189757 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:04:50.189864 INFO: Starting optimization step 7.
1:04:50.189956 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:04:50.190040 INFO: Using rust extraction backend
1:04:50.190111 PROGRESS: Extracting batch of 250439 precursors
1:04:50.617365 INFO: === Search parameters used ===
1:04:50.617633 INFO: rt_error       : 805.5982666015625
1:04:50.617689 INFO: mobility_error : 0.1
1:04:50.617758 INFO: num_candidates : 3
1:04:50.617803 INFO: ms1_error      : 3
1:04:50.617843 INFO: ms2_error      : 10
1:04:50.617883 INFO: fwhm_rt        : 3.0
1:04:50.617941 INFO: quant_window   : 3
1:04:50.617985 INFO: ==============================================
1:04:53.194150 INFO: performing precursor FDR with 40 features
1:04:53.194278 INFO: Decoy channel: -1
1:04:53.194305 INFO: competitive: True
1:04:53.379588 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:53.691327 INFO: Estimating optimal hyperparameters - samples: 599,888, batch_size: 2,457, learning_rate: 7.75e-04
1:04:53.692232 INFO: Using random state 785326 for train-test-split
1:05:07.029503 INFO: Test AUC: 0.598
1:05:07.029741 INFO: Train AUC: 0.609
1:05:07.029776 INFO: AUC difference: 1.78%
1:05:07.524887 INFO: Resetting torch num_threads to 100
1:05:07.552677 PROGRESS: === Extracted 749861 precursors and 4047653 fragments ===
1:05:07.553187 INFO: === FDR correction performed with classifier version 6 ===
1:05:07.553921 PROGRESS: ============================= Precursor FDR =============================
1:05:07.554028 PROGRESS: Total precursors accumulated: 1,423
1:05:07.554090 PROGRESS: Target precursors: 1,409 (99.02%)
1:05:07.554141 PROGRESS: Decoy precursors: 14 (0.98%)
1:05:07.554186 PROGRESS: 
1:05:07.554230 PROGRESS: Precursor Summary:
1:05:07.555577 PROGRESS: Channel   0:	 0.050 FDR: 1,409; 0.010 FDR: 1,409; 0.001 FDR:   829
1:05:07.555669 PROGRESS: 
1:05:07.555725 PROGRESS: Protein Summary:
1:05:07.557432 PROGRESS: Channel   0:	 0.050 FDR: 1,174; 0.010 FDR: 1,174; 0.001 FDR:   704
1:05:07.557523 PROGRESS: =========================================================================
1:05:07.570844 INFO: Target number of precursors reached.
1:05:08.011178 INFO: fragments_df: keeping 5000 of 4047653 [sum(precursor_idx_mask)=33690 sum(mass_error_mask)=4047653 stop_rank=5000
1:05:08.519173 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:08.745949 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:09.466328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:09.466763 INFO: Using score_cutoff 11.942324522781371 (fac=0.99, q=1)
1:05:09.467094 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:09.467179 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:09.467235 INFO: Updating optimization_manager: score_cutoff        : 11.897697575569152 -> 11.942324522781371
1:05:09.467290 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:09.616944 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:09.965428 INFO: === checking if optimization conditions were reached ===
1:05:09.968050 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:05:09.968173 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:05:09.968250 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:05:09.968317 INFO: ==============================================
1:05:09.968397 INFO: Starting optimization step 8.
1:05:09.968473 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:05:09.968553 INFO: Using rust extraction backend
1:05:09.968627 PROGRESS: Extracting batch of 250439 precursors
1:05:10.399966 INFO: === Search parameters used ===
1:05:10.400244 INFO: rt_error       : 805.5982666015625
1:05:10.400304 INFO: mobility_error : 0.1
1:05:10.400353 INFO: num_candidates : 3
1:05:10.400397 INFO: ms1_error      : 3
1:05:10.400438 INFO: ms2_error      : 10.0
1:05:10.400480 INFO: fwhm_rt        : 3.0
1:05:10.400521 INFO: quant_window   : 3
1:05:10.400572 INFO: ==============================================
1:05:12.921051 INFO: performing precursor FDR with 40 features
1:05:12.921175 INFO: Decoy channel: -1
1:05:12.921201 INFO: competitive: True
1:05:13.105978 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:13.409319 INFO: Estimating optimal hyperparameters - samples: 599,893, batch_size: 2,457, learning_rate: 7.75e-04
1:05:13.410391 INFO: Using random state 834047 for train-test-split
1:05:26.356859 INFO: Test AUC: 0.603
1:05:26.357083 INFO: Train AUC: 0.614
1:05:26.357117 INFO: AUC difference: 1.78%
1:05:26.851726 INFO: Resetting torch num_threads to 100
1:05:26.879922 PROGRESS: === Extracted 749867 precursors and 4048096 fragments ===
1:05:26.880426 INFO: === FDR correction performed with classifier version 7 ===
1:05:26.881082 PROGRESS: ============================= Precursor FDR =============================
1:05:26.881171 PROGRESS: Total precursors accumulated: 1,452
1:05:26.881231 PROGRESS: Target precursors: 1,438 (99.04%)
1:05:26.881282 PROGRESS: Decoy precursors: 14 (0.96%)
1:05:26.881329 PROGRESS: 
1:05:26.881374 PROGRESS: Precursor Summary:
1:05:26.882755 PROGRESS: Channel   0:	 0.050 FDR: 1,438; 0.010 FDR: 1,438; 0.001 FDR:   817
1:05:26.882847 PROGRESS: 
1:05:26.882904 PROGRESS: Protein Summary:
1:05:26.884611 PROGRESS: Channel   0:	 0.050 FDR: 1,196; 0.010 FDR: 1,196; 0.001 FDR:   701
1:05:26.884701 PROGRESS: =========================================================================
1:05:26.898022 INFO: Target number of precursors reached.
1:05:27.356720 INFO: fragments_df: keeping 5000 of 4048096 [sum(precursor_idx_mask)=34418 sum(mass_error_mask)=4048096 stop_rank=5000
1:05:27.777986 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:28.002776 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:28.722175 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:28.722728 INFO: Using score_cutoff 11.902525829029084 (fac=0.99, q=1)
1:05:28.723089 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:28.723174 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:28.723228 INFO: Updating optimization_manager: score_cutoff        : 11.942324522781371 -> 11.902525829029084
1:05:28.723295 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:28.871752 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:29.223727 INFO: === checking if optimization conditions were reached ===
1:05:29.226284 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:05:29.226406 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:05:29.226485 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:05:29.226557 INFO: ==============================================
1:05:29.226640 INFO: Starting optimization step 9.
1:05:29.226715 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:05:29.226801 INFO: Using rust extraction backend
1:05:29.226878 PROGRESS: Extracting batch of 250439 precursors
1:05:29.647384 INFO: === Search parameters used ===
1:05:29.647642 INFO: rt_error       : 805.5982666015625
1:05:29.647701 INFO: mobility_error : 0.1
1:05:29.647750 INFO: num_candidates : 3
1:05:29.647795 INFO: ms1_error      : 3
1:05:29.647840 INFO: ms2_error      : 10.0
1:05:29.647883 INFO: fwhm_rt        : 3.0
1:05:29.647926 INFO: quant_window   : 3
1:05:29.647968 INFO: ==============================================
1:05:32.069418 INFO: performing precursor FDR with 40 features
1:05:32.069535 INFO: Decoy channel: -1
1:05:32.069561 INFO: competitive: True
1:05:32.260163 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:32.568318 INFO: Estimating optimal hyperparameters - samples: 599,884, batch_size: 2,457, learning_rate: 7.75e-04
1:05:32.569459 INFO: Using random state 784930 for train-test-split
1:05:45.641480 INFO: Test AUC: 0.604
1:05:45.641698 INFO: Train AUC: 0.618
1:05:45.641732 INFO: AUC difference: 2.21%
1:05:46.143682 INFO: Resetting torch num_threads to 100
1:05:46.168302 PROGRESS: === Extracted 749855 precursors and 4048000 fragments ===
1:05:46.168828 INFO: === FDR correction performed with classifier version 8 ===
1:05:46.169526 PROGRESS: ============================= Precursor FDR =============================
1:05:46.169614 PROGRESS: Total precursors accumulated: 1,583
1:05:46.169673 PROGRESS: Target precursors: 1,568 (99.05%)
1:05:46.169727 PROGRESS: Decoy precursors: 15 (0.95%)
1:05:46.169783 PROGRESS: 
1:05:46.169828 PROGRESS: Precursor Summary:
1:05:46.171197 PROGRESS: Channel   0:	 0.050 FDR: 1,568; 0.010 FDR: 1,568; 0.001 FDR:   945
1:05:46.171291 PROGRESS: 
1:05:46.171345 PROGRESS: Protein Summary:
1:05:46.173120 PROGRESS: Channel   0:	 0.050 FDR: 1,297; 0.010 FDR: 1,297; 0.001 FDR:   806
1:05:46.173210 PROGRESS: =========================================================================
1:05:46.186669 INFO: Target number of precursors reached.
1:05:46.656058 INFO: fragments_df: keeping 5000 of 4048000 [sum(precursor_idx_mask)=37222 sum(mass_error_mask)=4048000 stop_rank=5000
1:05:47.095370 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:47.332197 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:48.053878 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:48.054333 INFO: Using score_cutoff 11.920624663066864 (fac=0.99, q=1)
1:05:48.054663 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:48.054738 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:48.054797 INFO: Updating optimization_manager: score_cutoff        : 11.902525829029084 -> 11.920624663066864
1:05:48.054850 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:48.203964 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:48.555364 INFO: === checking if optimization conditions were reached ===
1:05:48.558016 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:05:48.558139 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:05:48.558223 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:05:48.558290 INFO: ==============================================
1:05:48.558368 INFO: Starting optimization step 10.
1:05:48.558436 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:05:48.558513 INFO: Using rust extraction backend
1:05:48.558583 PROGRESS: Extracting batch of 250439 precursors
1:05:48.987187 INFO: === Search parameters used ===
1:05:48.987470 INFO: rt_error       : 805.5982666015625
1:05:48.987525 INFO: mobility_error : 0.1
1:05:48.987571 INFO: num_candidates : 3
1:05:48.987613 INFO: ms1_error      : 3
1:05:48.987654 INFO: ms2_error      : 10.0
1:05:48.987699 INFO: fwhm_rt        : 3.0
1:05:48.987737 INFO: quant_window   : 3
1:05:48.987776 INFO: ==============================================
1:05:51.528003 INFO: performing precursor FDR with 40 features
1:05:51.528128 INFO: Decoy channel: -1
1:05:51.528155 INFO: competitive: True
1:05:51.718388 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:52.026210 INFO: Estimating optimal hyperparameters - samples: 599,886, batch_size: 2,457, learning_rate: 7.75e-04
1:05:52.027164 INFO: Using random state 148125 for train-test-split
1:06:05.177055 INFO: Test AUC: 0.610
1:06:05.177266 INFO: Train AUC: 0.621
1:06:05.177300 INFO: AUC difference: 1.80%
1:06:05.664467 INFO: Resetting torch num_threads to 100
1:06:05.689393 PROGRESS: === Extracted 749858 precursors and 4047708 fragments ===
1:06:05.689886 INFO: === FDR correction performed with classifier version 9 ===
1:06:05.690573 PROGRESS: ============================= Precursor FDR =============================
1:06:05.690663 PROGRESS: Total precursors accumulated: 1,620
1:06:05.690723 PROGRESS: Target precursors: 1,604 (99.01%)
1:06:05.690774 PROGRESS: Decoy precursors: 16 (0.99%)
1:06:05.690822 PROGRESS: 
1:06:05.690871 PROGRESS: Precursor Summary:
1:06:05.692232 PROGRESS: Channel   0:	 0.050 FDR: 1,604; 0.010 FDR: 1,604; 0.001 FDR: 1,107
1:06:05.692320 PROGRESS: 
1:06:05.692378 PROGRESS: Protein Summary:
1:06:05.694361 PROGRESS: Channel   0:	 0.050 FDR: 1,336; 0.010 FDR: 1,336; 0.001 FDR:   931
1:06:05.694460 PROGRESS: =========================================================================
1:06:05.715122 INFO: Target number of precursors reached.
1:06:06.154536 INFO: fragments_df: keeping 5000 of 4047708 [sum(precursor_idx_mask)=38005 sum(mass_error_mask)=4047708 stop_rank=5000
1:06:06.608178 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:06:06.853342 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:06:07.571781 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:06:07.572211 INFO: Using score_cutoff 11.346115571308134 (fac=0.99, q=1)
1:06:07.572537 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:07.572620 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:07.572675 INFO: Updating optimization_manager: score_cutoff        : 11.920624663066864 -> 11.346115571308134
1:06:07.572729 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:07.721039 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:08.057963 INFO: === checking if optimization conditions were reached ===
1:06:08.060580 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:06:08.060692 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:06:08.060766 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:06:08.060834 INFO: ==============================================
1:06:08.060910 INFO: Starting optimization step 11.
1:06:08.060976 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:06:08.061051 INFO: Using rust extraction backend
1:06:08.061120 PROGRESS: Extracting batch of 250439 precursors
1:06:08.490695 INFO: === Search parameters used ===
1:06:08.490960 INFO: rt_error       : 805.5982666015625
1:06:08.491015 INFO: mobility_error : 0.1
1:06:08.491062 INFO: num_candidates : 3
1:06:08.491107 INFO: ms1_error      : 3
1:06:08.491148 INFO: ms2_error      : 10.0
1:06:08.491189 INFO: fwhm_rt        : 3.0
1:06:08.491245 INFO: quant_window   : 3
1:06:08.491285 INFO: ==============================================
1:06:11.891706 INFO: performing precursor FDR with 40 features
1:06:11.891836 INFO: Decoy channel: -1
1:06:11.891863 INFO: competitive: True
1:06:12.081615 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:12.387919 INFO: Estimating optimal hyperparameters - samples: 599,881, batch_size: 2,457, learning_rate: 7.75e-04
1:06:12.388938 INFO: Using random state 848181 for train-test-split
1:06:26.246280 INFO: Test AUC: 0.612
1:06:26.246525 INFO: Train AUC: 0.622
1:06:26.246560 INFO: AUC difference: 1.49%
1:06:26.725046 INFO: Resetting torch num_threads to 100
1:06:26.749885 PROGRESS: === Extracted 749852 precursors and 4047924 fragments ===
1:06:26.750394 INFO: === FDR correction performed with classifier version 10 ===
1:06:26.751118 PROGRESS: ============================= Precursor FDR =============================
1:06:26.751207 PROGRESS: Total precursors accumulated: 1,717
1:06:26.751267 PROGRESS: Target precursors: 1,700 (99.01%)
1:06:26.751318 PROGRESS: Decoy precursors: 17 (0.99%)
1:06:26.751367 PROGRESS: 
1:06:26.751413 PROGRESS: Precursor Summary:
1:06:26.752803 PROGRESS: Channel   0:	 0.050 FDR: 1,700; 0.010 FDR: 1,698; 0.001 FDR: 1,106
1:06:26.752893 PROGRESS: 
1:06:26.752949 PROGRESS: Protein Summary:
1:06:26.754794 PROGRESS: Channel   0:	 0.050 FDR: 1,409; 0.010 FDR: 1,407; 0.001 FDR:   928
1:06:26.754900 PROGRESS: =========================================================================
1:06:26.770609 INFO: Target number of precursors reached.
1:06:27.210214 INFO: fragments_df: keeping 5000 of 4047924 [sum(precursor_idx_mask)=39941 sum(mass_error_mask)=4047924 stop_rank=5000
1:06:27.661372 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:06:27.892982 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:06:28.541440 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:06:28.541884 INFO: Using score_cutoff 10.93530719833374 (fac=0.99, q=1)
1:06:28.542233 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:28.542309 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:28.542361 INFO: Updating optimization_manager: score_cutoff        : 11.346115571308134 -> 10.93530719833374
1:06:28.542429 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:28.689698 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:29.023936 INFO: === checking if optimization conditions were reached ===
1:06:29.026508 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:06:29.026676 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:06:29.026752 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:06:29.026819 INFO: ==============================================
1:06:29.026900 PROGRESS: Optimization finished for ms2_error.
1:06:29.427978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:29.575347 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:29.910256 INFO: Starting optimization step 0.
1:06:29.910556 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:06:29.910652 INFO: Using rust extraction backend
1:06:29.910730 PROGRESS: Extracting batch of 250439 precursors
1:06:30.338145 INFO: === Search parameters used ===
1:06:30.338415 INFO: rt_error       : 805.5982666015625
1:06:30.338491 INFO: mobility_error : 0.1
1:06:30.338538 INFO: num_candidates : 3
1:06:30.338581 INFO: ms1_error      : 3
1:06:30.338621 INFO: ms2_error      : 10.0
1:06:30.338660 INFO: fwhm_rt        : 3.0
1:06:30.338699 INFO: quant_window   : 3
1:06:30.338739 INFO: ==============================================
1:06:32.883679 INFO: performing precursor FDR with 40 features
1:06:32.883805 INFO: Decoy channel: -1
1:06:32.883831 INFO: competitive: True
1:06:33.075197 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:33.380399 INFO: Estimating optimal hyperparameters - samples: 599,887, batch_size: 2,457, learning_rate: 7.75e-04
1:06:33.381275 INFO: Using random state 223535 for train-test-split
1:06:46.082574 INFO: Test AUC: 0.611
1:06:46.082788 INFO: Train AUC: 0.625
1:06:46.082823 INFO: AUC difference: 2.26%
1:06:46.566125 INFO: Resetting torch num_threads to 100
1:06:46.597204 PROGRESS: === Extracted 749859 precursors and 4047956 fragments ===
1:06:46.597703 INFO: === FDR correction performed with classifier version 11 ===
1:06:46.598377 PROGRESS: ============================= Precursor FDR =============================
1:06:46.598471 PROGRESS: Total precursors accumulated: 1,572
1:06:46.598532 PROGRESS: Target precursors: 1,557 (99.05%)
1:06:46.598599 PROGRESS: Decoy precursors: 15 (0.95%)
1:06:46.598647 PROGRESS: 
1:06:46.598693 PROGRESS: Precursor Summary:
1:06:46.600047 PROGRESS: Channel   0:	 0.050 FDR: 1,557; 0.010 FDR: 1,557; 0.001 FDR: 1,106
1:06:46.600139 PROGRESS: 
1:06:46.600196 PROGRESS: Protein Summary:
1:06:46.602005 PROGRESS: Channel   0:	 0.050 FDR: 1,292; 0.010 FDR: 1,292; 0.001 FDR:   935
1:06:46.602111 PROGRESS: =========================================================================
1:06:46.615379 INFO: Target number of precursors reached.
1:06:47.065056 INFO: fragments_df: keeping 5000 of 4047956 [sum(precursor_idx_mask)=36811 sum(mass_error_mask)=4047956 stop_rank=5000
1:06:47.577343 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:06:47.817267 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:06:48.538097 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:06:48.538599 INFO: Using score_cutoff 11.377244967269897 (fac=0.99, q=1)
1:06:48.538944 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:48.539024 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:48.539080 INFO: Updating optimization_manager: score_cutoff        : 10.93530719833374 -> 11.377244967269897
1:06:48.539144 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:48.686755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:49.021467 INFO: === checking if optimization conditions were reached ===
1:06:49.021866 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:06:49.025022 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 353.23389277634715
1:06:49.025163 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 353.2339.
1:06:49.025240 INFO: ==============================================
1:06:49.025326 INFO: Starting optimization step 1.
1:06:49.025401 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:06:49.025480 INFO: Using rust extraction backend
1:06:49.025552 PROGRESS: Extracting batch of 250439 precursors
1:06:49.453726 INFO: === Search parameters used ===
1:06:49.454015 INFO: rt_error       : 353.23389277634715
1:06:49.454074 INFO: mobility_error : 0.1
1:06:49.454121 INFO: num_candidates : 3
1:06:49.454165 INFO: ms1_error      : 3
1:06:49.454207 INFO: ms2_error      : 10.0
1:06:49.454247 INFO: fwhm_rt        : 3.0
1:06:49.454288 INFO: quant_window   : 3
1:06:49.454328 INFO: ==============================================
1:06:51.836304 INFO: performing precursor FDR with 40 features
1:06:51.836418 INFO: Decoy channel: -1
1:06:51.836444 INFO: competitive: True
1:06:52.024612 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:52.322665 INFO: Estimating optimal hyperparameters - samples: 597,637, batch_size: 2,447, learning_rate: 7.73e-04
1:06:52.323799 INFO: Using random state 223535 for train-test-split
1:07:05.347142 INFO: Test AUC: 0.606
1:07:05.347350 INFO: Train AUC: 0.619
1:07:05.347384 INFO: AUC difference: 2.00%
1:07:05.828472 INFO: Resetting torch num_threads to 100
1:07:05.853461 PROGRESS: === Extracted 747047 precursors and 3819505 fragments ===
1:07:05.854000 INFO: === FDR correction performed with classifier version 11 ===
1:07:05.854764 PROGRESS: ============================= Precursor FDR =============================
1:07:05.854864 PROGRESS: Total precursors accumulated: 1,804
1:07:05.854924 PROGRESS: Target precursors: 1,787 (99.06%)
1:07:05.854975 PROGRESS: Decoy precursors: 17 (0.94%)
1:07:05.855022 PROGRESS: 
1:07:05.855066 PROGRESS: Precursor Summary:
1:07:05.856516 PROGRESS: Channel   0:	 0.050 FDR: 1,787; 0.010 FDR: 1,787; 0.001 FDR: 1,170
1:07:05.856610 PROGRESS: 
1:07:05.856666 PROGRESS: Protein Summary:
1:07:05.858556 PROGRESS: Channel   0:	 0.050 FDR: 1,478; 0.010 FDR: 1,478; 0.001 FDR:   977
1:07:05.858654 PROGRESS: =========================================================================
1:07:05.870744 INFO: Target number of precursors reached.
1:07:06.297575 INFO: fragments_df: keeping 5000 of 3819505 [sum(precursor_idx_mask)=41843 sum(mass_error_mask)=3819505 stop_rank=5000
1:07:06.755822 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:07.020531 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:07.742860 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:07:07.743291 INFO: Using score_cutoff 11.320696829223634 (fac=0.99, q=1)
1:07:07.743616 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:07:07.743692 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:07:07.743745 INFO: Updating optimization_manager: score_cutoff        : 11.377244967269897 -> 11.320696829223634
1:07:07.743798 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:07.891968 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:08.228427 INFO: === checking if optimization conditions were reached ===
1:07:08.228758 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:07:08.232110 INFO: Updating optimization_manager: rt_error            : 353.23389277634715 -> 346.96131415915397
1:07:08.232225 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 346.9613.
1:07:08.232302 INFO: ==============================================
1:07:08.232388 INFO: Starting optimization step 2.
1:07:08.232458 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:07:08.232555 INFO: Using rust extraction backend
1:07:08.232628 PROGRESS: Extracting batch of 250439 precursors
1:07:08.665722 INFO: === Search parameters used ===
1:07:08.666010 INFO: rt_error       : 346.96131415915397
1:07:08.666094 INFO: mobility_error : 0.1
1:07:08.666144 INFO: num_candidates : 3
1:07:08.666190 INFO: ms1_error      : 3
1:07:08.666231 INFO: ms2_error      : 10.0
1:07:08.666271 INFO: fwhm_rt        : 3.0
1:07:08.666310 INFO: quant_window   : 3
1:07:08.666350 INFO: ==============================================
1:07:11.016031 INFO: performing precursor FDR with 40 features
1:07:11.016152 INFO: Decoy channel: -1
1:07:11.016179 INFO: competitive: True
1:07:11.198354 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:11.485945 INFO: Estimating optimal hyperparameters - samples: 597,572, batch_size: 2,447, learning_rate: 7.73e-04
1:07:11.487100 INFO: Using random state 223535 for train-test-split
1:07:24.096434 INFO: Test AUC: 0.607
1:07:24.096569 INFO: Train AUC: 0.618
1:07:24.096600 INFO: AUC difference: 1.82%
1:07:24.581125 INFO: Resetting torch num_threads to 100
1:07:24.604723 PROGRESS: === Extracted 746965 precursors and 3812759 fragments ===
1:07:24.605204 INFO: === FDR correction performed with classifier version 11 ===
1:07:24.605848 PROGRESS: ============================= Precursor FDR =============================
1:07:24.605946 PROGRESS: Total precursors accumulated: 1,670
1:07:24.606009 PROGRESS: Target precursors: 1,654 (99.04%)
1:07:24.606060 PROGRESS: Decoy precursors: 16 (0.96%)
1:07:24.606106 PROGRESS: 
1:07:24.606151 PROGRESS: Precursor Summary:
1:07:24.607507 PROGRESS: Channel   0:	 0.050 FDR: 1,654; 0.010 FDR: 1,654; 0.001 FDR: 1,130
1:07:24.607594 PROGRESS: 
1:07:24.607650 PROGRESS: Protein Summary:
1:07:24.609472 PROGRESS: Channel   0:	 0.050 FDR: 1,374; 0.010 FDR: 1,374; 0.001 FDR:   955
1:07:24.609559 PROGRESS: =========================================================================
1:07:24.621672 INFO: Target number of precursors reached.
1:07:25.034649 INFO: fragments_df: keeping 5000 of 3812759 [sum(precursor_idx_mask)=39029 sum(mass_error_mask)=3812759 stop_rank=5000
1:07:25.452066 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:25.699447 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:26.419145 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:07:26.419587 INFO: Using score_cutoff 10.929664229679108 (fac=0.99, q=1)
1:07:26.419889 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:07:26.419968 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:07:26.420023 INFO: Updating optimization_manager: score_cutoff        : 11.320696829223634 -> 10.929664229679108
1:07:26.420078 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:26.574166 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:26.985247 INFO: === checking if optimization conditions were reached ===
1:07:26.985512 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:07:26.988410 INFO: Updating optimization_manager: rt_error            : 346.96131415915397 -> 409.7239945887468
1:07:26.988526 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 409.7240.
1:07:26.988592 INFO: ==============================================
1:07:26.988662 INFO: Starting optimization step 3.
1:07:26.988740 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:07:26.988803 INFO: Using rust extraction backend
1:07:26.988861 PROGRESS: Extracting batch of 250439 precursors
1:07:27.408544 INFO: === Search parameters used ===
1:07:27.408808 INFO: rt_error       : 409.7239945887468
1:07:27.408862 INFO: mobility_error : 0.1
1:07:27.408909 INFO: num_candidates : 3
1:07:27.408953 INFO: ms1_error      : 3
1:07:27.408996 INFO: ms2_error      : 10.0
1:07:27.409038 INFO: fwhm_rt        : 3.0
1:07:27.409080 INFO: quant_window   : 3
1:07:27.409121 INFO: ==============================================
1:07:29.728004 INFO: performing precursor FDR with 40 features
1:07:29.728123 INFO: Decoy channel: -1
1:07:29.728149 INFO: competitive: True
1:07:29.908311 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:30.194300 INFO: Estimating optimal hyperparameters - samples: 598,494, batch_size: 2,451, learning_rate: 7.74e-04
1:07:30.195230 INFO: Using random state 223535 for train-test-split
1:07:43.421763 INFO: Test AUC: 0.609
1:07:43.421998 INFO: Train AUC: 0.620
1:07:43.422033 INFO: AUC difference: 1.82%
1:07:43.895883 INFO: Resetting torch num_threads to 100
1:07:43.925682 PROGRESS: === Extracted 748118 precursors and 3910493 fragments ===
1:07:43.926211 INFO: === FDR correction performed with classifier version 11 ===
1:07:43.926862 PROGRESS: ============================= Precursor FDR =============================
1:07:43.926951 PROGRESS: Total precursors accumulated: 1,530
1:07:43.927011 PROGRESS: Target precursors: 1,515 (99.02%)
1:07:43.927062 PROGRESS: Decoy precursors: 15 (0.98%)
1:07:43.927109 PROGRESS: 
1:07:43.927155 PROGRESS: Precursor Summary:
1:07:43.928505 PROGRESS: Channel   0:	 0.050 FDR: 1,515; 0.010 FDR: 1,515; 0.001 FDR: 1,178
1:07:43.928608 PROGRESS: 
1:07:43.928665 PROGRESS: Protein Summary:
1:07:43.930452 PROGRESS: Channel   0:	 0.050 FDR: 1,272; 0.010 FDR: 1,272; 0.001 FDR:   998
1:07:43.930544 PROGRESS: =========================================================================
1:07:43.944520 INFO: Target number of precursors reached.
1:07:44.431852 INFO: fragments_df: keeping 5000 of 3910493 [sum(precursor_idx_mask)=35669 sum(mass_error_mask)=3910493 stop_rank=5000
1:07:44.892544 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:45.105947 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:45.757532 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:07:45.757979 INFO: Using score_cutoff 10.774368204689026 (fac=0.99, q=1)
1:07:45.758309 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:07:45.758387 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:07:45.758441 INFO: Updating optimization_manager: score_cutoff        : 10.929664229679108 -> 10.774368204689026
1:07:45.758495 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:45.912488 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:46.247313 INFO: === checking if optimization conditions were reached ===
1:07:46.247620 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:07:46.251090 INFO: Updating optimization_manager: rt_error            : 409.7239945887468 -> 501.17825518584266
1:07:46.251239 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 501.1783.
1:07:46.251336 INFO: ==============================================
1:07:46.251434 INFO: Starting optimization step 4.
1:07:46.251510 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:07:46.251590 INFO: Using rust extraction backend
1:07:46.251665 PROGRESS: Extracting batch of 250439 precursors
1:07:46.679108 INFO: === Search parameters used ===
1:07:46.679416 INFO: rt_error       : 501.17825518584266
1:07:46.679475 INFO: mobility_error : 0.1
1:07:46.679525 INFO: num_candidates : 3
1:07:46.679570 INFO: ms1_error      : 3
1:07:46.679617 INFO: ms2_error      : 10.0
1:07:46.679661 INFO: fwhm_rt        : 3.0
1:07:46.679703 INFO: quant_window   : 3
1:07:46.679744 INFO: ==============================================
1:07:49.150819 INFO: performing precursor FDR with 40 features
1:07:49.150944 INFO: Decoy channel: -1
1:07:49.150971 INFO: competitive: True
1:07:49.335891 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:49.620085 INFO: Estimating optimal hyperparameters - samples: 599,152, batch_size: 2,454, learning_rate: 7.74e-04
1:07:49.621223 INFO: Using random state 223535 for train-test-split
1:08:02.482179 INFO: Test AUC: 0.608
1:08:02.482323 INFO: Train AUC: 0.623
1:08:02.482360 INFO: AUC difference: 2.32%
1:08:02.952890 INFO: Resetting torch num_threads to 100
1:08:02.976501 PROGRESS: === Extracted 748941 precursors and 3985626 fragments ===
1:08:02.976964 INFO: === FDR correction performed with classifier version 11 ===
1:08:02.977628 PROGRESS: ============================= Precursor FDR =============================
1:08:02.977715 PROGRESS: Total precursors accumulated: 1,680
1:08:02.977774 PROGRESS: Target precursors: 1,664 (99.05%)
1:08:02.977823 PROGRESS: Decoy precursors: 16 (0.95%)
1:08:02.977870 PROGRESS: 
1:08:02.977933 PROGRESS: Precursor Summary:
1:08:02.979298 PROGRESS: Channel   0:	 0.050 FDR: 1,664; 0.010 FDR: 1,664; 0.001 FDR: 1,160
1:08:02.979383 PROGRESS: 
1:08:02.979437 PROGRESS: Protein Summary:
1:08:02.981210 PROGRESS: Channel   0:	 0.050 FDR: 1,388; 0.010 FDR: 1,388; 0.001 FDR:   977
1:08:02.981296 PROGRESS: =========================================================================
1:08:02.993030 INFO: Target number of precursors reached.
1:08:03.416420 INFO: fragments_df: keeping 5000 of 3985626 [sum(precursor_idx_mask)=39419 sum(mass_error_mask)=3985626 stop_rank=5000
1:08:03.832682 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:08:04.081485 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:08:04.798737 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:08:04.799169 INFO: Using score_cutoff 11.179502046489715 (fac=0.99, q=1)
1:08:04.799481 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:08:04.799559 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:08:04.799614 INFO: Updating optimization_manager: score_cutoff        : 10.774368204689026 -> 11.179502046489715
1:08:04.799669 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:08:04.946770 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:08:05.280818 INFO: === checking if optimization conditions were reached ===
1:08:05.281130 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:08:05.284531 INFO: Updating optimization_manager: rt_error            : 501.17825518584266 -> 578.4397339527053
1:08:05.284712 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 578.4397.
1:08:05.284791 INFO: ==============================================
1:08:05.284875 INFO: Starting optimization step 5.
1:08:05.284945 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:08:05.285020 INFO: Using rust extraction backend
1:08:05.285090 PROGRESS: Extracting batch of 250439 precursors
1:08:05.707051 INFO: === Search parameters used ===
1:08:05.707320 INFO: rt_error       : 578.4397339527053
1:08:05.707377 INFO: mobility_error : 0.1
1:08:05.707426 INFO: num_candidates : 3
1:08:05.707471 INFO: ms1_error      : 3
1:08:05.707528 INFO: ms2_error      : 10.0
1:08:05.707572 INFO: fwhm_rt        : 3.0
1:08:05.707614 INFO: quant_window   : 3
1:08:05.707656 INFO: ==============================================
1:08:08.061043 INFO: performing precursor FDR with 40 features
1:08:08.061166 INFO: Decoy channel: -1
1:08:08.061192 INFO: competitive: True
1:08:08.236562 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:08.527921 INFO: Estimating optimal hyperparameters - samples: 599,487, batch_size: 2,455, learning_rate: 7.74e-04
1:08:08.528939 INFO: Using random state 223535 for train-test-split
1:08:21.508016 INFO: Test AUC: 0.609
1:08:21.508202 INFO: Train AUC: 0.624
1:08:21.508235 INFO: AUC difference: 2.45%
1:08:21.993090 INFO: Resetting torch num_threads to 100
1:08:22.017510 PROGRESS: === Extracted 749359 precursors and 4020469 fragments ===
1:08:22.018009 INFO: === FDR correction performed with classifier version 11 ===
1:08:22.018673 PROGRESS: ============================= Precursor FDR =============================
1:08:22.018764 PROGRESS: Total precursors accumulated: 1,684
1:08:22.018825 PROGRESS: Target precursors: 1,668 (99.05%)
1:08:22.018891 PROGRESS: Decoy precursors: 16 (0.95%)
1:08:22.018938 PROGRESS: 
1:08:22.018981 PROGRESS: Precursor Summary:
1:08:22.020242 PROGRESS: Channel   0:	 0.050 FDR: 1,668; 0.010 FDR: 1,668; 0.001 FDR:     0
1:08:22.020329 PROGRESS: 
1:08:22.020383 PROGRESS: Protein Summary:
1:08:22.021986 PROGRESS: Channel   0:	 0.050 FDR: 1,378; 0.010 FDR: 1,378; 0.001 FDR:     0
1:08:22.022084 PROGRESS: =========================================================================
1:08:22.034717 INFO: Target number of precursors reached.
1:08:22.486559 INFO: fragments_df: keeping 5000 of 4020469 [sum(precursor_idx_mask)=39178 sum(mass_error_mask)=4020469 stop_rank=5000
1:08:22.917923 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:08:23.167471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:08:23.884573 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:08:23.885002 INFO: Using score_cutoff 11.069348987102508 (fac=0.99, q=1)
1:08:23.885327 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:08:23.885405 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:08:23.885459 INFO: Updating optimization_manager: score_cutoff        : 11.179502046489715 -> 11.069348987102508
1:08:23.885512 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:08:24.035929 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:08:24.375434 INFO: === checking if optimization conditions were reached ===
1:08:24.375762 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:08:24.379210 INFO: Updating optimization_manager: rt_error            : 578.4397339527053 -> 515.864200311149
1:08:24.379363 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 515.8642.
1:08:24.379441 INFO: ==============================================
1:08:24.379529 INFO: Starting optimization step 6.
1:08:24.379600 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:08:24.379687 INFO: Using rust extraction backend
1:08:24.379757 PROGRESS: Extracting batch of 250439 precursors
1:08:24.803789 INFO: === Search parameters used ===
1:08:24.804048 INFO: rt_error       : 515.864200311149
1:08:24.804110 INFO: mobility_error : 0.1
1:08:24.804158 INFO: num_candidates : 3
1:08:24.804203 INFO: ms1_error      : 3
1:08:24.804244 INFO: ms2_error      : 10.0
1:08:24.804285 INFO: fwhm_rt        : 3.0
1:08:24.804325 INFO: quant_window   : 3
1:08:24.804365 INFO: ==============================================
1:08:27.158319 INFO: performing precursor FDR with 40 features
1:08:27.158434 INFO: Decoy channel: -1
1:08:27.158460 INFO: competitive: True
1:08:27.324940 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:27.603807 INFO: Estimating optimal hyperparameters - samples: 599,277, batch_size: 2,454, learning_rate: 7.74e-04
1:08:27.604857 INFO: Using random state 223535 for train-test-split
1:08:40.622586 INFO: Test AUC: 0.610
1:08:40.622715 INFO: Train AUC: 0.623
1:08:40.622747 INFO: AUC difference: 1.97%
1:08:41.099073 INFO: Resetting torch num_threads to 100
1:08:41.123011 PROGRESS: === Extracted 749097 precursors and 3997904 fragments ===
1:08:41.123463 INFO: === FDR correction performed with classifier version 11 ===
1:08:41.124139 PROGRESS: ============================= Precursor FDR =============================
1:08:41.124228 PROGRESS: Total precursors accumulated: 1,739
1:08:41.124302 PROGRESS: Target precursors: 1,722 (99.02%)
1:08:41.124355 PROGRESS: Decoy precursors: 17 (0.98%)
1:08:41.124402 PROGRESS: 
1:08:41.124446 PROGRESS: Precursor Summary:
1:08:41.125837 PROGRESS: Channel   0:	 0.050 FDR: 1,722; 0.010 FDR: 1,722; 0.001 FDR: 1,263
1:08:41.125936 PROGRESS: 
1:08:41.125997 PROGRESS: Protein Summary:
1:08:41.127842 PROGRESS: Channel   0:	 0.050 FDR: 1,436; 0.010 FDR: 1,436; 0.001 FDR: 1,058
1:08:41.127945 PROGRESS: =========================================================================
1:08:41.140048 INFO: Target number of precursors reached.
1:08:41.581687 INFO: fragments_df: keeping 5000 of 3997904 [sum(precursor_idx_mask)=40422 sum(mass_error_mask)=3997904 stop_rank=5000
1:08:41.984416 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:08:42.238269 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:08:42.954011 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:08:42.954452 INFO: Using score_cutoff 10.89844018392563 (fac=0.99, q=1)
1:08:42.954751 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:08:42.954826 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:08:42.954878 INFO: Updating optimization_manager: score_cutoff        : 11.069348987102508 -> 10.89844018392563
1:08:42.954930 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:08:43.102090 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:08:43.433189 INFO: === checking if optimization conditions were reached ===
1:08:43.433490 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:08:43.436839 INFO: Updating optimization_manager: rt_error            : 515.864200311149 -> 496.7179830148569
1:08:43.436979 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 496.7180.
1:08:43.437054 INFO: ==============================================
1:08:43.437136 INFO: Starting optimization step 7.
1:08:43.437204 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:08:43.437273 INFO: Using rust extraction backend
1:08:43.437338 PROGRESS: Extracting batch of 250439 precursors
1:08:43.859070 INFO: === Search parameters used ===
1:08:43.859327 INFO: rt_error       : 496.7179830148569
1:08:43.859381 INFO: mobility_error : 0.1
1:08:43.859428 INFO: num_candidates : 3
1:08:43.859470 INFO: ms1_error      : 3
1:08:43.859511 INFO: ms2_error      : 10.0
1:08:43.859553 INFO: fwhm_rt        : 3.0
1:08:43.859594 INFO: quant_window   : 3
1:08:43.859634 INFO: ==============================================
1:08:46.188421 INFO: performing precursor FDR with 40 features
1:08:46.188546 INFO: Decoy channel: -1
1:08:46.188572 INFO: competitive: True
1:08:46.362316 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:46.653220 INFO: Estimating optimal hyperparameters - samples: 599,151, batch_size: 2,454, learning_rate: 7.74e-04
1:08:46.654336 INFO: Using random state 223535 for train-test-split
1:08:59.435286 INFO: Test AUC: 0.610
1:08:59.435481 INFO: Train AUC: 0.623
1:08:59.435515 INFO: AUC difference: 2.02%
1:08:59.913914 INFO: Resetting torch num_threads to 100
1:08:59.937942 PROGRESS: === Extracted 748939 precursors and 3987748 fragments ===
1:08:59.938415 INFO: === FDR correction performed with classifier version 11 ===
1:08:59.939106 PROGRESS: ============================= Precursor FDR =============================
1:08:59.939194 PROGRESS: Total precursors accumulated: 1,727
1:08:59.939254 PROGRESS: Target precursors: 1,710 (99.02%)
1:08:59.939306 PROGRESS: Decoy precursors: 17 (0.98%)
1:08:59.939352 PROGRESS: 
1:08:59.939396 PROGRESS: Precursor Summary:
1:08:59.940772 PROGRESS: Channel   0:	 0.050 FDR: 1,710; 0.010 FDR: 1,710; 0.001 FDR: 1,130
1:08:59.940859 PROGRESS: 
1:08:59.940913 PROGRESS: Protein Summary:
1:08:59.942729 PROGRESS: Channel   0:	 0.050 FDR: 1,427; 0.010 FDR: 1,427; 0.001 FDR:   949
1:08:59.942822 PROGRESS: =========================================================================
1:08:59.954855 INFO: Target number of precursors reached.
1:09:00.396132 INFO: fragments_df: keeping 5000 of 3987748 [sum(precursor_idx_mask)=39864 sum(mass_error_mask)=3987748 stop_rank=5000
1:09:00.821852 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:01.079621 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:01.799381 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:01.799814 INFO: Using score_cutoff 10.369353220367431 (fac=0.99, q=1)
1:09:01.800153 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:01.800233 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:01.800288 INFO: Updating optimization_manager: score_cutoff        : 10.89844018392563 -> 10.369353220367431
1:09:01.800349 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:01.949832 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:02.285185 INFO: === checking if optimization conditions were reached ===
1:09:02.285500 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:09:02.286721 INFO: Updating optimization_manager: rt_error            : 496.7179830148569 -> 353.23389277634715
1:09:02.286872 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
1:09:02.286986 INFO: Updating optimization_manager: score_cutoff        : 10.369353220367431 -> 11.320696829223634
1:09:02.287088 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:02.287189 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:02.287290 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 353.2339 found after 8 searches.
1:09:02.287360 INFO: ==============================================
1:09:02.287440 PROGRESS: Optimization finished for rt_error.
1:09:02.695019 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:02.844612 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:03.184262 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:09:03.184565 PROGRESS: ==============================================
1:09:03.184649 PROGRESS: ms2_error      : 10.0000
1:09:03.184716 PROGRESS: rt_error       : 353.2339
1:09:03.184773 PROGRESS: ==============================================
1:09:03.185648 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:10.655309 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:27.315741 INFO: Using rust extraction backend
1:09:27.316248 PROGRESS: Extracting batch of 11997144 precursors
1:09:43.335224 INFO: === Search parameters used ===
1:09:43.335789 INFO: rt_error       : 353.23389277634715
1:09:43.335857 INFO: mobility_error : 0.1
1:09:43.335932 INFO: num_candidates : 3
1:09:43.335980 INFO: ms1_error      : 3
1:09:43.336026 INFO: ms2_error      : 10.0
1:09:43.336070 INFO: fwhm_rt        : 3.0
1:09:43.336112 INFO: quant_window   : 3
1:09:43.336153 INFO: ==============================================
1:10:07.908128 INFO: Removed 11829941 precursors with score below cutoff 11.320696829223634
1:10:29.200276 INFO: performing precursor FDR with 40 features
1:10:29.200530 INFO: Decoy channel: -1
1:10:29.200575 INFO: competitive: True
1:10:31.941383 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:42.849411 INFO: Estimating optimal hyperparameters - samples: 19,324,305, batch_size: 4,096, learning_rate: 1.00e-03
1:10:42.909088 INFO: Using random state 104027 for train-test-split
1:18:12.725301 INFO: Test AUC: 0.618
1:18:12.726685 INFO: Train AUC: 0.619
1:18:12.726897 INFO: AUC difference: 0.11%
1:18:21.594156 INFO: Resetting torch num_threads to 100
1:18:30.363200 PROGRESS: ============================= Precursor FDR =============================
1:18:30.364599 PROGRESS: Total precursors accumulated: 95,149
1:18:30.364697 PROGRESS: Target precursors: 94,207 (99.01%)
1:18:30.364758 PROGRESS: Decoy precursors: 942 (0.99%)
1:18:30.364811 PROGRESS: 
1:18:30.364868 PROGRESS: Precursor Summary:
1:18:30.486323 PROGRESS: Channel   0:	 0.050 FDR: 94,207; 0.010 FDR: 94,207; 0.001 FDR: 67,049
1:18:30.487337 PROGRESS: 
1:18:30.487516 PROGRESS: Protein Summary:
1:18:30.655262 PROGRESS: Channel   0:	 0.050 FDR: 13,329; 0.010 FDR: 13,329; 0.001 FDR: 9,812
1:18:30.656355 PROGRESS: =========================================================================
1:18:31.326971 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
1:18:31.897382 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
1:18:33.055077 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:18:35.649587 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
1:18:35.650323 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant
1:18:35.650627 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
1:18:35.651215 INFO: Initializing TimingManager
1:18:35.653601 INFO: Initializing RawFileManager
1:19:05.167504 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.
1:19:05.182516 INFO: Determining DIA cycle
1:19:05.201533 INFO: Found cycle with start 0.00 min and length 300.
1:19:05.933291 INFO: RT (min)            : 0.0 - 26.9
1:19:05.933554 INFO: RT duration (sec)   : 1611.2
1:19:05.933588 INFO: RT duration (min)   : 26.9
1:19:05.933612 INFO: Cycle len (scans)   : 300
1:19:05.933634 INFO: Cycle len (sec)     : 1.65
1:19:05.933669 INFO: Number of cycles    : 977
1:19:05.933691 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:19:05.933749 INFO: Creating DIA data object took: 30.279985189437866
1:19:07.964384 INFO: Creating DIA data NG object took: 2.030228614807129
1:19:14.892679 INFO: Initializing CalibrationManager
1:19:14.893452 INFO: Setting up calibration estimators ..
1:19:14.894041 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:19:14.894209 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'}' ..
1:19:14.894381 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:19:14.894459 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:19:14.894526 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}}' ..
1:19:14.894587 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:19:14.894642 INFO: Done setting up calibration estimators.
1:19:14.895538 INFO: Initializing OptimizationManager
1:19:14.895837 INFO: initial parameter: ms1_error = 3
1:19:14.895891 INFO: initial parameter: ms2_error = 10
1:19:14.895947 INFO: initial parameter: rt_error = 805.6002197265625
1:19:14.895993 INFO: initial parameter: mobility_error = 0.1
1:19:14.896039 INFO: initial parameter: num_candidates = 1
1:19:14.896085 INFO: initial parameter: fwhm_rt = 5
1:19:14.896127 INFO: initial parameter: fwhm_mobility = 0.01
1:19:14.896168 INFO: initial parameter: score_cutoff = 0
1:19:14.896215 INFO: initial parameter: classifier_version = -1
1:19:14.896307 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:19:14.897181 INFO: FDRManager: loading saved state not requested, will be initialized.
1:19:14.897231 INFO: Initializing FDRManager
1:19:14.897319 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:19:19.465420 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:19:23.124089 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:19:23.125869 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
1:19:23.126413 PROGRESS: Starting initial search for precursors.
1:19:23.126819 INFO: Starting optimization step 0.
1:19:23.127033 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:19:23.127250 INFO: Using rust extraction backend
1:19:23.127397 PROGRESS: Extracting batch of 1965 precursors
1:19:23.152601 INFO: === Search parameters used ===
1:19:23.153309 INFO: rt_error       : 805.6002197265625
1:19:23.153380 INFO: mobility_error : 0.1
1:19:23.153448 INFO: num_candidates : 1
1:19:23.153494 INFO: ms1_error      : 3
1:19:23.153550 INFO: ms2_error      : 10
1:19:23.153602 INFO: fwhm_rt        : 5
1:19:23.153654 INFO: quant_window   : 3
1:19:23.153694 INFO: ==============================================
1:19:23.303891 INFO: performing precursor FDR with 40 features
1:19:23.304145 INFO: Decoy channel: -1
1:19:23.304174 INFO: competitive: True
1:19:23.306445 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:23.310551 INFO: Estimating optimal hyperparameters - samples: 1,569, batch_size: 128, learning_rate: 1.77e-04
1:19:23.312580 INFO: Using random state 871440 for train-test-split
1:19:23.531318 INFO: Test AUC: 0.514
1:19:23.531576 INFO: Train AUC: 0.576
1:19:23.531611 INFO: AUC difference: 10.82%
1:19:23.531639 WARNING: AUC difference > 5%. This may indicate overfitting.
1:19:23.971053 INFO: Resetting torch num_threads to 100
1:19:23.976081 PROGRESS: === Extracted 1962 precursors and 10917 fragments ===
1:19:23.977397 INFO: === FDR correction performed with classifier version -1 ===
1:19:23.979067 PROGRESS: ============================= Precursor FDR =============================
1:19:23.979390 PROGRESS: Total precursors accumulated: 6
1:19:23.979502 PROGRESS: Target precursors: 6 (100.00%)
1:19:23.979563 PROGRESS: Decoy precursors: 0 (0.00%)
1:19:23.979611 PROGRESS: 
1:19:23.979658 PROGRESS: Precursor Summary:
1:19:23.981783 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:19:23.982046 PROGRESS: 
1:19:23.982130 PROGRESS: Protein Summary:
1:19:23.984366 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
1:19:23.984579 PROGRESS: =========================================================================
1:19:23.985547 INFO: Target number of precursors not reached yet.
1:19:24.090259 INFO: Starting optimization step 1.
1:19:24.090863 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:19:24.091050 INFO: Using rust extraction backend
1:19:24.091135 PROGRESS: Extracting batch of 3948 precursors
1:19:24.115476 INFO: === Search parameters used ===
1:19:24.116096 INFO: rt_error       : 805.6002197265625
1:19:24.116176 INFO: mobility_error : 0.1
1:19:24.116230 INFO: num_candidates : 1
1:19:24.116276 INFO: ms1_error      : 3
1:19:24.116320 INFO: ms2_error      : 10
1:19:24.116361 INFO: fwhm_rt        : 5
1:19:24.116402 INFO: quant_window   : 3
1:19:24.116443 INFO: ==============================================
1:19:24.243339 INFO: performing precursor FDR with 40 features
1:19:24.243586 INFO: Decoy channel: -1
1:19:24.243614 INFO: competitive: True
1:19:24.263198 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:24.271469 INFO: Estimating optimal hyperparameters - samples: 4,724, batch_size: 128, learning_rate: 1.77e-04
1:19:24.271831 INFO: Using random state 345034 for train-test-split
1:19:24.868133 INFO: Test AUC: 0.545
1:19:24.868410 INFO: Train AUC: 0.564
1:19:24.868445 INFO: AUC difference: 3.46%
1:19:25.320922 INFO: Resetting torch num_threads to 100
1:19:25.335604 PROGRESS: === Extracted 5905 precursors and 32898 fragments ===
1:19:25.337354 INFO: === FDR correction performed with classifier version -1 ===
1:19:25.339509 PROGRESS: ============================= Precursor FDR =============================
1:19:25.339867 PROGRESS: Total precursors accumulated: 20
1:19:25.339987 PROGRESS: Target precursors: 20 (100.00%)
1:19:25.340045 PROGRESS: Decoy precursors: 0 (0.00%)
1:19:25.340141 PROGRESS: 
1:19:25.340195 PROGRESS: Precursor Summary:
1:19:25.342827 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
1:19:25.343097 PROGRESS: 
1:19:25.343164 PROGRESS: Protein Summary:
1:19:25.345403 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
1:19:25.345652 PROGRESS: =========================================================================
1:19:25.347408 INFO: Target number of precursors not reached yet.
1:19:25.480082 INFO: Starting optimization step 2.
1:19:25.480745 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:19:25.480891 INFO: Using rust extraction backend
1:19:25.481006 PROGRESS: Extracting batch of 7900 precursors
1:19:25.539917 INFO: === Search parameters used ===
1:19:25.540703 INFO: rt_error       : 805.6002197265625
1:19:25.540766 INFO: mobility_error : 0.1
1:19:25.540815 INFO: num_candidates : 1
1:19:25.540862 INFO: ms1_error      : 3
1:19:25.540906 INFO: ms2_error      : 10
1:19:25.540951 INFO: fwhm_rt        : 5
1:19:25.540994 INFO: quant_window   : 3
1:19:25.541038 INFO: ==============================================
1:19:25.768969 INFO: performing precursor FDR with 40 features
1:19:25.769284 INFO: Decoy channel: -1
1:19:25.769318 INFO: competitive: True
1:19:25.805558 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:25.821125 INFO: Estimating optimal hyperparameters - samples: 11,032, batch_size: 128, learning_rate: 1.77e-04
1:19:25.821540 INFO: Using random state 897128 for train-test-split
1:19:27.618631 INFO: Test AUC: 0.547
1:19:27.619044 INFO: Train AUC: 0.577
1:19:27.619094 INFO: AUC difference: 5.34%
1:19:27.619126 WARNING: AUC difference > 5%. This may indicate overfitting.
1:19:28.084163 INFO: Resetting torch num_threads to 100
1:19:28.104842 PROGRESS: === Extracted 13790 precursors and 76900 fragments ===
1:19:28.106480 INFO: === FDR correction performed with classifier version -1 ===
1:19:28.108253 PROGRESS: ============================= Precursor FDR =============================
1:19:28.108559 PROGRESS: Total precursors accumulated: 47
1:19:28.108690 PROGRESS: Target precursors: 47 (100.00%)
1:19:28.108772 PROGRESS: Decoy precursors: 0 (0.00%)
1:19:28.108857 PROGRESS: 
1:19:28.108908 PROGRESS: Precursor Summary:
1:19:28.111642 PROGRESS: Channel   0:	 0.050 FDR:    47; 0.010 FDR:    47; 0.001 FDR:    47
1:19:28.111926 PROGRESS: 
1:19:28.112008 PROGRESS: Protein Summary:
1:19:28.114538 PROGRESS: Channel   0:	 0.050 FDR:    46; 0.010 FDR:    46; 0.001 FDR:    46
1:19:28.114794 PROGRESS: =========================================================================
1:19:28.117573 INFO: Target number of precursors not reached yet.
1:19:28.283854 INFO: Starting optimization step 3.
1:19:28.284656 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:19:28.284835 INFO: Using rust extraction backend
1:19:28.284944 PROGRESS: Extracting batch of 15775 precursors
1:19:28.384517 INFO: === Search parameters used ===
1:19:28.385293 INFO: rt_error       : 805.6002197265625
1:19:28.385419 INFO: mobility_error : 0.1
1:19:28.385476 INFO: num_candidates : 1
1:19:28.385521 INFO: ms1_error      : 3
1:19:28.385565 INFO: ms2_error      : 10
1:19:28.385639 INFO: fwhm_rt        : 5
1:19:28.385690 INFO: quant_window   : 3
1:19:28.385739 INFO: ==============================================
1:19:28.717104 INFO: performing precursor FDR with 40 features
1:19:28.717378 INFO: Decoy channel: -1
1:19:28.717412 INFO: competitive: True
1:19:28.768065 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:28.797594 INFO: Estimating optimal hyperparameters - samples: 23,624, batch_size: 128, learning_rate: 1.77e-04
1:19:28.798251 INFO: Using random state 529516 for train-test-split
1:19:32.334463 INFO: Test AUC: 0.558
1:19:32.334807 INFO: Train AUC: 0.586
1:19:32.334855 INFO: AUC difference: 4.75%
1:19:32.817471 INFO: Resetting torch num_threads to 100
1:19:32.859308 PROGRESS: === Extracted 29531 precursors and 165084 fragments ===
1:19:32.861008 INFO: === FDR correction performed with classifier version -1 ===
1:19:32.863295 PROGRESS: ============================= Precursor FDR =============================
1:19:32.863821 PROGRESS: Total precursors accumulated: 84
1:19:32.863980 PROGRESS: Target precursors: 84 (100.00%)
1:19:32.864047 PROGRESS: Decoy precursors: 0 (0.00%)
1:19:32.864103 PROGRESS: 
1:19:32.864156 PROGRESS: Precursor Summary:
1:19:32.867015 PROGRESS: Channel   0:	 0.050 FDR:    84; 0.010 FDR:    84; 0.001 FDR:    84
1:19:32.867311 PROGRESS: 
1:19:32.867388 PROGRESS: Protein Summary:
1:19:32.869939 PROGRESS: Channel   0:	 0.050 FDR:    83; 0.010 FDR:    83; 0.001 FDR:    83
1:19:32.870267 PROGRESS: =========================================================================
1:19:32.873751 INFO: Target number of precursors not reached yet.
1:19:33.101619 INFO: Starting optimization step 4.
1:19:33.102468 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:19:33.102627 INFO: Using rust extraction backend
1:19:33.102736 PROGRESS: Extracting batch of 31568 precursors
1:19:33.337044 INFO: === Search parameters used ===
1:19:33.337816 INFO: rt_error       : 805.6002197265625
1:19:33.337886 INFO: mobility_error : 0.1
1:19:33.338101 INFO: num_candidates : 1
1:19:33.338163 INFO: ms1_error      : 3
1:19:33.338220 INFO: ms2_error      : 10
1:19:33.338311 INFO: fwhm_rt        : 5
1:19:33.338365 INFO: quant_window   : 3
1:19:33.338418 INFO: ==============================================
1:19:33.887460 INFO: performing precursor FDR with 40 features
1:19:33.887798 INFO: Decoy channel: -1
1:19:33.887830 INFO: competitive: True
1:19:33.996889 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:34.084233 INFO: Estimating optimal hyperparameters - samples: 48,824, batch_size: 199, learning_rate: 2.20e-04
1:19:34.084916 INFO: Using random state 756508 for train-test-split
1:19:40.624020 INFO: Test AUC: 0.575
1:19:40.624495 INFO: Train AUC: 0.609
1:19:40.624541 INFO: AUC difference: 5.54%
1:19:40.624584 WARNING: AUC difference > 5%. This may indicate overfitting.
1:19:47.525468 INFO: Resetting torch num_threads to 100
1:19:47.606052 PROGRESS: === Extracted 61031 precursors and 341431 fragments ===
1:19:47.607938 INFO: === FDR correction performed with classifier version -1 ===
1:19:47.610529 PROGRESS: ============================= Precursor FDR =============================
1:19:47.610966 PROGRESS: Total precursors accumulated: 309
1:19:47.611038 PROGRESS: Target precursors: 306 (99.03%)
1:19:47.611095 PROGRESS: Decoy precursors: 3 (0.97%)
1:19:47.611151 PROGRESS: 
1:19:47.611207 PROGRESS: Precursor Summary:
1:19:47.613426 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   306; 0.001 FDR:   211
1:19:47.613704 PROGRESS: 
1:19:47.613764 PROGRESS: Protein Summary:
1:19:47.615554 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   285; 0.001 FDR:   200
1:19:47.615787 PROGRESS: =========================================================================
1:19:47.621728 INFO: Target number of precursors not reached yet.
1:19:48.184108 INFO: Starting optimization step 5.
1:19:48.184922 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:19:48.185141 INFO: Using rust extraction backend
1:19:48.185260 PROGRESS: Extracting batch of 63098 precursors
1:19:48.565102 INFO: === Search parameters used ===
1:19:48.565984 INFO: rt_error       : 805.6002197265625
1:19:48.566119 INFO: mobility_error : 0.1
1:19:48.566187 INFO: num_candidates : 1
1:19:48.566238 INFO: ms1_error      : 3
1:19:48.566286 INFO: ms2_error      : 10
1:19:48.566330 INFO: fwhm_rt        : 5
1:19:48.566374 INFO: quant_window   : 3
1:19:48.566418 INFO: ==============================================
1:19:49.932201 INFO: performing precursor FDR with 40 features
1:19:49.932558 INFO: Decoy channel: -1
1:19:49.932590 INFO: competitive: True
1:19:50.149088 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:50.405360 INFO: Estimating optimal hyperparameters - samples: 99,178, batch_size: 406, learning_rate: 3.15e-04
1:19:50.407707 INFO: Using random state 609093 for train-test-split
1:19:59.433146 INFO: Test AUC: 0.587
1:19:59.433588 INFO: Train AUC: 0.613
1:19:59.433640 INFO: AUC difference: 4.30%
1:19:59.940498 INFO: Resetting torch num_threads to 100
1:20:00.065140 PROGRESS: === Extracted 123973 precursors and 694515 fragments ===
1:20:00.067268 INFO: === FDR correction performed with classifier version -1 ===
1:20:00.069787 PROGRESS: ============================= Precursor FDR =============================
1:20:00.070363 PROGRESS: Total precursors accumulated: 728
1:20:00.070442 PROGRESS: Target precursors: 721 (99.04%)
1:20:00.070499 PROGRESS: Decoy precursors: 7 (0.96%)
1:20:00.070549 PROGRESS: 
1:20:00.070618 PROGRESS: Precursor Summary:
1:20:00.073920 PROGRESS: Channel   0:	 0.050 FDR:   721; 0.010 FDR:   721; 0.001 FDR:   514
1:20:00.074547 PROGRESS: 
1:20:00.074612 PROGRESS: Protein Summary:
1:20:00.077377 PROGRESS: Channel   0:	 0.050 FDR:   650; 0.010 FDR:   650; 0.001 FDR:   470
1:20:00.077957 PROGRESS: =========================================================================
1:20:00.086730 INFO: Target number of precursors not reached yet.
1:20:00.857406 INFO: Starting optimization step 6.
1:20:00.858150 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:20:00.858397 INFO: Using rust extraction backend
1:20:00.858531 PROGRESS: Extracting batch of 126185 precursors
1:20:01.552902 INFO: === Search parameters used ===
1:20:01.553593 INFO: rt_error       : 805.6002197265625
1:20:01.553718 INFO: mobility_error : 0.1
1:20:01.553780 INFO: num_candidates : 1
1:20:01.553829 INFO: ms1_error      : 3
1:20:01.553875 INFO: ms2_error      : 10
1:20:01.554020 INFO: fwhm_rt        : 5
1:20:01.554088 INFO: quant_window   : 3
1:20:01.554132 INFO: ==============================================
1:20:03.802409 INFO: performing precursor FDR with 40 features
1:20:03.802686 INFO: Decoy channel: -1
1:20:03.802716 INFO: competitive: True
1:20:04.236532 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:04.619366 INFO: Estimating optimal hyperparameters - samples: 199,910, batch_size: 818, learning_rate: 4.47e-04
1:20:04.621833 INFO: Using random state 984688 for train-test-split
1:20:15.543087 INFO: Test AUC: 0.592
1:20:15.543461 INFO: Train AUC: 0.611
1:20:15.543508 INFO: AUC difference: 3.09%
1:20:16.044984 INFO: Resetting torch num_threads to 100
1:20:16.273332 PROGRESS: === Extracted 249888 precursors and 1400176 fragments ===
1:20:16.275063 INFO: === FDR correction performed with classifier version -1 ===
1:20:16.277787 PROGRESS: ============================= Precursor FDR =============================
1:20:16.278018 PROGRESS: Total precursors accumulated: 1,491
1:20:16.278100 PROGRESS: Target precursors: 1,477 (99.06%)
1:20:16.278175 PROGRESS: Decoy precursors: 14 (0.94%)
1:20:16.278231 PROGRESS: 
1:20:16.278283 PROGRESS: Precursor Summary:
1:20:16.280841 PROGRESS: Channel   0:	 0.050 FDR: 1,477; 0.010 FDR: 1,477; 0.001 FDR:     0
1:20:16.281010 PROGRESS: 
1:20:16.281070 PROGRESS: Protein Summary:
1:20:16.283379 PROGRESS: Channel   0:	 0.050 FDR: 1,229; 0.010 FDR: 1,229; 0.001 FDR:     0
1:20:16.283562 PROGRESS: =========================================================================
1:20:16.297957 INFO: Target number of precursors reached.
1:20:16.499511 INFO: fragments_df: keeping 5000 of 1400176 [sum(precursor_idx_mask)=15374 sum(mass_error_mask)=1400176 stop_rank=5000
1:20:17.618845 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:18.641724 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:19.532456 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:20:19.533726 INFO: Using score_cutoff 11.298797747039794 (fac=0.99, q=1)
1:20:19.534549 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:20:19.534648 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:20:19.534708 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.298797747039794
1:20:19.534817 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:19.765030 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:20.503776 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:20:20.504522 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:20:20.504725 INFO: Starting optimization step 7.
1:20:20.504810 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:20.504933 INFO: Using rust extraction backend
1:20:20.505042 PROGRESS: Extracting batch of 250439 precursors
1:20:21.638889 INFO: === Search parameters used ===
1:20:21.639463 INFO: rt_error       : 805.6002197265625
1:20:21.639599 INFO: mobility_error : 0.1
1:20:21.639669 INFO: num_candidates : 3
1:20:21.639720 INFO: ms1_error      : 3
1:20:21.639767 INFO: ms2_error      : 10
1:20:21.639847 INFO: fwhm_rt        : 3.0
1:20:21.639893 INFO: quant_window   : 3
1:20:21.639953 INFO: ==============================================
1:20:28.857155 INFO: performing precursor FDR with 40 features
1:20:28.857485 INFO: Decoy channel: -1
1:20:28.857519 INFO: competitive: True
1:20:29.577915 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:30.691298 INFO: Estimating optimal hyperparameters - samples: 599,832, batch_size: 2,456, learning_rate: 7.74e-04
1:20:30.698465 INFO: Using random state 494858 for train-test-split
1:20:52.829499 INFO: Test AUC: 0.598
1:20:52.830008 INFO: Train AUC: 0.607
1:20:52.830057 INFO: AUC difference: 1.52%
1:20:53.623801 INFO: Resetting torch num_threads to 100
1:20:53.708653 PROGRESS: === Extracted 749791 precursors and 4032078 fragments ===
1:20:53.710067 INFO: === FDR correction performed with classifier version 6 ===
1:20:53.712110 PROGRESS: ============================= Precursor FDR =============================
1:20:53.712293 PROGRESS: Total precursors accumulated: 1,335
1:20:53.712390 PROGRESS: Target precursors: 1,322 (99.03%)
1:20:53.712449 PROGRESS: Decoy precursors: 13 (0.97%)
1:20:53.712497 PROGRESS: 
1:20:53.712544 PROGRESS: Precursor Summary:
1:20:53.714690 PROGRESS: Channel   0:	 0.050 FDR: 1,322; 0.010 FDR: 1,322; 0.001 FDR:     0
1:20:53.714871 PROGRESS: 
1:20:53.714927 PROGRESS: Protein Summary:
1:20:53.716923 PROGRESS: Channel   0:	 0.050 FDR: 1,102; 0.010 FDR: 1,102; 0.001 FDR:     0
1:20:53.717071 PROGRESS: =========================================================================
1:20:53.767489 INFO: Target number of precursors reached.
1:20:54.276641 INFO: fragments_df: keeping 5000 of 4032078 [sum(precursor_idx_mask)=31877 sum(mass_error_mask)=4032078 stop_rank=5000
1:20:55.877557 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:56.290040 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:57.370109 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:57.371655 INFO: Using score_cutoff 11.97706080751419 (fac=0.99, q=1)
1:20:57.373105 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:57.373413 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:57.373531 INFO: Updating optimization_manager: score_cutoff        : 11.298797747039794 -> 11.97706080751419
1:20:57.373634 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:57.582344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:58.191635 INFO: === checking if optimization conditions were reached ===
1:20:58.201093 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:20:58.201630 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:20:58.201930 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:20:58.202229 INFO: ==============================================
1:20:58.202545 INFO: Starting optimization step 8.
1:20:58.202842 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:20:58.203175 INFO: Using rust extraction backend
1:20:58.203416 PROGRESS: Extracting batch of 250439 precursors
1:20:59.698437 INFO: === Search parameters used ===
1:20:59.699145 INFO: rt_error       : 805.6002197265625
1:20:59.699217 INFO: mobility_error : 0.1
1:20:59.699277 INFO: num_candidates : 3
1:20:59.699330 INFO: ms1_error      : 3
1:20:59.699379 INFO: ms2_error      : 10.0
1:20:59.699429 INFO: fwhm_rt        : 3.0
1:20:59.699475 INFO: quant_window   : 3
1:20:59.699519 INFO: ==============================================
1:21:08.829489 INFO: performing precursor FDR with 40 features
1:21:08.829787 INFO: Decoy channel: -1
1:21:08.829818 INFO: competitive: True
1:21:09.588761 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:10.792938 INFO: Estimating optimal hyperparameters - samples: 599,826, batch_size: 2,456, learning_rate: 7.74e-04
1:21:10.801313 INFO: Using random state 961143 for train-test-split
1:21:40.330531 INFO: Test AUC: 0.607
1:21:40.331036 INFO: Train AUC: 0.615
1:21:40.331127 INFO: AUC difference: 1.32%
1:21:41.144691 INFO: Resetting torch num_threads to 100
1:21:41.230601 PROGRESS: === Extracted 749783 precursors and 4032217 fragments ===
1:21:41.232045 INFO: === FDR correction performed with classifier version 7 ===
1:21:41.234551 PROGRESS: ============================= Precursor FDR =============================
1:21:41.234782 PROGRESS: Total precursors accumulated: 1,471
1:21:41.234854 PROGRESS: Target precursors: 1,457 (99.05%)
1:21:41.234911 PROGRESS: Decoy precursors: 14 (0.95%)
1:21:41.234970 PROGRESS: 
1:21:41.235016 PROGRESS: Precursor Summary:
1:21:41.238129 PROGRESS: Channel   0:	 0.050 FDR: 1,457; 0.010 FDR: 1,457; 0.001 FDR:   682
1:21:41.238470 PROGRESS: 
1:21:41.238528 PROGRESS: Protein Summary:
1:21:41.241325 PROGRESS: Channel   0:	 0.050 FDR: 1,211; 0.010 FDR: 1,211; 0.001 FDR:   599
1:21:41.241611 PROGRESS: =========================================================================
1:21:41.294468 INFO: Target number of precursors reached.
1:21:41.828711 INFO: fragments_df: keeping 5000 of 4032217 [sum(precursor_idx_mask)=34917 sum(mass_error_mask)=4032217 stop_rank=5000
1:21:43.389548 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:43.831841 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:44.842170 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:44.844010 INFO: Using score_cutoff 11.458646847152709 (fac=0.99, q=1)
1:21:44.845127 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:44.845315 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:44.845387 INFO: Updating optimization_manager: score_cutoff        : 11.97706080751419 -> 11.458646847152709
1:21:44.845526 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:45.079000 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:45.731334 INFO: === checking if optimization conditions were reached ===
1:21:45.736822 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:21:45.737292 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:21:45.737396 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:21:45.737502 INFO: ==============================================
1:21:45.737595 INFO: Starting optimization step 9.
1:21:45.737695 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:21:45.737828 INFO: Using rust extraction backend
1:21:45.737972 PROGRESS: Extracting batch of 250439 precursors
1:21:47.066446 INFO: === Search parameters used ===
1:21:47.067156 INFO: rt_error       : 805.6002197265625
1:21:47.067221 INFO: mobility_error : 0.1
1:21:47.067272 INFO: num_candidates : 3
1:21:47.067340 INFO: ms1_error      : 3
1:21:47.067401 INFO: ms2_error      : 10.0
1:21:47.067446 INFO: fwhm_rt        : 3.0
1:21:47.067489 INFO: quant_window   : 3
1:21:47.067534 INFO: ==============================================
1:21:56.519833 INFO: performing precursor FDR with 40 features
1:21:56.520193 INFO: Decoy channel: -1
1:21:56.520224 INFO: competitive: True
1:21:57.342036 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:58.535678 INFO: Estimating optimal hyperparameters - samples: 599,839, batch_size: 2,456, learning_rate: 7.74e-04
1:21:58.543977 INFO: Using random state 916853 for train-test-split
1:22:30.866250 INFO: Test AUC: 0.609
1:22:30.866729 INFO: Train AUC: 0.618
1:22:30.866777 INFO: AUC difference: 1.54%
1:22:31.769318 INFO: Resetting torch num_threads to 100
1:22:31.870571 PROGRESS: === Extracted 749799 precursors and 4032302 fragments ===
1:22:31.872072 INFO: === FDR correction performed with classifier version 8 ===
1:22:31.874135 PROGRESS: ============================= Precursor FDR =============================
1:22:31.874295 PROGRESS: Total precursors accumulated: 1,401
1:22:31.874365 PROGRESS: Target precursors: 1,388 (99.07%)
1:22:31.874421 PROGRESS: Decoy precursors: 13 (0.93%)
1:22:31.874470 PROGRESS: 
1:22:31.874519 PROGRESS: Precursor Summary:
1:22:31.876535 PROGRESS: Channel   0:	 0.050 FDR: 1,388; 0.010 FDR: 1,388; 0.001 FDR:     0
1:22:31.876724 PROGRESS: 
1:22:31.876782 PROGRESS: Protein Summary:
1:22:31.878896 PROGRESS: Channel   0:	 0.050 FDR: 1,157; 0.010 FDR: 1,157; 0.001 FDR:     0
1:22:31.879046 PROGRESS: =========================================================================
1:22:31.930012 INFO: Target number of precursors reached.
1:22:32.419497 INFO: fragments_df: keeping 5000 of 4032302 [sum(precursor_idx_mask)=33372 sum(mass_error_mask)=4032302 stop_rank=5000
1:22:33.796513 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:34.802901 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:36.662104 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:36.664134 INFO: Using score_cutoff 11.757393312835694 (fac=0.99, q=1)
1:22:36.666194 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:36.666643 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:36.667019 INFO: Updating optimization_manager: score_cutoff        : 11.458646847152709 -> 11.757393312835694
1:22:36.667333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:36.939034 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:37.605183 INFO: === checking if optimization conditions were reached ===
1:22:37.612380 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:22:37.613110 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:22:37.613336 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:22:37.613466 INFO: ==============================================
1:22:37.613588 INFO: Starting optimization step 10.
1:22:37.613699 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:37.613849 INFO: Using rust extraction backend
1:22:37.613993 PROGRESS: Extracting batch of 250439 precursors
1:22:38.809769 INFO: === Search parameters used ===
1:22:38.811249 INFO: rt_error       : 805.6002197265625
1:22:38.811412 INFO: mobility_error : 0.1
1:22:38.811477 INFO: num_candidates : 3
1:22:38.811528 INFO: ms1_error      : 3
1:22:38.811575 INFO: ms2_error      : 10.0
1:22:38.811621 INFO: fwhm_rt        : 3.0
1:22:38.811667 INFO: quant_window   : 3
1:22:38.811711 INFO: ==============================================
1:22:46.987617 INFO: performing precursor FDR with 40 features
1:22:46.987936 INFO: Decoy channel: -1
1:22:46.987983 INFO: competitive: True
1:22:47.786002 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:49.008688 INFO: Estimating optimal hyperparameters - samples: 599,835, batch_size: 2,456, learning_rate: 7.74e-04
1:22:49.015009 INFO: Using random state 696210 for train-test-split
1:23:18.707425 INFO: Test AUC: 0.609
1:23:18.707929 INFO: Train AUC: 0.621
1:23:18.707980 INFO: AUC difference: 2.04%
1:23:19.482262 INFO: Resetting torch num_threads to 100
1:23:19.565669 PROGRESS: === Extracted 749794 precursors and 4031999 fragments ===
1:23:19.567004 INFO: === FDR correction performed with classifier version 9 ===
1:23:19.568895 PROGRESS: ============================= Precursor FDR =============================
1:23:19.569072 PROGRESS: Total precursors accumulated: 1,565
1:23:19.569145 PROGRESS: Target precursors: 1,550 (99.04%)
1:23:19.569200 PROGRESS: Decoy precursors: 15 (0.96%)
1:23:19.569252 PROGRESS: 
1:23:19.569299 PROGRESS: Precursor Summary:
1:23:19.571554 PROGRESS: Channel   0:	 0.050 FDR: 1,550; 0.010 FDR: 1,550; 0.001 FDR:   124
1:23:19.571727 PROGRESS: 
1:23:19.571798 PROGRESS: Protein Summary:
1:23:19.574090 PROGRESS: Channel   0:	 0.050 FDR: 1,281; 0.010 FDR: 1,281; 0.001 FDR:   119
1:23:19.574260 PROGRESS: =========================================================================
1:23:19.629227 INFO: Target number of precursors reached.
1:23:20.129863 INFO: fragments_df: keeping 5000 of 4031999 [sum(precursor_idx_mask)=36807 sum(mass_error_mask)=4031999 stop_rank=5000
1:23:21.530986 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:21.968548 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:22.894459 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:22.896254 INFO: Using score_cutoff 11.14004964351654 (fac=0.99, q=1)
1:23:22.897597 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:22.898075 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:22.898209 INFO: Updating optimization_manager: score_cutoff        : 11.757393312835694 -> 11.14004964351654
1:23:22.898339 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:23.124315 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:23.837178 INFO: === checking if optimization conditions were reached ===
1:23:23.841702 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:23:23.842133 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:23:23.842215 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:23:23.842300 INFO: ==============================================
1:23:23.842393 INFO: Starting optimization step 11.
1:23:23.842483 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:23.842593 INFO: Using rust extraction backend
1:23:23.842685 PROGRESS: Extracting batch of 250439 precursors
1:23:24.940030 INFO: === Search parameters used ===
1:23:24.940814 INFO: rt_error       : 805.6002197265625
1:23:24.940879 INFO: mobility_error : 0.1
1:23:24.940931 INFO: num_candidates : 3
1:23:24.940978 INFO: ms1_error      : 3
1:23:24.941028 INFO: ms2_error      : 10.0
1:23:24.941075 INFO: fwhm_rt        : 3.0
1:23:24.941118 INFO: quant_window   : 3
1:23:24.941188 INFO: ==============================================
1:23:32.699668 INFO: performing precursor FDR with 40 features
1:23:32.700111 INFO: Decoy channel: -1
1:23:32.700154 INFO: competitive: True
1:23:33.532768 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:34.703810 INFO: Estimating optimal hyperparameters - samples: 599,829, batch_size: 2,456, learning_rate: 7.74e-04
1:23:34.713783 INFO: Using random state 505887 for train-test-split
1:24:03.542629 INFO: Test AUC: 0.609
1:24:03.543211 INFO: Train AUC: 0.622
1:24:03.543271 INFO: AUC difference: 2.19%
1:24:04.333354 INFO: Resetting torch num_threads to 100
1:24:04.409580 PROGRESS: === Extracted 749787 precursors and 4032003 fragments ===
1:24:04.410943 INFO: === FDR correction performed with classifier version 10 ===
1:24:04.413047 PROGRESS: ============================= Precursor FDR =============================
1:24:04.413243 PROGRESS: Total precursors accumulated: 1,634
1:24:04.413314 PROGRESS: Target precursors: 1,618 (99.02%)
1:24:04.413369 PROGRESS: Decoy precursors: 16 (0.98%)
1:24:04.413431 PROGRESS: 
1:24:04.413479 PROGRESS: Precursor Summary:
1:24:04.415668 PROGRESS: Channel   0:	 0.050 FDR: 1,618; 0.010 FDR: 1,618; 0.001 FDR:    33
1:24:04.415837 PROGRESS: 
1:24:04.415899 PROGRESS: Protein Summary:
1:24:04.417992 PROGRESS: Channel   0:	 0.050 FDR: 1,356; 0.010 FDR: 1,356; 0.001 FDR:    33
1:24:04.418156 PROGRESS: =========================================================================
1:24:04.469550 INFO: Target number of precursors reached.
1:24:04.942735 INFO: fragments_df: keeping 5000 of 4032003 [sum(precursor_idx_mask)=37907 sum(mass_error_mask)=4032003 stop_rank=5000
1:24:06.169219 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:06.695203 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:07.634289 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:24:07.635675 INFO: Using score_cutoff 10.453231912994385 (fac=0.99, q=1)
1:24:07.637392 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:07.637819 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:07.637919 INFO: Updating optimization_manager: score_cutoff        : 11.14004964351654 -> 10.453231912994385
1:24:07.638024 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:07.856513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:08.433824 INFO: === checking if optimization conditions were reached ===
1:24:08.438357 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:24:08.438886 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:24:08.438969 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:24:08.439044 INFO: ==============================================
1:24:08.439141 PROGRESS: Optimization finished for ms2_error.
1:24:09.693482 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:09.926529 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:10.536186 INFO: Starting optimization step 0.
1:24:10.536797 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:24:10.537008 INFO: Using rust extraction backend
1:24:10.537131 PROGRESS: Extracting batch of 250439 precursors
1:24:11.799793 INFO: === Search parameters used ===
1:24:11.800747 INFO: rt_error       : 805.6002197265625
1:24:11.800935 INFO: mobility_error : 0.1
1:24:11.801193 INFO: num_candidates : 3
1:24:11.801255 INFO: ms1_error      : 3
1:24:11.801304 INFO: ms2_error      : 10.0
1:24:11.801347 INFO: fwhm_rt        : 3.0
1:24:11.801393 INFO: quant_window   : 3
1:24:11.801435 INFO: ==============================================
1:24:20.421808 INFO: performing precursor FDR with 40 features
1:24:20.422150 INFO: Decoy channel: -1
1:24:20.422182 INFO: competitive: True
1:24:21.240123 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:22.428083 INFO: Estimating optimal hyperparameters - samples: 599,853, batch_size: 2,456, learning_rate: 7.74e-04
1:24:22.434942 INFO: Using random state 945761 for train-test-split
1:24:54.382702 INFO: Test AUC: 0.612
1:24:54.383163 INFO: Train AUC: 0.625
1:24:54.383210 INFO: AUC difference: 2.01%
1:24:55.172533 INFO: Resetting torch num_threads to 100
1:24:55.271013 PROGRESS: === Extracted 749817 precursors and 4033041 fragments ===
1:24:55.272691 INFO: === FDR correction performed with classifier version 11 ===
1:24:55.275313 PROGRESS: ============================= Precursor FDR =============================
1:24:55.275663 PROGRESS: Total precursors accumulated: 1,617
1:24:55.275739 PROGRESS: Target precursors: 1,601 (99.01%)
1:24:55.275798 PROGRESS: Decoy precursors: 16 (0.99%)
1:24:55.275851 PROGRESS: 
1:24:55.275908 PROGRESS: Precursor Summary:
1:24:55.279366 PROGRESS: Channel   0:	 0.050 FDR: 1,601; 0.010 FDR: 1,601; 0.001 FDR:     0
1:24:55.279648 PROGRESS: 
1:24:55.279712 PROGRESS: Protein Summary:
1:24:55.282650 PROGRESS: Channel   0:	 0.050 FDR: 1,317; 0.010 FDR: 1,317; 0.001 FDR:     0
1:24:55.282865 PROGRESS: =========================================================================
1:24:55.353512 INFO: Target number of precursors reached.
1:24:55.836234 INFO: fragments_df: keeping 5000 of 4033041 [sum(precursor_idx_mask)=38019 sum(mass_error_mask)=4033041 stop_rank=5000
1:24:57.184046 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:57.612822 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:58.521152 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:24:58.522168 INFO: Using score_cutoff 11.469066009521484 (fac=0.99, q=1)
1:24:58.523173 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:58.523386 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:58.523458 INFO: Updating optimization_manager: score_cutoff        : 10.453231912994385 -> 11.469066009521484
1:24:58.523532 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:58.712137 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:59.226305 INFO: === checking if optimization conditions were reached ===
1:24:59.227153 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:24:59.233229 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 577.5438489485857
1:24:59.233840 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 577.5438.
1:24:59.233991 INFO: ==============================================
1:24:59.234119 INFO: Starting optimization step 1.
1:24:59.234210 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:24:59.234321 INFO: Using rust extraction backend
1:24:59.234427 PROGRESS: Extracting batch of 250439 precursors
1:25:00.483760 INFO: === Search parameters used ===
1:25:00.484543 INFO: rt_error       : 577.5438489485857
1:25:00.484707 INFO: mobility_error : 0.1
1:25:00.484779 INFO: num_candidates : 3
1:25:00.484828 INFO: ms1_error      : 3
1:25:00.484871 INFO: ms2_error      : 10.0
1:25:00.484910 INFO: fwhm_rt        : 3.0
1:25:00.484951 INFO: quant_window   : 3
1:25:00.484990 INFO: ==============================================
1:25:08.129575 INFO: performing precursor FDR with 40 features
1:25:08.129864 INFO: Decoy channel: -1
1:25:08.129895 INFO: competitive: True
1:25:08.917015 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:10.121887 INFO: Estimating optimal hyperparameters - samples: 599,503, batch_size: 2,455, learning_rate: 7.74e-04
1:25:10.130769 INFO: Using random state 945761 for train-test-split
1:25:31.872538 INFO: Test AUC: 0.609
1:25:31.873055 INFO: Train AUC: 0.624
1:25:31.873111 INFO: AUC difference: 2.30%
1:25:32.636810 INFO: Resetting torch num_threads to 100
1:25:32.726250 PROGRESS: === Extracted 749379 precursors and 4005963 fragments ===
1:25:32.727668 INFO: === FDR correction performed with classifier version 11 ===
1:25:32.729964 PROGRESS: ============================= Precursor FDR =============================
1:25:32.730162 PROGRESS: Total precursors accumulated: 1,686
1:25:32.730234 PROGRESS: Target precursors: 1,670 (99.05%)
1:25:32.730289 PROGRESS: Decoy precursors: 16 (0.95%)
1:25:32.730344 PROGRESS: 
1:25:32.730393 PROGRESS: Precursor Summary:
1:25:32.732622 PROGRESS: Channel   0:	 0.050 FDR: 1,670; 0.010 FDR: 1,670; 0.001 FDR:     0
1:25:32.732817 PROGRESS: 
1:25:32.732878 PROGRESS: Protein Summary:
1:25:32.735118 PROGRESS: Channel   0:	 0.050 FDR: 1,375; 0.010 FDR: 1,375; 0.001 FDR:     0
1:25:32.735309 PROGRESS: =========================================================================
1:25:32.792037 INFO: Target number of precursors reached.
1:25:33.280415 INFO: fragments_df: keeping 5000 of 4005963 [sum(precursor_idx_mask)=39277 sum(mass_error_mask)=4005963 stop_rank=5000
1:25:34.500951 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:34.966356 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:35.888672 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:35.889982 INFO: Using score_cutoff 11.014202223014832 (fac=0.99, q=1)
1:25:35.891130 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:35.891375 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:35.891473 INFO: Updating optimization_manager: score_cutoff        : 11.469066009521484 -> 11.014202223014832
1:25:35.891556 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:36.117207 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:36.723089 INFO: === checking if optimization conditions were reached ===
1:25:36.724077 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:25:36.731021 INFO: Updating optimization_manager: rt_error            : 577.5438489485857 -> 600.9354424206526
1:25:36.731592 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 600.9354.
1:25:36.731682 INFO: ==============================================
1:25:36.731785 INFO: Starting optimization step 2.
1:25:36.731868 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:25:36.731990 INFO: Using rust extraction backend
1:25:36.732099 PROGRESS: Extracting batch of 250439 precursors
1:25:38.019996 INFO: === Search parameters used ===
1:25:38.021137 INFO: rt_error       : 600.9354424206526
1:25:38.021370 INFO: mobility_error : 0.1
1:25:38.021459 INFO: num_candidates : 3
1:25:38.021517 INFO: ms1_error      : 3
1:25:38.021626 INFO: ms2_error      : 10.0
1:25:38.021698 INFO: fwhm_rt        : 3.0
1:25:38.021744 INFO: quant_window   : 3
1:25:38.021796 INFO: ==============================================
1:25:45.730159 INFO: performing precursor FDR with 40 features
1:25:45.730483 INFO: Decoy channel: -1
1:25:45.730523 INFO: competitive: True
1:25:46.502365 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:47.677542 INFO: Estimating optimal hyperparameters - samples: 599,571, batch_size: 2,455, learning_rate: 7.74e-04
1:25:47.688360 INFO: Using random state 945761 for train-test-split
1:26:18.658937 INFO: Test AUC: 0.609
1:26:18.659441 INFO: Train AUC: 0.623
1:26:18.659489 INFO: AUC difference: 2.21%
1:26:19.428898 INFO: Resetting torch num_threads to 100
1:26:19.507364 PROGRESS: === Extracted 749464 precursors and 4011554 fragments ===
1:26:19.508828 INFO: === FDR correction performed with classifier version 11 ===
1:26:19.510957 PROGRESS: ============================= Precursor FDR =============================
1:26:19.511153 PROGRESS: Total precursors accumulated: 1,629
1:26:19.511226 PROGRESS: Target precursors: 1,613 (99.02%)
1:26:19.511284 PROGRESS: Decoy precursors: 16 (0.98%)
1:26:19.511334 PROGRESS: 
1:26:19.511383 PROGRESS: Precursor Summary:
1:26:19.513545 PROGRESS: Channel   0:	 0.050 FDR: 1,613; 0.010 FDR: 1,613; 0.001 FDR:     0
1:26:19.513705 PROGRESS: 
1:26:19.513772 PROGRESS: Protein Summary:
1:26:19.515926 PROGRESS: Channel   0:	 0.050 FDR: 1,332; 0.010 FDR: 1,332; 0.001 FDR:     0
1:26:19.516116 PROGRESS: =========================================================================
1:26:19.565496 INFO: Target number of precursors reached.
1:26:20.047392 INFO: fragments_df: keeping 5000 of 4011554 [sum(precursor_idx_mask)=38316 sum(mass_error_mask)=4011554 stop_rank=5000
1:26:21.305383 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:21.730206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:22.595388 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:22.596513 INFO: Using score_cutoff 11.473058805084227 (fac=0.99, q=1)
1:26:22.598402 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:22.598554 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:22.598613 INFO: Updating optimization_manager: score_cutoff        : 11.014202223014832 -> 11.473058805084227
1:26:22.598700 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:22.844157 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:23.479802 INFO: === checking if optimization conditions were reached ===
1:26:23.480531 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:26:23.486948 INFO: Updating optimization_manager: rt_error            : 600.9354424206526 -> 594.6717553686636
1:26:23.487466 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 594.6718.
1:26:23.487564 INFO: ==============================================
1:26:23.487677 INFO: Starting optimization step 3.
1:26:23.487783 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:26:23.487911 INFO: Using rust extraction backend
1:26:23.487997 PROGRESS: Extracting batch of 250439 precursors
1:26:24.567166 INFO: === Search parameters used ===
1:26:24.568865 INFO: rt_error       : 594.6717553686636
1:26:24.569116 INFO: mobility_error : 0.1
1:26:24.569198 INFO: num_candidates : 3
1:26:24.569255 INFO: ms1_error      : 3
1:26:24.569307 INFO: ms2_error      : 10.0
1:26:24.569357 INFO: fwhm_rt        : 3.0
1:26:24.569403 INFO: quant_window   : 3
1:26:24.569450 INFO: ==============================================
1:26:34.074790 INFO: performing precursor FDR with 40 features
1:26:34.075084 INFO: Decoy channel: -1
1:26:34.075114 INFO: competitive: True
1:26:34.806468 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:35.982787 INFO: Estimating optimal hyperparameters - samples: 599,540, batch_size: 2,455, learning_rate: 7.74e-04
1:26:35.992931 INFO: Using random state 945761 for train-test-split
1:27:08.992835 INFO: Test AUC: 0.610
1:27:08.993344 INFO: Train AUC: 0.625
1:27:08.993405 INFO: AUC difference: 2.28%
1:27:10.095581 INFO: Resetting torch num_threads to 100
1:27:10.192173 PROGRESS: === Extracted 749425 precursors and 4009750 fragments ===
1:27:10.194382 INFO: === FDR correction performed with classifier version 11 ===
1:27:10.198439 PROGRESS: ============================= Precursor FDR =============================
1:27:10.199198 PROGRESS: Total precursors accumulated: 1,570
1:27:10.199353 PROGRESS: Target precursors: 1,555 (99.04%)
1:27:10.199464 PROGRESS: Decoy precursors: 15 (0.96%)
1:27:10.199620 PROGRESS: 
1:27:10.199691 PROGRESS: Precursor Summary:
1:27:10.205737 PROGRESS: Channel   0:	 0.050 FDR: 1,555; 0.010 FDR: 1,555; 0.001 FDR:     0
1:27:10.206588 PROGRESS: 
1:27:10.206771 PROGRESS: Protein Summary:
1:27:10.215233 PROGRESS: Channel   0:	 0.050 FDR: 1,288; 0.010 FDR: 1,288; 0.001 FDR:     0
1:27:10.216065 PROGRESS: =========================================================================
1:27:10.326250 INFO: Target number of precursors reached.
1:27:11.401324 INFO: fragments_df: keeping 5000 of 4009750 [sum(precursor_idx_mask)=37055 sum(mass_error_mask)=4009750 stop_rank=5000
1:27:13.353544 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:27:14.691051 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:27:16.800120 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:27:16.801555 INFO: Using score_cutoff 11.807960169410705 (fac=0.99, q=1)
1:27:16.802929 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:27:16.803265 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:27:16.803355 INFO: Updating optimization_manager: score_cutoff        : 11.473058805084227 -> 11.807960169410705
1:27:16.803463 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:17.084344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:27:17.785946 INFO: === checking if optimization conditions were reached ===
1:27:17.786570 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:27:17.793376 INFO: Updating optimization_manager: rt_error            : 594.6717553686636 -> 496.4202592210907
1:27:17.793884 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 496.4203.
1:27:17.794081 INFO: ==============================================
1:27:17.794254 INFO: Starting optimization step 4.
1:27:17.794379 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:27:17.794512 INFO: Using rust extraction backend
1:27:17.794605 PROGRESS: Extracting batch of 250439 precursors
1:27:19.228122 INFO: === Search parameters used ===
1:27:19.228761 INFO: rt_error       : 496.4202592210907
1:27:19.228891 INFO: mobility_error : 0.1
1:27:19.228952 INFO: num_candidates : 3
1:27:19.229002 INFO: ms1_error      : 3
1:27:19.229060 INFO: ms2_error      : 10.0
1:27:19.229105 INFO: fwhm_rt        : 3.0
1:27:19.229147 INFO: quant_window   : 3
1:27:19.229191 INFO: ==============================================
1:27:30.500644 INFO: performing precursor FDR with 40 features
1:27:30.501183 INFO: Decoy channel: -1
1:27:30.501410 INFO: competitive: True
1:27:31.560393 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:33.122170 INFO: Estimating optimal hyperparameters - samples: 599,042, batch_size: 2,453, learning_rate: 7.74e-04
1:27:33.131568 INFO: Using random state 945761 for train-test-split
1:28:06.236279 INFO: Test AUC: 0.608
1:28:06.236725 INFO: Train AUC: 0.622
1:28:06.236770 INFO: AUC difference: 2.31%
1:28:07.041705 INFO: Resetting torch num_threads to 100
1:28:07.121147 PROGRESS: === Extracted 748803 precursors and 3968028 fragments ===
1:28:07.122428 INFO: === FDR correction performed with classifier version 11 ===
1:28:07.124527 PROGRESS: ============================= Precursor FDR =============================
1:28:07.124667 PROGRESS: Total precursors accumulated: 1,725
1:28:07.124750 PROGRESS: Target precursors: 1,708 (99.01%)
1:28:07.124802 PROGRESS: Decoy precursors: 17 (0.99%)
1:28:07.124850 PROGRESS: 
1:28:07.124898 PROGRESS: Precursor Summary:
1:28:07.127358 PROGRESS: Channel   0:	 0.050 FDR: 1,708; 0.010 FDR: 1,708; 0.001 FDR:   813
1:28:07.127506 PROGRESS: 
1:28:07.127566 PROGRESS: Protein Summary:
1:28:07.129852 PROGRESS: Channel   0:	 0.050 FDR: 1,425; 0.010 FDR: 1,425; 0.001 FDR:   714
1:28:07.130011 PROGRESS: =========================================================================
1:28:07.185623 INFO: Target number of precursors reached.
1:28:07.674913 INFO: fragments_df: keeping 5000 of 3968028 [sum(precursor_idx_mask)=39891 sum(mass_error_mask)=3968028 stop_rank=5000
1:28:08.904043 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:09.459631 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:10.391053 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:10.392046 INFO: Using score_cutoff 10.338830517768859 (fac=0.99, q=1)
1:28:10.392633 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:10.392715 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:10.392769 INFO: Updating optimization_manager: score_cutoff        : 11.807960169410705 -> 10.338830517768859
1:28:10.392839 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:10.619473 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:11.255048 INFO: === checking if optimization conditions were reached ===
1:28:11.255774 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:28:11.261165 INFO: Updating optimization_manager: rt_error            : 496.4202592210907 -> 534.2698124206593
1:28:11.261662 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 534.2698.
1:28:11.261751 INFO: ==============================================
1:28:11.261858 INFO: Starting optimization step 5.
1:28:11.261970 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:28:11.262101 INFO: Using rust extraction backend
1:28:11.262187 PROGRESS: Extracting batch of 250439 precursors
1:28:12.278100 INFO: === Search parameters used ===
1:28:12.278758 INFO: rt_error       : 534.2698124206593
1:28:12.278889 INFO: mobility_error : 0.1
1:28:12.278952 INFO: num_candidates : 3
1:28:12.279005 INFO: ms1_error      : 3
1:28:12.279057 INFO: ms2_error      : 10.0
1:28:12.279105 INFO: fwhm_rt        : 3.0
1:28:12.279152 INFO: quant_window   : 3
1:28:12.279200 INFO: ==============================================
1:28:20.035328 INFO: performing precursor FDR with 40 features
1:28:20.035621 INFO: Decoy channel: -1
1:28:20.035652 INFO: competitive: True
1:28:20.828907 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:21.956203 INFO: Estimating optimal hyperparameters - samples: 599,492, batch_size: 2,455, learning_rate: 7.74e-04
1:28:21.964444 INFO: Using random state 945761 for train-test-split
1:28:52.337157 INFO: Test AUC: 0.610
1:28:52.337594 INFO: Train AUC: 0.622
1:28:52.337642 INFO: AUC difference: 2.04%
1:28:53.042369 INFO: Resetting torch num_threads to 100
1:28:53.173580 PROGRESS: === Extracted 749366 precursors and 3999602 fragments ===
1:28:53.175057 INFO: === FDR correction performed with classifier version 11 ===
1:28:53.178084 PROGRESS: ============================= Precursor FDR =============================
1:28:53.178357 PROGRESS: Total precursors accumulated: 1,598
1:28:53.178428 PROGRESS: Target precursors: 1,583 (99.06%)
1:28:53.178483 PROGRESS: Decoy precursors: 15 (0.94%)
1:28:53.178533 PROGRESS: 
1:28:53.178616 PROGRESS: Precursor Summary:
1:28:53.180968 PROGRESS: Channel   0:	 0.050 FDR: 1,583; 0.010 FDR: 1,583; 0.001 FDR:     0
1:28:53.181197 PROGRESS: 
1:28:53.181258 PROGRESS: Protein Summary:
1:28:53.183528 PROGRESS: Channel   0:	 0.050 FDR: 1,325; 0.010 FDR: 1,325; 0.001 FDR:     0
1:28:53.183743 PROGRESS: =========================================================================
1:28:53.287526 INFO: Target number of precursors reached.
1:28:53.773582 INFO: fragments_df: keeping 5000 of 3999602 [sum(precursor_idx_mask)=37050 sum(mass_error_mask)=3999602 stop_rank=5000
1:28:55.038581 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:55.566617 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:56.567053 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:56.568372 INFO: Using score_cutoff 9.870999303817749 (fac=0.99, q=1)
1:28:56.569122 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:28:56.569256 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:28:56.569334 INFO: Updating optimization_manager: score_cutoff        : 10.338830517768859 -> 9.870999303817749
1:28:56.569434 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:56.786377 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:57.418187 INFO: === checking if optimization conditions were reached ===
1:28:57.419043 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:28:57.425966 INFO: Updating optimization_manager: rt_error            : 534.2698124206593 -> 611.139068520748
1:28:57.426463 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 611.1391.
1:28:57.426558 INFO: ==============================================
1:28:57.426676 INFO: Starting optimization step 6.
1:28:57.426755 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:28:57.426887 INFO: Using rust extraction backend
1:28:57.426997 PROGRESS: Extracting batch of 250439 precursors
1:28:58.675113 INFO: === Search parameters used ===
1:28:58.676074 INFO: rt_error       : 611.139068520748
1:28:58.676246 INFO: mobility_error : 0.1
1:28:58.676323 INFO: num_candidates : 3
1:28:58.676380 INFO: ms1_error      : 3
1:28:58.676429 INFO: ms2_error      : 10.0
1:28:58.676479 INFO: fwhm_rt        : 3.0
1:28:58.676523 INFO: quant_window   : 3
1:28:58.676567 INFO: ==============================================
1:29:07.660453 INFO: performing precursor FDR with 40 features
1:29:07.660763 INFO: Decoy channel: -1
1:29:07.660804 INFO: competitive: True
1:29:08.567118 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:09.822495 INFO: Estimating optimal hyperparameters - samples: 599,676, batch_size: 2,456, learning_rate: 7.74e-04
1:29:09.831002 INFO: Using random state 945761 for train-test-split
1:29:36.884284 INFO: Test AUC: 0.613
1:29:36.884771 INFO: Train AUC: 0.624
1:29:36.884820 INFO: AUC difference: 1.65%
1:29:37.682377 INFO: Resetting torch num_threads to 100
1:29:37.765374 PROGRESS: === Extracted 749595 precursors and 4018829 fragments ===
1:29:37.766899 INFO: === FDR correction performed with classifier version 11 ===
1:29:37.769217 PROGRESS: ============================= Precursor FDR =============================
1:29:37.769536 PROGRESS: Total precursors accumulated: 1,763
1:29:37.769611 PROGRESS: Target precursors: 1,746 (99.04%)
1:29:37.769689 PROGRESS: Decoy precursors: 17 (0.96%)
1:29:37.769742 PROGRESS: 
1:29:37.769792 PROGRESS: Precursor Summary:
1:29:37.772762 PROGRESS: Channel   0:	 0.050 FDR: 1,746; 0.010 FDR: 1,746; 0.001 FDR:     3
1:29:37.773308 PROGRESS: 
1:29:37.773371 PROGRESS: Protein Summary:
1:29:37.776828 PROGRESS: Channel   0:	 0.050 FDR: 1,461; 0.010 FDR: 1,461; 0.001 FDR:     3
1:29:37.777388 PROGRESS: =========================================================================
1:29:37.836687 INFO: Target number of precursors reached.
1:29:38.334095 INFO: fragments_df: keeping 5000 of 4018829 [sum(precursor_idx_mask)=39921 sum(mass_error_mask)=4018829 stop_rank=5000
1:29:39.683388 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:29:40.142678 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:29:41.072973 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:29:41.074152 INFO: Using score_cutoff 8.388840497016906 (fac=0.99, q=1)
1:29:41.074799 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:29:41.074904 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:29:41.074960 INFO: Updating optimization_manager: score_cutoff        : 9.870999303817749 -> 8.388840497016906
1:29:41.075043 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:29:41.303643 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:29:41.982210 INFO: === checking if optimization conditions were reached ===
1:29:41.983435 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:29:41.995806 INFO: Updating optimization_manager: rt_error            : 611.139068520748 -> 731.8933262736513
1:29:41.996671 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 731.8933.
1:29:41.996943 INFO: ==============================================
1:29:41.997273 INFO: Starting optimization step 7.
1:29:41.997577 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:29:41.997889 INFO: Using rust extraction backend
1:29:41.998181 PROGRESS: Extracting batch of 250439 precursors
1:29:43.089671 INFO: === Search parameters used ===
1:29:43.090567 INFO: rt_error       : 731.8933262736513
1:29:43.090727 INFO: mobility_error : 0.1
1:29:43.090791 INFO: num_candidates : 3
1:29:43.090847 INFO: ms1_error      : 3
1:29:43.090893 INFO: ms2_error      : 10.0
1:29:43.090941 INFO: fwhm_rt        : 3.0
1:29:43.090987 INFO: quant_window   : 3
1:29:43.091031 INFO: ==============================================
1:29:51.298059 INFO: performing precursor FDR with 40 features
1:29:51.298353 INFO: Decoy channel: -1
1:29:51.298386 INFO: competitive: True
1:29:52.124073 INFO: Setting torch num_threads to 2 for FDR classification task
1:29:53.331896 INFO: Estimating optimal hyperparameters - samples: 599,876, batch_size: 2,457, learning_rate: 7.75e-04
1:29:53.341064 INFO: Using random state 945761 for train-test-split
1:30:21.944916 INFO: Test AUC: 0.613
1:30:21.945478 INFO: Train AUC: 0.624
1:30:21.945534 INFO: AUC difference: 1.83%
1:30:22.745523 INFO: Resetting torch num_threads to 100
1:30:22.830641 PROGRESS: === Extracted 749846 precursors and 4033342 fragments ===
1:30:22.831905 INFO: === FDR correction performed with classifier version 11 ===
1:30:22.833679 PROGRESS: ============================= Precursor FDR =============================
1:30:22.833862 PROGRESS: Total precursors accumulated: 1,631
1:30:22.833954 PROGRESS: Target precursors: 1,615 (99.02%)
1:30:22.834016 PROGRESS: Decoy precursors: 16 (0.98%)
1:30:22.834066 PROGRESS: 
1:30:22.834113 PROGRESS: Precursor Summary:
1:30:22.836355 PROGRESS: Channel   0:	 0.050 FDR: 1,615; 0.010 FDR: 1,615; 0.001 FDR:     4
1:30:22.836525 PROGRESS: 
1:30:22.836587 PROGRESS: Protein Summary:
1:30:22.838832 PROGRESS: Channel   0:	 0.050 FDR: 1,343; 0.010 FDR: 1,343; 0.001 FDR:     4
1:30:22.838999 PROGRESS: =========================================================================
1:30:22.896131 INFO: Target number of precursors reached.
1:30:23.391633 INFO: fragments_df: keeping 5000 of 4033342 [sum(precursor_idx_mask)=37987 sum(mass_error_mask)=4033342 stop_rank=5000
1:30:24.643047 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:30:25.015945 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:30:25.928307 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:30:25.929921 INFO: Using score_cutoff 10.655469693374634 (fac=0.99, q=1)
1:30:25.931508 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:30:25.931899 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:30:25.931990 INFO: Updating optimization_manager: score_cutoff        : 8.388840497016906 -> 10.655469693374634
1:30:25.932116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:30:26.156060 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:30:26.792225 INFO: === checking if optimization conditions were reached ===
1:30:26.793005 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:30:26.799246 INFO: Updating optimization_manager: rt_error            : 731.8933262736513 -> 691.1706373796787
1:30:26.799720 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 691.1706.
1:30:26.799813 INFO: ==============================================
1:30:26.799918 INFO: Starting optimization step 8.
1:30:26.799994 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:30:26.800108 INFO: Using rust extraction backend
1:30:26.800192 PROGRESS: Extracting batch of 250439 precursors
1:30:27.919930 INFO: === Search parameters used ===
1:30:27.920786 INFO: rt_error       : 691.1706373796787
1:30:27.920947 INFO: mobility_error : 0.1
1:30:27.921018 INFO: num_candidates : 3
1:30:27.921078 INFO: ms1_error      : 3
1:30:27.921194 INFO: ms2_error      : 10.0
1:30:27.921245 INFO: fwhm_rt        : 3.0
1:30:27.921295 INFO: quant_window   : 3
1:30:27.921340 INFO: ==============================================
1:30:38.609461 INFO: performing precursor FDR with 40 features
1:30:38.609808 INFO: Decoy channel: -1
1:30:38.609845 INFO: competitive: True
1:30:39.311923 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:40.430856 INFO: Estimating optimal hyperparameters - samples: 599,754, batch_size: 2,456, learning_rate: 7.74e-04
1:30:40.439983 INFO: Using random state 945761 for train-test-split
1:31:07.747540 INFO: Test AUC: 0.611
1:31:07.748188 INFO: Train AUC: 0.624
1:31:07.748250 INFO: AUC difference: 2.09%
1:31:08.518253 INFO: Resetting torch num_threads to 100
1:31:08.592501 PROGRESS: === Extracted 749693 precursors and 4027263 fragments ===
1:31:08.593931 INFO: === FDR correction performed with classifier version 11 ===
1:31:08.596038 PROGRESS: ============================= Precursor FDR =============================
1:31:08.596237 PROGRESS: Total precursors accumulated: 1,692
1:31:08.596306 PROGRESS: Target precursors: 1,676 (99.05%)
1:31:08.596362 PROGRESS: Decoy precursors: 16 (0.95%)
1:31:08.596415 PROGRESS: 
1:31:08.596466 PROGRESS: Precursor Summary:
1:31:08.598735 PROGRESS: Channel   0:	 0.050 FDR: 1,676; 0.010 FDR: 1,676; 0.001 FDR: 1,042
1:31:08.598929 PROGRESS: 
1:31:08.598991 PROGRESS: Protein Summary:
1:31:08.601345 PROGRESS: Channel   0:	 0.050 FDR: 1,384; 0.010 FDR: 1,384; 0.001 FDR:   890
1:31:08.601532 PROGRESS: =========================================================================
1:31:08.651063 INFO: Target number of precursors reached.
1:31:09.148526 INFO: fragments_df: keeping 5000 of 4027263 [sum(precursor_idx_mask)=39266 sum(mass_error_mask)=4027263 stop_rank=5000
1:31:10.540808 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:11.256589 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:12.182603 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:12.183902 INFO: Using score_cutoff 10.454626064300538 (fac=0.99, q=1)
1:31:12.185128 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:12.185389 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:12.185491 INFO: Updating optimization_manager: score_cutoff        : 10.655469693374634 -> 10.454626064300538
1:31:12.185628 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:12.413130 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:12.990660 INFO: === checking if optimization conditions were reached ===
1:31:12.991590 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
1:31:12.998845 INFO: Updating optimization_manager: rt_error            : 691.1706373796787 -> 762.1227006709987
1:31:12.999566 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 762.1227.
1:31:12.999663 INFO: ==============================================
1:31:12.999785 INFO: Starting optimization step 9.
1:31:12.999909 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:31:13.000046 INFO: Using rust extraction backend
1:31:13.000489 PROGRESS: Extracting batch of 250439 precursors
1:31:14.521612 INFO: === Search parameters used ===
1:31:14.522422 INFO: rt_error       : 762.1227006709987
1:31:14.522563 INFO: mobility_error : 0.1
1:31:14.522621 INFO: num_candidates : 3
1:31:14.522672 INFO: ms1_error      : 3
1:31:14.522717 INFO: ms2_error      : 10.0
1:31:14.522757 INFO: fwhm_rt        : 3.0
1:31:14.522810 INFO: quant_window   : 3
1:31:14.522854 INFO: ==============================================
1:31:22.336108 INFO: performing precursor FDR with 40 features
1:31:22.336432 INFO: Decoy channel: -1
1:31:22.336467 INFO: competitive: True
1:31:23.058073 INFO: Setting torch num_threads to 2 for FDR classification task
1:31:24.199437 INFO: Estimating optimal hyperparameters - samples: 599,836, batch_size: 2,456, learning_rate: 7.74e-04
1:31:24.206151 INFO: Using random state 945761 for train-test-split
1:31:50.678862 INFO: Test AUC: 0.611
1:31:50.679353 INFO: Train AUC: 0.625
1:31:50.679403 INFO: AUC difference: 2.19%
1:31:51.450916 INFO: Resetting torch num_threads to 100
1:31:51.528099 PROGRESS: === Extracted 749795 precursors and 4031445 fragments ===
1:31:51.529439 INFO: === FDR correction performed with classifier version 11 ===
1:31:51.531480 PROGRESS: ============================= Precursor FDR =============================
1:31:51.531659 PROGRESS: Total precursors accumulated: 1,732
1:31:51.531728 PROGRESS: Target precursors: 1,715 (99.02%)
1:31:51.531784 PROGRESS: Decoy precursors: 17 (0.98%)
1:31:51.531836 PROGRESS: 
1:31:51.531884 PROGRESS: Precursor Summary:
1:31:51.533987 PROGRESS: Channel   0:	 0.050 FDR: 1,715; 0.010 FDR: 1,715; 0.001 FDR:     1
1:31:51.534149 PROGRESS: 
1:31:51.534211 PROGRESS: Protein Summary:
1:31:51.536372 PROGRESS: Channel   0:	 0.050 FDR: 1,406; 0.010 FDR: 1,406; 0.001 FDR:     1
1:31:51.536539 PROGRESS: =========================================================================
1:31:51.586953 INFO: Target number of precursors reached.
1:31:52.057735 INFO: fragments_df: keeping 5000 of 4031445 [sum(precursor_idx_mask)=40458 sum(mass_error_mask)=4031445 stop_rank=5000
1:31:53.297391 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:53.759000 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:54.663062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:54.664306 INFO: Using score_cutoff 10.845288873481751 (fac=0.99, q=1)
1:31:54.664989 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:31:54.665095 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:31:54.665154 INFO: Updating optimization_manager: score_cutoff        : 10.454626064300538 -> 10.845288873481751
1:31:54.665236 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:54.874633 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:55.467691 INFO: === checking if optimization conditions were reached ===
1:31:55.468505 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
1:31:55.474438 INFO: Updating optimization_manager: rt_error            : 762.1227006709987 -> 548.4418843380759
1:31:55.474929 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 548.4419.
1:31:55.475056 INFO: ==============================================
1:31:55.475161 INFO: Starting optimization step 10.
1:31:55.475237 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:31:55.475362 INFO: Using rust extraction backend
1:31:55.475451 PROGRESS: Extracting batch of 250439 precursors
1:31:56.775690 INFO: === Search parameters used ===
1:31:56.776728 INFO: rt_error       : 548.4418843380759
1:31:56.777024 INFO: mobility_error : 0.1
1:31:56.777144 INFO: num_candidates : 3
1:31:56.777218 INFO: ms1_error      : 3
1:31:56.777277 INFO: ms2_error      : 10.0
1:31:56.777334 INFO: fwhm_rt        : 3.0
1:31:56.777390 INFO: quant_window   : 3
1:31:56.777471 INFO: ==============================================
1:32:08.454763 INFO: performing precursor FDR with 40 features
1:32:08.455121 INFO: Decoy channel: -1
1:32:08.455163 INFO: competitive: True
1:32:09.366625 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:10.765487 INFO: Estimating optimal hyperparameters - samples: 599,462, batch_size: 2,455, learning_rate: 7.74e-04
1:32:10.777353 INFO: Using random state 945761 for train-test-split
1:32:37.974450 INFO: Test AUC: 0.609
1:32:37.975020 INFO: Train AUC: 0.622
1:32:37.975091 INFO: AUC difference: 2.14%
1:32:38.864630 INFO: Resetting torch num_threads to 100
1:32:38.983414 PROGRESS: === Extracted 749328 precursors and 3999419 fragments ===
1:32:38.984978 INFO: === FDR correction performed with classifier version 11 ===
1:32:38.987422 PROGRESS: ============================= Precursor FDR =============================
1:32:38.987728 PROGRESS: Total precursors accumulated: 1,751
1:32:38.987797 PROGRESS: Target precursors: 1,734 (99.03%)
1:32:38.987855 PROGRESS: Decoy precursors: 17 (0.97%)
1:32:38.987909 PROGRESS: 
1:32:38.987962 PROGRESS: Precursor Summary:
1:32:38.991779 PROGRESS: Channel   0:	 0.050 FDR: 1,734; 0.010 FDR: 1,734; 0.001 FDR: 1,343
1:32:38.992358 PROGRESS: 
1:32:38.992420 PROGRESS: Protein Summary:
1:32:38.998967 PROGRESS: Channel   0:	 0.050 FDR: 1,437; 0.010 FDR: 1,437; 0.001 FDR: 1,118
1:32:38.999461 PROGRESS: =========================================================================
1:32:39.061616 INFO: Target number of precursors reached.
1:32:39.553718 INFO: fragments_df: keeping 5000 of 3999419 [sum(precursor_idx_mask)=40312 sum(mass_error_mask)=3999419 stop_rank=5000
1:32:40.919744 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:32:41.353205 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:32:42.230965 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:32:42.232172 INFO: Using score_cutoff 9.620928889274598 (fac=0.99, q=1)
1:32:42.232855 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:32:42.232954 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:32:42.233010 INFO: Updating optimization_manager: score_cutoff        : 10.845288873481751 -> 9.620928889274598
1:32:42.233083 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:32:42.454985 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:32:43.072818 INFO: === checking if optimization conditions were reached ===
1:32:43.073929 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
1:32:43.080950 INFO: Updating optimization_manager: rt_error            : 548.4418843380759 -> 590.3569314697387
1:32:43.081443 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 590.3569.
1:32:43.081548 INFO: ==============================================
1:32:43.081665 INFO: Starting optimization step 11.
1:32:43.081758 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:32:43.081887 INFO: Using rust extraction backend
1:32:43.082018 PROGRESS: Extracting batch of 250439 precursors
1:32:44.470505 INFO: === Search parameters used ===
1:32:44.471241 INFO: rt_error       : 590.3569314697387
1:32:44.471376 INFO: mobility_error : 0.1
1:32:44.471444 INFO: num_candidates : 3
1:32:44.471490 INFO: ms1_error      : 3
1:32:44.471534 INFO: ms2_error      : 10.0
1:32:44.471612 INFO: fwhm_rt        : 3.0
1:32:44.471664 INFO: quant_window   : 3
1:32:44.471706 INFO: ==============================================
1:32:52.681368 INFO: performing precursor FDR with 40 features
1:32:52.681666 INFO: Decoy channel: -1
1:32:52.681697 INFO: competitive: True
1:32:53.521824 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:54.714712 INFO: Estimating optimal hyperparameters - samples: 599,605, batch_size: 2,455, learning_rate: 7.74e-04
1:32:54.723610 INFO: Using random state 945761 for train-test-split
1:33:22.912583 INFO: Test AUC: 0.611
1:33:22.912989 INFO: Train AUC: 0.624
1:33:22.913035 INFO: AUC difference: 2.10%
1:33:23.683779 INFO: Resetting torch num_threads to 100
1:33:23.760058 PROGRESS: === Extracted 749507 precursors and 4013542 fragments ===
1:33:23.761251 INFO: === FDR correction performed with classifier version 11 ===
1:33:23.763082 PROGRESS: ============================= Precursor FDR =============================
1:33:23.763263 PROGRESS: Total precursors accumulated: 1,625
1:33:23.763333 PROGRESS: Target precursors: 1,609 (99.02%)
1:33:23.763389 PROGRESS: Decoy precursors: 16 (0.98%)
1:33:23.763442 PROGRESS: 
1:33:23.763493 PROGRESS: Precursor Summary:
1:33:23.765857 PROGRESS: Channel   0:	 0.050 FDR: 1,609; 0.010 FDR: 1,609; 0.001 FDR:   510
1:33:23.766749 PROGRESS: 
1:33:23.766814 PROGRESS: Protein Summary:
1:33:23.769153 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR:   456
1:33:23.769350 PROGRESS: =========================================================================
1:33:23.816203 INFO: Target number of precursors reached.
1:33:24.287217 INFO: fragments_df: keeping 5000 of 4013542 [sum(precursor_idx_mask)=38282 sum(mass_error_mask)=4013542 stop_rank=5000
1:33:25.471378 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:33:25.934047 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:33:28.480345 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:33:28.482785 INFO: Using score_cutoff 11.60870274810791 (fac=0.99, q=1)
1:33:28.484875 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:33:28.485374 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:33:28.485616 INFO: Updating optimization_manager: score_cutoff        : 9.620928889274598 -> 11.60870274810791
1:33:28.485837 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:28.735103 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:29.462359 INFO: === checking if optimization conditions were reached ===
1:33:29.463233 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
1:33:29.469294 INFO: Updating optimization_manager: rt_error            : 590.3569314697387 -> 495.27022500282453
1:33:29.469662 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 495.2702.
1:33:29.469764 INFO: ==============================================
1:33:29.469868 INFO: Starting optimization step 12.
1:33:29.469967 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:33:29.470085 INFO: Using rust extraction backend
1:33:29.470185 PROGRESS: Extracting batch of 250439 precursors
1:33:30.772532 INFO: === Search parameters used ===
1:33:30.773431 INFO: rt_error       : 495.27022500282453
1:33:30.773621 INFO: mobility_error : 0.1
1:33:30.773704 INFO: num_candidates : 3
1:33:30.773807 INFO: ms1_error      : 3
1:33:30.773877 INFO: ms2_error      : 10.0
1:33:30.773947 INFO: fwhm_rt        : 3.0
1:33:30.774003 INFO: quant_window   : 3
1:33:30.774052 INFO: ==============================================
1:33:41.076132 INFO: performing precursor FDR with 40 features
1:33:41.076606 INFO: Decoy channel: -1
1:33:41.076649 INFO: competitive: True
1:33:42.308674 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:44.320329 INFO: Estimating optimal hyperparameters - samples: 599,009, batch_size: 2,453, learning_rate: 7.74e-04
1:33:44.332419 INFO: Using random state 945761 for train-test-split
1:34:14.179122 INFO: Test AUC: 0.608
1:34:14.179528 INFO: Train AUC: 0.623
1:34:14.179572 INFO: AUC difference: 2.38%
1:34:14.986526 INFO: Resetting torch num_threads to 100
1:34:15.057521 PROGRESS: === Extracted 748762 precursors and 3966648 fragments ===
1:34:15.058692 INFO: === FDR correction performed with classifier version 11 ===
1:34:15.060633 PROGRESS: ============================= Precursor FDR =============================
1:34:15.060807 PROGRESS: Total precursors accumulated: 1,747
1:34:15.060876 PROGRESS: Target precursors: 1,730 (99.03%)
1:34:15.060932 PROGRESS: Decoy precursors: 17 (0.97%)
1:34:15.060983 PROGRESS: 
1:34:15.061033 PROGRESS: Precursor Summary:
1:34:15.063293 PROGRESS: Channel   0:	 0.050 FDR: 1,730; 0.010 FDR: 1,730; 0.001 FDR:    56
1:34:15.063527 PROGRESS: 
1:34:15.063586 PROGRESS: Protein Summary:
1:34:15.065783 PROGRESS: Channel   0:	 0.050 FDR: 1,432; 0.010 FDR: 1,432; 0.001 FDR:    55
1:34:15.065959 PROGRESS: =========================================================================
1:34:15.114375 INFO: Target number of precursors reached.
1:34:15.589482 INFO: fragments_df: keeping 5000 of 3966648 [sum(precursor_idx_mask)=40653 sum(mass_error_mask)=3966648 stop_rank=5000
1:34:16.774379 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:17.280643 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:18.233659 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:18.234862 INFO: Using score_cutoff 10.74827034444809 (fac=0.99, q=1)
1:34:18.235458 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:18.235546 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:18.235604 INFO: Updating optimization_manager: score_cutoff        : 11.60870274810791 -> 10.74827034444809
1:34:18.235680 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:18.454941 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:18.995973 INFO: === checking if optimization conditions were reached ===
1:34:18.996721 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
1:34:19.003797 INFO: Updating optimization_manager: rt_error            : 495.27022500282453 -> 565.2965504191446
1:34:19.004177 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 565.2966.
1:34:19.004271 INFO: ==============================================
1:34:19.004362 INFO: Starting optimization step 13.
1:34:19.004438 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:34:19.004539 INFO: Using rust extraction backend
1:34:19.004617 PROGRESS: Extracting batch of 250439 precursors
1:34:20.169172 INFO: === Search parameters used ===
1:34:20.170192 INFO: rt_error       : 565.2965504191446
1:34:20.170288 INFO: mobility_error : 0.1
1:34:20.170343 INFO: num_candidates : 3
1:34:20.170392 INFO: ms1_error      : 3
1:34:20.170439 INFO: ms2_error      : 10.0
1:34:20.170486 INFO: fwhm_rt        : 3.0
1:34:20.170531 INFO: quant_window   : 3
1:34:20.170576 INFO: ==============================================
1:34:28.013366 INFO: performing precursor FDR with 40 features
1:34:28.013705 INFO: Decoy channel: -1
1:34:28.013741 INFO: competitive: True
1:34:28.770834 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:29.963014 INFO: Estimating optimal hyperparameters - samples: 599,468, batch_size: 2,455, learning_rate: 7.74e-04
1:34:29.972296 INFO: Using random state 945761 for train-test-split
1:34:52.292621 INFO: Test AUC: 0.609
1:34:52.293058 INFO: Train AUC: 0.623
1:34:52.293106 INFO: AUC difference: 2.16%
1:34:59.953804 INFO: Resetting torch num_threads to 100
1:35:00.153424 PROGRESS: === Extracted 749335 precursors and 4002119 fragments ===
1:35:00.154969 INFO: === FDR correction performed with classifier version 11 ===
1:35:00.157137 PROGRESS: ============================= Precursor FDR =============================
1:35:00.157356 PROGRESS: Total precursors accumulated: 1,632
1:35:00.157428 PROGRESS: Target precursors: 1,616 (99.02%)
1:35:00.157485 PROGRESS: Decoy precursors: 16 (0.98%)
1:35:00.157539 PROGRESS: 
1:35:00.157590 PROGRESS: Precursor Summary:
1:35:00.160139 PROGRESS: Channel   0:	 0.050 FDR: 1,616; 0.010 FDR: 1,616; 0.001 FDR:     0
1:35:00.160366 PROGRESS: 
1:35:00.160427 PROGRESS: Protein Summary:
1:35:00.163078 PROGRESS: Channel   0:	 0.050 FDR: 1,332; 0.010 FDR: 1,332; 0.001 FDR:     0
1:35:00.163323 PROGRESS: =========================================================================
1:35:00.229999 INFO: Target number of precursors reached.
1:35:00.752316 INFO: fragments_df: keeping 5000 of 4002119 [sum(precursor_idx_mask)=38355 sum(mass_error_mask)=4002119 stop_rank=5000
1:35:02.050132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:02.490446 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:03.467211 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:35:03.468228 INFO: Using score_cutoff 11.532087098121643 (fac=0.99, q=1)
1:35:03.468788 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:35:03.468882 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:35:03.468940 INFO: Updating optimization_manager: score_cutoff        : 10.74827034444809 -> 11.532087098121643
1:35:03.469012 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:03.699537 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:04.336263 INFO: === checking if optimization conditions were reached ===
1:35:04.337032 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
1:35:04.343943 INFO: Updating optimization_manager: rt_error            : 565.2965504191446 -> 525.3749558111767
1:35:04.344460 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 525.3750.
1:35:04.344599 INFO: ==============================================
1:35:04.344727 INFO: Starting optimization step 14.
1:35:04.344831 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:35:04.344965 INFO: Using rust extraction backend
1:35:04.345076 PROGRESS: Extracting batch of 250439 precursors
1:35:05.433921 INFO: === Search parameters used ===
1:35:05.434741 INFO: rt_error       : 525.3749558111767
1:35:05.434907 INFO: mobility_error : 0.1
1:35:05.434976 INFO: num_candidates : 3
1:35:05.435026 INFO: ms1_error      : 3
1:35:05.435076 INFO: ms2_error      : 10.0
1:35:05.435120 INFO: fwhm_rt        : 3.0
1:35:05.435169 INFO: quant_window   : 3
1:35:05.435228 INFO: ==============================================
1:35:14.585487 INFO: performing precursor FDR with 40 features
1:35:14.585822 INFO: Decoy channel: -1
1:35:14.585860 INFO: competitive: True
1:35:15.360282 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:16.579158 INFO: Estimating optimal hyperparameters - samples: 599,268, batch_size: 2,454, learning_rate: 7.74e-04
1:35:16.587806 INFO: Using random state 945761 for train-test-split
1:35:40.250336 INFO: Test AUC: 0.609
1:35:40.250499 INFO: Train AUC: 0.624
1:35:40.250539 INFO: AUC difference: 2.40%
1:35:40.738901 INFO: Resetting torch num_threads to 100
1:35:40.768716 PROGRESS: === Extracted 749085 precursors and 3985844 fragments ===
1:35:40.769230 INFO: === FDR correction performed with classifier version 11 ===
1:35:40.770157 PROGRESS: ============================= Precursor FDR =============================
1:35:40.770254 PROGRESS: Total precursors accumulated: 1,779
1:35:40.770330 PROGRESS: Target precursors: 1,762 (99.04%)
1:35:40.770383 PROGRESS: Decoy precursors: 17 (0.96%)
1:35:40.770430 PROGRESS: 
1:35:40.770474 PROGRESS: Precursor Summary:
1:35:40.771888 PROGRESS: Channel   0:	 0.050 FDR: 1,762; 0.010 FDR: 1,762; 0.001 FDR:   542
1:35:40.771980 PROGRESS: 
1:35:40.772034 PROGRESS: Protein Summary:
1:35:40.773812 PROGRESS: Channel   0:	 0.050 FDR: 1,461; 0.010 FDR: 1,461; 0.001 FDR:   484
1:35:40.773931 PROGRESS: =========================================================================
1:35:40.788076 INFO: Target number of precursors reached.
1:35:41.215312 INFO: fragments_df: keeping 5000 of 3985844 [sum(precursor_idx_mask)=41180 sum(mass_error_mask)=3985844 stop_rank=5000
1:35:41.681213 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:41.956892 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:42.679197 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:35:42.679669 INFO: Using score_cutoff 10.456555390548706 (fac=0.99, q=1)
1:35:42.680013 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:35:42.680092 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:35:42.680147 INFO: Updating optimization_manager: score_cutoff        : 11.532087098121643 -> 10.456555390548706
1:35:42.680209 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:42.828918 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:43.162415 INFO: === checking if optimization conditions were reached ===
1:35:43.162697 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
1:35:43.165956 INFO: Updating optimization_manager: rt_error            : 525.3749558111767 -> 553.5262891922016
1:35:43.166063 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 553.5263.
1:35:43.166128 INFO: ==============================================
1:35:43.166199 INFO: Starting optimization step 15.
1:35:43.166259 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:35:43.166339 INFO: Using rust extraction backend
1:35:43.166399 PROGRESS: Extracting batch of 250439 precursors
1:35:43.592344 INFO: === Search parameters used ===
1:35:43.592630 INFO: rt_error       : 553.5262891922016
1:35:43.592685 INFO: mobility_error : 0.1
1:35:43.592731 INFO: num_candidates : 3
1:35:43.592773 INFO: ms1_error      : 3
1:35:43.592815 INFO: ms2_error      : 10.0
1:35:43.592856 INFO: fwhm_rt        : 3.0
1:35:43.592895 INFO: quant_window   : 3
1:35:43.592934 INFO: ==============================================
1:35:46.194092 INFO: performing precursor FDR with 40 features
1:35:46.194216 INFO: Decoy channel: -1
1:35:46.194242 INFO: competitive: True
1:35:46.382280 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:46.680100 INFO: Estimating optimal hyperparameters - samples: 599,476, batch_size: 2,455, learning_rate: 7.74e-04
1:35:46.681433 INFO: Using random state 945761 for train-test-split
1:36:00.252528 INFO: Test AUC: 0.613
1:36:00.252692 INFO: Train AUC: 0.623
1:36:00.252726 INFO: AUC difference: 1.48%
1:36:00.746245 INFO: Resetting torch num_threads to 100
1:36:00.775643 PROGRESS: === Extracted 749346 precursors and 4001124 fragments ===
1:36:00.776152 INFO: === FDR correction performed with classifier version 11 ===
1:36:00.776919 PROGRESS: ============================= Precursor FDR =============================
1:36:00.777012 PROGRESS: Total precursors accumulated: 1,760
1:36:00.777071 PROGRESS: Target precursors: 1,743 (99.03%)
1:36:00.777124 PROGRESS: Decoy precursors: 17 (0.97%)
1:36:00.777175 PROGRESS: 
1:36:00.777221 PROGRESS: Precursor Summary:
1:36:00.778691 PROGRESS: Channel   0:	 0.050 FDR: 1,743; 0.010 FDR: 1,743; 0.001 FDR: 1,302
1:36:00.778787 PROGRESS: 
1:36:00.778845 PROGRESS: Protein Summary:
1:36:00.780763 PROGRESS: Channel   0:	 0.050 FDR: 1,438; 0.010 FDR: 1,438; 0.001 FDR: 1,095
1:36:00.780858 PROGRESS: =========================================================================
1:36:00.799281 INFO: Target number of precursors reached.
1:36:01.243432 INFO: fragments_df: keeping 5000 of 4001124 [sum(precursor_idx_mask)=40821 sum(mass_error_mask)=4001124 stop_rank=5000
1:36:01.721751 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:01.990073 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:02.714854 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:02.715339 INFO: Using score_cutoff 10.974787519454955 (fac=0.99, q=1)
1:36:02.715674 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:02.715754 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:02.715811 INFO: Updating optimization_manager: score_cutoff        : 10.456555390548706 -> 10.974787519454955
1:36:02.715876 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:02.865345 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:03.215461 INFO: === checking if optimization conditions were reached ===
1:36:03.215801 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 5 ===
1:36:03.219655 INFO: Updating optimization_manager: rt_error            : 553.5262891922016 -> 578.668457544914
1:36:03.219797 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 578.6685.
1:36:03.219908 INFO: ==============================================
1:36:03.219998 INFO: Starting optimization step 16.
1:36:03.220080 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:03.220164 INFO: Using rust extraction backend
1:36:03.220242 PROGRESS: Extracting batch of 250439 precursors
1:36:03.646893 INFO: === Search parameters used ===
1:36:03.647163 INFO: rt_error       : 578.668457544914
1:36:03.647224 INFO: mobility_error : 0.1
1:36:03.647272 INFO: num_candidates : 3
1:36:03.647316 INFO: ms1_error      : 3
1:36:03.647359 INFO: ms2_error      : 10.0
1:36:03.647401 INFO: fwhm_rt        : 3.0
1:36:03.647444 INFO: quant_window   : 3
1:36:03.647485 INFO: ==============================================
1:36:06.169750 INFO: performing precursor FDR with 40 features
1:36:06.169872 INFO: Decoy channel: -1
1:36:06.169898 INFO: competitive: True
1:36:06.358951 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:06.659673 INFO: Estimating optimal hyperparameters - samples: 599,527, batch_size: 2,455, learning_rate: 7.74e-04
1:36:06.660705 INFO: Using random state 945761 for train-test-split
1:36:23.740283 INFO: Test AUC: 0.607
1:36:23.740484 INFO: Train AUC: 0.623
1:36:23.740521 INFO: AUC difference: 2.46%
1:36:24.230589 INFO: Resetting torch num_threads to 100
1:36:24.259266 PROGRESS: === Extracted 749409 precursors and 4007279 fragments ===
1:36:24.259797 INFO: === FDR correction performed with classifier version 11 ===
1:36:24.260520 PROGRESS: ============================= Precursor FDR =============================
1:36:24.260612 PROGRESS: Total precursors accumulated: 1,769
1:36:24.260675 PROGRESS: Target precursors: 1,752 (99.04%)
1:36:24.260728 PROGRESS: Decoy precursors: 17 (0.96%)
1:36:24.260775 PROGRESS: 
1:36:24.260823 PROGRESS: Precursor Summary:
1:36:24.262263 PROGRESS: Channel   0:	 0.050 FDR: 1,752; 0.010 FDR: 1,752; 0.001 FDR: 1,282
1:36:24.262369 PROGRESS: 
1:36:24.262429 PROGRESS: Protein Summary:
1:36:24.264322 PROGRESS: Channel   0:	 0.050 FDR: 1,444; 0.010 FDR: 1,444; 0.001 FDR: 1,066
1:36:24.264416 PROGRESS: =========================================================================
1:36:24.281763 INFO: Target number of precursors reached.
1:36:24.707021 INFO: fragments_df: keeping 5000 of 4007279 [sum(precursor_idx_mask)=41276 sum(mass_error_mask)=4007279 stop_rank=5000
1:36:25.190553 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:25.437270 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:26.107104 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:26.107582 INFO: Using score_cutoff 11.07569922809601 (fac=0.99, q=1)
1:36:26.107930 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:26.108009 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:26.108064 INFO: Updating optimization_manager: score_cutoff        : 10.974787519454955 -> 11.07569922809601
1:36:26.108124 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:26.257831 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:26.598812 INFO: === checking if optimization conditions were reached ===
1:36:26.599141 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 5 ===
1:36:26.600370 INFO: Updating optimization_manager: rt_error            : 578.668457544914 -> 525.3749558111767
1:36:26.600518 INFO: Updating optimization_manager: classifier_version  : 11 -> 26
1:36:26.600648 INFO: Updating optimization_manager: score_cutoff        : 11.07569922809601 -> 10.456555390548706
1:36:26.600754 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:26.600857 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:26.600965 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 525.3750 found after 17 searches.
1:36:26.601038 INFO: ==============================================
1:36:26.601122 PROGRESS: Optimization finished for rt_error.
1:36:27.005859 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:27.156397 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:27.489301 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:36:27.489611 PROGRESS: ==============================================
1:36:27.489712 PROGRESS: ms2_error      : 10.0000
1:36:27.489788 PROGRESS: rt_error       : 525.3750
1:36:27.489846 PROGRESS: ==============================================
1:36:27.493616 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:35.017634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:51.404818 INFO: Using rust extraction backend
1:36:51.405272 PROGRESS: Extracting batch of 11997144 precursors
1:37:07.485293 INFO: === Search parameters used ===
1:37:07.485831 INFO: rt_error       : 525.3749558111767
1:37:07.485909 INFO: mobility_error : 0.1
1:37:07.485984 INFO: num_candidates : 3
1:37:07.486033 INFO: ms1_error      : 3
1:37:07.486078 INFO: ms2_error      : 10.0
1:37:07.486120 INFO: fwhm_rt        : 3.0
1:37:07.486162 INFO: quant_window   : 3
1:37:07.486204 INFO: ==============================================
1:37:34.854651 INFO: Removed 8350803 precursors with score below cutoff 10.456555390548706
1:37:57.134600 INFO: performing precursor FDR with 40 features
1:37:57.134835 INFO: Decoy channel: -1
1:37:57.134868 INFO: competitive: True
1:38:00.191353 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:11.404200 INFO: Estimating optimal hyperparameters - samples: 22,110,656, batch_size: 4,096, learning_rate: 1.00e-03
1:38:11.471671 INFO: Using random state 21820 for train-test-split
1:46:21.186259 INFO: Test AUC: 0.619
1:46:21.186697 INFO: Train AUC: 0.620
1:46:21.186746 INFO: AUC difference: 0.05%
1:46:27.535807 INFO: Resetting torch num_threads to 100
1:46:30.741627 PROGRESS: ============================= Precursor FDR =============================
1:46:30.742048 PROGRESS: Total precursors accumulated: 93,736
1:46:30.742127 PROGRESS: Target precursors: 92,808 (99.01%)
1:46:30.742183 PROGRESS: Decoy precursors: 928 (0.99%)
1:46:30.742232 PROGRESS: 
1:46:30.742280 PROGRESS: Precursor Summary:
1:46:30.767319 PROGRESS: Channel   0:	 0.050 FDR: 92,808; 0.010 FDR: 92,808; 0.001 FDR: 59,059
1:46:30.767570 PROGRESS: 
1:46:30.767632 PROGRESS: Protein Summary:
1:46:30.800812 PROGRESS: Channel   0:	 0.050 FDR: 13,122; 0.010 FDR: 13,122; 0.001 FDR: 9,119
1:46:30.801079 PROGRESS: =========================================================================
1:46:31.037700 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
1:46:31.199289 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
1:46:31.436802 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:46:32.063185 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
1:46:32.063351 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant
1:46:32.063456 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
1:46:32.063657 INFO: Initializing TimingManager
1:46:32.064172 INFO: Initializing RawFileManager
1:46:43.182621 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.
1:46:43.191578 INFO: Determining DIA cycle
1:46:43.209067 INFO: Found cycle with start 0.00 min and length 300.
1:46:43.383389 INFO: RT (min)            : 0.0 - 26.9
1:46:43.383480 INFO: RT duration (sec)   : 1611.2
1:46:43.383509 INFO: RT duration (min)   : 26.9
1:46:43.383545 INFO: Cycle len (scans)   : 300
1:46:43.383568 INFO: Cycle len (sec)     : 1.65
1:46:43.383587 INFO: Number of cycles    : 978
1:46:43.383605 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:46:43.383645 INFO: Creating DIA data object took: 11.319373369216919
1:46:44.088053 INFO: Creating DIA data NG object took: 0.7042708396911621
1:46:45.551275 INFO: Initializing CalibrationManager
1:46:45.551575 INFO: Setting up calibration estimators ..
1:46:45.551642 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:46:45.551722 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'}' ..
1:46:45.551802 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:46:45.551855 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:46:45.551907 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}}' ..
1:46:45.551973 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:46:45.552018 INFO: Done setting up calibration estimators.
1:46:45.552237 INFO: Initializing OptimizationManager
1:46:45.552393 INFO: initial parameter: ms1_error = 3
1:46:45.552446 INFO: initial parameter: ms2_error = 10
1:46:45.552494 INFO: initial parameter: rt_error = 805.611083984375
1:46:45.552537 INFO: initial parameter: mobility_error = 0.1
1:46:45.552579 INFO: initial parameter: num_candidates = 1
1:46:45.552619 INFO: initial parameter: fwhm_rt = 5
1:46:45.552660 INFO: initial parameter: fwhm_mobility = 0.01
1:46:45.552700 INFO: initial parameter: score_cutoff = 0
1:46:45.552739 INFO: initial parameter: classifier_version = -1
1:46:45.552809 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:46:45.553097 INFO: FDRManager: loading saved state not requested, will be initialized.
1:46:45.553133 INFO: Initializing FDRManager
1:46:45.553176 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:46:46.990306 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:46:47.916645 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:46:47.917111 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
1:46:47.917234 PROGRESS: Starting initial search for precursors.
1:46:47.917343 INFO: Starting optimization step 0.
1:46:47.917423 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:46:47.917488 INFO: Using rust extraction backend
1:46:47.917555 PROGRESS: Extracting batch of 1965 precursors
1:46:47.926130 INFO: === Search parameters used ===
1:46:47.926248 INFO: rt_error       : 805.611083984375
1:46:47.926303 INFO: mobility_error : 0.1
1:46:47.926349 INFO: num_candidates : 1
1:46:47.926394 INFO: ms1_error      : 3
1:46:47.926435 INFO: ms2_error      : 10
1:46:47.926476 INFO: fwhm_rt        : 5
1:46:47.926516 INFO: quant_window   : 3
1:46:47.926555 INFO: ==============================================
1:46:47.960559 INFO: performing precursor FDR with 40 features
1:46:47.960635 INFO: Decoy channel: -1
1:46:47.960664 INFO: competitive: True
1:46:47.962142 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:47.964230 INFO: Estimating optimal hyperparameters - samples: 1,568, batch_size: 128, learning_rate: 1.77e-04
1:46:47.965388 INFO: Using random state 765620 for train-test-split
1:46:48.122964 INFO: Test AUC: 0.479
1:46:48.123049 INFO: Train AUC: 0.569
1:46:48.123077 INFO: AUC difference: 15.87%
1:46:48.123099 WARNING: AUC difference > 5%. This may indicate overfitting.
1:46:48.383689 INFO: Resetting torch num_threads to 100
1:46:48.385364 PROGRESS: === Extracted 1961 precursors and 10876 fragments ===
1:46:48.385760 INFO: === FDR correction performed with classifier version -1 ===
1:46:48.386279 PROGRESS: ============================= Precursor FDR =============================
1:46:48.386370 PROGRESS: Total precursors accumulated: 11
1:46:48.386427 PROGRESS: Target precursors: 11 (100.00%)
1:46:48.386474 PROGRESS: Decoy precursors: 0 (0.00%)
1:46:48.386518 PROGRESS: 
1:46:48.386559 PROGRESS: Precursor Summary:
1:46:48.387628 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1:46:48.387713 PROGRESS: 
1:46:48.387767 PROGRESS: Protein Summary:
1:46:48.388950 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1:46:48.389034 PROGRESS: =========================================================================
1:46:48.389269 INFO: Target number of precursors not reached yet.
1:46:48.475609 INFO: Starting optimization step 1.
1:46:48.475998 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:46:48.476101 INFO: Using rust extraction backend
1:46:48.476170 PROGRESS: Extracting batch of 3948 precursors
1:46:48.485077 INFO: === Search parameters used ===
1:46:48.485222 INFO: rt_error       : 805.611083984375
1:46:48.485275 INFO: mobility_error : 0.1
1:46:48.485328 INFO: num_candidates : 1
1:46:48.485374 INFO: ms1_error      : 3
1:46:48.485415 INFO: ms2_error      : 10
1:46:48.485456 INFO: fwhm_rt        : 5
1:46:48.485500 INFO: quant_window   : 3
1:46:48.485547 INFO: ==============================================
1:46:48.538316 INFO: performing precursor FDR with 40 features
1:46:48.538408 INFO: Decoy channel: -1
1:46:48.538433 INFO: competitive: True
1:46:48.543825 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:48.546195 INFO: Estimating optimal hyperparameters - samples: 4,717, batch_size: 128, learning_rate: 1.77e-04
1:46:48.546325 INFO: Using random state 39259 for train-test-split
1:46:49.027904 INFO: Test AUC: 0.553
1:46:49.027989 INFO: Train AUC: 0.571
1:46:49.028018 INFO: AUC difference: 3.19%
1:46:49.284834 INFO: Resetting torch num_threads to 100
1:46:49.288371 PROGRESS: === Extracted 5897 precursors and 32928 fragments ===
1:46:49.288758 INFO: === FDR correction performed with classifier version -1 ===
1:46:49.289257 PROGRESS: ============================= Precursor FDR =============================
1:46:49.289339 PROGRESS: Total precursors accumulated: 23
1:46:49.289394 PROGRESS: Target precursors: 23 (100.00%)
1:46:49.289441 PROGRESS: Decoy precursors: 0 (0.00%)
1:46:49.289483 PROGRESS: 
1:46:49.289525 PROGRESS: Precursor Summary:
1:46:49.290593 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1:46:49.290681 PROGRESS: 
1:46:49.290735 PROGRESS: Protein Summary:
1:46:49.291895 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1:46:49.291975 PROGRESS: =========================================================================
1:46:49.292278 INFO: Target number of precursors not reached yet.
1:46:49.399107 INFO: Starting optimization step 2.
1:46:49.399350 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:46:49.399426 INFO: Using rust extraction backend
1:46:49.399485 PROGRESS: Extracting batch of 7900 precursors
1:46:49.415229 INFO: === Search parameters used ===
1:46:49.415398 INFO: rt_error       : 805.611083984375
1:46:49.415450 INFO: mobility_error : 0.1
1:46:49.415494 INFO: num_candidates : 1
1:46:49.415535 INFO: ms1_error      : 3
1:46:49.415575 INFO: ms2_error      : 10
1:46:49.415614 INFO: fwhm_rt        : 5
1:46:49.415653 INFO: quant_window   : 3
1:46:49.415692 INFO: ==============================================
1:46:49.494718 INFO: performing precursor FDR with 40 features
1:46:49.494825 INFO: Decoy channel: -1
1:46:49.494849 INFO: competitive: True
1:46:49.502304 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:49.506037 INFO: Estimating optimal hyperparameters - samples: 11,023, batch_size: 128, learning_rate: 1.77e-04
1:46:49.506156 INFO: Using random state 488396 for train-test-split
1:46:50.691641 INFO: Test AUC: 0.556
1:46:50.691730 INFO: Train AUC: 0.589
1:46:50.691773 INFO: AUC difference: 5.49%
1:46:50.691795 WARNING: AUC difference > 5%. This may indicate overfitting.
1:46:50.949557 INFO: Resetting torch num_threads to 100
1:46:50.954647 PROGRESS: === Extracted 13779 precursors and 76997 fragments ===
1:46:50.955083 INFO: === FDR correction performed with classifier version -1 ===
1:46:50.955585 PROGRESS: ============================= Precursor FDR =============================
1:46:50.955668 PROGRESS: Total precursors accumulated: 0
1:46:50.955723 PROGRESS: Target precursors: 0 (0.00%)
1:46:50.955771 PROGRESS: Decoy precursors: 0 (0.00%)
1:46:50.955818 PROGRESS: 
1:46:50.955861 PROGRESS: Precursor Summary:
1:46:50.955972 PROGRESS: 
1:46:50.956031 PROGRESS: Protein Summary:
1:46:50.956101 PROGRESS: =========================================================================
1:46:50.956915 INFO: Target number of precursors not reached yet.
1:46:51.077148 INFO: Starting optimization step 3.
1:46:51.077401 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:46:51.077481 INFO: Using rust extraction backend
1:46:51.077539 PROGRESS: Extracting batch of 15775 precursors
1:46:51.106729 INFO: === Search parameters used ===
1:46:51.106936 INFO: rt_error       : 805.611083984375
1:46:51.106988 INFO: mobility_error : 0.1
1:46:51.107035 INFO: num_candidates : 1
1:46:51.107079 INFO: ms1_error      : 3
1:46:51.107120 INFO: ms2_error      : 10
1:46:51.107162 INFO: fwhm_rt        : 5
1:46:51.107201 INFO: quant_window   : 3
1:46:51.107256 INFO: ==============================================
1:46:51.246807 INFO: performing precursor FDR with 40 features
1:46:51.246922 INFO: Decoy channel: -1
1:46:51.246946 INFO: competitive: True
1:46:51.258507 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:51.265818 INFO: Estimating optimal hyperparameters - samples: 23,615, batch_size: 128, learning_rate: 1.77e-04
1:46:51.266022 INFO: Using random state 218104 for train-test-split
1:46:53.727057 INFO: Test AUC: 0.565
1:46:53.727174 INFO: Train AUC: 0.597
1:46:53.727202 INFO: AUC difference: 5.22%
1:46:53.727223 WARNING: AUC difference > 5%. This may indicate overfitting.
1:46:53.987508 INFO: Resetting torch num_threads to 100
1:46:53.993928 PROGRESS: === Extracted 29519 precursors and 165090 fragments ===
1:46:53.994457 INFO: === FDR correction performed with classifier version -1 ===
1:46:53.994998 PROGRESS: ============================= Precursor FDR =============================
1:46:53.995082 PROGRESS: Total precursors accumulated: 104
1:46:53.995152 PROGRESS: Target precursors: 103 (99.04%)
1:46:53.995200 PROGRESS: Decoy precursors: 1 (0.96%)
1:46:53.995243 PROGRESS: 
1:46:53.995286 PROGRESS: Precursor Summary:
1:46:53.996259 PROGRESS: Channel   0:	 0.050 FDR:   103; 0.010 FDR:   103; 0.001 FDR:    90
1:46:53.996342 PROGRESS: 
1:46:53.996395 PROGRESS: Protein Summary:
1:46:53.997484 PROGRESS: Channel   0:	 0.050 FDR:   101; 0.010 FDR:   101; 0.001 FDR:    88
1:46:53.997566 PROGRESS: =========================================================================
1:46:53.998090 INFO: Target number of precursors not reached yet.
1:46:54.128797 INFO: Starting optimization step 4.
1:46:54.129052 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:46:54.129129 INFO: Using rust extraction backend
1:46:54.129189 PROGRESS: Extracting batch of 31568 precursors
1:46:54.184174 INFO: === Search parameters used ===
1:46:54.184412 INFO: rt_error       : 805.611083984375
1:46:54.184479 INFO: mobility_error : 0.1
1:46:54.184526 INFO: num_candidates : 1
1:46:54.184571 INFO: ms1_error      : 3
1:46:54.184613 INFO: ms2_error      : 10
1:46:54.184654 INFO: fwhm_rt        : 5
1:46:54.184693 INFO: quant_window   : 3
1:46:54.184732 INFO: ==============================================
1:46:54.406222 INFO: performing precursor FDR with 40 features
1:46:54.406335 INFO: Decoy channel: -1
1:46:54.406359 INFO: competitive: True
1:46:54.432775 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:54.448341 INFO: Estimating optimal hyperparameters - samples: 48,796, batch_size: 199, learning_rate: 2.20e-04
1:46:54.448570 INFO: Using random state 888749 for train-test-split
1:46:58.177379 INFO: Test AUC: 0.593
1:46:58.177496 INFO: Train AUC: 0.602
1:46:58.177526 INFO: AUC difference: 1.63%
1:46:58.449363 INFO: Resetting torch num_threads to 100
1:46:58.460423 PROGRESS: === Extracted 60995 precursors and 341336 fragments ===
1:46:58.461062 INFO: === FDR correction performed with classifier version -1 ===
1:46:58.461643 PROGRESS: ============================= Precursor FDR =============================
1:46:58.461743 PROGRESS: Total precursors accumulated: 276
1:46:58.461807 PROGRESS: Target precursors: 274 (99.28%)
1:46:58.461861 PROGRESS: Decoy precursors: 2 (0.72%)
1:46:58.461933 PROGRESS: 
1:46:58.461991 PROGRESS: Precursor Summary:
1:46:58.463019 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:     1
1:46:58.463108 PROGRESS: 
1:46:58.463166 PROGRESS: Protein Summary:
1:46:58.464317 PROGRESS: Channel   0:	 0.050 FDR:   259; 0.010 FDR:   259; 0.001 FDR:     1
1:46:58.464407 PROGRESS: =========================================================================
1:46:58.465389 INFO: Target number of precursors not reached yet.
1:46:58.629093 INFO: Starting optimization step 5.
1:46:58.629384 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:46:58.629470 INFO: Using rust extraction backend
1:46:58.629534 PROGRESS: Extracting batch of 63098 precursors
1:46:58.738168 INFO: === Search parameters used ===
1:46:58.738456 INFO: rt_error       : 805.611083984375
1:46:58.738510 INFO: mobility_error : 0.1
1:46:58.738557 INFO: num_candidates : 1
1:46:58.738601 INFO: ms1_error      : 3
1:46:58.738643 INFO: ms2_error      : 10
1:46:58.738685 INFO: fwhm_rt        : 5
1:46:58.738726 INFO: quant_window   : 3
1:46:58.738766 INFO: ==============================================
1:46:59.121270 INFO: performing precursor FDR with 40 features
1:46:59.121385 INFO: Decoy channel: -1
1:46:59.121410 INFO: competitive: True
1:46:59.167303 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:59.198346 INFO: Estimating optimal hyperparameters - samples: 99,132, batch_size: 406, learning_rate: 3.15e-04
1:46:59.198670 INFO: Using random state 565937 for train-test-split
1:47:04.112062 INFO: Test AUC: 0.584
1:47:04.112189 INFO: Train AUC: 0.609
1:47:04.112221 INFO: AUC difference: 4.16%
1:47:04.403057 INFO: Resetting torch num_threads to 100
1:47:04.434606 PROGRESS: === Extracted 123916 precursors and 694071 fragments ===
1:47:04.435335 INFO: === FDR correction performed with classifier version -1 ===
1:47:04.436001 PROGRESS: ============================= Precursor FDR =============================
1:47:04.436094 PROGRESS: Total precursors accumulated: 529
1:47:04.436156 PROGRESS: Target precursors: 524 (99.05%)
1:47:04.436208 PROGRESS: Decoy precursors: 5 (0.95%)
1:47:04.436255 PROGRESS: 
1:47:04.436303 PROGRESS: Precursor Summary:
1:47:04.437399 PROGRESS: Channel   0:	 0.050 FDR:   524; 0.010 FDR:   524; 0.001 FDR:    12
1:47:04.437500 PROGRESS: 
1:47:04.437557 PROGRESS: Protein Summary:
1:47:04.438827 PROGRESS: Channel   0:	 0.050 FDR:   482; 0.010 FDR:   482; 0.001 FDR:    12
1:47:04.438921 PROGRESS: =========================================================================
1:47:04.441140 INFO: Target number of precursors not reached yet.
1:47:04.734757 INFO: Starting optimization step 6.
1:47:04.735030 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:47:04.735159 INFO: Using rust extraction backend
1:47:04.735238 PROGRESS: Extracting batch of 126185 precursors
1:47:04.950377 INFO: === Search parameters used ===
1:47:04.950656 INFO: rt_error       : 805.611083984375
1:47:04.950715 INFO: mobility_error : 0.1
1:47:04.950763 INFO: num_candidates : 1
1:47:04.950807 INFO: ms1_error      : 3
1:47:04.950848 INFO: ms2_error      : 10
1:47:04.950890 INFO: fwhm_rt        : 5
1:47:04.950931 INFO: quant_window   : 3
1:47:04.950971 INFO: ==============================================
1:47:05.635158 INFO: performing precursor FDR with 40 features
1:47:05.635288 INFO: Decoy channel: -1
1:47:05.635332 INFO: competitive: True
1:47:05.729390 INFO: Setting torch num_threads to 2 for FDR classification task
1:47:05.813103 INFO: Estimating optimal hyperparameters - samples: 199,856, batch_size: 818, learning_rate: 4.47e-04
1:47:05.813634 INFO: Using random state 883105 for train-test-split
1:47:12.293335 INFO: Test AUC: 0.597
1:47:12.293445 INFO: Train AUC: 0.609
1:47:12.293476 INFO: AUC difference: 2.01%
1:47:12.618226 INFO: Resetting torch num_threads to 100
1:47:12.660407 PROGRESS: === Extracted 249820 precursors and 1399269 fragments ===
1:47:12.661080 INFO: === FDR correction performed with classifier version -1 ===
1:47:12.661853 PROGRESS: ============================= Precursor FDR =============================
1:47:12.661978 PROGRESS: Total precursors accumulated: 1,169
1:47:12.662058 PROGRESS: Target precursors: 1,158 (99.06%)
1:47:12.662111 PROGRESS: Decoy precursors: 11 (0.94%)
1:47:12.662157 PROGRESS: 
1:47:12.662202 PROGRESS: Precursor Summary:
1:47:12.663409 PROGRESS: Channel   0:	 0.050 FDR: 1,158; 0.010 FDR: 1,158; 0.001 FDR:     0
1:47:12.663500 PROGRESS: 
1:47:12.663556 PROGRESS: Protein Summary:
1:47:12.665035 PROGRESS: Channel   0:	 0.050 FDR:   979; 0.010 FDR:   979; 0.001 FDR:     0
1:47:12.665124 PROGRESS: =========================================================================
1:47:12.668802 INFO: Target number of precursors reached.
1:47:12.830721 INFO: fragments_df: keeping 5000 of 1399269 [sum(precursor_idx_mask)=12473 sum(mass_error_mask)=1399269 stop_rank=5000
1:47:13.233216 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:47:13.440487 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:47:14.161097 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:47:14.161548 INFO: Using score_cutoff 12.148524470901489 (fac=0.99, q=1)
1:47:14.161883 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:47:14.161976 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:47:14.162033 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.148524470901489
1:47:14.162091 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:47:14.311162 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:47:14.650249 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:47:14.650506 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:47:14.650601 INFO: Starting optimization step 7.
1:47:14.650664 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:47:14.650730 INFO: Using rust extraction backend
1:47:14.650785 PROGRESS: Extracting batch of 250439 precursors
1:47:15.071434 INFO: === Search parameters used ===
1:47:15.071702 INFO: rt_error       : 805.611083984375
1:47:15.071762 INFO: mobility_error : 0.1
1:47:15.071809 INFO: num_candidates : 3
1:47:15.071854 INFO: ms1_error      : 3
1:47:15.071898 INFO: ms2_error      : 10
1:47:15.071940 INFO: fwhm_rt        : 3.0
1:47:15.071980 INFO: quant_window   : 3
1:47:15.072022 INFO: ==============================================
1:47:17.690283 INFO: performing precursor FDR with 40 features
1:47:17.690404 INFO: Decoy channel: -1
1:47:17.690434 INFO: competitive: True
1:47:17.918249 INFO: Setting torch num_threads to 2 for FDR classification task
1:47:18.209049 INFO: Estimating optimal hyperparameters - samples: 599,876, batch_size: 2,457, learning_rate: 7.75e-04
1:47:18.210248 INFO: Using random state 571581 for train-test-split
1:47:31.311783 INFO: Test AUC: 0.599
1:47:31.312007 INFO: Train AUC: 0.607
1:47:31.312043 INFO: AUC difference: 1.37%
1:47:31.794745 INFO: Resetting torch num_threads to 100
1:47:31.825477 PROGRESS: === Extracted 749845 precursors and 4031574 fragments ===
1:47:31.826034 INFO: === FDR correction performed with classifier version 6 ===
1:47:31.826709 PROGRESS: ============================= Precursor FDR =============================
1:47:31.826802 PROGRESS: Total precursors accumulated: 1,368
1:47:31.826862 PROGRESS: Target precursors: 1,355 (99.05%)
1:47:31.826928 PROGRESS: Decoy precursors: 13 (0.95%)
1:47:31.826981 PROGRESS: 
1:47:31.827029 PROGRESS: Precursor Summary:
1:47:31.828380 PROGRESS: Channel   0:	 0.050 FDR: 1,355; 0.010 FDR: 1,355; 0.001 FDR: 1,097
1:47:31.828483 PROGRESS: 
1:47:31.828539 PROGRESS: Protein Summary:
1:47:31.830307 PROGRESS: Channel   0:	 0.050 FDR: 1,139; 0.010 FDR: 1,139; 0.001 FDR:   940
1:47:31.830407 PROGRESS: =========================================================================
1:47:31.847325 INFO: Target number of precursors reached.
1:47:32.284510 INFO: fragments_df: keeping 5000 of 4031574 [sum(precursor_idx_mask)=32543 sum(mass_error_mask)=4031574 stop_rank=5000
1:47:32.865481 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:47:33.090486 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:47:33.807121 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:47:33.807566 INFO: Using score_cutoff 11.695393648910523 (fac=0.99, q=1)
1:47:33.807934 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:47:33.808012 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:47:33.808065 INFO: Updating optimization_manager: score_cutoff        : 12.148524470901489 -> 11.695393648910523
1:47:33.808121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:47:33.957189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:47:34.282085 INFO: === checking if optimization conditions were reached ===
1:47:34.284681 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:47:34.284791 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:47:34.284858 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:47:34.284916 INFO: ==============================================
1:47:34.285010 INFO: Starting optimization step 8.
1:47:34.285072 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:47:34.285146 INFO: Using rust extraction backend
1:47:34.285212 PROGRESS: Extracting batch of 250439 precursors
1:47:34.705543 INFO: === Search parameters used ===
1:47:34.705810 INFO: rt_error       : 805.611083984375
1:47:34.705865 INFO: mobility_error : 0.1
1:47:34.705921 INFO: num_candidates : 3
1:47:34.705967 INFO: ms1_error      : 3
1:47:34.706008 INFO: ms2_error      : 10.0
1:47:34.706048 INFO: fwhm_rt        : 3.0
1:47:34.706088 INFO: quant_window   : 3
1:47:34.706128 INFO: ==============================================
1:47:37.236195 INFO: performing precursor FDR with 40 features
1:47:37.236331 INFO: Decoy channel: -1
1:47:37.236358 INFO: competitive: True
1:47:37.418401 INFO: Setting torch num_threads to 2 for FDR classification task
1:47:37.709346 INFO: Estimating optimal hyperparameters - samples: 599,866, batch_size: 2,457, learning_rate: 7.75e-04
1:47:37.710551 INFO: Using random state 579698 for train-test-split
1:47:50.493882 INFO: Test AUC: 0.606
1:47:50.494054 INFO: Train AUC: 0.614
1:47:50.494087 INFO: AUC difference: 1.36%
1:47:50.980444 INFO: Resetting torch num_threads to 100
1:47:51.012422 PROGRESS: === Extracted 749833 precursors and 4031263 fragments ===
1:47:51.012926 INFO: === FDR correction performed with classifier version 7 ===
1:47:51.013824 PROGRESS: ============================= Precursor FDR =============================
1:47:51.013927 PROGRESS: Total precursors accumulated: 1,439
1:47:51.014002 PROGRESS: Target precursors: 1,425 (99.03%)
1:47:51.014054 PROGRESS: Decoy precursors: 14 (0.97%)
1:47:51.014101 PROGRESS: 
1:47:51.014145 PROGRESS: Precursor Summary:
1:47:51.015477 PROGRESS: Channel   0:	 0.050 FDR: 1,425; 0.010 FDR: 1,425; 0.001 FDR: 1,094
1:47:51.015563 PROGRESS: 
1:47:51.015620 PROGRESS: Protein Summary:
1:47:51.017353 PROGRESS: Channel   0:	 0.050 FDR: 1,195; 0.010 FDR: 1,195; 0.001 FDR:   939
1:47:51.017443 PROGRESS: =========================================================================
1:47:51.032597 INFO: Target number of precursors reached.
1:47:51.471073 INFO: fragments_df: keeping 5000 of 4031263 [sum(precursor_idx_mask)=34387 sum(mass_error_mask)=4031263 stop_rank=5000
1:47:51.923918 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:47:52.148669 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:47:52.865466 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:47:52.865930 INFO: Using score_cutoff 11.806944636154174 (fac=0.99, q=1)
1:47:52.866271 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:47:52.866351 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:47:52.866405 INFO: Updating optimization_manager: score_cutoff        : 11.695393648910523 -> 11.806944636154174
1:47:52.866460 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:47:53.017635 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:47:53.345684 INFO: === checking if optimization conditions were reached ===
1:47:53.347858 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:47:53.347959 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:47:53.348025 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:47:53.348083 INFO: ==============================================
1:47:53.348156 INFO: Starting optimization step 9.
1:47:53.348216 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:47:53.348280 INFO: Using rust extraction backend
1:47:53.348341 PROGRESS: Extracting batch of 250439 precursors
1:47:53.768259 INFO: === Search parameters used ===
1:47:53.768525 INFO: rt_error       : 805.611083984375
1:47:53.768580 INFO: mobility_error : 0.1
1:47:53.768628 INFO: num_candidates : 3
1:47:53.768672 INFO: ms1_error      : 3
1:47:53.768716 INFO: ms2_error      : 10.0
1:47:53.768758 INFO: fwhm_rt        : 3.0
1:47:53.768800 INFO: quant_window   : 3
1:47:53.768842 INFO: ==============================================
1:47:56.312615 INFO: performing precursor FDR with 40 features
1:47:56.312735 INFO: Decoy channel: -1
1:47:56.312759 INFO: competitive: True
1:47:56.485220 INFO: Setting torch num_threads to 2 for FDR classification task
1:47:56.770046 INFO: Estimating optimal hyperparameters - samples: 599,868, batch_size: 2,457, learning_rate: 7.75e-04
1:47:56.771104 INFO: Using random state 266709 for train-test-split
1:48:09.675630 INFO: Test AUC: 0.607
1:48:09.675781 INFO: Train AUC: 0.618
1:48:09.675816 INFO: AUC difference: 1.74%
1:48:10.155491 INFO: Resetting torch num_threads to 100
1:48:10.186852 PROGRESS: === Extracted 749836 precursors and 4032275 fragments ===
1:48:10.187391 INFO: === FDR correction performed with classifier version 8 ===
1:48:10.188066 PROGRESS: ============================= Precursor FDR =============================
1:48:10.188180 PROGRESS: Total precursors accumulated: 1,394
1:48:10.188242 PROGRESS: Target precursors: 1,381 (99.07%)
1:48:10.188293 PROGRESS: Decoy precursors: 13 (0.93%)
1:48:10.188339 PROGRESS: 
1:48:10.188384 PROGRESS: Precursor Summary:
1:48:10.189801 PROGRESS: Channel   0:	 0.050 FDR: 1,381; 0.010 FDR: 1,381; 0.001 FDR: 1,243
1:48:10.189896 PROGRESS: 
1:48:10.189971 PROGRESS: Protein Summary:
1:48:10.191726 PROGRESS: Channel   0:	 0.050 FDR: 1,165; 0.010 FDR: 1,165; 0.001 FDR: 1,055
1:48:10.191820 PROGRESS: =========================================================================
1:48:10.204667 INFO: Target number of precursors reached.
1:48:10.654000 INFO: fragments_df: keeping 5000 of 4032275 [sum(precursor_idx_mask)=33397 sum(mass_error_mask)=4032275 stop_rank=5000
1:48:11.057712 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:48:11.273206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:48:11.993806 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:48:11.994255 INFO: Using score_cutoff 11.757879959106445 (fac=0.99, q=1)
1:48:11.994562 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:48:11.994638 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:48:11.994691 INFO: Updating optimization_manager: score_cutoff        : 11.806944636154174 -> 11.757879959106445
1:48:11.994752 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:48:12.144398 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:48:12.470901 INFO: === checking if optimization conditions were reached ===
1:48:12.473074 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:48:12.473171 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:48:12.473236 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:48:12.473294 INFO: ==============================================
1:48:12.473360 INFO: Starting optimization step 10.
1:48:12.473416 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:48:12.473474 INFO: Using rust extraction backend
1:48:12.473528 PROGRESS: Extracting batch of 250439 precursors
1:48:12.892094 INFO: === Search parameters used ===
1:48:12.892357 INFO: rt_error       : 805.611083984375
1:48:12.892409 INFO: mobility_error : 0.1
1:48:12.892455 INFO: num_candidates : 3
1:48:12.892517 INFO: ms1_error      : 3
1:48:12.892556 INFO: ms2_error      : 10.0
1:48:12.892595 INFO: fwhm_rt        : 3.0
1:48:12.892633 INFO: quant_window   : 3
1:48:12.892671 INFO: ==============================================
1:48:15.398364 INFO: performing precursor FDR with 40 features
1:48:15.398490 INFO: Decoy channel: -1
1:48:15.398516 INFO: competitive: True
1:48:15.576046 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:15.859573 INFO: Estimating optimal hyperparameters - samples: 599,870, batch_size: 2,457, learning_rate: 7.75e-04
1:48:15.860707 INFO: Using random state 971606 for train-test-split
1:48:28.679760 INFO: Test AUC: 0.609
1:48:28.679923 INFO: Train AUC: 0.621
1:48:28.679956 INFO: AUC difference: 2.01%
1:48:29.173796 INFO: Resetting torch num_threads to 100
1:48:29.240423 PROGRESS: === Extracted 749838 precursors and 4032447 fragments ===
1:48:29.240945 INFO: === FDR correction performed with classifier version 9 ===
1:48:29.241722 PROGRESS: ============================= Precursor FDR =============================
1:48:29.241819 PROGRESS: Total precursors accumulated: 1,568
1:48:29.241879 PROGRESS: Target precursors: 1,553 (99.04%)
1:48:29.241946 PROGRESS: Decoy precursors: 15 (0.96%)
1:48:29.242001 PROGRESS: 
1:48:29.242046 PROGRESS: Precursor Summary:
1:48:29.243433 PROGRESS: Channel   0:	 0.050 FDR: 1,553; 0.010 FDR: 1,553; 0.001 FDR: 1,060
1:48:29.243527 PROGRESS: 
1:48:29.243585 PROGRESS: Protein Summary:
1:48:29.245356 PROGRESS: Channel   0:	 0.050 FDR: 1,306; 0.010 FDR: 1,306; 0.001 FDR:   921
1:48:29.245454 PROGRESS: =========================================================================
1:48:29.259538 INFO: Target number of precursors reached.
1:48:29.707064 INFO: fragments_df: keeping 5000 of 4032447 [sum(precursor_idx_mask)=36753 sum(mass_error_mask)=4032447 stop_rank=5000
1:48:30.234097 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:48:30.451025 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:48:31.101177 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:48:31.101625 INFO: Using score_cutoff 10.997487268066406 (fac=0.99, q=1)
1:48:31.101953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:48:31.102034 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:48:31.102088 INFO: Updating optimization_manager: score_cutoff        : 11.757879959106445 -> 10.997487268066406
1:48:31.102147 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:48:31.250408 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:48:31.586795 INFO: === checking if optimization conditions were reached ===
1:48:31.589057 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:48:31.589195 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:48:31.589263 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:48:31.589326 INFO: ==============================================
1:48:31.589401 INFO: Starting optimization step 11.
1:48:31.589479 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:48:31.589545 INFO: Using rust extraction backend
1:48:31.589604 PROGRESS: Extracting batch of 250439 precursors
1:48:32.009243 INFO: === Search parameters used ===
1:48:32.009511 INFO: rt_error       : 805.611083984375
1:48:32.009564 INFO: mobility_error : 0.1
1:48:32.009609 INFO: num_candidates : 3
1:48:32.009651 INFO: ms1_error      : 3
1:48:32.009691 INFO: ms2_error      : 10.0
1:48:32.009730 INFO: fwhm_rt        : 3.0
1:48:32.009769 INFO: quant_window   : 3
1:48:32.009807 INFO: ==============================================
1:48:34.558169 INFO: performing precursor FDR with 40 features
1:48:34.558293 INFO: Decoy channel: -1
1:48:34.558320 INFO: competitive: True
1:48:34.731886 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:35.011533 INFO: Estimating optimal hyperparameters - samples: 599,869, batch_size: 2,457, learning_rate: 7.75e-04
1:48:35.012666 INFO: Using random state 634373 for train-test-split
1:48:47.861066 INFO: Test AUC: 0.613
1:48:47.861204 INFO: Train AUC: 0.623
1:48:47.861236 INFO: AUC difference: 1.73%
1:48:48.341735 INFO: Resetting torch num_threads to 100
1:48:48.365778 PROGRESS: === Extracted 749837 precursors and 4032071 fragments ===
1:48:48.366613 INFO: === FDR correction performed with classifier version 10 ===
1:48:48.367297 PROGRESS: ============================= Precursor FDR =============================
1:48:48.367393 PROGRESS: Total precursors accumulated: 1,622
1:48:48.367453 PROGRESS: Target precursors: 1,606 (99.01%)
1:48:48.367504 PROGRESS: Decoy precursors: 16 (0.99%)
1:48:48.367551 PROGRESS: 
1:48:48.367596 PROGRESS: Precursor Summary:
1:48:48.368978 PROGRESS: Channel   0:	 0.050 FDR: 1,606; 0.010 FDR: 1,606; 0.001 FDR: 1,107
1:48:48.369070 PROGRESS: 
1:48:48.369126 PROGRESS: Protein Summary:
1:48:48.370956 PROGRESS: Channel   0:	 0.050 FDR: 1,351; 0.010 FDR: 1,351; 0.001 FDR:   948
1:48:48.371060 PROGRESS: =========================================================================
1:48:48.383745 INFO: Target number of precursors reached.
1:48:48.829120 INFO: fragments_df: keeping 5000 of 4032071 [sum(precursor_idx_mask)=37802 sum(mass_error_mask)=4032071 stop_rank=5000
1:48:49.238241 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:48:49.486889 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:48:50.207028 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:48:50.207469 INFO: Using score_cutoff 10.683670818328858 (fac=0.99, q=1)
1:48:50.207781 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:48:50.207860 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:48:50.207921 INFO: Updating optimization_manager: score_cutoff        : 10.997487268066406 -> 10.683670818328858
1:48:50.207978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:48:50.357117 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:48:50.692156 INFO: === checking if optimization conditions were reached ===
1:48:50.694342 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:48:50.694448 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:48:50.694512 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:48:50.694571 INFO: ==============================================
1:48:50.694670 PROGRESS: Optimization finished for ms2_error.
1:48:51.086298 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:48:51.236565 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:48:51.572204 INFO: Starting optimization step 0.
1:48:51.572456 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:48:51.572533 INFO: Using rust extraction backend
1:48:51.572596 PROGRESS: Extracting batch of 250439 precursors
1:48:51.991489 INFO: === Search parameters used ===
1:48:51.991757 INFO: rt_error       : 805.611083984375
1:48:51.991812 INFO: mobility_error : 0.1
1:48:51.991859 INFO: num_candidates : 3
1:48:51.991903 INFO: ms1_error      : 3
1:48:51.991964 INFO: ms2_error      : 10.0
1:48:51.992014 INFO: fwhm_rt        : 3.0
1:48:51.992054 INFO: quant_window   : 3
1:48:51.992092 INFO: ==============================================
1:48:54.505893 INFO: performing precursor FDR with 40 features
1:48:54.506027 INFO: Decoy channel: -1
1:48:54.506051 INFO: competitive: True
1:48:54.675869 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:54.952584 INFO: Estimating optimal hyperparameters - samples: 599,868, batch_size: 2,457, learning_rate: 7.75e-04
1:48:54.953677 INFO: Using random state 295042 for train-test-split
1:49:07.020015 INFO: Test AUC: 0.611
1:49:07.020149 INFO: Train AUC: 0.625
1:49:07.020182 INFO: AUC difference: 2.24%
1:49:07.496525 INFO: Resetting torch num_threads to 100
1:49:07.524649 PROGRESS: === Extracted 749835 precursors and 4032219 fragments ===
1:49:07.525111 INFO: === FDR correction performed with classifier version 11 ===
1:49:07.525810 PROGRESS: ============================= Precursor FDR =============================
1:49:07.525918 PROGRESS: Total precursors accumulated: 1,525
1:49:07.525985 PROGRESS: Target precursors: 1,510 (99.02%)
1:49:07.526039 PROGRESS: Decoy precursors: 15 (0.98%)
1:49:07.526087 PROGRESS: 
1:49:07.526135 PROGRESS: Precursor Summary:
1:49:07.527452 PROGRESS: Channel   0:	 0.050 FDR: 1,510; 0.010 FDR: 1,510; 0.001 FDR:   349
1:49:07.527542 PROGRESS: 
1:49:07.527598 PROGRESS: Protein Summary:
1:49:07.529259 PROGRESS: Channel   0:	 0.050 FDR: 1,272; 0.010 FDR: 1,272; 0.001 FDR:   320
1:49:07.529350 PROGRESS: =========================================================================
1:49:07.542332 INFO: Target number of precursors reached.
1:49:07.999798 INFO: fragments_df: keeping 5000 of 4032219 [sum(precursor_idx_mask)=35904 sum(mass_error_mask)=4032219 stop_rank=5000
1:49:08.401586 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:49:08.644406 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:49:09.360151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:49:09.360597 INFO: Using score_cutoff 11.038800245189666 (fac=0.99, q=1)
1:49:09.360898 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:49:09.360976 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:49:09.361032 INFO: Updating optimization_manager: score_cutoff        : 10.683670818328858 -> 11.038800245189666
1:49:09.361087 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:49:09.508074 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:49:09.830403 INFO: === checking if optimization conditions were reached ===
1:49:09.830710 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:49:09.833449 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 931.3225552835181
1:49:09.833563 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 931.3226.
1:49:09.833627 INFO: ==============================================
1:49:09.833695 INFO: Starting optimization step 1.
1:49:09.833752 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:49:09.833811 INFO: Using rust extraction backend
1:49:09.833863 PROGRESS: Extracting batch of 250439 precursors
1:49:10.253011 INFO: === Search parameters used ===
1:49:10.253280 INFO: rt_error       : 931.3225552835181
1:49:10.253333 INFO: mobility_error : 0.1
1:49:10.253398 INFO: num_candidates : 3
1:49:10.253445 INFO: ms1_error      : 3
1:49:10.253488 INFO: ms2_error      : 10.0
1:49:10.253528 INFO: fwhm_rt        : 3.0
1:49:10.253568 INFO: quant_window   : 3
1:49:10.253608 INFO: ==============================================
1:49:12.791039 INFO: performing precursor FDR with 40 features
1:49:12.791164 INFO: Decoy channel: -1
1:49:12.791190 INFO: competitive: True
1:49:12.968369 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:13.255491 INFO: Estimating optimal hyperparameters - samples: 599,866, batch_size: 2,457, learning_rate: 7.75e-04
1:49:13.256613 INFO: Using random state 295042 for train-test-split
1:49:25.637275 INFO: Test AUC: 0.614
1:49:25.637412 INFO: Train AUC: 0.627
1:49:25.637444 INFO: AUC difference: 2.06%
1:49:26.118730 INFO: Resetting torch num_threads to 100
1:49:26.147086 PROGRESS: === Extracted 749833 precursors and 4032712 fragments ===
1:49:26.147581 INFO: === FDR correction performed with classifier version 11 ===
1:49:26.148296 PROGRESS: ============================= Precursor FDR =============================
1:49:26.148395 PROGRESS: Total precursors accumulated: 1,550
1:49:26.148456 PROGRESS: Target precursors: 1,535 (99.03%)
1:49:26.148508 PROGRESS: Decoy precursors: 15 (0.97%)
1:49:26.148555 PROGRESS: 
1:49:26.148601 PROGRESS: Precursor Summary:
1:49:26.150084 PROGRESS: Channel   0:	 0.050 FDR: 1,535; 0.010 FDR: 1,535; 0.001 FDR: 1,236
1:49:26.150183 PROGRESS: 
1:49:26.150240 PROGRESS: Protein Summary:
1:49:26.152036 PROGRESS: Channel   0:	 0.050 FDR: 1,291; 0.010 FDR: 1,291; 0.001 FDR: 1,049
1:49:26.152129 PROGRESS: =========================================================================
1:49:26.166547 INFO: Target number of precursors reached.
1:49:26.611217 INFO: fragments_df: keeping 5000 of 4032712 [sum(precursor_idx_mask)=36548 sum(mass_error_mask)=4032712 stop_rank=5000
1:49:27.013504 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:49:27.252814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:49:27.968843 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:49:27.969294 INFO: Using score_cutoff 11.334480841255187 (fac=0.99, q=1)
1:49:27.969599 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:49:27.969683 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:49:27.969736 INFO: Updating optimization_manager: score_cutoff        : 11.038800245189666 -> 11.334480841255187
1:49:27.969789 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:49:28.119305 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:49:28.465573 INFO: === checking if optimization conditions were reached ===
1:49:28.465846 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:49:28.468609 INFO: Updating optimization_manager: rt_error            : 931.3225552835181 -> 351.64760229902527
1:49:28.468709 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 351.6476.
1:49:28.468772 INFO: ==============================================
1:49:28.468841 INFO: Starting optimization step 2.
1:49:28.468900 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:49:28.468962 INFO: Using rust extraction backend
1:49:28.469018 PROGRESS: Extracting batch of 250439 precursors
1:49:28.887810 INFO: === Search parameters used ===
1:49:28.888089 INFO: rt_error       : 351.64760229902527
1:49:28.888145 INFO: mobility_error : 0.1
1:49:28.888192 INFO: num_candidates : 3
1:49:28.888236 INFO: ms1_error      : 3
1:49:28.888279 INFO: ms2_error      : 10.0
1:49:28.888319 INFO: fwhm_rt        : 3.0
1:49:28.888360 INFO: quant_window   : 3
1:49:28.888401 INFO: ==============================================
1:49:31.215799 INFO: performing precursor FDR with 40 features
1:49:31.215922 INFO: Decoy channel: -1
1:49:31.215948 INFO: competitive: True
1:49:31.400226 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:31.684959 INFO: Estimating optimal hyperparameters - samples: 597,483, batch_size: 2,447, learning_rate: 7.73e-04
1:49:31.686089 INFO: Using random state 295042 for train-test-split
1:49:44.115420 INFO: Test AUC: 0.606
1:49:44.115553 INFO: Train AUC: 0.620
1:49:44.115586 INFO: AUC difference: 2.18%
1:49:44.600419 INFO: Resetting torch num_threads to 100
1:49:44.629063 PROGRESS: === Extracted 746854 precursors and 3802223 fragments ===
1:49:44.629568 INFO: === FDR correction performed with classifier version 11 ===
1:49:44.630300 PROGRESS: ============================= Precursor FDR =============================
1:49:44.630402 PROGRESS: Total precursors accumulated: 1,571
1:49:44.630479 PROGRESS: Target precursors: 1,556 (99.05%)
1:49:44.630532 PROGRESS: Decoy precursors: 15 (0.95%)
1:49:44.630584 PROGRESS: 
1:49:44.630630 PROGRESS: Precursor Summary:
1:49:44.632029 PROGRESS: Channel   0:	 0.050 FDR: 1,556; 0.010 FDR: 1,556; 0.001 FDR: 1,094
1:49:44.632122 PROGRESS: 
1:49:44.632181 PROGRESS: Protein Summary:
1:49:44.633974 PROGRESS: Channel   0:	 0.050 FDR: 1,289; 0.010 FDR: 1,289; 0.001 FDR:   932
1:49:44.634072 PROGRESS: =========================================================================
1:49:44.648830 INFO: Target number of precursors reached.
1:49:45.071057 INFO: fragments_df: keeping 5000 of 3802223 [sum(precursor_idx_mask)=36932 sum(mass_error_mask)=3802223 stop_rank=5000
1:49:45.473933 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:49:45.708240 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:49:46.426957 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:49:46.427402 INFO: Using score_cutoff 11.341392693042756 (fac=0.99, q=1)
1:49:46.427713 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:49:46.427786 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:49:46.427836 INFO: Updating optimization_manager: score_cutoff        : 11.334480841255187 -> 11.341392693042756
1:49:46.427887 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:49:46.576771 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:49:46.921016 INFO: === checking if optimization conditions were reached ===
1:49:46.921287 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:49:46.924179 INFO: Updating optimization_manager: rt_error            : 351.64760229902527 -> 315.6408082087595
1:49:46.924283 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 315.6408.
1:49:46.924348 INFO: ==============================================
1:49:46.924415 INFO: Starting optimization step 3.
1:49:46.924470 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:49:46.924528 INFO: Using rust extraction backend
1:49:46.924600 PROGRESS: Extracting batch of 250439 precursors
1:49:47.343429 INFO: === Search parameters used ===
1:49:47.343703 INFO: rt_error       : 315.6408082087595
1:49:47.343764 INFO: mobility_error : 0.1
1:49:47.343814 INFO: num_candidates : 3
1:49:47.343859 INFO: ms1_error      : 3
1:49:47.343903 INFO: ms2_error      : 10.0
1:49:47.343945 INFO: fwhm_rt        : 3.0
1:49:47.343987 INFO: quant_window   : 3
1:49:47.344028 INFO: ==============================================
1:49:49.638702 INFO: performing precursor FDR with 40 features
1:49:49.638824 INFO: Decoy channel: -1
1:49:49.638851 INFO: competitive: True
1:49:49.814391 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:50.106895 INFO: Estimating optimal hyperparameters - samples: 596,896, batch_size: 2,444, learning_rate: 7.72e-04
1:49:50.107867 INFO: Using random state 295042 for train-test-split
1:50:02.101841 INFO: Test AUC: 0.603
1:50:02.102037 INFO: Train AUC: 0.619
1:50:02.102070 INFO: AUC difference: 2.66%
1:50:02.583371 INFO: Resetting torch num_threads to 100
1:50:02.608026 PROGRESS: === Extracted 746121 precursors and 3736228 fragments ===
1:50:02.608521 INFO: === FDR correction performed with classifier version 11 ===
1:50:02.609182 PROGRESS: ============================= Precursor FDR =============================
1:50:02.609271 PROGRESS: Total precursors accumulated: 1,696
1:50:02.609330 PROGRESS: Target precursors: 1,680 (99.06%)
1:50:02.609383 PROGRESS: Decoy precursors: 16 (0.94%)
1:50:02.609432 PROGRESS: 
1:50:02.609482 PROGRESS: Precursor Summary:
1:50:02.610877 PROGRESS: Channel   0:	 0.050 FDR: 1,680; 0.010 FDR: 1,680; 0.001 FDR: 1,202
1:50:02.610972 PROGRESS: 
1:50:02.611030 PROGRESS: Protein Summary:
1:50:02.612856 PROGRESS: Channel   0:	 0.050 FDR: 1,404; 0.010 FDR: 1,404; 0.001 FDR: 1,020
1:50:02.612977 PROGRESS: =========================================================================
1:50:02.626969 INFO: Target number of precursors reached.
1:50:03.035154 INFO: fragments_df: keeping 5000 of 3736228 [sum(precursor_idx_mask)=39010 sum(mass_error_mask)=3736228 stop_rank=5000
1:50:03.442026 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:03.657953 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:04.311702 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:50:04.312152 INFO: Using score_cutoff 10.38956852760315 (fac=0.99, q=1)
1:50:04.312480 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:50:04.312560 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:50:04.312617 INFO: Updating optimization_manager: score_cutoff        : 11.341392693042756 -> 10.38956852760315
1:50:04.312675 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:04.460648 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:04.784325 INFO: === checking if optimization conditions were reached ===
1:50:04.784587 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:50:04.787579 INFO: Updating optimization_manager: rt_error            : 315.6408082087595 -> 395.4301920554706
1:50:04.787685 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 395.4302.
1:50:04.787751 INFO: ==============================================
1:50:04.787822 INFO: Starting optimization step 4.
1:50:04.787897 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:50:04.787958 INFO: Using rust extraction backend
1:50:04.788013 PROGRESS: Extracting batch of 250439 precursors
1:50:05.206944 INFO: === Search parameters used ===
1:50:05.207211 INFO: rt_error       : 395.4301920554706
1:50:05.207266 INFO: mobility_error : 0.1
1:50:05.207314 INFO: num_candidates : 3
1:50:05.207359 INFO: ms1_error      : 3
1:50:05.207402 INFO: ms2_error      : 10.0
1:50:05.207444 INFO: fwhm_rt        : 3.0
1:50:05.207485 INFO: quant_window   : 3
1:50:05.207526 INFO: ==============================================
1:50:07.567813 INFO: performing precursor FDR with 40 features
1:50:07.567932 INFO: Decoy channel: -1
1:50:07.567958 INFO: competitive: True
1:50:07.749553 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:08.040065 INFO: Estimating optimal hyperparameters - samples: 598,183, batch_size: 2,450, learning_rate: 7.73e-04
1:50:08.041202 INFO: Using random state 295042 for train-test-split
1:50:20.418795 INFO: Test AUC: 0.605
1:50:20.419046 INFO: Train AUC: 0.622
1:50:20.419081 INFO: AUC difference: 2.67%
1:50:20.897888 INFO: Resetting torch num_threads to 100
1:50:20.922906 PROGRESS: === Extracted 747729 precursors and 3878680 fragments ===
1:50:20.923473 INFO: === FDR correction performed with classifier version 11 ===
1:50:20.924301 PROGRESS: ============================= Precursor FDR =============================
1:50:20.924401 PROGRESS: Total precursors accumulated: 1,598
1:50:20.924462 PROGRESS: Target precursors: 1,583 (99.06%)
1:50:20.924514 PROGRESS: Decoy precursors: 15 (0.94%)
1:50:20.924563 PROGRESS: 
1:50:20.924612 PROGRESS: Precursor Summary:
1:50:20.926075 PROGRESS: Channel   0:	 0.050 FDR: 1,583; 0.010 FDR: 1,583; 0.001 FDR: 1,257
1:50:20.926169 PROGRESS: 
1:50:20.926232 PROGRESS: Protein Summary:
1:50:20.928050 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR: 1,059
1:50:20.928144 PROGRESS: =========================================================================
1:50:20.941114 INFO: Target number of precursors reached.
1:50:21.362618 INFO: fragments_df: keeping 5000 of 3878680 [sum(precursor_idx_mask)=37581 sum(mass_error_mask)=3878680 stop_rank=5000
1:50:21.860466 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:22.075940 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:22.728497 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:50:22.728961 INFO: Using score_cutoff 11.277440222167968 (fac=0.99, q=1)
1:50:22.729326 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:50:22.729418 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:50:22.729472 INFO: Updating optimization_manager: score_cutoff        : 10.38956852760315 -> 11.277440222167968
1:50:22.729527 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:22.878634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:23.219251 INFO: === checking if optimization conditions were reached ===
1:50:23.219515 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:50:23.222543 INFO: Updating optimization_manager: rt_error            : 395.4301920554706 -> 440.0701989055972
1:50:23.222647 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 440.0702.
1:50:23.222709 INFO: ==============================================
1:50:23.222807 INFO: Starting optimization step 5.
1:50:23.222871 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:50:23.222947 INFO: Using rust extraction backend
1:50:23.223014 PROGRESS: Extracting batch of 250439 precursors
1:50:23.645882 INFO: === Search parameters used ===
1:50:23.646174 INFO: rt_error       : 440.0701989055972
1:50:23.646229 INFO: mobility_error : 0.1
1:50:23.646275 INFO: num_candidates : 3
1:50:23.646319 INFO: ms1_error      : 3
1:50:23.646360 INFO: ms2_error      : 10.0
1:50:23.646402 INFO: fwhm_rt        : 3.0
1:50:23.646444 INFO: quant_window   : 3
1:50:23.646484 INFO: ==============================================
1:50:26.057297 INFO: performing precursor FDR with 40 features
1:50:26.057426 INFO: Decoy channel: -1
1:50:26.057453 INFO: competitive: True
1:50:26.245454 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:26.545790 INFO: Estimating optimal hyperparameters - samples: 598,680, batch_size: 2,452, learning_rate: 7.74e-04
1:50:26.546934 INFO: Using random state 295042 for train-test-split
1:50:38.623247 INFO: Test AUC: 0.607
1:50:38.623465 INFO: Train AUC: 0.622
1:50:38.623499 INFO: AUC difference: 2.27%
1:50:39.109801 INFO: Resetting torch num_threads to 100
1:50:39.138514 PROGRESS: === Extracted 748350 precursors and 3927374 fragments ===
1:50:39.139060 INFO: === FDR correction performed with classifier version 11 ===
1:50:39.139731 PROGRESS: ============================= Precursor FDR =============================
1:50:39.139834 PROGRESS: Total precursors accumulated: 1,506
1:50:39.139893 PROGRESS: Target precursors: 1,492 (99.07%)
1:50:39.139943 PROGRESS: Decoy precursors: 14 (0.93%)
1:50:39.139990 PROGRESS: 
1:50:39.140037 PROGRESS: Precursor Summary:
1:50:39.141361 PROGRESS: Channel   0:	 0.050 FDR: 1,492; 0.010 FDR: 1,492; 0.001 FDR:   724
1:50:39.141448 PROGRESS: 
1:50:39.141501 PROGRESS: Protein Summary:
1:50:39.143244 PROGRESS: Channel   0:	 0.050 FDR: 1,258; 0.010 FDR: 1,258; 0.001 FDR:   631
1:50:39.143342 PROGRESS: =========================================================================
1:50:39.156505 INFO: Target number of precursors reached.
1:50:39.591427 INFO: fragments_df: keeping 5000 of 3927374 [sum(precursor_idx_mask)=35662 sum(mass_error_mask)=3927374 stop_rank=5000
1:50:40.043866 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:40.249639 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:40.901630 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:50:40.902101 INFO: Using score_cutoff 11.280608672332763 (fac=0.99, q=1)
1:50:40.902444 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:50:40.902523 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:50:40.902577 INFO: Updating optimization_manager: score_cutoff        : 11.277440222167968 -> 11.280608672332763
1:50:40.902635 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:41.054084 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:41.387322 INFO: === checking if optimization conditions were reached ===
1:50:41.387608 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:50:41.390859 INFO: Updating optimization_manager: rt_error            : 440.0701989055972 -> 464.56047642766197
1:50:41.391000 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 464.5605.
1:50:41.391068 INFO: ==============================================
1:50:41.391155 INFO: Starting optimization step 6.
1:50:41.391222 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:50:41.391299 INFO: Using rust extraction backend
1:50:41.391371 PROGRESS: Extracting batch of 250439 precursors
1:50:41.816571 INFO: === Search parameters used ===
1:50:41.816856 INFO: rt_error       : 464.56047642766197
1:50:41.816911 INFO: mobility_error : 0.1
1:50:41.816963 INFO: num_candidates : 3
1:50:41.817007 INFO: ms1_error      : 3
1:50:41.817048 INFO: ms2_error      : 10.0
1:50:41.817094 INFO: fwhm_rt        : 3.0
1:50:41.817143 INFO: quant_window   : 3
1:50:41.817190 INFO: ==============================================
1:50:44.253198 INFO: performing precursor FDR with 40 features
1:50:44.253317 INFO: Decoy channel: -1
1:50:44.253347 INFO: competitive: True
1:50:44.424204 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:44.706140 INFO: Estimating optimal hyperparameters - samples: 598,975, batch_size: 2,453, learning_rate: 7.74e-04
1:50:44.707076 INFO: Using random state 295042 for train-test-split
1:50:56.878725 INFO: Test AUC: 0.610
1:50:56.878856 INFO: Train AUC: 0.623
1:50:56.878906 INFO: AUC difference: 2.17%
1:50:57.362135 INFO: Resetting torch num_threads to 100
1:50:57.386559 PROGRESS: === Extracted 748719 precursors and 3952474 fragments ===
1:50:57.387042 INFO: === FDR correction performed with classifier version 11 ===
1:50:57.387767 PROGRESS: ============================= Precursor FDR =============================
1:50:57.387865 PROGRESS: Total precursors accumulated: 1,717
1:50:57.387927 PROGRESS: Target precursors: 1,700 (99.01%)
1:50:57.387978 PROGRESS: Decoy precursors: 17 (0.99%)
1:50:57.388039 PROGRESS: 
1:50:57.388085 PROGRESS: Precursor Summary:
1:50:57.389494 PROGRESS: Channel   0:	 0.050 FDR: 1,700; 0.010 FDR: 1,652; 0.001 FDR: 1,061
1:50:57.389590 PROGRESS: 
1:50:57.389645 PROGRESS: Protein Summary:
1:50:57.391528 PROGRESS: Channel   0:	 0.050 FDR: 1,417; 0.010 FDR: 1,375; 0.001 FDR:   900
1:50:57.391625 PROGRESS: =========================================================================
1:50:57.405684 INFO: Target number of precursors reached.
1:50:57.835967 INFO: fragments_df: keeping 5000 of 3952474 [sum(precursor_idx_mask)=38719 sum(mass_error_mask)=3952474 stop_rank=5000
1:50:58.254447 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:58.480899 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:59.133209 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:50:59.133657 INFO: Using score_cutoff 10.484516459083556 (fac=0.99, q=1)
1:50:59.133971 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:50:59.134052 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:50:59.134107 INFO: Updating optimization_manager: score_cutoff        : 11.280608672332763 -> 10.484516459083556
1:50:59.134163 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:59.283176 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:59.612845 INFO: === checking if optimization conditions were reached ===
1:50:59.613103 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:50:59.616121 INFO: Updating optimization_manager: rt_error            : 464.56047642766197 -> 484.4547012808575
1:50:59.616261 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 484.4547.
1:50:59.616327 INFO: ==============================================
1:50:59.616395 INFO: Starting optimization step 7.
1:50:59.616453 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:50:59.616515 INFO: Using rust extraction backend
1:50:59.616571 PROGRESS: Extracting batch of 250439 precursors
1:51:00.036103 INFO: === Search parameters used ===
1:51:00.036371 INFO: rt_error       : 484.4547012808575
1:51:00.036428 INFO: mobility_error : 0.1
1:51:00.036477 INFO: num_candidates : 3
1:51:00.036524 INFO: ms1_error      : 3
1:51:00.036569 INFO: ms2_error      : 10.0
1:51:00.036613 INFO: fwhm_rt        : 3.0
1:51:00.036656 INFO: quant_window   : 3
1:51:00.036700 INFO: ==============================================
1:51:02.403293 INFO: performing precursor FDR with 40 features
1:51:02.403410 INFO: Decoy channel: -1
1:51:02.403436 INFO: competitive: True
1:51:02.581130 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:02.871010 INFO: Estimating optimal hyperparameters - samples: 598,872, batch_size: 2,452, learning_rate: 7.74e-04
1:51:02.872152 INFO: Using random state 295042 for train-test-split
1:51:14.818209 INFO: Test AUC: 0.612
1:51:14.818428 INFO: Train AUC: 0.624
1:51:14.818463 INFO: AUC difference: 1.95%
1:51:15.306670 INFO: Resetting torch num_threads to 100
1:51:15.381173 PROGRESS: === Extracted 748590 precursors and 3955057 fragments ===
1:51:15.381725 INFO: === FDR correction performed with classifier version 11 ===
1:51:15.382434 PROGRESS: ============================= Precursor FDR =============================
1:51:15.382535 PROGRESS: Total precursors accumulated: 1,492
1:51:15.382609 PROGRESS: Target precursors: 1,478 (99.06%)
1:51:15.382663 PROGRESS: Decoy precursors: 14 (0.94%)
1:51:15.382710 PROGRESS: 
1:51:15.382758 PROGRESS: Precursor Summary:
1:51:15.384118 PROGRESS: Channel   0:	 0.050 FDR: 1,478; 0.010 FDR: 1,478; 0.001 FDR: 1,136
1:51:15.384208 PROGRESS: 
1:51:15.384263 PROGRESS: Protein Summary:
1:51:15.386079 PROGRESS: Channel   0:	 0.050 FDR: 1,228; 0.010 FDR: 1,228; 0.001 FDR:   968
1:51:15.386176 PROGRESS: =========================================================================
1:51:15.400587 INFO: Target number of precursors reached.
1:51:15.831995 INFO: fragments_df: keeping 5000 of 3955057 [sum(precursor_idx_mask)=35396 sum(mass_error_mask)=3955057 stop_rank=5000
1:51:16.328746 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:16.549223 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:17.199877 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:17.200335 INFO: Using score_cutoff 11.314202210712432 (fac=0.99, q=1)
1:51:17.200683 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:17.200762 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:17.200818 INFO: Updating optimization_manager: score_cutoff        : 10.484516459083556 -> 11.314202210712432
1:51:17.200878 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:17.350331 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:17.671639 INFO: === checking if optimization conditions were reached ===
1:51:17.671911 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:51:17.672998 INFO: Updating optimization_manager: rt_error            : 484.4547012808575 -> 315.6408082087595
1:51:17.673153 INFO: Updating optimization_manager: classifier_version  : 11 -> 15
1:51:17.673256 INFO: Updating optimization_manager: score_cutoff        : 11.314202210712432 -> 10.38956852760315
1:51:17.673346 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:17.673436 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:17.673531 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 315.6408 found after 8 searches.
1:51:17.673593 INFO: ==============================================
1:51:17.673674 PROGRESS: Optimization finished for rt_error.
1:51:18.064181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:18.213505 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:18.533917 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:51:18.534168 PROGRESS: ==============================================
1:51:18.534262 PROGRESS: ms2_error      : 10.0000
1:51:18.534319 PROGRESS: rt_error       : 315.6408
1:51:18.534367 PROGRESS: ==============================================
1:51:18.535139 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:26.095897 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:42.939386 INFO: Using rust extraction backend
1:51:42.939768 PROGRESS: Extracting batch of 11997144 precursors
1:51:58.940166 INFO: === Search parameters used ===
1:51:58.940604 INFO: rt_error       : 315.6408082087595
1:51:58.940675 INFO: mobility_error : 0.1
1:51:58.940731 INFO: num_candidates : 3
1:51:58.940783 INFO: ms1_error      : 3
1:51:58.940833 INFO: ms2_error      : 10.0
1:51:58.940879 INFO: fwhm_rt        : 3.0
1:51:58.940921 INFO: quant_window   : 3
1:51:58.940963 INFO: ==============================================
1:52:20.875138 INFO: Removed 10846891 precursors with score below cutoff 10.38956852760315
1:52:42.957369 INFO: performing precursor FDR with 40 features
1:52:42.957561 INFO: Decoy channel: -1
1:52:42.957593 INFO: competitive: True
1:52:45.601202 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:55.664240 INFO: Estimating optimal hyperparameters - samples: 20,098,099, batch_size: 4,096, learning_rate: 1.00e-03
1:52:55.725776 INFO: Using random state 535988 for train-test-split
1:59:55.665613 INFO: Test AUC: 0.615
1:59:55.665950 INFO: Train AUC: 0.616
1:59:55.665996 INFO: AUC difference: 0.16%
2:00:01.552667 INFO: Resetting torch num_threads to 100
2:00:03.639647 PROGRESS: ============================= Precursor FDR =============================
2:00:03.639968 PROGRESS: Total precursors accumulated: 94,637
2:00:03.640039 PROGRESS: Target precursors: 93,700 (99.01%)
2:00:03.640095 PROGRESS: Decoy precursors: 937 (0.99%)
2:00:03.640145 PROGRESS: 
2:00:03.640194 PROGRESS: Precursor Summary:
2:00:03.665267 PROGRESS: Channel   0:	 0.050 FDR: 93,700; 0.010 FDR: 93,700; 0.001 FDR: 57,637
2:00:03.665516 PROGRESS: 
2:00:03.665580 PROGRESS: Protein Summary:
2:00:03.700358 PROGRESS: Channel   0:	 0.050 FDR: 13,582; 0.010 FDR: 13,582; 0.001 FDR: 9,053
2:00:03.700624 PROGRESS: =========================================================================
2:00:03.853248 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
2:00:04.022178 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
2:00:04.259188 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:00:31.812908 PROGRESS: Processing search outputs
2:00:31.813153 PROGRESS: === Performing protein grouping and FDR ===
2:00:31.813214 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:00:31.880230 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:00:31.939326 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:00:31.999050 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:00:32.064320 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:00:32.131471 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:00:32.236528 INFO: Performing protein inference
2:00:33.053797 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2:01:27.042762 INFO: Performing protein FDR
2:01:34.089309 INFO: Normalizing q-values using 19,751 targets and 3,930 decoys
2:01:34.093706 INFO: Test AUC: 0.849
2:01:34.093758 INFO: Train AUC: 0.853
2:01:34.093788 INFO: AUC difference: 0.47%
2:01:34.770729 INFO: ================ Protein FDR =================
2:01:34.770882 INFO: Unique protein groups in output
2:01:34.770913 INFO:   1% protein FDR: 10,554
2:01:34.770935 INFO: 
2:01:34.770956 INFO: Unique precursor in output
2:01:34.770976 INFO:   1% protein FDR: 133,153
2:01:34.770997 INFO: ================================================
2:01:34.837323 PROGRESS: Building search statistics
2:01:34.939538 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:01:34.939754 INFO: Initializing OptimizationManager
2:01:34.940066 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:01:34.940145 INFO: Initializing CalibrationManager
2:01:34.940393 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:01:34.940483 INFO: Initializing RawFileManager
2:01:34.973004 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:01:34.973188 INFO: Initializing OptimizationManager
2:01:34.973392 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:01:34.973473 INFO: Initializing CalibrationManager
2:01:34.973679 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:01:34.973758 INFO: Initializing RawFileManager
2:01:35.005820 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:01:35.006006 INFO: Initializing OptimizationManager
2:01:35.006215 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:01:35.006287 INFO: Initializing CalibrationManager
2:01:35.006502 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:01:35.006574 INFO: Initializing RawFileManager
2:01:35.040609 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:01:35.040785 INFO: Initializing OptimizationManager
2:01:35.040986 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:01:35.041060 INFO: Initializing CalibrationManager
2:01:35.041261 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:01:35.041334 INFO: Initializing RawFileManager
2:01:35.074750 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:01:35.074942 INFO: Initializing OptimizationManager
2:01:35.075147 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:01:35.075238 INFO: Initializing CalibrationManager
2:01:35.075438 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:01:35.075510 INFO: Initializing RawFileManager
2:01:35.108896 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:01:35.109090 INFO: Initializing OptimizationManager
2:01:35.109293 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:01:35.109364 INFO: Initializing CalibrationManager
2:01:35.109561 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:01:35.109634 INFO: Initializing RawFileManager
2:01:35.112893 INFO: Writing stat output to disk
2:01:35.112970 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
2:01:35.123080 PROGRESS: Building internal statistics
2:01:35.123450 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:01:35.123495 INFO: Initializing TimingManager
2:01:35.123890 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:01:35.123930 INFO: Initializing TimingManager
2:01:35.124144 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:01:35.124179 INFO: Initializing TimingManager
2:01:35.124370 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:01:35.124403 INFO: Initializing TimingManager
2:01:35.124592 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:01:35.124624 INFO: Initializing TimingManager
2:01:35.124807 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:01:35.124838 INFO: Initializing TimingManager
2:01:35.125304 INFO: Writing internal output to disk
2:01:35.125345 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
2:01:35.190664 INFO: Performing label free quantification
2:01:35.190827 INFO: Accumulating fragment data
2:01:35.190900 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:01:35.426001 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:01:36.716361 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:01:38.055927 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:01:39.545978 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:01:41.110352 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:01:43.055998 INFO: Performing label free quantification on the precursor level
2:01:43.056153 INFO: Filtering fragments by quality
2:01:43.453203 INFO: Performing label-free quantification with directlfq normalization
2:01:44.020300 INFO: Applying directLFQ normalization
2:01:45.166230 INFO: 133153 lfq-groups total
2:04:42.813871 INFO: using 100 processes
2:04:43.712071 INFO: lfq-object 0
2:04:43.997676 INFO: lfq-object 100
2:04:44.048596 INFO: lfq-object 400
2:04:44.100225 INFO: lfq-object 700
2:04:44.145912 INFO: lfq-object 200
2:04:44.260166 INFO: lfq-object 800
2:04:44.280727 INFO: lfq-object 1000
2:04:44.290156 INFO: lfq-object 300
2:04:44.321685 INFO: lfq-object 500
2:04:44.415039 INFO: lfq-object 900
2:04:44.512396 INFO: lfq-object 1100
2:04:44.584516 INFO: lfq-object 1400
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2:04:44.700985 INFO: lfq-object 1200
2:04:44.726665 INFO: lfq-object 1500
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2:22:39.560871 INFO: lfq-object 6300
2:22:39.566067 INFO: lfq-object 6400
2:22:39.766197 INFO: lfq-object 6500
2:22:39.926627 INFO: lfq-object 6600
2:22:40.214319 INFO: lfq-object 6700
2:22:40.623539 INFO: lfq-object 6800
2:22:40.640483 INFO: lfq-object 7000
2:22:41.228436 INFO: lfq-object 7100
2:22:41.269559 INFO: lfq-object 6900
2:22:41.279705 INFO: lfq-object 7200
2:22:41.391010 INFO: lfq-object 7400
2:22:41.397137 INFO: lfq-object 7300
2:22:41.641476 INFO: lfq-object 7500
2:22:41.853765 INFO: lfq-object 7600
2:22:41.934261 INFO: lfq-object 7700
2:22:42.104503 INFO: lfq-object 7800
2:22:42.230482 INFO: lfq-object 8000
2:22:42.275167 INFO: lfq-object 8100
2:22:42.327676 INFO: lfq-object 7900
2:22:42.711125 INFO: lfq-object 8200
2:22:42.723714 INFO: lfq-object 8300
2:22:42.868738 INFO: lfq-object 8400
2:22:43.091558 INFO: lfq-object 8600
2:22:43.201456 INFO: lfq-object 8700
2:22:43.289118 INFO: lfq-object 8800
2:22:43.564815 INFO: lfq-object 8500
2:22:43.663296 INFO: lfq-object 8900
2:22:43.781613 INFO: lfq-object 9000
2:22:43.836982 INFO: lfq-object 9100
2:22:43.988149 INFO: lfq-object 9200
2:22:44.072644 INFO: lfq-object 9300
2:22:44.145359 INFO: lfq-object 9400
2:22:44.272307 INFO: lfq-object 9500
2:22:44.506397 INFO: lfq-object 9600
2:22:44.649697 INFO: lfq-object 9700
2:22:44.883802 INFO: lfq-object 9900
2:22:44.931800 INFO: lfq-object 9800
2:22:44.949441 INFO: lfq-object 10000
2:22:45.019584 INFO: lfq-object 10100
2:22:45.124090 INFO: lfq-object 10200
2:22:55.336465 INFO: lfq-object 10400
2:22:55.411075 INFO: lfq-object 10300
2:22:55.659780 INFO: lfq-object 10500
2:23:05.243702 INFO: Writing psm output to disk
2:23:05.585185 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
2:23:07.406612 INFO: Writing precursor output to disk
2:23:07.424842 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
2:23:07.679170 INFO: Writing peptide output to disk
2:23:07.697122 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
2:23:07.885839 INFO: Writing pg output to disk
2:23:07.897529 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIANoMBR/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
2:23:08.186652 PROGRESS: Building MBR spectral library
2:23:08.187457 INFO: Running MbrLibraryBuilder
2:23:13.842250 INFO: MBR spectral library contains 133,153 precursors, 10,554 proteins
2:23:13.842646 INFO: Writing MBR spectral library to disk
2:23:16.694275 PROGRESS: =================== Search step 'library' finished ===================
2:23:20.607996 INFO: =================== Search Finished ===================
