0:00:00.000041 INFO: Output directory: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest, cwd: /app.
0:00:00.000147 INFO: User provided config file: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/alphadia_config.yaml.
0:00:00.016138 PROGRESS:           _      _         ___ ___   _   
0:00:00.016201 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.016223 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.016241 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.016258 PROGRESS:            |_|                           
0:00:00.016280 PROGRESS: 
0:00:00.016299 PROGRESS: version: 2.1.2
0:00:00.016319 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.016343 INFO: hostname: 91fa8f4f98ee
0:00:00.016369 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.016392 PROGRESS: python: 3.10.10 (CPython)
0:00:00.016447 INFO: date: 2026-07-20 09:15:07
0:00:00.016468 INFO: ================ AlphaX Environment ===============
0:00:00.016488 INFO: alphabase       : 1.9.0
0:00:00.016506 INFO: alpharaw        : 0.6.0
0:00:00.016524 INFO: alphapeptdeep   : 1.4.2
0:00:00.016543 INFO: directlfq       : 0.3.1
0:00:00.016560 INFO: ===================================================
0:00:00.016579 INFO: ================= Pip Environment =================
0:00:00.081605 INFO: click==8.1.8 peptdeep==1.4.2 et_xmlfile==2.0.0 nvidia-nvjitlink-cu12==12.4.127 huggingface-hub==0.30.2 pyarrow==20.0.0 rdkit==2024.9.6 tqdm==4.67.1 psutil==7.0.0 alpharaw==0.6.0 torchmetrics==1.7.1 numpy==1.26.4 directlfq==0.3.1 contextlib2==21.6.0 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 packaging==24.2 narwhals==2.22.0 joblib==1.4.2 transformers==4.51.2 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 numba==0.61.2 pyteomics==4.7.5 mpmath==1.3.0 multiprocess==0.70.17 lightning-utilities==0.14.3 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 fsspec==2025.3.2 xxhash==3.5.0 threadpoolctl==3.6.0 alphabase==1.9.0 pythonnet==3.0.5 requests==2.32.3 triton==3.2.0 h5py==3.13.0 pyahocorasick==2.1.0 pycparser==2.22 pytz==2026.2 regex==2024.11.6 certifi==2025.1.31 python-dateutil==2.9.0.post0 torch==2.6.0 plotly==6.7.0 openpyxl==3.1.5 setuptools==78.1.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 alphadia==2.1.2 clr_loader==0.2.7.post0 quantselect==0.1.3 pandas==2.2.3 dill==0.3.9 pyparsing==3.2.3 typing_extensions==4.13.2 networkx==3.4.2 biopython==1.85 urllib3==2.4.0 seaborn==0.13.2 alphadia-search-rs==1.1.1 llvmlite==0.44.0 fonttools==4.57.0 scipy==1.12.0 tzdata==2025.2 filelock==3.18.0 matplotlib==3.10.1 contourpy==1.3.1 lxml==5.3.2 Jinja2==3.1.6 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 safetensors==0.5.3 idna==3.10 nvidia-cufft-cu12==11.2.1.3 sympy==1.13.1 pillow==11.1.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 tokenizers==0.21.1 nvidia-curand-cu12==10.3.5.147 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 nvidia-cusparselt-cu12==0.6.2 PyYAML==6.0.2 pip==22.3.1 wheel==0.38.4 more-itertools==10.3.0 wheel==0.45.1 autocommand==2.2.2 packaging==24.2 typing_extensions==4.12.2 tomli==2.0.1 backports.tarfile==1.2.0 jaraco.functools==4.0.1 jaraco.text==3.12.1 platformdirs==4.2.2 jaraco.collections==5.1.0 typeguard==4.3.0 jaraco.context==5.3.0 importlib_metadata==8.0.0 inflect==7.3.1 zipp==3.19.2
0:00:00.081704 INFO: ===================================================
0:00:00.081733 INFO: =================== Running step 'library' ===================
0:00:00.081821 INFO: loading default config from /usr/local/lib/python3.10/site-packages/alphadia/constants/default.yaml
0:00:00.100630 INFO: loading additional config provided via CLI
0:00:00.100760 INFO: loading additional config provided via CLI parameters
0:00:00.101166 INFO: Updating config with 'user defined'
0:00:00.101255 INFO: Updating config with 'user defined (cli)'
0:00:00.101323 INFO: updating config with user defined values: [{'raw_paths': ['/public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01.raw', '/public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02.raw', '/public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03.raw'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta'], 'output_directory': '/home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest', 'general': {'thread_count': 80, 'mbr_step_enabled': False, 'transfer_step_enabled': False}, 'library_prediction': {'enabled': True, 'enzyme': 'no-cleave', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': '', 'max_var_mod_num': 0, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400.0, 1000.0], 'fragment_mz': [100.0, 1700.0]}, 'search': {'target_ms1_tolerance': 5, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}}, {'raw_paths': ['/public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01.raw', '/public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02.raw', '/public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03.raw']}]
0:00:00.101558 INFO: Updating config with 'user defined'
0:00:00.101608 INFO: Updating config with 'user defined (cli)'
0:00:00.101641 INFO: ├──version: None
0:00:00.101665 INFO: ├──workflow_name: None
0:00:00.101685 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest [user defined, default: None][0m
0:00:00.101707 INFO: ├──library_path: None
0:00:00.101733 INFO: ├──raw_paths:
0:00:00.101761 INFO: │   [32;20m- /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_01.raw [user defined (cli), default: None][0m
0:00:00.101788 INFO: │   [32;20m- /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_02.raw [user defined (cli), default: None][0m
0:00:00.101807 INFO: │   [32;20m- /public/local/ProteoBench/Entrapment_DIA/LFQ_Astral_DIA_15min_50ng_Human_03.raw [user defined (cli), default: None][0m
0:00:00.101830 INFO: ├──fasta_paths:
0:00:00.101849 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta [user defined, default: None][0m
0:00:00.101872 INFO: ├──quant_directory: None
0:00:00.101895 INFO: ├──general
0:00:00.101938 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.101960 INFO: │   ├──transfer_step_enabled: False
0:00:00.101980 INFO: │   ├──mbr_step_enabled: False
0:00:00.102000 INFO: │   ├──reuse_calibration: False
0:00:00.102018 INFO: │   ├──reuse_quant: False
0:00:00.102037 INFO: │   ├──log_level: INFO
0:00:00.102063 INFO: │   ├──use_gpu: True
0:00:00.102082 INFO: │   ├──save_figures: True
0:00:00.102101 INFO: │   ├──save_library: True
0:00:00.102119 INFO: │   ├──save_flat_library: False
0:00:00.102137 INFO: │   ├──input_library_type: base
0:00:00.102156 INFO: │   ├──save_mbr_library: True
0:00:00.102177 INFO: │   ├──random_state: None
0:00:00.102201 INFO: │   └──fail_fast: False
0:00:00.102225 INFO: ├──library_loading
0:00:00.102244 INFO: │   └──drop_decoys: False
0:00:00.102265 INFO: ├──library_prediction
0:00:00.102286 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.102309 INFO: │   [32;20m├──enzyme: no-cleave [user defined, default: trypsin][0m
0:00:00.102336 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.102359 INFO: │   [32;20m├──variable_modifications:  [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.102385 INFO: │   [32;20m├──max_var_mod_num: 0 [user defined, default: 2][0m
0:00:00.102408 INFO: │   ├──missed_cleavages: 1
0:00:00.102435 INFO: │   ├──precursor_len:
0:00:00.102458 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.102482 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.102503 INFO: │   ├──precursor_charge:
0:00:00.102526 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.102549 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.102576 INFO: │   ├──precursor_mz:
0:00:00.102604 INFO: │   │   - 400.0
0:00:00.102630 INFO: │   │   [32;20m- 1000.0 [user defined, default: 1200][0m
0:00:00.102659 INFO: │   ├──fragment_mz:
0:00:00.102681 INFO: │   │   [32;20m- 100.0 [user defined, default: 200][0m
0:00:00.102704 INFO: │   │   [32;20m- 1700.0 [user defined, default: 2000][0m
0:00:00.102731 INFO: │   ├──nce: 25.0
0:00:00.102755 INFO: │   ├──fragment_types:
0:00:00.102778 INFO: │   │   - b
0:00:00.102796 INFO: │   │   - y
0:00:00.102818 INFO: │   ├──max_fragment_charge: 2
0:00:00.102840 INFO: │   ├──instrument: Lumos
0:00:00.102863 INFO: │   ├──peptdeep_model_path: None
0:00:00.102889 INFO: │   ├──peptdeep_model_type: generic
0:00:00.102911 INFO: │   ├──predict_charge: False
0:00:00.102934 INFO: │   └──min_charge_probability: 0.1
0:00:00.102959 INFO: ├──custom_modifications:
0:00:00.102984 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.103005 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.103029 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.103055 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.103080 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.103105 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.103128 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.103153 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.103175 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.103201 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.103226 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.103248 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.103271 INFO: │   ├──name: Label:13C(12)@K
0:00:00.103292 INFO: │   └──composition: C(12)
0:00:00.103316 INFO: ├──search
0:00:00.103342 INFO: │   ├──extraction_backend: rust
0:00:00.103365 INFO: │   ├──target_ms1_tolerance: 5
0:00:00.103386 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.103410 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.103436 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.103462 INFO: │   ├──quant_window: 3
0:00:00.103487 INFO: │   ├──target_num_candidates: 3
0:00:00.103512 INFO: │   ├──channel_filter: 
0:00:00.103534 INFO: │   ├──compete_for_fragments: True
0:00:00.103556 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.103580 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.103606 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.103628 INFO: │   ├──optimized_peak_group_score: False
0:00:00.103654 INFO: │   ├──exclude_shared_ions: True
0:00:00.103678 INFO: │   ├──quant_all: True
0:00:00.103703 INFO: │   └──experimental_xic: True
0:00:00.103725 INFO: ├──calibration
0:00:00.103748 INFO: │   ├──batch_size: 1000
0:00:00.103772 INFO: │   ├──optimization_lock_target: 1000
0:00:00.103794 INFO: │   ├──max_steps: 20
0:00:00.103819 INFO: │   ├──min_steps: 5
0:00:00.103843 INFO: │   ├──max_skips: 1
0:00:00.103865 INFO: │   ├──max_fragments: 5000
0:00:00.103888 INFO: │   └──min_correlation: 0.7
0:00:00.103910 INFO: ├──search_initial
0:00:00.103933 INFO: │   ├──num_candidates: 1
0:00:00.103958 INFO: │   ├──ms1_tolerance: 30
0:00:00.103977 INFO: │   ├──ms2_tolerance: 30
0:00:00.103997 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.104018 INFO: │   └──rt_tolerance: 0.5
0:00:00.104037 INFO: ├──library_multiplexing
0:00:00.104066 INFO: │   ├──enabled: False
0:00:00.104085 INFO: │   ├──input_channel: 0
0:00:00.104105 INFO: │   └──multiplex_mapping:
0:00:00.104123 INFO: ├──multiplexing
0:00:00.104141 INFO: │   ├──enabled: False
0:00:00.104163 INFO: │   ├──target_channels: 4,8
0:00:00.104186 INFO: │   ├──decoy_channel: 12
0:00:00.104212 INFO: │   ├──reference_channel: 0
0:00:00.104236 INFO: │   └──competitive_scoring: True
0:00:00.104255 INFO: ├──fdr
0:00:00.104278 INFO: │   ├──fdr: 0.01
0:00:00.104296 INFO: │   ├──group_level: proteins
0:00:00.104314 INFO: │   ├──inference_strategy: heuristic
0:00:00.104333 INFO: │   ├──competitive_scoring: True
0:00:00.104354 INFO: │   ├──keep_decoys: False
0:00:00.104373 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.104391 INFO: │   ├──channel_wise_fdr: False
0:00:00.104409 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.104426 INFO: ├──search_output
0:00:00.104444 INFO: │   ├──file_format: parquet
0:00:00.104466 INFO: │   ├──precursor_level_lfq: True
0:00:00.104487 INFO: │   ├──peptide_level_lfq: True
0:00:00.104505 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.104523 INFO: │   ├──min_k_fragments: 12
0:00:00.104542 INFO: │   ├──min_correlation: 0.9
0:00:00.104569 INFO: │   ├──num_samples_quadratic: 50
0:00:00.104596 INFO: │   ├──min_nonnan: 3
0:00:00.104622 INFO: │   ├──normalization_method: directlfq
0:00:00.104646 INFO: │   └──normalize_directlfq: True
0:00:00.104666 INFO: ├──optimization
0:00:00.104686 INFO: │   ├──order_of_optimization: None
0:00:00.104705 INFO: │   ├──ms2_error
0:00:00.104730 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.104750 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.104768 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.104786 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.104805 INFO: │   │   ├──try_narrower_values: True
0:00:00.104829 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.104855 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.104882 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.104908 INFO: │   ├──ms1_error
0:00:00.104935 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.104963 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.104991 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.105019 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.105045 INFO: │   │   ├──try_narrower_values: False
0:00:00.105068 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.105088 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.105106 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.105126 INFO: │   ├──mobility_error
0:00:00.105147 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.105175 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.105203 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.105230 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.105257 INFO: │   │   ├──try_narrower_values: False
0:00:00.105282 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.105301 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.105325 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.105348 INFO: │   └──rt_error
0:00:00.105374 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.105395 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.105417 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.105442 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.105467 INFO: │       ├──try_narrower_values: True
0:00:00.105489 INFO: │       ├──maximal_decrease: 0.1
0:00:00.105513 INFO: │       ├──favour_narrower_optimum: False
0:00:00.105539 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.105563 INFO: ├──optimization_manager
0:00:00.105585 INFO: │   ├──fwhm_rt: 5
0:00:00.105611 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.105638 INFO: │   └──score_cutoff: 0
0:00:00.105667 INFO: ├──transfer_library
0:00:00.105694 INFO: │   ├──enabled: False
0:00:00.105720 INFO: │   ├──fragment_types:
0:00:00.105746 INFO: │   │   - b
0:00:00.105772 INFO: │   │   - y
0:00:00.105799 INFO: │   ├──max_charge: 2
0:00:00.105824 INFO: │   ├──top_k_samples: 3
0:00:00.105849 INFO: │   ├──norm_delta_max: True
0:00:00.105871 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.105890 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.105920 INFO: └──transfer_learning
0:00:00.105940 INFO:     ├──enabled: False
0:00:00.105958 INFO:     ├──batch_size: 2000
0:00:00.105976 INFO:     ├──max_lr: 0.0001
0:00:00.105995 INFO:     ├──train_fraction: 0.7
0:00:00.106013 INFO:     ├──validation_fraction: 0.2
0:00:00.106031 INFO:     ├──test_fraction: 0.1
0:00:00.106049 INFO:     ├──test_interval: 1
0:00:00.106066 INFO:     ├──lr_patience: 3
0:00:00.106084 INFO:     ├──epochs: 51
0:00:00.106104 INFO:     ├──warmup_epochs: 5
0:00:00.106122 INFO:     ├──nce: 25
0:00:00.106141 INFO:     └──instrument: Lumos
0:00:00.112825 INFO: Registering 7 custom modifications
0:00:00.144954 INFO: Searching 3 files:
0:00:00.145048 INFO:   LFQ_Astral_DIA_15min_50ng_Human_01.raw
0:00:00.145072 INFO:   LFQ_Astral_DIA_15min_50ng_Human_02.raw
0:00:00.145092 INFO:   LFQ_Astral_DIA_15min_50ng_Human_03.raw
0:00:00.145110 INFO: Using 1 fasta files:
0:00:00.145128 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_Entrapment_Human_with_contaminants_entrapment_pep.fasta
0:00:00.145145 INFO: Using library: None
0:00:00.145163 INFO: Saving output to: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest
0:00:00.145188 PROGRESS: Loading spectral library
0:00:00.145216 PROGRESS: No library provided. Building library from fasta files.
0:00:00.145274 INFO: Running FastaDigest
0:00:00.146806 INFO: Digesting fasta file
0:00:37.220490 INFO: Adding modifications
0:03:39.748789 INFO: Removing non-canonical amino acids
0:03:47.629077 INFO: Fasta library contains 6,166,515 precursors
0:03:47.629478 PROGRESS: Predicting library properties.
0:03:47.629585 INFO: Running PeptDeepPrediction
0:03:47.631222 INFO: Device set to cpu
0:03:47.631571 INFO: Downloading pretrained models from https://github.com/MannLabs/alphapeptdeep/releases/download/pre-trained-models/pretrained_models_v3.zip to /tmp/peptdeep/pretrained_models/pretrained_models_v3.zip ...
0:03:48.323411 INFO: Successfully downloaded pretrained models.
0:03:51.158855 INFO: Loading PeptDeep models of type generic
0:03:53.422528 INFO: Predicting RT, MS2 and mobility
0:03:53.422838 INFO: Using multiprocessing with 80 processes ...
0:03:54.881685 INFO: Predicting rt,ms2,mobility ...
0:15:22.043665 INFO: Adding fragment mz information
0:15:22.416969 INFO: Adding fragment intensity information
0:15:22.728847 INFO: Adding precursor information
0:15:23.352971 INFO: Running PrecursorInitializer
0:15:23.374680 INFO: Running AnnotateFasta
0:17:23.194538 INFO: Running IsotopeGenerator
0:17:23.196312 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:21:53.391229 INFO: Running RTNormalization
0:21:53.391636 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:21:53.391755 INFO: Saving library to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/speclib.hdf
0:22:37.962572 INFO: Running DecoyGenerator
0:24:36.968463 INFO: Running FlattenLibrary
0:25:12.687561 INFO: Running InitFlatColumns
0:25:12.904109 INFO: Running LogFlatLibraryStats
0:25:12.904285 INFO: ============ Library Stats ============
0:25:12.904325 INFO: Number of precursors: 12,318,629
0:25:15.051676 INFO: 	thereof targets:6,166,515
0:25:15.051843 INFO: 	thereof decoys: 6,152,114
0:25:15.128547 INFO: Number of elution groups: 6,166,515
0:25:15.128693 INFO: 	average size: 2.00
0:25:17.314741 INFO: Number of proteins: 2,699,155
0:25:17.345274 INFO: Number of channels: 1 ([0])
0:25:17.345535 INFO: Isotopes Distribution for 4 isotopes
0:25:17.345583 INFO: =======================================
0:25:17.345702 PROGRESS: =================== Starting Search Workflows for step library ===================
0:25:17.345968 PROGRESS: Loading raw file 1/3: LFQ_Astral_DIA_15min_50ng_Human_01 
0:25:17.346060 INFO: Quantification results path: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant
0:25:17.346173 INFO: Creating folder /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/figures
0:25:17.346437 INFO: Initializing TimingManager
0:25:17.346971 INFO: Initializing RawFileManager
0:25:29.932515 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.
0:25:29.940850 INFO: Determining DIA cycle
0:25:30.172308 INFO: Found cycle with start 0.00 min and length 300.
0:25:30.291795 INFO: RT (min)            : 0.0 - 26.9
0:25:30.291904 INFO: RT duration (sec)   : 1611.2
0:25:30.291934 INFO: RT duration (min)   : 26.9
0:25:30.291958 INFO: Cycle len (scans)   : 300
0:25:30.291983 INFO: Cycle len (sec)     : 1.65
0:25:30.292008 INFO: Number of cycles    : 976
0:25:30.292033 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:25:30.292070 INFO: Creating DIA data object took: 12.944974422454834
0:25:31.057864 INFO: Creating DIA data NG object took: 0.765639066696167
0:25:32.659434 INFO: Initializing CalibrationManager
0:25:32.659788 INFO: Setting up calibration estimators ..
0:25:32.659866 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:25:32.659939 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'}' ..
0:25:32.660021 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:25:32.660080 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:25:32.660137 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}}' ..
0:25:32.660193 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:25:32.660262 INFO: Done setting up calibration estimators.
0:25:32.660495 INFO: Initializing OptimizationManager
0:25:32.660685 INFO: initial parameter: ms1_error = 30
0:25:32.660769 INFO: initial parameter: ms2_error = 30
0:25:32.660839 INFO: initial parameter: rt_error = 805.6138305664062
0:25:32.660904 INFO: initial parameter: mobility_error = 0.1
0:25:32.660963 INFO: initial parameter: num_candidates = 1
0:25:32.661023 INFO: initial parameter: fwhm_rt = 5
0:25:32.661093 INFO: initial parameter: fwhm_mobility = 0.01
0:25:32.661156 INFO: initial parameter: score_cutoff = 0
0:25:32.661223 INFO: initial parameter: classifier_version = -1
0:25:32.661318 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Human_01
0:25:32.661654 INFO: FDRManager: loading saved state not requested, will be initialized.
0:25:32.661694 INFO: Initializing FDRManager
0:25:32.661746 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
0:25:34.454870 PROGRESS: Initializing spectral library: 6,065,786 target precursors potentially observable (100,729 removed)
0:25:36.369245 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:25:36.369812 INFO: Updating optimization_manager: rt_error            : 805.6138305664062 -> 805.6138305664062
0:25:36.369962 PROGRESS: Starting initial search for precursors.
0:25:36.370072 INFO: Starting optimization step 0.
0:25:36.370147 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:25:36.370211 INFO: Using rust extraction backend
0:25:36.370282 PROGRESS: Extracting batch of 1985 precursors
0:25:36.375159 INFO: === Search parameters used ===
0:25:36.375278 INFO: rt_error       : 805.6138305664062
0:25:36.375362 INFO: mobility_error : 0.1
0:25:36.375441 INFO: num_candidates : 1
0:25:36.375513 INFO: ms1_error      : 30
0:25:36.375579 INFO: ms2_error      : 30
0:25:36.375645 INFO: fwhm_rt        : 5
0:25:36.375708 INFO: quant_window   : 3
0:25:36.375774 INFO: ==============================================
0:25:36.402871 INFO: performing precursor FDR with 40 features
0:25:36.402945 INFO: Decoy channel: -1
0:25:36.402983 INFO: competitive: True
0:25:36.404287 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:36.406402 INFO: Estimating optimal hyperparameters - samples: 1,558, batch_size: 128, learning_rate: 1.77e-04
0:25:36.407166 INFO: Using random state 79163 for train-test-split
0:25:36.556941 INFO: Test AUC: 0.514
0:25:36.557045 INFO: Train AUC: 0.514
0:25:36.557084 INFO: AUC difference: 0.03%
0:25:36.845396 INFO: Resetting torch num_threads to 80
0:25:36.847139 PROGRESS: === Extracted 1948 precursors and 8669 fragments ===
0:25:36.847521 INFO: === FDR correction performed with classifier version -1 ===
0:25:36.848126 PROGRESS: ============================= Precursor FDR =============================
0:25:36.848232 PROGRESS: Total precursors accumulated: 941
0:25:36.848309 PROGRESS: Target precursors: 932 (99.04%)
0:25:36.848379 PROGRESS: Decoy precursors: 9 (0.96%)
0:25:36.848439 PROGRESS: 
0:25:36.848496 PROGRESS: Precursor Summary:
0:25:36.849789 PROGRESS: Channel   0:	 0.050 FDR:   932; 0.010 FDR:   932; 0.001 FDR:   932
0:25:36.849890 PROGRESS: 
0:25:36.849962 PROGRESS: Protein Summary:
0:25:36.851725 PROGRESS: Channel   0:	 0.050 FDR:   931; 0.010 FDR:   931; 0.001 FDR:   931
0:25:36.851827 PROGRESS: =========================================================================
0:25:36.852005 INFO: Target number of precursors not reached yet.
0:25:36.940948 INFO: Starting optimization step 1.
0:25:36.941220 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:25:36.941327 INFO: Using rust extraction backend
0:25:36.941404 PROGRESS: Extracting batch of 3969 precursors
0:25:36.949688 INFO: === Search parameters used ===
0:25:36.949825 INFO: rt_error       : 805.6138305664062
0:25:36.949884 INFO: mobility_error : 0.1
0:25:36.949961 INFO: num_candidates : 1
0:25:36.950026 INFO: ms1_error      : 30
0:25:36.950089 INFO: ms2_error      : 30
0:25:36.950161 INFO: fwhm_rt        : 5
0:25:36.950237 INFO: quant_window   : 3
0:25:36.950308 INFO: ==============================================
0:25:36.992718 INFO: performing precursor FDR with 40 features
0:25:36.992810 INFO: Decoy channel: -1
0:25:36.992838 INFO: competitive: True
0:25:36.996877 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:36.999415 INFO: Estimating optimal hyperparameters - samples: 4,677, batch_size: 128, learning_rate: 1.77e-04
0:25:36.999505 INFO: Using random state 591119 for train-test-split
0:25:37.470171 INFO: Test AUC: 0.502
0:25:37.470285 INFO: Train AUC: 0.509
0:25:37.470316 INFO: AUC difference: 1.40%
0:25:37.729886 INFO: Resetting torch num_threads to 80
0:25:37.733159 PROGRESS: === Extracted 5847 precursors and 25885 fragments ===
0:25:37.733596 INFO: === FDR correction performed with classifier version -1 ===
0:25:37.734163 PROGRESS: ============================= Precursor FDR =============================
0:25:37.734266 PROGRESS: Total precursors accumulated: 14
0:25:37.734340 PROGRESS: Target precursors: 14 (100.00%)
0:25:37.734407 PROGRESS: Decoy precursors: 0 (0.00%)
0:25:37.734468 PROGRESS: 
0:25:37.734531 PROGRESS: Precursor Summary:
0:25:37.735942 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
0:25:37.736055 PROGRESS: 
0:25:37.736121 PROGRESS: Protein Summary:
0:25:37.737422 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
0:25:37.737527 PROGRESS: =========================================================================
0:25:37.737815 INFO: Target number of precursors not reached yet.
0:25:37.843741 INFO: Starting optimization step 2.
0:25:37.844022 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:25:37.844128 INFO: Using rust extraction backend
0:25:37.844205 PROGRESS: Extracting batch of 7917 precursors
0:25:37.859056 INFO: === Search parameters used ===
0:25:37.859200 INFO: rt_error       : 805.6138305664062
0:25:37.859272 INFO: mobility_error : 0.1
0:25:37.859336 INFO: num_candidates : 1
0:25:37.859397 INFO: ms1_error      : 30
0:25:37.859456 INFO: ms2_error      : 30
0:25:37.859514 INFO: fwhm_rt        : 5
0:25:37.859568 INFO: quant_window   : 3
0:25:37.859628 INFO: ==============================================
0:25:37.933483 INFO: performing precursor FDR with 40 features
0:25:37.933614 INFO: Decoy channel: -1
0:25:37.933647 INFO: competitive: True
0:25:37.941873 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:37.947379 INFO: Estimating optimal hyperparameters - samples: 10,912, batch_size: 128, learning_rate: 1.77e-04
0:25:37.947531 INFO: Using random state 661508 for train-test-split
0:25:39.024767 INFO: Test AUC: 0.542
0:25:39.024884 INFO: Train AUC: 0.551
0:25:39.024914 INFO: AUC difference: 1.58%
0:25:39.350016 INFO: Resetting torch num_threads to 80
0:25:39.354343 PROGRESS: === Extracted 13640 precursors and 60388 fragments ===
0:25:39.354806 INFO: === FDR correction performed with classifier version -1 ===
0:25:39.355380 PROGRESS: ============================= Precursor FDR =============================
0:25:39.355487 PROGRESS: Total precursors accumulated: 8
0:25:39.355567 PROGRESS: Target precursors: 8 (100.00%)
0:25:39.355645 PROGRESS: Decoy precursors: 0 (0.00%)
0:25:39.355717 PROGRESS: 
0:25:39.355784 PROGRESS: Precursor Summary:
0:25:39.356958 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:25:39.357067 PROGRESS: 
0:25:39.357144 PROGRESS: Protein Summary:
0:25:39.358431 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:25:39.358546 PROGRESS: =========================================================================
0:25:39.358890 INFO: Target number of precursors not reached yet.
0:25:39.479263 INFO: Starting optimization step 3.
0:25:39.479576 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:25:39.479686 INFO: Using rust extraction backend
0:25:39.479792 PROGRESS: Extracting batch of 15855 precursors
0:25:39.508392 INFO: === Search parameters used ===
0:25:39.508567 INFO: rt_error       : 805.6138305664062
0:25:39.508651 INFO: mobility_error : 0.1
0:25:39.508720 INFO: num_candidates : 1
0:25:39.508788 INFO: ms1_error      : 30
0:25:39.508844 INFO: ms2_error      : 30
0:25:39.508915 INFO: fwhm_rt        : 5
0:25:39.508967 INFO: quant_window   : 3
0:25:39.509024 INFO: ==============================================
0:25:39.633288 INFO: performing precursor FDR with 40 features
0:25:39.633416 INFO: Decoy channel: -1
0:25:39.633443 INFO: competitive: True
0:25:39.644913 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:39.652344 INFO: Estimating optimal hyperparameters - samples: 23,352, batch_size: 128, learning_rate: 1.77e-04
0:25:39.652530 INFO: Using random state 250386 for train-test-split
0:25:41.956418 INFO: Test AUC: 0.552
0:25:41.956555 INFO: Train AUC: 0.561
0:25:41.956588 INFO: AUC difference: 1.66%
0:25:42.221040 INFO: Resetting torch num_threads to 80
0:25:42.228880 PROGRESS: === Extracted 29190 precursors and 129750 fragments ===
0:25:42.229366 INFO: === FDR correction performed with classifier version -1 ===
0:25:42.229939 PROGRESS: ============================= Precursor FDR =============================
0:25:42.230050 PROGRESS: Total precursors accumulated: 17
0:25:42.230119 PROGRESS: Target precursors: 17 (100.00%)
0:25:42.230178 PROGRESS: Decoy precursors: 0 (0.00%)
0:25:42.230231 PROGRESS: 
0:25:42.230282 PROGRESS: Precursor Summary:
0:25:42.231405 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
0:25:42.231510 PROGRESS: 
0:25:42.231583 PROGRESS: Protein Summary:
0:25:42.232844 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
0:25:42.232947 PROGRESS: =========================================================================
0:25:42.233478 INFO: Target number of precursors not reached yet.
0:25:42.388514 INFO: Starting optimization step 4.
0:25:42.388821 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:25:42.388920 INFO: Using rust extraction backend
0:25:42.388997 PROGRESS: Extracting batch of 31732 precursors
0:25:42.445176 INFO: === Search parameters used ===
0:25:42.445467 INFO: rt_error       : 805.6138305664062
0:25:42.445529 INFO: mobility_error : 0.1
0:25:42.445579 INFO: num_candidates : 1
0:25:42.445628 INFO: ms1_error      : 30
0:25:42.445676 INFO: ms2_error      : 30
0:25:42.445719 INFO: fwhm_rt        : 5
0:25:42.445762 INFO: quant_window   : 3
0:25:42.445804 INFO: ==============================================
0:25:42.667944 INFO: performing precursor FDR with 40 features
0:25:42.668075 INFO: Decoy channel: -1
0:25:42.668105 INFO: competitive: True
0:25:42.691828 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:42.710009 INFO: Estimating optimal hyperparameters - samples: 48,325, batch_size: 197, learning_rate: 2.19e-04
0:25:42.710244 INFO: Using random state 574070 for train-test-split
0:25:46.326656 INFO: Test AUC: 0.565
0:25:46.326791 INFO: Train AUC: 0.581
0:25:46.326821 INFO: AUC difference: 2.80%
0:25:46.604710 INFO: Resetting torch num_threads to 80
0:25:46.617335 PROGRESS: === Extracted 60407 precursors and 267887 fragments ===
0:25:46.617929 INFO: === FDR correction performed with classifier version -1 ===
0:25:46.618577 PROGRESS: ============================= Precursor FDR =============================
0:25:46.618695 PROGRESS: Total precursors accumulated: 96
0:25:46.618778 PROGRESS: Target precursors: 96 (100.00%)
0:25:46.618855 PROGRESS: Decoy precursors: 0 (0.00%)
0:25:46.618922 PROGRESS: 
0:25:46.618985 PROGRESS: Precursor Summary:
0:25:46.620156 PROGRESS: Channel   0:	 0.050 FDR:    96; 0.010 FDR:    96; 0.001 FDR:    96
0:25:46.620260 PROGRESS: 
0:25:46.620334 PROGRESS: Protein Summary:
0:25:46.621656 PROGRESS: Channel   0:	 0.050 FDR:    96; 0.010 FDR:    96; 0.001 FDR:    96
0:25:46.621763 PROGRESS: =========================================================================
0:25:46.622739 INFO: Target number of precursors not reached yet.
0:25:46.833394 INFO: Starting optimization step 5.
0:25:46.833711 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:25:46.833822 INFO: Using rust extraction backend
0:25:46.833929 PROGRESS: Extracting batch of 63446 precursors
0:25:46.944707 INFO: === Search parameters used ===
0:25:46.945009 INFO: rt_error       : 805.6138305664062
0:25:46.945070 INFO: mobility_error : 0.1
0:25:46.945126 INFO: num_candidates : 1
0:25:46.945187 INFO: ms1_error      : 30
0:25:46.945245 INFO: ms2_error      : 30
0:25:46.945294 INFO: fwhm_rt        : 5
0:25:46.945347 INFO: quant_window   : 3
0:25:46.945396 INFO: ==============================================
0:25:47.363592 INFO: performing precursor FDR with 40 features
0:25:47.363731 INFO: Decoy channel: -1
0:25:47.363760 INFO: competitive: True
0:25:47.424585 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:47.461218 INFO: Estimating optimal hyperparameters - samples: 98,211, batch_size: 402, learning_rate: 3.13e-04
0:25:47.461563 INFO: Using random state 557386 for train-test-split
0:25:51.964029 INFO: Test AUC: 0.574
0:25:51.964200 INFO: Train AUC: 0.592
0:25:51.964234 INFO: AUC difference: 3.01%
0:25:52.260403 INFO: Resetting torch num_threads to 80
0:25:52.287374 PROGRESS: === Extracted 122764 precursors and 545281 fragments ===
0:25:52.288151 INFO: === FDR correction performed with classifier version -1 ===
0:25:52.288789 PROGRESS: ============================= Precursor FDR =============================
0:25:52.288906 PROGRESS: Total precursors accumulated: 101
0:25:52.288987 PROGRESS: Target precursors: 100 (99.01%)
0:25:52.289063 PROGRESS: Decoy precursors: 1 (0.99%)
0:25:52.289130 PROGRESS: 
0:25:52.289200 PROGRESS: Precursor Summary:
0:25:52.290287 PROGRESS: Channel   0:	 0.050 FDR:   100; 0.010 FDR:     0; 0.001 FDR:     0
0:25:52.290398 PROGRESS: 
0:25:52.290475 PROGRESS: Protein Summary:
0:25:52.291647 PROGRESS: Channel   0:	 0.050 FDR:   100; 0.010 FDR:     0; 0.001 FDR:     0
0:25:52.291755 PROGRESS: =========================================================================
0:25:52.293675 INFO: Target number of precursors not reached yet.
0:25:52.594088 INFO: Starting optimization step 6.
0:25:52.594413 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:25:52.594541 INFO: Using rust extraction backend
0:25:52.594635 PROGRESS: Extracting batch of 126831 precursors
0:25:52.813912 INFO: === Search parameters used ===
0:25:52.814241 INFO: rt_error       : 805.6138305664062
0:25:52.814322 INFO: mobility_error : 0.1
0:25:52.814387 INFO: num_candidates : 1
0:25:52.814442 INFO: ms1_error      : 30
0:25:52.814496 INFO: ms2_error      : 30
0:25:52.814547 INFO: fwhm_rt        : 5
0:25:52.814598 INFO: quant_window   : 3
0:25:52.814643 INFO: ==============================================
0:25:53.597936 INFO: performing precursor FDR with 40 features
0:25:53.598078 INFO: Decoy channel: -1
0:25:53.598107 INFO: competitive: True
0:25:53.723947 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:53.809861 INFO: Estimating optimal hyperparameters - samples: 197,900, batch_size: 810, learning_rate: 4.45e-04
0:25:53.811329 INFO: Using random state 164817 for train-test-split
0:25:59.805112 INFO: Test AUC: 0.582
0:25:59.805259 INFO: Train AUC: 0.595
0:25:59.805292 INFO: AUC difference: 2.08%
0:26:00.135296 INFO: Resetting torch num_threads to 80
0:26:00.184200 PROGRESS: === Extracted 247375 precursors and 1099176 fragments ===
0:26:00.185029 INFO: === FDR correction performed with classifier version -1 ===
0:26:00.185925 PROGRESS: ============================= Precursor FDR =============================
0:26:00.186044 PROGRESS: Total precursors accumulated: 590
0:26:00.186121 PROGRESS: Target precursors: 585 (99.15%)
0:26:00.186191 PROGRESS: Decoy precursors: 5 (0.85%)
0:26:00.186253 PROGRESS: 
0:26:00.186313 PROGRESS: Precursor Summary:
0:26:00.187853 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   585; 0.001 FDR:   284
0:26:00.187971 PROGRESS: 
0:26:00.188050 PROGRESS: Protein Summary:
0:26:00.190111 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   584; 0.001 FDR:   284
0:26:00.190237 PROGRESS: =========================================================================
0:26:00.198150 INFO: Target number of precursors not reached yet.
0:26:00.748599 INFO: Starting optimization step 7.
0:26:00.748944 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:26:00.749053 INFO: Using rust extraction backend
0:26:00.749140 PROGRESS: Extracting batch of 253660 precursors
0:26:01.185533 INFO: === Search parameters used ===
0:26:01.185881 INFO: rt_error       : 805.6138305664062
0:26:01.185969 INFO: mobility_error : 0.1
0:26:01.186044 INFO: num_candidates : 1
0:26:01.186115 INFO: ms1_error      : 30
0:26:01.186181 INFO: ms2_error      : 30
0:26:01.186252 INFO: fwhm_rt        : 5
0:26:01.186321 INFO: quant_window   : 3
0:26:01.186388 INFO: ==============================================
0:26:02.748094 INFO: performing precursor FDR with 40 features
0:26:02.748253 INFO: Decoy channel: -1
0:26:02.748282 INFO: competitive: True
0:26:03.016571 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:03.216737 INFO: Estimating optimal hyperparameters - samples: 397,252, batch_size: 1,627, learning_rate: 6.30e-04
0:26:03.217483 INFO: Using random state 703368 for train-test-split
0:26:10.329203 INFO: Test AUC: 0.586
0:26:10.329369 INFO: Train AUC: 0.596
0:26:10.329406 INFO: AUC difference: 1.68%
0:26:11.068664 INFO: Resetting torch num_threads to 80
0:26:11.174858 PROGRESS: === Extracted 496566 precursors and 2207521 fragments ===
0:26:11.175650 INFO: === FDR correction performed with classifier version -1 ===
0:26:11.176538 PROGRESS: ============================= Precursor FDR =============================
0:26:11.176650 PROGRESS: Total precursors accumulated: 1,414
0:26:11.176732 PROGRESS: Target precursors: 1,400 (99.01%)
0:26:11.176797 PROGRESS: Decoy precursors: 14 (0.99%)
0:26:11.176849 PROGRESS: 
0:26:11.176907 PROGRESS: Precursor Summary:
0:26:11.178376 PROGRESS: Channel   0:	 0.050 FDR: 1,400; 0.010 FDR: 1,397; 0.001 FDR: 1,023
0:26:11.178500 PROGRESS: 
0:26:11.178583 PROGRESS: Protein Summary:
0:26:11.180952 PROGRESS: Channel   0:	 0.050 FDR: 1,397; 0.010 FDR: 1,394; 0.001 FDR: 1,020
0:26:11.181060 PROGRESS: =========================================================================
0:26:11.190406 INFO: Target number of precursors reached.
0:26:11.377539 INFO: fragments_df: keeping 5000 of 2207521 [sum(precursor_idx_mask)=15029 sum(mass_error_mask)=2207521 stop_rank=5000
0:26:12.083714 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:12.324435 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:13.043614 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:26:13.044126 INFO: Using score_cutoff 13.29689085960388 (fac=0.99, q=1)
0:26:13.044480 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:26:13.044565 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:26:13.044625 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.29689085960388
0:26:13.044692 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:13.362212 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:14.039422 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:26:14.039709 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:26:14.039843 INFO: Starting optimization step 8.
0:26:14.039923 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:26:14.040027 INFO: Using rust extraction backend
0:26:14.040111 PROGRESS: Extracting batch of 505395 precursors
0:26:14.896791 INFO: === Search parameters used ===
0:26:14.897139 INFO: rt_error       : 805.6138305664062
0:26:14.897214 INFO: mobility_error : 0.1
0:26:14.897278 INFO: num_candidates : 3
0:26:14.897331 INFO: ms1_error      : 30
0:26:14.897386 INFO: ms2_error      : 30
0:26:14.897432 INFO: fwhm_rt        : 3.0
0:26:14.897491 INFO: quant_window   : 3
0:26:14.897542 INFO: ==============================================
0:26:21.490531 INFO: performing precursor FDR with 40 features
0:26:21.490709 INFO: Decoy channel: -1
0:26:21.490738 INFO: competitive: True
0:26:22.012051 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:22.755823 INFO: Estimating optimal hyperparameters - samples: 1,192,298, batch_size: 4,096, learning_rate: 1.00e-03
0:26:22.757962 INFO: Using random state 940731 for train-test-split
0:26:48.041313 INFO: Test AUC: 0.594
0:26:48.041511 INFO: Train AUC: 0.599
0:26:48.041544 INFO: AUC difference: 0.86%
0:26:48.783961 INFO: Resetting torch num_threads to 80
0:26:48.843114 PROGRESS: === Extracted 1490373 precursors and 6499134 fragments ===
0:26:48.843705 INFO: === FDR correction performed with classifier version 7 ===
0:26:48.844569 PROGRESS: ============================= Precursor FDR =============================
0:26:48.844703 PROGRESS: Total precursors accumulated: 1,808
0:26:48.844782 PROGRESS: Target precursors: 1,791 (99.06%)
0:26:48.844857 PROGRESS: Decoy precursors: 17 (0.94%)
0:26:48.844934 PROGRESS: 
0:26:48.845007 PROGRESS: Precursor Summary:
0:26:48.846673 PROGRESS: Channel   0:	 0.050 FDR: 1,791; 0.010 FDR: 1,791; 0.001 FDR: 1,117
0:26:48.846793 PROGRESS: 
0:26:48.846874 PROGRESS: Protein Summary:
0:26:48.849531 PROGRESS: Channel   0:	 0.050 FDR: 1,786; 0.010 FDR: 1,786; 0.001 FDR: 1,114
0:26:48.849655 PROGRESS: =========================================================================
0:26:48.889398 INFO: Target number of precursors reached.
0:26:49.385583 INFO: fragments_df: keeping 5000 of 6499134 [sum(precursor_idx_mask)=38895 sum(mass_error_mask)=6499134 stop_rank=5000
0:26:50.267302 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:50.547473 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:51.272513 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:51.273017 INFO: Using score_cutoff 12.487104251861574 (fac=0.99, q=1)
0:26:51.273359 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:51.273448 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:51.273507 INFO: Updating optimization_manager: score_cutoff        : 13.29689085960388 -> 12.487104251861574
0:26:51.273567 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:51.584638 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:52.336966 INFO: === checking if optimization conditions were reached ===
0:26:52.339517 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:26:52.339703 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:26:52.339792 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:26:52.339870 INFO: ==============================================
0:26:52.339954 INFO: Starting optimization step 9.
0:26:52.340033 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:26:52.340121 INFO: Using rust extraction backend
0:26:52.340209 PROGRESS: Extracting batch of 505395 precursors
0:26:53.201177 INFO: === Search parameters used ===
0:26:53.201502 INFO: rt_error       : 805.6138305664062
0:26:53.201569 INFO: mobility_error : 0.1
0:26:53.201624 INFO: num_candidates : 3
0:26:53.201673 INFO: ms1_error      : 30
0:26:53.201727 INFO: ms2_error      : 10.0
0:26:53.201804 INFO: fwhm_rt        : 3.0
0:26:53.201863 INFO: quant_window   : 3
0:26:53.201938 INFO: ==============================================
0:26:58.858701 INFO: performing precursor FDR with 40 features
0:26:58.858860 INFO: Decoy channel: -1
0:26:58.858889 INFO: competitive: True
0:26:59.283888 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:59.951869 INFO: Estimating optimal hyperparameters - samples: 1,207,080, batch_size: 4,096, learning_rate: 1.00e-03
0:26:59.955201 INFO: Using random state 931913 for train-test-split
0:27:25.442317 INFO: Test AUC: 0.604
0:27:25.442601 INFO: Train AUC: 0.606
0:27:25.442641 INFO: AUC difference: 0.33%
0:27:26.187150 INFO: Resetting torch num_threads to 80
0:27:26.370641 PROGRESS: === Extracted 1508851 precursors and 7589005 fragments ===
0:27:26.371745 INFO: === FDR correction performed with classifier version 8 ===
0:27:26.372901 PROGRESS: ============================= Precursor FDR =============================
0:27:26.373033 PROGRESS: Total precursors accumulated: 2,108
0:27:26.373106 PROGRESS: Target precursors: 2,088 (99.05%)
0:27:26.373182 PROGRESS: Decoy precursors: 20 (0.95%)
0:27:26.373252 PROGRESS: 
0:27:26.373318 PROGRESS: Precursor Summary:
0:27:26.375112 PROGRESS: Channel   0:	 0.050 FDR: 2,088; 0.010 FDR: 2,088; 0.001 FDR:     0
0:27:26.375235 PROGRESS: 
0:27:26.375313 PROGRESS: Protein Summary:
0:27:26.377982 PROGRESS: Channel   0:	 0.050 FDR: 2,084; 0.010 FDR: 2,084; 0.001 FDR:     0
0:27:26.378104 PROGRESS: =========================================================================
0:27:26.443346 INFO: Target number of precursors reached.
0:27:27.013067 INFO: fragments_df: keeping 5000 of 7589005 [sum(precursor_idx_mask)=48854 sum(mass_error_mask)=7589005 stop_rank=5000
0:27:27.599091 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:27.926489 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:28.656730 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:28.657336 INFO: Using score_cutoff 11.701297926521303 (fac=0.99, q=1)
0:27:28.657825 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:28.657925 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:28.657988 INFO: Updating optimization_manager: score_cutoff        : 12.487104251861574 -> 11.701297926521303
0:27:28.658078 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:28.821543 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:29.175143 INFO: === checking if optimization conditions were reached ===
0:27:29.178118 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:27:29.178261 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:27:29.178352 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:27:29.178442 INFO: ==============================================
0:27:29.178527 INFO: Starting optimization step 10.
0:27:29.178604 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:27:29.178734 INFO: Using rust extraction backend
0:27:29.178828 PROGRESS: Extracting batch of 251735 precursors
0:27:29.636808 INFO: === Search parameters used ===
0:27:29.637146 INFO: rt_error       : 805.6138305664062
0:27:29.637211 INFO: mobility_error : 0.1
0:27:29.637264 INFO: num_candidates : 3
0:27:29.637320 INFO: ms1_error      : 30
0:27:29.637379 INFO: ms2_error      : 10.0
0:27:29.637441 INFO: fwhm_rt        : 3.0
0:27:29.637500 INFO: quant_window   : 3
0:27:29.637554 INFO: ==============================================
0:27:32.862376 INFO: performing precursor FDR with 40 features
0:27:32.862542 INFO: Decoy channel: -1
0:27:32.862571 INFO: competitive: True
0:27:33.123928 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:33.464610 INFO: Estimating optimal hyperparameters - samples: 601,179, batch_size: 2,462, learning_rate: 7.75e-04
0:27:33.466026 INFO: Using random state 432918 for train-test-split
0:27:49.372367 INFO: Test AUC: 0.605
0:27:49.372650 INFO: Train AUC: 0.611
0:27:49.372687 INFO: AUC difference: 0.97%
0:27:49.868336 INFO: Resetting torch num_threads to 80
0:27:49.899264 PROGRESS: === Extracted 751474 precursors and 3776677 fragments ===
0:27:49.899881 INFO: === FDR correction performed with classifier version 9 ===
0:27:49.900617 PROGRESS: ============================= Precursor FDR =============================
0:27:49.900729 PROGRESS: Total precursors accumulated: 1,071
0:27:49.900826 PROGRESS: Target precursors: 1,061 (99.07%)
0:27:49.900897 PROGRESS: Decoy precursors: 10 (0.93%)
0:27:49.900975 PROGRESS: 
0:27:49.901039 PROGRESS: Precursor Summary:
0:27:49.902399 PROGRESS: Channel   0:	 0.050 FDR: 1,061; 0.010 FDR: 1,061; 0.001 FDR:   332
0:27:49.902508 PROGRESS: 
0:27:49.902588 PROGRESS: Protein Summary:
0:27:49.904550 PROGRESS: Channel   0:	 0.050 FDR: 1,060; 0.010 FDR: 1,060; 0.001 FDR:   332
0:27:49.904662 PROGRESS: =========================================================================
0:27:49.925415 INFO: Target number of precursors reached.
0:27:50.217725 INFO: fragments_df: keeping 5000 of 3776677 [sum(precursor_idx_mask)=24574 sum(mass_error_mask)=3776677 stop_rank=5000
0:27:50.767437 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:50.969048 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:51.692092 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:51.692616 INFO: Using score_cutoff 11.20745058631897 (fac=0.99, q=1)
0:27:51.692998 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:51.693089 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:51.693153 INFO: Updating optimization_manager: score_cutoff        : 11.701297926521303 -> 11.20745058631897
0:27:51.693217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:51.848720 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:52.217158 INFO: === checking if optimization conditions were reached ===
0:27:52.220390 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:27:52.220542 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:27:52.220627 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:27:52.220708 INFO: ==============================================
0:27:52.220794 INFO: Starting optimization step 11.
0:27:52.220872 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:27:52.220963 INFO: Using rust extraction backend
0:27:52.221050 PROGRESS: Extracting batch of 251735 precursors
0:27:52.662209 INFO: === Search parameters used ===
0:27:52.662545 INFO: rt_error       : 805.6138305664062
0:27:52.662616 INFO: mobility_error : 0.1
0:27:52.662699 INFO: num_candidates : 3
0:27:52.662770 INFO: ms1_error      : 30
0:27:52.662830 INFO: ms2_error      : 10.0
0:27:52.662889 INFO: fwhm_rt        : 3.0
0:27:52.662957 INFO: quant_window   : 3
0:27:52.663025 INFO: ==============================================
0:27:55.540156 INFO: performing precursor FDR with 40 features
0:27:55.540297 INFO: Decoy channel: -1
0:27:55.540329 INFO: competitive: True
0:27:55.749638 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:56.070969 INFO: Estimating optimal hyperparameters - samples: 601,196, batch_size: 2,462, learning_rate: 7.75e-04
0:27:56.072249 INFO: Using random state 803720 for train-test-split
0:28:10.156913 INFO: Test AUC: 0.609
0:28:10.157177 INFO: Train AUC: 0.614
0:28:10.157221 INFO: AUC difference: 0.89%
0:28:10.665955 INFO: Resetting torch num_threads to 80
0:28:10.721789 PROGRESS: === Extracted 751495 precursors and 3777486 fragments ===
0:28:10.722669 INFO: === FDR correction performed with classifier version 10 ===
0:28:10.723783 PROGRESS: ============================= Precursor FDR =============================
0:28:10.723941 PROGRESS: Total precursors accumulated: 1,232
0:28:10.724026 PROGRESS: Target precursors: 1,220 (99.03%)
0:28:10.724099 PROGRESS: Decoy precursors: 12 (0.97%)
0:28:10.724166 PROGRESS: 
0:28:10.724236 PROGRESS: Precursor Summary:
0:28:10.725895 PROGRESS: Channel   0:	 0.050 FDR: 1,220; 0.010 FDR: 1,220; 0.001 FDR:   173
0:28:10.726037 PROGRESS: 
0:28:10.726121 PROGRESS: Protein Summary:
0:28:10.728516 PROGRESS: Channel   0:	 0.050 FDR: 1,219; 0.010 FDR: 1,219; 0.001 FDR:   173
0:28:10.728655 PROGRESS: =========================================================================
0:28:10.766034 INFO: Target number of precursors reached.
0:28:11.052315 INFO: fragments_df: keeping 5000 of 3777486 [sum(precursor_idx_mask)=28166 sum(mass_error_mask)=3777486 stop_rank=5000
0:28:11.893334 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:12.092747 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:12.769072 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:12.769735 INFO: Using score_cutoff 11.469974354839325 (fac=0.99, q=1)
0:28:12.770208 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:12.770302 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:12.770380 INFO: Updating optimization_manager: score_cutoff        : 11.20745058631897 -> 11.469974354839325
0:28:12.770480 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:12.929284 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:13.302997 INFO: === checking if optimization conditions were reached ===
0:28:13.305702 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:28:13.305846 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:28:13.305966 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:28:13.306051 INFO: ==============================================
0:28:13.306169 INFO: Starting optimization step 12.
0:28:13.306278 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:28:13.306383 INFO: Using rust extraction backend
0:28:13.306473 PROGRESS: Extracting batch of 251735 precursors
0:28:13.750974 INFO: === Search parameters used ===
0:28:13.751339 INFO: rt_error       : 805.6138305664062
0:28:13.751410 INFO: mobility_error : 0.1
0:28:13.751474 INFO: num_candidates : 3
0:28:13.751523 INFO: ms1_error      : 30
0:28:13.751568 INFO: ms2_error      : 10.0
0:28:13.751612 INFO: fwhm_rt        : 3.0
0:28:13.751657 INFO: quant_window   : 3
0:28:13.751704 INFO: ==============================================
0:28:16.870602 INFO: performing precursor FDR with 40 features
0:28:16.870757 INFO: Decoy channel: -1
0:28:16.870788 INFO: competitive: True
0:28:17.110053 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:17.434571 INFO: Estimating optimal hyperparameters - samples: 601,192, batch_size: 2,462, learning_rate: 7.75e-04
0:28:17.436286 INFO: Using random state 588681 for train-test-split
0:28:32.709963 INFO: Test AUC: 0.607
0:28:32.710267 INFO: Train AUC: 0.615
0:28:32.710304 INFO: AUC difference: 1.20%
0:28:33.211099 INFO: Resetting torch num_threads to 80
0:28:33.250818 PROGRESS: === Extracted 751491 precursors and 3776461 fragments ===
0:28:33.251509 INFO: === FDR correction performed with classifier version 11 ===
0:28:33.252309 PROGRESS: ============================= Precursor FDR =============================
0:28:33.252436 PROGRESS: Total precursors accumulated: 1,163
0:28:33.252518 PROGRESS: Target precursors: 1,152 (99.05%)
0:28:33.252589 PROGRESS: Decoy precursors: 11 (0.95%)
0:28:33.252653 PROGRESS: 
0:28:33.252715 PROGRESS: Precursor Summary:
0:28:33.254074 PROGRESS: Channel   0:	 0.050 FDR: 1,152; 0.010 FDR: 1,152; 0.001 FDR:     0
0:28:33.254194 PROGRESS: 
0:28:33.254268 PROGRESS: Protein Summary:
0:28:33.256227 PROGRESS: Channel   0:	 0.050 FDR: 1,151; 0.010 FDR: 1,151; 0.001 FDR:     0
0:28:33.256337 PROGRESS: =========================================================================
0:28:33.278136 INFO: Target number of precursors reached.
0:28:33.589454 INFO: fragments_df: keeping 5000 of 3776461 [sum(precursor_idx_mask)=26699 sum(mass_error_mask)=3776461 stop_rank=5000
0:28:34.135175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:34.356402 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:35.084858 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:35.085368 INFO: Using score_cutoff 11.423428466892242 (fac=0.99, q=1)
0:28:35.085766 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:35.085855 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:35.085929 INFO: Updating optimization_manager: score_cutoff        : 11.469974354839325 -> 11.423428466892242
0:28:35.086029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:35.240692 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:35.642907 INFO: === checking if optimization conditions were reached ===
0:28:35.645304 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:28:35.645426 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
0:28:35.645501 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:28:35.645577 INFO: ==============================================
0:28:35.645662 PROGRESS: Optimization finished for ms2_error.
0:28:36.064223 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:36.217731 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:36.592977 INFO: Starting optimization step 0.
0:28:36.593348 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:28:36.593564 INFO: Using rust extraction backend
0:28:36.593704 PROGRESS: Extracting batch of 251735 precursors
0:28:37.049886 INFO: === Search parameters used ===
0:28:37.050227 INFO: rt_error       : 805.6138305664062
0:28:37.050294 INFO: mobility_error : 0.1
0:28:37.050347 INFO: num_candidates : 3
0:28:37.050404 INFO: ms1_error      : 30
0:28:37.050466 INFO: ms2_error      : 10.0
0:28:37.050534 INFO: fwhm_rt        : 3.0
0:28:37.050594 INFO: quant_window   : 3
0:28:37.050649 INFO: ==============================================
0:28:39.992878 INFO: performing precursor FDR with 40 features
0:28:39.993027 INFO: Decoy channel: -1
0:28:39.993062 INFO: competitive: True
0:28:40.187744 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:40.494240 INFO: Estimating optimal hyperparameters - samples: 601,208, batch_size: 2,462, learning_rate: 7.75e-04
0:28:40.495573 INFO: Using random state 832707 for train-test-split
0:28:53.976324 INFO: Test AUC: 0.608
0:28:53.976493 INFO: Train AUC: 0.616
0:28:53.976528 INFO: AUC difference: 1.33%
0:28:54.917267 INFO: Resetting torch num_threads to 80
0:28:54.975149 PROGRESS: === Extracted 751510 precursors and 3776583 fragments ===
0:28:54.975739 INFO: === FDR correction performed with classifier version 12 ===
0:28:54.976577 PROGRESS: ============================= Precursor FDR =============================
0:28:54.976700 PROGRESS: Total precursors accumulated: 1,178
0:28:54.976789 PROGRESS: Target precursors: 1,167 (99.07%)
0:28:54.976871 PROGRESS: Decoy precursors: 11 (0.93%)
0:28:54.976929 PROGRESS: 
0:28:54.976980 PROGRESS: Precursor Summary:
0:28:54.978320 PROGRESS: Channel   0:	 0.050 FDR: 1,167; 0.010 FDR: 1,167; 0.001 FDR:     1
0:28:54.978432 PROGRESS: 
0:28:54.978497 PROGRESS: Protein Summary:
0:28:54.980405 PROGRESS: Channel   0:	 0.050 FDR: 1,166; 0.010 FDR: 1,166; 0.001 FDR:     1
0:28:54.980509 PROGRESS: =========================================================================
0:28:54.999147 INFO: Target number of precursors reached.
0:28:55.280110 INFO: fragments_df: keeping 5000 of 3776583 [sum(precursor_idx_mask)=26874 sum(mass_error_mask)=3776583 stop_rank=5000
0:28:55.750779 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:55.963805 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:56.691127 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:56.691643 INFO: Using score_cutoff 10.82698147945404 (fac=0.99, q=1)
0:28:56.691978 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:56.692068 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:56.692151 INFO: Updating optimization_manager: score_cutoff        : 11.423428466892242 -> 10.82698147945404
0:28:56.692228 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:56.848880 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:57.213943 INFO: === checking if optimization conditions were reached ===
0:28:57.214299 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:28:57.217456 INFO: Updating optimization_manager: rt_error            : 805.6138305664062 -> 733.9218235419708
0:28:57.217591 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 733.9218.
0:28:57.217697 INFO: ==============================================
0:28:57.217790 INFO: Starting optimization step 1.
0:28:57.217874 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:28:57.217975 INFO: Using rust extraction backend
0:28:57.218096 PROGRESS: Extracting batch of 251735 precursors
0:28:57.659816 INFO: === Search parameters used ===
0:28:57.660140 INFO: rt_error       : 733.9218235419708
0:28:57.660212 INFO: mobility_error : 0.1
0:28:57.660291 INFO: num_candidates : 3
0:28:57.660360 INFO: ms1_error      : 30
0:28:57.660424 INFO: ms2_error      : 10.0
0:28:57.660481 INFO: fwhm_rt        : 3.0
0:28:57.660541 INFO: quant_window   : 3
0:28:57.660597 INFO: ==============================================
0:29:00.510121 INFO: performing precursor FDR with 40 features
0:29:00.510346 INFO: Decoy channel: -1
0:29:00.510386 INFO: competitive: True
0:29:00.700641 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:01.006009 INFO: Estimating optimal hyperparameters - samples: 601,204, batch_size: 2,462, learning_rate: 7.75e-04
0:29:01.007066 INFO: Using random state 832707 for train-test-split
0:29:13.331849 INFO: Test AUC: 0.610
0:29:13.332029 INFO: Train AUC: 0.618
0:29:13.332061 INFO: AUC difference: 1.42%
0:29:13.830514 INFO: Resetting torch num_threads to 80
0:29:13.867032 PROGRESS: === Extracted 751505 precursors and 3776313 fragments ===
0:29:13.867764 INFO: === FDR correction performed with classifier version 12 ===
0:29:13.868694 PROGRESS: ============================= Precursor FDR =============================
0:29:13.868827 PROGRESS: Total precursors accumulated: 1,237
0:29:13.868911 PROGRESS: Target precursors: 1,225 (99.03%)
0:29:13.868982 PROGRESS: Decoy precursors: 12 (0.97%)
0:29:13.869046 PROGRESS: 
0:29:13.869107 PROGRESS: Precursor Summary:
0:29:13.870549 PROGRESS: Channel   0:	 0.050 FDR: 1,225; 0.010 FDR: 1,225; 0.001 FDR:     1
0:29:13.870659 PROGRESS: 
0:29:13.870739 PROGRESS: Protein Summary:
0:29:13.872755 PROGRESS: Channel   0:	 0.050 FDR: 1,224; 0.010 FDR: 1,224; 0.001 FDR:     1
0:29:13.872864 PROGRESS: =========================================================================
0:29:13.897696 INFO: Target number of precursors reached.
0:29:14.193363 INFO: fragments_df: keeping 5000 of 3776313 [sum(precursor_idx_mask)=28216 sum(mass_error_mask)=3776313 stop_rank=5000
0:29:14.669000 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:14.895520 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:15.624097 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:15.624598 INFO: Using score_cutoff 10.79149642753601 (fac=0.99, q=1)
0:29:15.625006 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:15.625103 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:15.625174 INFO: Updating optimization_manager: score_cutoff        : 10.82698147945404 -> 10.79149642753601
0:29:15.625250 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:15.780762 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:16.147544 INFO: === checking if optimization conditions were reached ===
0:29:16.148008 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:29:16.151426 INFO: Updating optimization_manager: rt_error            : 733.9218235419708 -> 588.288511220227
0:29:16.151600 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 588.2885.
0:29:16.151691 INFO: ==============================================
0:29:16.151783 INFO: Starting optimization step 2.
0:29:16.151862 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:29:16.151957 INFO: Using rust extraction backend
0:29:16.152047 PROGRESS: Extracting batch of 251735 precursors
0:29:16.605275 INFO: === Search parameters used ===
0:29:16.605616 INFO: rt_error       : 588.288511220227
0:29:16.605683 INFO: mobility_error : 0.1
0:29:16.605735 INFO: num_candidates : 3
0:29:16.605781 INFO: ms1_error      : 30
0:29:16.605824 INFO: ms2_error      : 10.0
0:29:16.605866 INFO: fwhm_rt        : 3.0
0:29:16.605918 INFO: quant_window   : 3
0:29:16.605963 INFO: ==============================================
0:29:19.260997 INFO: performing precursor FDR with 40 features
0:29:19.261148 INFO: Decoy channel: -1
0:29:19.261178 INFO: competitive: True
0:29:19.451249 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:19.755253 INFO: Estimating optimal hyperparameters - samples: 600,912, batch_size: 2,461, learning_rate: 7.75e-04
0:29:19.756464 INFO: Using random state 832707 for train-test-split
0:29:33.908605 INFO: Test AUC: 0.609
0:29:33.908844 INFO: Train AUC: 0.617
0:29:33.908884 INFO: AUC difference: 1.34%
0:29:34.423637 INFO: Resetting torch num_threads to 80
0:29:34.456683 PROGRESS: === Extracted 751141 precursors and 3759912 fragments ===
0:29:34.457345 INFO: === FDR correction performed with classifier version 12 ===
0:29:34.458151 PROGRESS: ============================= Precursor FDR =============================
0:29:34.458288 PROGRESS: Total precursors accumulated: 1,197
0:29:34.458381 PROGRESS: Target precursors: 1,186 (99.08%)
0:29:34.458452 PROGRESS: Decoy precursors: 11 (0.92%)
0:29:34.458531 PROGRESS: 
0:29:34.458585 PROGRESS: Precursor Summary:
0:29:34.459941 PROGRESS: Channel   0:	 0.050 FDR: 1,186; 0.010 FDR: 1,186; 0.001 FDR:     1
0:29:34.460044 PROGRESS: 
0:29:34.460105 PROGRESS: Protein Summary:
0:29:34.462058 PROGRESS: Channel   0:	 0.050 FDR: 1,185; 0.010 FDR: 1,185; 0.001 FDR:     1
0:29:34.462166 PROGRESS: =========================================================================
0:29:34.481533 INFO: Target number of precursors reached.
0:29:34.779742 INFO: fragments_df: keeping 5000 of 3759912 [sum(precursor_idx_mask)=27406 sum(mass_error_mask)=3759912 stop_rank=5000
0:29:35.345609 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:35.569761 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:36.299980 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:36.300523 INFO: Using score_cutoff 11.455711797237397 (fac=0.99, q=1)
0:29:36.300884 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:36.300969 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:36.301034 INFO: Updating optimization_manager: score_cutoff        : 10.79149642753601 -> 11.455711797237397
0:29:36.301132 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:36.456611 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:36.817948 INFO: === checking if optimization conditions were reached ===
0:29:36.818403 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:29:36.822109 INFO: Updating optimization_manager: rt_error            : 588.288511220227 -> 575.7716112522105
0:29:36.822293 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 575.7716.
0:29:36.822409 INFO: ==============================================
0:29:36.822529 INFO: Starting optimization step 3.
0:29:36.822643 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:29:36.822757 INFO: Using rust extraction backend
0:29:36.822865 PROGRESS: Extracting batch of 251735 precursors
0:29:37.258549 INFO: === Search parameters used ===
0:29:37.258908 INFO: rt_error       : 575.7716112522105
0:29:37.258996 INFO: mobility_error : 0.1
0:29:37.259091 INFO: num_candidates : 3
0:29:37.259152 INFO: ms1_error      : 30
0:29:37.259224 INFO: ms2_error      : 10.0
0:29:37.259280 INFO: fwhm_rt        : 3.0
0:29:37.259345 INFO: quant_window   : 3
0:29:37.259397 INFO: ==============================================
0:29:39.985794 INFO: performing precursor FDR with 40 features
0:29:39.985943 INFO: Decoy channel: -1
0:29:39.985973 INFO: competitive: True
0:29:40.168761 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:40.472273 INFO: Estimating optimal hyperparameters - samples: 600,883, batch_size: 2,461, learning_rate: 7.75e-04
0:29:40.473424 INFO: Using random state 832707 for train-test-split
0:29:52.757727 INFO: Test AUC: 0.607
0:29:52.757955 INFO: Train AUC: 0.616
0:29:52.757989 INFO: AUC difference: 1.51%
0:29:53.253534 INFO: Resetting torch num_threads to 80
0:29:53.285713 PROGRESS: === Extracted 751104 precursors and 3757657 fragments ===
0:29:53.286328 INFO: === FDR correction performed with classifier version 12 ===
0:29:53.287067 PROGRESS: ============================= Precursor FDR =============================
0:29:53.287177 PROGRESS: Total precursors accumulated: 1,216
0:29:53.287252 PROGRESS: Target precursors: 1,204 (99.01%)
0:29:53.287313 PROGRESS: Decoy precursors: 12 (0.99%)
0:29:53.287367 PROGRESS: 
0:29:53.287416 PROGRESS: Precursor Summary:
0:29:53.288709 PROGRESS: Channel   0:	 0.050 FDR: 1,204; 0.010 FDR: 1,204; 0.001 FDR:    40
0:29:53.288805 PROGRESS: 
0:29:53.288867 PROGRESS: Protein Summary:
0:29:53.290793 PROGRESS: Channel   0:	 0.050 FDR: 1,203; 0.010 FDR: 1,203; 0.001 FDR:    40
0:29:53.290897 PROGRESS: =========================================================================
0:29:53.309358 INFO: Target number of precursors reached.
0:29:53.591899 INFO: fragments_df: keeping 5000 of 3757657 [sum(precursor_idx_mask)=27739 sum(mass_error_mask)=3757657 stop_rank=5000
0:29:54.042878 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:54.258991 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:54.987083 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:54.987574 INFO: Using score_cutoff 11.256049378681183 (fac=0.99, q=1)
0:29:54.987946 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:54.988044 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:54.988118 INFO: Updating optimization_manager: score_cutoff        : 11.455711797237397 -> 11.256049378681183
0:29:54.988193 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:55.138377 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:55.476876 INFO: === checking if optimization conditions were reached ===
0:29:55.477327 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:29:55.480854 INFO: Updating optimization_manager: rt_error            : 575.7716112522105 -> 491.9981949130319
0:29:55.481063 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 491.9982.
0:29:55.481175 INFO: ==============================================
0:29:55.481288 INFO: Starting optimization step 4.
0:29:55.481389 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:29:55.481499 INFO: Using rust extraction backend
0:29:55.481607 PROGRESS: Extracting batch of 251735 precursors
0:29:55.912095 INFO: === Search parameters used ===
0:29:55.912606 INFO: rt_error       : 491.9981949130319
0:29:55.912672 INFO: mobility_error : 0.1
0:29:55.912723 INFO: num_candidates : 3
0:29:55.912768 INFO: ms1_error      : 30
0:29:55.912811 INFO: ms2_error      : 10.0
0:29:55.912855 INFO: fwhm_rt        : 3.0
0:29:55.912897 INFO: quant_window   : 3
0:29:55.912939 INFO: ==============================================
0:29:58.523422 INFO: performing precursor FDR with 40 features
0:29:58.523568 INFO: Decoy channel: -1
0:29:58.523597 INFO: competitive: True
0:29:58.707243 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:59.005229 INFO: Estimating optimal hyperparameters - samples: 600,480, batch_size: 2,459, learning_rate: 7.75e-04
0:29:59.006226 INFO: Using random state 832707 for train-test-split
0:30:11.150758 INFO: Test AUC: 0.607
0:30:11.150927 INFO: Train AUC: 0.616
0:30:11.150966 INFO: AUC difference: 1.33%
0:30:11.648014 INFO: Resetting torch num_threads to 80
0:30:11.693389 PROGRESS: === Extracted 750601 precursors and 3725121 fragments ===
0:30:11.693984 INFO: === FDR correction performed with classifier version 12 ===
0:30:11.694727 PROGRESS: ============================= Precursor FDR =============================
0:30:11.694838 PROGRESS: Total precursors accumulated: 1,100
0:30:11.694903 PROGRESS: Target precursors: 1,090 (99.09%)
0:30:11.694958 PROGRESS: Decoy precursors: 10 (0.91%)
0:30:11.695010 PROGRESS: 
0:30:11.695058 PROGRESS: Precursor Summary:
0:30:11.696333 PROGRESS: Channel   0:	 0.050 FDR: 1,090; 0.010 FDR: 1,090; 0.001 FDR:     1
0:30:11.696437 PROGRESS: 
0:30:11.696499 PROGRESS: Protein Summary:
0:30:11.698598 PROGRESS: Channel   0:	 0.050 FDR: 1,089; 0.010 FDR: 1,089; 0.001 FDR:     1
0:30:11.698713 PROGRESS: =========================================================================
0:30:11.718584 INFO: Target number of precursors reached.
0:30:11.998204 INFO: fragments_df: keeping 5000 of 3725121 [sum(precursor_idx_mask)=25240 sum(mass_error_mask)=3725121 stop_rank=5000
0:30:12.467235 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:12.673363 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:13.401374 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:13.401865 INFO: Using score_cutoff 10.804517718029022 (fac=0.99, q=1)
0:30:13.402217 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:13.402302 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:13.402361 INFO: Updating optimization_manager: score_cutoff        : 11.256049378681183 -> 10.804517718029022
0:30:13.402429 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:13.553857 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:13.890874 INFO: === checking if optimization conditions were reached ===
0:30:13.891331 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:30:13.894783 INFO: Updating optimization_manager: rt_error            : 491.9981949130319 -> 601.4928815966248
0:30:13.894988 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 601.4929.
0:30:13.895101 INFO: ==============================================
0:30:13.895214 INFO: Starting optimization step 5.
0:30:13.895328 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:30:13.895452 INFO: Using rust extraction backend
0:30:13.895562 PROGRESS: Extracting batch of 251735 precursors
0:30:14.327978 INFO: === Search parameters used ===
0:30:14.328486 INFO: rt_error       : 601.4928815966248
0:30:14.328562 INFO: mobility_error : 0.1
0:30:14.328643 INFO: num_candidates : 3
0:30:14.328700 INFO: ms1_error      : 30
0:30:14.328750 INFO: ms2_error      : 10.0
0:30:14.328817 INFO: fwhm_rt        : 3.0
0:30:14.328874 INFO: quant_window   : 3
0:30:14.328928 INFO: ==============================================
0:30:17.001925 INFO: performing precursor FDR with 40 features
0:30:17.002074 INFO: Decoy channel: -1
0:30:17.002103 INFO: competitive: True
0:30:17.210990 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:17.521137 INFO: Estimating optimal hyperparameters - samples: 601,000, batch_size: 2,461, learning_rate: 7.75e-04
0:30:17.522390 INFO: Using random state 832707 for train-test-split
0:30:31.193291 INFO: Test AUC: 0.607
0:30:31.193454 INFO: Train AUC: 0.617
0:30:31.193494 INFO: AUC difference: 1.70%
0:30:31.686091 INFO: Resetting torch num_threads to 80
0:30:31.717548 PROGRESS: === Extracted 751251 precursors and 3765203 fragments ===
0:30:31.718140 INFO: === FDR correction performed with classifier version 12 ===
0:30:31.718886 PROGRESS: ============================= Precursor FDR =============================
0:30:31.718996 PROGRESS: Total precursors accumulated: 1,105
0:30:31.719073 PROGRESS: Target precursors: 1,095 (99.10%)
0:30:31.719139 PROGRESS: Decoy precursors: 10 (0.90%)
0:30:31.719200 PROGRESS: 
0:30:31.719256 PROGRESS: Precursor Summary:
0:30:31.720571 PROGRESS: Channel   0:	 0.050 FDR: 1,095; 0.010 FDR: 1,095; 0.001 FDR:     1
0:30:31.720680 PROGRESS: 
0:30:31.720752 PROGRESS: Protein Summary:
0:30:31.722631 PROGRESS: Channel   0:	 0.050 FDR: 1,094; 0.010 FDR: 1,094; 0.001 FDR:     1
0:30:31.722746 PROGRESS: =========================================================================
0:30:31.741932 INFO: Target number of precursors reached.
0:30:32.016464 INFO: fragments_df: keeping 5000 of 3765203 [sum(precursor_idx_mask)=25473 sum(mass_error_mask)=3765203 stop_rank=5000
0:30:32.454536 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:32.661631 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:33.393087 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:33.393600 INFO: Using score_cutoff 11.92482651901245 (fac=0.99, q=1)
0:30:33.393952 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:33.394056 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:33.394145 INFO: Updating optimization_manager: score_cutoff        : 10.804517718029022 -> 11.92482651901245
0:30:33.394226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:33.547370 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:33.897809 INFO: === checking if optimization conditions were reached ===
0:30:33.898146 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:30:33.901362 INFO: Updating optimization_manager: rt_error            : 601.4928815966248 -> 703.6538478974358
0:30:33.901494 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 703.6538.
0:30:33.901591 INFO: ==============================================
0:30:33.901741 INFO: Starting optimization step 6.
0:30:33.901844 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:30:33.901972 INFO: Using rust extraction backend
0:30:33.902101 PROGRESS: Extracting batch of 251735 precursors
0:30:34.333019 INFO: === Search parameters used ===
0:30:34.333361 INFO: rt_error       : 703.6538478974358
0:30:34.333445 INFO: mobility_error : 0.1
0:30:34.333513 INFO: num_candidates : 3
0:30:34.333576 INFO: ms1_error      : 30
0:30:34.333645 INFO: ms2_error      : 10.0
0:30:34.333710 INFO: fwhm_rt        : 3.0
0:30:34.333770 INFO: quant_window   : 3
0:30:34.333864 INFO: ==============================================
0:30:37.085954 INFO: performing precursor FDR with 40 features
0:30:37.086101 INFO: Decoy channel: -1
0:30:37.086129 INFO: competitive: True
0:30:37.285122 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:37.597419 INFO: Estimating optimal hyperparameters - samples: 601,162, batch_size: 2,462, learning_rate: 7.75e-04
0:30:37.598596 INFO: Using random state 832707 for train-test-split
0:30:50.250615 INFO: Test AUC: 0.609
0:30:50.250775 INFO: Train AUC: 0.618
0:30:50.250813 INFO: AUC difference: 1.49%
0:30:50.740214 INFO: Resetting torch num_threads to 80
0:30:50.772099 PROGRESS: === Extracted 751453 precursors and 3774321 fragments ===
0:30:50.772631 INFO: === FDR correction performed with classifier version 12 ===
0:30:50.773347 PROGRESS: ============================= Precursor FDR =============================
0:30:50.773457 PROGRESS: Total precursors accumulated: 1,135
0:30:50.773538 PROGRESS: Target precursors: 1,124 (99.03%)
0:30:50.773608 PROGRESS: Decoy precursors: 11 (0.97%)
0:30:50.773676 PROGRESS: 
0:30:50.773738 PROGRESS: Precursor Summary:
0:30:50.775076 PROGRESS: Channel   0:	 0.050 FDR: 1,124; 0.010 FDR: 1,124; 0.001 FDR:     1
0:30:50.775182 PROGRESS: 
0:30:50.775258 PROGRESS: Protein Summary:
0:30:50.777158 PROGRESS: Channel   0:	 0.050 FDR: 1,123; 0.010 FDR: 1,123; 0.001 FDR:     1
0:30:50.777269 PROGRESS: =========================================================================
0:30:50.796391 INFO: Target number of precursors reached.
0:30:51.090971 INFO: fragments_df: keeping 5000 of 3774321 [sum(precursor_idx_mask)=26082 sum(mass_error_mask)=3774321 stop_rank=5000
0:30:51.522680 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:52.231984 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:52.965422 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:52.966048 INFO: Using score_cutoff 11.993412156200408 (fac=0.99, q=1)
0:30:52.966471 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:52.966559 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:52.966619 INFO: Updating optimization_manager: score_cutoff        : 11.92482651901245 -> 11.993412156200408
0:30:52.966700 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:53.119850 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:53.470304 INFO: === checking if optimization conditions were reached ===
0:30:53.470734 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:30:53.474280 INFO: Updating optimization_manager: rt_error            : 703.6538478974358 -> 809.0759845121491
0:30:53.474455 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 809.0760.
0:30:53.474569 INFO: ==============================================
0:30:53.474682 INFO: Starting optimization step 7.
0:30:53.474787 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:30:53.474900 INFO: Using rust extraction backend
0:30:53.475005 PROGRESS: Extracting batch of 251735 precursors
0:30:53.905603 INFO: === Search parameters used ===
0:30:53.905932 INFO: rt_error       : 809.0759845121491
0:30:53.906020 INFO: mobility_error : 0.1
0:30:53.906083 INFO: num_candidates : 3
0:30:53.906135 INFO: ms1_error      : 30
0:30:53.906183 INFO: ms2_error      : 10.0
0:30:53.906263 INFO: fwhm_rt        : 3.0
0:30:53.906335 INFO: quant_window   : 3
0:30:53.906387 INFO: ==============================================
0:30:56.654976 INFO: performing precursor FDR with 40 features
0:30:56.655119 INFO: Decoy channel: -1
0:30:56.655148 INFO: competitive: True
0:30:56.846365 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:57.151707 INFO: Estimating optimal hyperparameters - samples: 601,198, batch_size: 2,462, learning_rate: 7.75e-04
0:30:57.152910 INFO: Using random state 832707 for train-test-split
0:31:09.446081 INFO: Test AUC: 0.609
0:31:09.446258 INFO: Train AUC: 0.618
0:31:09.446293 INFO: AUC difference: 1.32%
0:31:09.939785 INFO: Resetting torch num_threads to 80
0:31:09.972422 PROGRESS: === Extracted 751498 precursors and 3776567 fragments ===
0:31:09.972961 INFO: === FDR correction performed with classifier version 12 ===
0:31:09.973725 PROGRESS: ============================= Precursor FDR =============================
0:31:09.973835 PROGRESS: Total precursors accumulated: 1,139
0:31:09.973909 PROGRESS: Target precursors: 1,128 (99.03%)
0:31:09.973973 PROGRESS: Decoy precursors: 11 (0.97%)
0:31:09.974032 PROGRESS: 
0:31:09.974100 PROGRESS: Precursor Summary:
0:31:09.975454 PROGRESS: Channel   0:	 0.050 FDR: 1,128; 0.010 FDR: 1,128; 0.001 FDR:     1
0:31:09.975568 PROGRESS: 
0:31:09.975649 PROGRESS: Protein Summary:
0:31:09.977573 PROGRESS: Channel   0:	 0.050 FDR: 1,127; 0.010 FDR: 1,127; 0.001 FDR:     1
0:31:09.977687 PROGRESS: =========================================================================
0:31:09.997198 INFO: Target number of precursors reached.
0:31:10.286352 INFO: fragments_df: keeping 5000 of 3776567 [sum(precursor_idx_mask)=26318 sum(mass_error_mask)=3776567 stop_rank=5000
0:31:10.741587 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:10.957289 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:11.683219 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:11.683723 INFO: Using score_cutoff 12.073950773334504 (fac=0.99, q=1)
0:31:11.684071 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:11.684158 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:11.684218 INFO: Updating optimization_manager: score_cutoff        : 11.993412156200408 -> 12.073950773334504
0:31:11.684280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:11.837744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:12.200313 INFO: === checking if optimization conditions were reached ===
0:31:12.200730 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:31:12.204078 INFO: Updating optimization_manager: rt_error            : 809.0759845121491 -> 675.639374169353
0:31:12.204227 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 675.6394.
0:31:12.204326 INFO: ==============================================
0:31:12.204432 INFO: Starting optimization step 8.
0:31:12.204524 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:31:12.204627 INFO: Using rust extraction backend
0:31:12.204723 PROGRESS: Extracting batch of 251735 precursors
0:31:12.645953 INFO: === Search parameters used ===
0:31:12.646442 INFO: rt_error       : 675.639374169353
0:31:12.646538 INFO: mobility_error : 0.1
0:31:12.646598 INFO: num_candidates : 3
0:31:12.646672 INFO: ms1_error      : 30
0:31:12.646729 INFO: ms2_error      : 10.0
0:31:12.646783 INFO: fwhm_rt        : 3.0
0:31:12.646832 INFO: quant_window   : 3
0:31:12.646890 INFO: ==============================================
0:31:15.504853 INFO: performing precursor FDR with 40 features
0:31:15.505000 INFO: Decoy channel: -1
0:31:15.505041 INFO: competitive: True
0:31:15.705403 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:16.017205 INFO: Estimating optimal hyperparameters - samples: 601,159, batch_size: 2,462, learning_rate: 7.75e-04
0:31:16.018462 INFO: Using random state 832707 for train-test-split
0:31:28.410968 INFO: Test AUC: 0.609
0:31:28.411160 INFO: Train AUC: 0.618
0:31:28.411194 INFO: AUC difference: 1.48%
0:31:28.907565 INFO: Resetting torch num_threads to 80
0:31:28.941856 PROGRESS: === Extracted 751449 precursors and 3773642 fragments ===
0:31:28.942422 INFO: === FDR correction performed with classifier version 12 ===
0:31:28.943154 PROGRESS: ============================= Precursor FDR =============================
0:31:28.943257 PROGRESS: Total precursors accumulated: 1,153
0:31:28.943323 PROGRESS: Target precursors: 1,142 (99.05%)
0:31:28.943379 PROGRESS: Decoy precursors: 11 (0.95%)
0:31:28.943431 PROGRESS: 
0:31:28.943480 PROGRESS: Precursor Summary:
0:31:28.944774 PROGRESS: Channel   0:	 0.050 FDR: 1,142; 0.010 FDR: 1,142; 0.001 FDR:     1
0:31:28.944874 PROGRESS: 
0:31:28.944936 PROGRESS: Protein Summary:
0:31:28.946819 PROGRESS: Channel   0:	 0.050 FDR: 1,141; 0.010 FDR: 1,141; 0.001 FDR:     1
0:31:28.946922 PROGRESS: =========================================================================
0:31:28.965890 INFO: Target number of precursors reached.
0:31:29.253094 INFO: fragments_df: keeping 5000 of 3773642 [sum(precursor_idx_mask)=26483 sum(mass_error_mask)=3773642 stop_rank=5000
0:31:29.697986 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:29.911906 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:30.640901 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:30.641392 INFO: Using score_cutoff 11.248107907104492 (fac=0.99, q=1)
0:31:30.641731 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:30.641814 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:30.641875 INFO: Updating optimization_manager: score_cutoff        : 12.073950773334504 -> 11.248107907104492
0:31:30.641949 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:30.794344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:31.155360 INFO: === checking if optimization conditions were reached ===
0:31:31.155713 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:31:31.159051 INFO: Updating optimization_manager: rt_error            : 675.639374169353 -> 807.6572479876254
0:31:31.159187 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 807.6572.
0:31:31.159271 INFO: ==============================================
0:31:31.159393 INFO: Starting optimization step 9.
0:31:31.159493 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:31:31.159601 INFO: Using rust extraction backend
0:31:31.159704 PROGRESS: Extracting batch of 251735 precursors
0:31:31.594595 INFO: === Search parameters used ===
0:31:31.594933 INFO: rt_error       : 807.6572479876254
0:31:31.595002 INFO: mobility_error : 0.1
0:31:31.595060 INFO: num_candidates : 3
0:31:31.595107 INFO: ms1_error      : 30
0:31:31.595153 INFO: ms2_error      : 10.0
0:31:31.595197 INFO: fwhm_rt        : 3.0
0:31:31.595239 INFO: quant_window   : 3
0:31:31.595283 INFO: ==============================================
0:31:34.414646 INFO: performing precursor FDR with 40 features
0:31:34.414792 INFO: Decoy channel: -1
0:31:34.414820 INFO: competitive: True
0:31:34.610024 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:34.920321 INFO: Estimating optimal hyperparameters - samples: 601,189, batch_size: 2,462, learning_rate: 7.75e-04
0:31:34.921339 INFO: Using random state 832707 for train-test-split
0:31:47.298394 INFO: Test AUC: 0.610
0:31:47.298550 INFO: Train AUC: 0.618
0:31:47.298582 INFO: AUC difference: 1.30%
0:31:47.789843 INFO: Resetting torch num_threads to 80
0:31:47.821041 PROGRESS: === Extracted 751487 precursors and 3776706 fragments ===
0:31:47.821588 INFO: === FDR correction performed with classifier version 12 ===
0:31:47.822331 PROGRESS: ============================= Precursor FDR =============================
0:31:47.822442 PROGRESS: Total precursors accumulated: 1,147
0:31:47.822512 PROGRESS: Target precursors: 1,136 (99.04%)
0:31:47.822608 PROGRESS: Decoy precursors: 11 (0.96%)
0:31:47.822681 PROGRESS: 
0:31:47.822752 PROGRESS: Precursor Summary:
0:31:47.824090 PROGRESS: Channel   0:	 0.050 FDR: 1,136; 0.010 FDR: 1,136; 0.001 FDR:     0
0:31:47.824205 PROGRESS: 
0:31:47.824287 PROGRESS: Protein Summary:
0:31:47.826210 PROGRESS: Channel   0:	 0.050 FDR: 1,135; 0.010 FDR: 1,135; 0.001 FDR:     0
0:31:47.826338 PROGRESS: =========================================================================
0:31:47.845007 INFO: Target number of precursors reached.
0:31:48.130937 INFO: fragments_df: keeping 5000 of 3776706 [sum(precursor_idx_mask)=26201 sum(mass_error_mask)=3776706 stop_rank=5000
0:31:48.565526 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:48.779657 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:49.504002 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:49.504522 INFO: Using score_cutoff 9.971249814033508 (fac=0.99, q=1)
0:31:49.504870 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:49.504955 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:49.505016 INFO: Updating optimization_manager: score_cutoff        : 11.248107907104492 -> 9.971249814033508
0:31:49.505078 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:49.657308 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:50.000674 INFO: === checking if optimization conditions were reached ===
0:31:50.001062 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
0:31:50.004367 INFO: Updating optimization_manager: rt_error            : 807.6572479876254 -> 820.0963981186989
0:31:50.004543 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 820.0964.
0:31:50.004652 INFO: ==============================================
0:31:50.004764 INFO: Starting optimization step 10.
0:31:50.004862 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:31:50.004964 INFO: Using rust extraction backend
0:31:50.005061 PROGRESS: Extracting batch of 251735 precursors
0:31:50.435906 INFO: === Search parameters used ===
0:31:50.436244 INFO: rt_error       : 820.0963981186989
0:31:50.436317 INFO: mobility_error : 0.1
0:31:50.436376 INFO: num_candidates : 3
0:31:50.436431 INFO: ms1_error      : 30
0:31:50.436481 INFO: ms2_error      : 10.0
0:31:50.436533 INFO: fwhm_rt        : 3.0
0:31:50.436577 INFO: quant_window   : 3
0:31:50.436626 INFO: ==============================================
0:31:53.219237 INFO: performing precursor FDR with 40 features
0:31:53.219396 INFO: Decoy channel: -1
0:31:53.219431 INFO: competitive: True
0:31:53.404788 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:53.712611 INFO: Estimating optimal hyperparameters - samples: 601,177, batch_size: 2,462, learning_rate: 7.75e-04
0:31:53.713627 INFO: Using random state 832707 for train-test-split
0:32:06.234848 INFO: Test AUC: 0.608
0:32:06.235015 INFO: Train AUC: 0.618
0:32:06.235048 INFO: AUC difference: 1.56%
0:32:06.733841 INFO: Resetting torch num_threads to 80
0:32:06.777621 PROGRESS: === Extracted 751472 precursors and 3776726 fragments ===
0:32:06.778186 INFO: === FDR correction performed with classifier version 12 ===
0:32:06.778911 PROGRESS: ============================= Precursor FDR =============================
0:32:06.779020 PROGRESS: Total precursors accumulated: 1,178
0:32:06.779090 PROGRESS: Target precursors: 1,167 (99.07%)
0:32:06.779147 PROGRESS: Decoy precursors: 11 (0.93%)
0:32:06.779198 PROGRESS: 
0:32:06.779248 PROGRESS: Precursor Summary:
0:32:06.780573 PROGRESS: Channel   0:	 0.050 FDR: 1,167; 0.010 FDR: 1,167; 0.001 FDR:   350
0:32:06.780675 PROGRESS: 
0:32:06.780737 PROGRESS: Protein Summary:
0:32:06.782796 PROGRESS: Channel   0:	 0.050 FDR: 1,166; 0.010 FDR: 1,166; 0.001 FDR:   350
0:32:06.782919 PROGRESS: =========================================================================
0:32:06.801365 INFO: Target number of precursors reached.
0:32:07.092546 INFO: fragments_df: keeping 5000 of 3776726 [sum(precursor_idx_mask)=26743 sum(mass_error_mask)=3776726 stop_rank=5000
0:32:07.549335 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:07.762169 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:08.491218 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:08.491718 INFO: Using score_cutoff 9.544978195381166 (fac=0.99, q=1)
0:32:08.492045 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:08.492126 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:08.492181 INFO: Updating optimization_manager: score_cutoff        : 9.971249814033508 -> 9.544978195381166
0:32:08.492244 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:08.643704 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:08.981311 INFO: === checking if optimization conditions were reached ===
0:32:08.981787 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
0:32:08.983160 INFO: Updating optimization_manager: rt_error            : 820.0963981186989 -> 733.9218235419708
0:32:08.983413 INFO: Updating optimization_manager: classifier_version  : 12 -> 14
0:32:08.983579 INFO: Updating optimization_manager: score_cutoff        : 9.544978195381166 -> 10.79149642753601
0:32:08.983734 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:08.983881 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:08.984044 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 733.9218 found after 11 searches.
0:32:08.984153 INFO: ==============================================
0:32:08.984268 PROGRESS: Optimization finished for rt_error.
0:32:09.427579 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:09.580439 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:09.925565 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:32:09.925990 PROGRESS: ==============================================
0:32:09.926135 PROGRESS: ms2_error      : 10.0000
0:32:09.926238 PROGRESS: rt_error       : 733.9218
0:32:09.926325 PROGRESS: ==============================================
0:32:09.927318 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:17.574586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:35.078887 INFO: Using rust extraction backend
0:32:35.079415 PROGRESS: Extracting batch of 12096565 precursors
0:32:52.695213 INFO: === Search parameters used ===
0:32:52.695797 INFO: rt_error       : 733.9218235419708
0:32:52.695870 INFO: mobility_error : 0.1
0:32:52.695933 INFO: num_candidates : 3
0:32:52.695985 INFO: ms1_error      : 30
0:32:52.696035 INFO: ms2_error      : 10.0
0:32:52.696093 INFO: fwhm_rt        : 3.0
0:32:52.696169 INFO: quant_window   : 3
0:32:52.696229 INFO: ==============================================
0:33:33.985261 INFO: Removed 11145359 precursors with score below cutoff 10.79149642753601
0:33:55.910502 INFO: performing precursor FDR with 40 features
0:33:55.910677 INFO: Decoy channel: -1
0:33:55.910716 INFO: competitive: True
0:33:58.996129 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:09.890330 INFO: Estimating optimal hyperparameters - samples: 20,114,754, batch_size: 4,096, learning_rate: 1.00e-03
0:34:09.952267 INFO: Using random state 928454 for train-test-split
0:40:39.082242 INFO: Test AUC: 0.619
0:40:39.082605 INFO: Train AUC: 0.620
0:40:39.082649 INFO: AUC difference: 0.04%
0:40:44.935735 INFO: Resetting torch num_threads to 80
0:40:47.691526 PROGRESS: ============================= Precursor FDR =============================
0:40:47.691887 PROGRESS: Total precursors accumulated: 71,838
0:40:47.691998 PROGRESS: Target precursors: 71,127 (99.01%)
0:40:47.692060 PROGRESS: Decoy precursors: 711 (0.99%)
0:40:47.692115 PROGRESS: 
0:40:47.692165 PROGRESS: Precursor Summary:
0:40:47.714938 PROGRESS: Channel   0:	 0.050 FDR: 71,127; 0.010 FDR: 71,127; 0.001 FDR: 51,055
0:40:47.715255 PROGRESS: 
0:40:47.715329 PROGRESS: Protein Summary:
0:40:47.796455 PROGRESS: Channel   0:	 0.050 FDR: 65,983; 0.010 FDR: 65,983; 0.001 FDR: 47,620
0:40:47.796766 PROGRESS: =========================================================================
0:40:48.008955 INFO: Saving results to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/psm.parquet
0:40:48.183789 INFO: Saving results to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/frag.parquet
0:40:48.379546 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Human_01
0:40:49.329486 PROGRESS: Loading raw file 2/3: LFQ_Astral_DIA_15min_50ng_Human_02 
0:40:49.329666 INFO: Quantification results path: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant
0:40:49.329777 INFO: Creating folder /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/figures
0:40:49.329994 INFO: Initializing TimingManager
0:40:49.330608 INFO: Initializing RawFileManager
0:40:59.996484 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.
0:41:00.005889 INFO: Determining DIA cycle
0:41:00.022779 INFO: Found cycle with start 0.00 min and length 300.
0:41:00.141756 INFO: RT (min)            : 0.0 - 26.9
0:41:00.141866 INFO: RT duration (sec)   : 1611.2
0:41:00.141893 INFO: RT duration (min)   : 26.9
0:41:00.141927 INFO: Cycle len (scans)   : 300
0:41:00.141945 INFO: Cycle len (sec)     : 1.65
0:41:00.141964 INFO: Number of cycles    : 976
0:41:00.141982 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:41:00.142013 INFO: Creating DIA data object took: 10.811300277709961
0:41:00.720727 INFO: Creating DIA data NG object took: 0.5785698890686035
0:41:02.521188 INFO: Initializing CalibrationManager
0:41:02.521572 INFO: Setting up calibration estimators ..
0:41:02.521651 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:41:02.521747 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'}' ..
0:41:02.521854 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:41:02.521926 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:41:02.521991 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}}' ..
0:41:02.522048 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:41:02.522099 INFO: Done setting up calibration estimators.
0:41:02.522356 INFO: Initializing OptimizationManager
0:41:02.522534 INFO: initial parameter: ms1_error = 30
0:41:02.522594 INFO: initial parameter: ms2_error = 30
0:41:02.522647 INFO: initial parameter: rt_error = 805.5951538085938
0:41:02.522713 INFO: initial parameter: mobility_error = 0.1
0:41:02.522790 INFO: initial parameter: num_candidates = 1
0:41:02.522852 INFO: initial parameter: fwhm_rt = 5
0:41:02.522899 INFO: initial parameter: fwhm_mobility = 0.01
0:41:02.522943 INFO: initial parameter: score_cutoff = 0
0:41:02.522986 INFO: initial parameter: classifier_version = -1
0:41:02.523068 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Human_02
0:41:02.523381 INFO: FDRManager: loading saved state not requested, will be initialized.
0:41:02.523421 INFO: Initializing FDRManager
0:41:02.523472 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
0:41:04.277727 PROGRESS: Initializing spectral library: 6,065,786 target precursors potentially observable (100,729 removed)
0:41:05.267367 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:41:05.267872 INFO: Updating optimization_manager: rt_error            : 805.5951538085938 -> 805.5951538085938
0:41:05.268000 PROGRESS: Starting initial search for precursors.
0:41:05.268091 INFO: Starting optimization step 0.
0:41:05.268159 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:41:05.268224 INFO: Using rust extraction backend
0:41:05.268311 PROGRESS: Extracting batch of 1985 precursors
0:41:05.278038 INFO: === Search parameters used ===
0:41:05.278185 INFO: rt_error       : 805.5951538085938
0:41:05.278242 INFO: mobility_error : 0.1
0:41:05.278300 INFO: num_candidates : 1
0:41:05.278373 INFO: ms1_error      : 30
0:41:05.278439 INFO: ms2_error      : 30
0:41:05.278506 INFO: fwhm_rt        : 5
0:41:05.278571 INFO: quant_window   : 3
0:41:05.278638 INFO: ==============================================
0:41:05.306946 INFO: performing precursor FDR with 40 features
0:41:05.307024 INFO: Decoy channel: -1
0:41:05.307049 INFO: competitive: True
0:41:05.308400 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:05.310708 INFO: Estimating optimal hyperparameters - samples: 1,562, batch_size: 128, learning_rate: 1.77e-04
0:41:05.311653 INFO: Using random state 539023 for train-test-split
0:41:05.459273 INFO: Test AUC: 0.475
0:41:05.459368 INFO: Train AUC: 0.517
0:41:05.459401 INFO: AUC difference: 8.00%
0:41:05.459431 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:05.714754 INFO: Resetting torch num_threads to 80
0:41:05.716456 PROGRESS: === Extracted 1953 precursors and 8856 fragments ===
0:41:05.716880 INFO: === FDR correction performed with classifier version -1 ===
0:41:05.717412 PROGRESS: ============================= Precursor FDR =============================
0:41:05.717510 PROGRESS: Total precursors accumulated: 1
0:41:05.717577 PROGRESS: Target precursors: 1 (100.00%)
0:41:05.717633 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:05.717697 PROGRESS: 
0:41:05.717756 PROGRESS: Precursor Summary:
0:41:05.718871 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:05.718982 PROGRESS: 
0:41:05.719065 PROGRESS: Protein Summary:
0:41:05.720336 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:41:05.720443 PROGRESS: =========================================================================
0:41:05.720676 INFO: Target number of precursors not reached yet.
0:41:05.806459 INFO: Starting optimization step 1.
0:41:05.806746 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:41:05.806838 INFO: Using rust extraction backend
0:41:05.806906 PROGRESS: Extracting batch of 3969 precursors
0:41:05.815337 INFO: === Search parameters used ===
0:41:05.815485 INFO: rt_error       : 805.5951538085938
0:41:05.815541 INFO: mobility_error : 0.1
0:41:05.815588 INFO: num_candidates : 1
0:41:05.815633 INFO: ms1_error      : 30
0:41:05.815694 INFO: ms2_error      : 30
0:41:05.815761 INFO: fwhm_rt        : 5
0:41:05.815825 INFO: quant_window   : 3
0:41:05.815877 INFO: ==============================================
0:41:05.863609 INFO: performing precursor FDR with 40 features
0:41:05.863712 INFO: Decoy channel: -1
0:41:05.863737 INFO: competitive: True
0:41:05.868060 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:05.870776 INFO: Estimating optimal hyperparameters - samples: 4,688, batch_size: 128, learning_rate: 1.77e-04
0:41:05.870864 INFO: Using random state 324542 for train-test-split
0:41:06.320757 INFO: Test AUC: 0.512
0:41:06.320862 INFO: Train AUC: 0.551
0:41:06.320894 INFO: AUC difference: 7.03%
0:41:06.320918 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:06.575416 INFO: Resetting torch num_threads to 80
0:41:06.578418 PROGRESS: === Extracted 5860 precursors and 26158 fragments ===
0:41:06.578844 INFO: === FDR correction performed with classifier version -1 ===
0:41:06.579367 PROGRESS: ============================= Precursor FDR =============================
0:41:06.579470 PROGRESS: Total precursors accumulated: 9
0:41:06.579535 PROGRESS: Target precursors: 9 (100.00%)
0:41:06.579591 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:06.579641 PROGRESS: 
0:41:06.579690 PROGRESS: Precursor Summary:
0:41:06.580784 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
0:41:06.580877 PROGRESS: 
0:41:06.580936 PROGRESS: Protein Summary:
0:41:06.582153 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
0:41:06.582250 PROGRESS: =========================================================================
0:41:06.582510 INFO: Target number of precursors not reached yet.
0:41:06.672817 INFO: Starting optimization step 2.
0:41:06.673097 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:41:06.673187 INFO: Using rust extraction backend
0:41:06.673256 PROGRESS: Extracting batch of 7917 precursors
0:41:06.688624 INFO: === Search parameters used ===
0:41:06.688796 INFO: rt_error       : 805.5951538085938
0:41:06.688855 INFO: mobility_error : 0.1
0:41:06.688904 INFO: num_candidates : 1
0:41:06.688949 INFO: ms1_error      : 30
0:41:06.688992 INFO: ms2_error      : 30
0:41:06.689034 INFO: fwhm_rt        : 5
0:41:06.689077 INFO: quant_window   : 3
0:41:06.689119 INFO: ==============================================
0:41:06.770412 INFO: performing precursor FDR with 40 features
0:41:06.770535 INFO: Decoy channel: -1
0:41:06.770562 INFO: competitive: True
0:41:06.777357 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:06.781451 INFO: Estimating optimal hyperparameters - samples: 10,908, batch_size: 128, learning_rate: 1.77e-04
0:41:06.781572 INFO: Using random state 572053 for train-test-split
0:41:07.846286 INFO: Test AUC: 0.552
0:41:07.846404 INFO: Train AUC: 0.566
0:41:07.846434 INFO: AUC difference: 2.41%
0:41:08.107589 INFO: Resetting torch num_threads to 80
0:41:08.111897 PROGRESS: === Extracted 13635 precursors and 60630 fragments ===
0:41:08.112391 INFO: === FDR correction performed with classifier version -1 ===
0:41:08.112946 PROGRESS: ============================= Precursor FDR =============================
0:41:08.113040 PROGRESS: Total precursors accumulated: 25
0:41:08.113111 PROGRESS: Target precursors: 25 (100.00%)
0:41:08.113173 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:08.113229 PROGRESS: 
0:41:08.113276 PROGRESS: Precursor Summary:
0:41:08.114404 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:    25; 0.001 FDR:    25
0:41:08.114505 PROGRESS: 
0:41:08.114575 PROGRESS: Protein Summary:
0:41:08.115825 PROGRESS: Channel   0:	 0.050 FDR:    25; 0.010 FDR:    25; 0.001 FDR:    25
0:41:08.115918 PROGRESS: =========================================================================
0:41:08.116263 INFO: Target number of precursors not reached yet.
0:41:08.217410 INFO: Starting optimization step 3.
0:41:08.217706 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:41:08.217796 INFO: Using rust extraction backend
0:41:08.217879 PROGRESS: Extracting batch of 15855 precursors
0:41:08.246605 INFO: === Search parameters used ===
0:41:08.246803 INFO: rt_error       : 805.5951538085938
0:41:08.246863 INFO: mobility_error : 0.1
0:41:08.246925 INFO: num_candidates : 1
0:41:08.246978 INFO: ms1_error      : 30
0:41:08.247039 INFO: ms2_error      : 30
0:41:08.247105 INFO: fwhm_rt        : 5
0:41:08.247164 INFO: quant_window   : 3
0:41:08.247216 INFO: ==============================================
0:41:08.384507 INFO: performing precursor FDR with 40 features
0:41:08.384641 INFO: Decoy channel: -1
0:41:08.384670 INFO: competitive: True
0:41:08.396788 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:08.405017 INFO: Estimating optimal hyperparameters - samples: 23,367, batch_size: 128, learning_rate: 1.77e-04
0:41:08.405203 INFO: Using random state 97771 for train-test-split
0:41:10.765641 INFO: Test AUC: 0.546
0:41:10.765768 INFO: Train AUC: 0.590
0:41:10.765796 INFO: AUC difference: 7.58%
0:41:10.765818 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:11.035492 INFO: Resetting torch num_threads to 80
0:41:11.042426 PROGRESS: === Extracted 29209 precursors and 130366 fragments ===
0:41:11.042918 INFO: === FDR correction performed with classifier version -1 ===
0:41:11.043494 PROGRESS: ============================= Precursor FDR =============================
0:41:11.043596 PROGRESS: Total precursors accumulated: 54
0:41:11.043668 PROGRESS: Target precursors: 54 (100.00%)
0:41:11.043731 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:11.043787 PROGRESS: 
0:41:11.043840 PROGRESS: Precursor Summary:
0:41:11.044970 PROGRESS: Channel   0:	 0.050 FDR:    54; 0.010 FDR:    54; 0.001 FDR:    54
0:41:11.045071 PROGRESS: 
0:41:11.045136 PROGRESS: Protein Summary:
0:41:11.046412 PROGRESS: Channel   0:	 0.050 FDR:    54; 0.010 FDR:    54; 0.001 FDR:    54
0:41:11.046510 PROGRESS: =========================================================================
0:41:11.047041 INFO: Target number of precursors not reached yet.
0:41:11.167958 INFO: Starting optimization step 4.
0:41:11.168284 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:41:11.168374 INFO: Using rust extraction backend
0:41:11.168476 PROGRESS: Extracting batch of 31732 precursors
0:41:11.224840 INFO: === Search parameters used ===
0:41:11.225121 INFO: rt_error       : 805.5951538085938
0:41:11.225178 INFO: mobility_error : 0.1
0:41:11.225249 INFO: num_candidates : 1
0:41:11.225304 INFO: ms1_error      : 30
0:41:11.225357 INFO: ms2_error      : 30
0:41:11.225410 INFO: fwhm_rt        : 5
0:41:11.225457 INFO: quant_window   : 3
0:41:11.225507 INFO: ==============================================
0:41:11.455598 INFO: performing precursor FDR with 40 features
0:41:11.455729 INFO: Decoy channel: -1
0:41:11.455756 INFO: competitive: True
0:41:11.479502 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:11.494428 INFO: Estimating optimal hyperparameters - samples: 48,355, batch_size: 198, learning_rate: 2.20e-04
0:41:11.494647 INFO: Using random state 178640 for train-test-split
0:41:15.124764 INFO: Test AUC: 0.574
0:41:15.124904 INFO: Train AUC: 0.594
0:41:15.124934 INFO: AUC difference: 3.42%
0:41:15.957360 INFO: Resetting torch num_threads to 80
0:41:15.969528 PROGRESS: === Extracted 60444 precursors and 269643 fragments ===
0:41:15.970238 INFO: === FDR correction performed with classifier version -1 ===
0:41:15.970829 PROGRESS: ============================= Precursor FDR =============================
0:41:15.970928 PROGRESS: Total precursors accumulated: 112
0:41:15.970993 PROGRESS: Target precursors: 111 (99.11%)
0:41:15.971050 PROGRESS: Decoy precursors: 1 (0.89%)
0:41:15.971101 PROGRESS: 
0:41:15.971150 PROGRESS: Precursor Summary:
0:41:15.972171 PROGRESS: Channel   0:	 0.050 FDR:   111; 0.010 FDR:   111; 0.001 FDR:    85
0:41:15.972269 PROGRESS: 
0:41:15.972330 PROGRESS: Protein Summary:
0:41:15.973536 PROGRESS: Channel   0:	 0.050 FDR:   111; 0.010 FDR:   111; 0.001 FDR:    85
0:41:15.973633 PROGRESS: =========================================================================
0:41:15.974564 INFO: Target number of precursors not reached yet.
0:41:16.138430 INFO: Starting optimization step 5.
0:41:16.138769 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:41:16.138864 INFO: Using rust extraction backend
0:41:16.138939 PROGRESS: Extracting batch of 63446 precursors
0:41:16.248932 INFO: === Search parameters used ===
0:41:16.249257 INFO: rt_error       : 805.5951538085938
0:41:16.249314 INFO: mobility_error : 0.1
0:41:16.249363 INFO: num_candidates : 1
0:41:16.249418 INFO: ms1_error      : 30
0:41:16.249480 INFO: ms2_error      : 30
0:41:16.249540 INFO: fwhm_rt        : 5
0:41:16.249604 INFO: quant_window   : 3
0:41:16.249667 INFO: ==============================================
0:41:16.645923 INFO: performing precursor FDR with 40 features
0:41:16.646071 INFO: Decoy channel: -1
0:41:16.646111 INFO: competitive: True
0:41:16.696246 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:16.732273 INFO: Estimating optimal hyperparameters - samples: 98,284, batch_size: 402, learning_rate: 3.13e-04
0:41:16.732691 INFO: Using random state 746176 for train-test-split
0:41:21.337250 INFO: Test AUC: 0.580
0:41:21.337392 INFO: Train AUC: 0.602
0:41:21.337422 INFO: AUC difference: 3.75%
0:41:21.630070 INFO: Resetting torch num_threads to 80
0:41:21.653010 PROGRESS: === Extracted 122856 precursors and 548888 fragments ===
0:41:21.653661 INFO: === FDR correction performed with classifier version -1 ===
0:41:21.654332 PROGRESS: ============================= Precursor FDR =============================
0:41:21.654454 PROGRESS: Total precursors accumulated: 317
0:41:21.654522 PROGRESS: Target precursors: 314 (99.05%)
0:41:21.654581 PROGRESS: Decoy precursors: 3 (0.95%)
0:41:21.654634 PROGRESS: 
0:41:21.654696 PROGRESS: Precursor Summary:
0:41:21.655830 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   314; 0.001 FDR:   221
0:41:21.655930 PROGRESS: 
0:41:21.655992 PROGRESS: Protein Summary:
0:41:21.657372 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   313; 0.001 FDR:   220
0:41:21.657470 PROGRESS: =========================================================================
0:41:21.659366 INFO: Target number of precursors not reached yet.
0:41:21.907609 INFO: Starting optimization step 6.
0:41:21.907929 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:41:21.908020 INFO: Using rust extraction backend
0:41:21.908096 PROGRESS: Extracting batch of 126831 precursors
0:41:22.125932 INFO: === Search parameters used ===
0:41:22.126239 INFO: rt_error       : 805.5951538085938
0:41:22.126298 INFO: mobility_error : 0.1
0:41:22.126351 INFO: num_candidates : 1
0:41:22.126399 INFO: ms1_error      : 30
0:41:22.126445 INFO: ms2_error      : 30
0:41:22.126490 INFO: fwhm_rt        : 5
0:41:22.126535 INFO: quant_window   : 3
0:41:22.126577 INFO: ==============================================
0:41:22.860512 INFO: performing precursor FDR with 40 features
0:41:22.860655 INFO: Decoy channel: -1
0:41:22.860684 INFO: competitive: True
0:41:22.966980 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:23.051638 INFO: Estimating optimal hyperparameters - samples: 198,115, batch_size: 811, learning_rate: 4.45e-04
0:41:23.052224 INFO: Using random state 62 for train-test-split
0:41:29.286731 INFO: Test AUC: 0.584
0:41:29.286875 INFO: Train AUC: 0.601
0:41:29.286906 INFO: AUC difference: 2.76%
0:41:29.616179 INFO: Resetting torch num_threads to 80
0:41:29.662914 PROGRESS: === Extracted 247644 precursors and 1107880 fragments ===
0:41:29.663589 INFO: === FDR correction performed with classifier version -1 ===
0:41:29.664406 PROGRESS: ============================= Precursor FDR =============================
0:41:29.664530 PROGRESS: Total precursors accumulated: 730
0:41:29.664597 PROGRESS: Target precursors: 723 (99.04%)
0:41:29.664653 PROGRESS: Decoy precursors: 7 (0.96%)
0:41:29.664702 PROGRESS: 
0:41:29.664753 PROGRESS: Precursor Summary:
0:41:29.666055 PROGRESS: Channel   0:	 0.050 FDR:   723; 0.010 FDR:   723; 0.001 FDR:   487
0:41:29.666163 PROGRESS: 
0:41:29.666225 PROGRESS: Protein Summary:
0:41:29.667997 PROGRESS: Channel   0:	 0.050 FDR:   722; 0.010 FDR:   722; 0.001 FDR:   486
0:41:29.668111 PROGRESS: =========================================================================
0:41:29.672220 INFO: Target number of precursors not reached yet.
0:41:30.081953 INFO: Starting optimization step 7.
0:41:30.082291 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:41:30.082395 INFO: Using rust extraction backend
0:41:30.082473 PROGRESS: Extracting batch of 253660 precursors
0:41:30.516220 INFO: === Search parameters used ===
0:41:30.516528 INFO: rt_error       : 805.5951538085938
0:41:30.516588 INFO: mobility_error : 0.1
0:41:30.516641 INFO: num_candidates : 1
0:41:30.516689 INFO: ms1_error      : 30
0:41:30.516750 INFO: ms2_error      : 30
0:41:30.516797 INFO: fwhm_rt        : 5
0:41:30.516857 INFO: quant_window   : 3
0:41:30.516929 INFO: ==============================================
0:41:31.901476 INFO: performing precursor FDR with 40 features
0:41:31.901631 INFO: Decoy channel: -1
0:41:31.901660 INFO: competitive: True
0:41:32.106840 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:32.299438 INFO: Estimating optimal hyperparameters - samples: 397,726, batch_size: 1,629, learning_rate: 6.31e-04
0:41:32.300075 INFO: Using random state 687574 for train-test-split
0:41:42.260725 INFO: Test AUC: 0.587
0:41:42.260869 INFO: Train AUC: 0.600
0:41:42.260904 INFO: AUC difference: 2.19%
0:41:42.660510 INFO: Resetting torch num_threads to 80
0:41:42.759689 PROGRESS: === Extracted 497158 precursors and 2226276 fragments ===
0:41:42.760444 INFO: === FDR correction performed with classifier version -1 ===
0:41:42.761376 PROGRESS: ============================= Precursor FDR =============================
0:41:42.761478 PROGRESS: Total precursors accumulated: 1,642
0:41:42.761544 PROGRESS: Target precursors: 1,626 (99.03%)
0:41:42.761600 PROGRESS: Decoy precursors: 16 (0.97%)
0:41:42.761652 PROGRESS: 
0:41:42.761702 PROGRESS: Precursor Summary:
0:41:42.763246 PROGRESS: Channel   0:	 0.050 FDR: 1,626; 0.010 FDR: 1,626; 0.001 FDR: 1,252
0:41:42.763350 PROGRESS: 
0:41:42.763414 PROGRESS: Protein Summary:
0:41:42.765924 PROGRESS: Channel   0:	 0.050 FDR: 1,622; 0.010 FDR: 1,622; 0.001 FDR: 1,249
0:41:42.766030 PROGRESS: =========================================================================
0:41:42.775021 INFO: Target number of precursors reached.
0:41:42.957523 INFO: fragments_df: keeping 5000 of 2226276 [sum(precursor_idx_mask)=17363 sum(mass_error_mask)=2226276 stop_rank=5000
0:41:43.663642 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:43.884938 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:44.605191 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:41:44.605692 INFO: Using score_cutoff 12.127829031944275 (fac=0.99, q=1)
0:41:44.606050 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:41:44.606137 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:41:44.606197 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.127829031944275
0:41:44.606260 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:44.912941 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:45.609554 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:41:45.609839 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:41:45.609965 INFO: Starting optimization step 8.
0:41:45.610046 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:41:45.610124 INFO: Using rust extraction backend
0:41:45.610200 PROGRESS: Extracting batch of 505395 precursors
0:41:46.475601 INFO: === Search parameters used ===
0:41:46.476100 INFO: rt_error       : 805.5951538085938
0:41:46.476166 INFO: mobility_error : 0.1
0:41:46.476220 INFO: num_candidates : 3
0:41:46.476287 INFO: ms1_error      : 30
0:41:46.476336 INFO: ms2_error      : 30
0:41:46.476382 INFO: fwhm_rt        : 3.0
0:41:46.476452 INFO: quant_window   : 3
0:41:46.476501 INFO: ==============================================
0:41:51.855437 INFO: performing precursor FDR with 40 features
0:41:51.855594 INFO: Decoy channel: -1
0:41:51.855628 INFO: competitive: True
0:41:52.260154 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:52.920079 INFO: Estimating optimal hyperparameters - samples: 1,192,656, batch_size: 4,096, learning_rate: 1.00e-03
0:41:52.922096 INFO: Using random state 229094 for train-test-split
0:42:14.763258 INFO: Test AUC: 0.596
0:42:14.763525 INFO: Train AUC: 0.600
0:42:14.763560 INFO: AUC difference: 0.66%
0:42:15.477201 INFO: Resetting torch num_threads to 80
0:42:15.547802 PROGRESS: === Extracted 1490820 precursors and 6515000 fragments ===
0:42:15.548505 INFO: === FDR correction performed with classifier version 7 ===
0:42:15.549467 PROGRESS: ============================= Precursor FDR =============================
0:42:15.549586 PROGRESS: Total precursors accumulated: 2,034
0:42:15.549657 PROGRESS: Target precursors: 2,014 (99.02%)
0:42:15.549715 PROGRESS: Decoy precursors: 20 (0.98%)
0:42:15.549781 PROGRESS: 
0:42:15.549830 PROGRESS: Precursor Summary:
0:42:15.551531 PROGRESS: Channel   0:	 0.050 FDR: 2,014; 0.010 FDR: 2,014; 0.001 FDR: 1,362
0:42:15.551647 PROGRESS: 
0:42:15.551711 PROGRESS: Protein Summary:
0:42:15.554531 PROGRESS: Channel   0:	 0.050 FDR: 2,010; 0.010 FDR: 2,010; 0.001 FDR: 1,359
0:42:15.554653 PROGRESS: =========================================================================
0:42:15.593886 INFO: Target number of precursors reached.
0:42:16.093491 INFO: fragments_df: keeping 5000 of 6515000 [sum(precursor_idx_mask)=43658 sum(mass_error_mask)=6515000 stop_rank=5000
0:42:16.716573 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:16.983787 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:17.705679 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:17.706220 INFO: Using score_cutoff 12.475635595607757 (fac=0.99, q=1)
0:42:17.706670 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:17.706770 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:17.706841 INFO: Updating optimization_manager: score_cutoff        : 12.127829031944275 -> 12.475635595607757
0:42:17.706928 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:17.861001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:18.204484 INFO: === checking if optimization conditions were reached ===
0:42:18.207256 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:42:18.207391 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:42:18.207517 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:42:18.207619 INFO: ==============================================
0:42:18.207723 INFO: Starting optimization step 9.
0:42:18.207819 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:18.207922 INFO: Using rust extraction backend
0:42:18.208026 PROGRESS: Extracting batch of 251735 precursors
0:42:18.643404 INFO: === Search parameters used ===
0:42:18.643733 INFO: rt_error       : 805.5951538085938
0:42:18.643798 INFO: mobility_error : 0.1
0:42:18.643850 INFO: num_candidates : 3
0:42:18.643897 INFO: ms1_error      : 30
0:42:18.643944 INFO: ms2_error      : 10.0
0:42:18.644003 INFO: fwhm_rt        : 3.0
0:42:18.644049 INFO: quant_window   : 3
0:42:18.644091 INFO: ==============================================
0:42:21.247306 INFO: performing precursor FDR with 40 features
0:42:21.247452 INFO: Decoy channel: -1
0:42:21.247480 INFO: competitive: True
0:42:21.437313 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:21.748756 INFO: Estimating optimal hyperparameters - samples: 601,231, batch_size: 2,462, learning_rate: 7.75e-04
0:42:21.749998 INFO: Using random state 855706 for train-test-split
0:42:33.934818 INFO: Test AUC: 0.600
0:42:33.934997 INFO: Train AUC: 0.607
0:42:33.935029 INFO: AUC difference: 1.19%
0:42:34.428360 INFO: Resetting torch num_threads to 80
0:42:34.461465 PROGRESS: === Extracted 751539 precursors and 3783981 fragments ===
0:42:34.462052 INFO: === FDR correction performed with classifier version 8 ===
0:42:34.462862 PROGRESS: ============================= Precursor FDR =============================
0:42:34.462966 PROGRESS: Total precursors accumulated: 1,262
0:42:34.463031 PROGRESS: Target precursors: 1,250 (99.05%)
0:42:34.463087 PROGRESS: Decoy precursors: 12 (0.95%)
0:42:34.463138 PROGRESS: 
0:42:34.463187 PROGRESS: Precursor Summary:
0:42:34.464562 PROGRESS: Channel   0:	 0.050 FDR: 1,250; 0.010 FDR: 1,250; 0.001 FDR:   822
0:42:34.464662 PROGRESS: 
0:42:34.464723 PROGRESS: Protein Summary:
0:42:34.466901 PROGRESS: Channel   0:	 0.050 FDR: 1,247; 0.010 FDR: 1,247; 0.001 FDR:   820
0:42:34.467003 PROGRESS: =========================================================================
0:42:34.486645 INFO: Target number of precursors reached.
0:42:34.787136 INFO: fragments_df: keeping 5000 of 3783981 [sum(precursor_idx_mask)=28733 sum(mass_error_mask)=3783981 stop_rank=5000
0:42:35.236078 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:35.450997 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:36.174807 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:36.175297 INFO: Using score_cutoff 11.347006412315368 (fac=0.99, q=1)
0:42:36.175637 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:36.175720 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:36.175776 INFO: Updating optimization_manager: score_cutoff        : 12.475635595607757 -> 11.347006412315368
0:42:36.175841 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:36.331924 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:36.684111 INFO: === checking if optimization conditions were reached ===
0:42:36.686940 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:42:36.687118 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:42:36.687224 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:42:36.687319 INFO: ==============================================
0:42:36.687423 INFO: Starting optimization step 10.
0:42:36.687521 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:36.687624 INFO: Using rust extraction backend
0:42:36.687721 PROGRESS: Extracting batch of 251735 precursors
0:42:37.123806 INFO: === Search parameters used ===
0:42:37.124131 INFO: rt_error       : 805.5951538085938
0:42:37.124192 INFO: mobility_error : 0.1
0:42:37.124245 INFO: num_candidates : 3
0:42:37.124310 INFO: ms1_error      : 30
0:42:37.124357 INFO: ms2_error      : 10.0
0:42:37.124400 INFO: fwhm_rt        : 3.0
0:42:37.124441 INFO: quant_window   : 3
0:42:37.124484 INFO: ==============================================
0:42:39.761840 INFO: performing precursor FDR with 40 features
0:42:39.762023 INFO: Decoy channel: -1
0:42:39.762052 INFO: competitive: True
0:42:39.961888 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:40.277364 INFO: Estimating optimal hyperparameters - samples: 601,248, batch_size: 2,462, learning_rate: 7.75e-04
0:42:40.278574 INFO: Using random state 62882 for train-test-split
0:42:52.487608 INFO: Test AUC: 0.606
0:42:52.487820 INFO: Train AUC: 0.613
0:42:52.487853 INFO: AUC difference: 1.06%
0:42:52.984159 INFO: Resetting torch num_threads to 80
0:42:53.016948 PROGRESS: === Extracted 751560 precursors and 3784246 fragments ===
0:42:53.017576 INFO: === FDR correction performed with classifier version 9 ===
0:42:53.018323 PROGRESS: ============================= Precursor FDR =============================
0:42:53.018433 PROGRESS: Total precursors accumulated: 1,268
0:42:53.018499 PROGRESS: Target precursors: 1,256 (99.05%)
0:42:53.018555 PROGRESS: Decoy precursors: 12 (0.95%)
0:42:53.018608 PROGRESS: 
0:42:53.018657 PROGRESS: Precursor Summary:
0:42:53.020075 PROGRESS: Channel   0:	 0.050 FDR: 1,256; 0.010 FDR: 1,256; 0.001 FDR: 1,024
0:42:53.020177 PROGRESS: 
0:42:53.020239 PROGRESS: Protein Summary:
0:42:53.022478 PROGRESS: Channel   0:	 0.050 FDR: 1,252; 0.010 FDR: 1,252; 0.001 FDR: 1,021
0:42:53.022584 PROGRESS: =========================================================================
0:42:53.040987 INFO: Target number of precursors reached.
0:42:53.325376 INFO: fragments_df: keeping 5000 of 3784246 [sum(precursor_idx_mask)=29030 sum(mass_error_mask)=3784246 stop_rank=5000
0:42:53.862437 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:54.053177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:54.716449 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:54.717018 INFO: Using score_cutoff 11.557284052848814 (fac=0.99, q=1)
0:42:54.717378 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:54.717462 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:54.717521 INFO: Updating optimization_manager: score_cutoff        : 11.347006412315368 -> 11.557284052848814
0:42:54.717592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:54.870355 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:55.215292 INFO: === checking if optimization conditions were reached ===
0:42:55.218054 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:42:55.218186 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:42:55.218270 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:42:55.218347 INFO: ==============================================
0:42:55.218427 INFO: Starting optimization step 11.
0:42:55.218497 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:55.218587 INFO: Using rust extraction backend
0:42:55.218671 PROGRESS: Extracting batch of 251735 precursors
0:42:55.655267 INFO: === Search parameters used ===
0:42:55.655611 INFO: rt_error       : 805.5951538085938
0:42:55.655675 INFO: mobility_error : 0.1
0:42:55.655762 INFO: num_candidates : 3
0:42:55.655813 INFO: ms1_error      : 30
0:42:55.655858 INFO: ms2_error      : 10.0
0:42:55.655900 INFO: fwhm_rt        : 3.0
0:42:55.655941 INFO: quant_window   : 3
0:42:55.655983 INFO: ==============================================
0:42:58.270554 INFO: performing precursor FDR with 40 features
0:42:58.270703 INFO: Decoy channel: -1
0:42:58.270733 INFO: competitive: True
0:42:58.464299 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:58.775342 INFO: Estimating optimal hyperparameters - samples: 601,249, batch_size: 2,462, learning_rate: 7.75e-04
0:42:58.776580 INFO: Using random state 497891 for train-test-split
0:43:11.402078 INFO: Test AUC: 0.608
0:43:11.402338 INFO: Train AUC: 0.615
0:43:11.402374 INFO: AUC difference: 1.12%
0:43:11.897976 INFO: Resetting torch num_threads to 80
0:43:11.931584 PROGRESS: === Extracted 751562 precursors and 3783960 fragments ===
0:43:11.932209 INFO: === FDR correction performed with classifier version 10 ===
0:43:11.932935 PROGRESS: ============================= Precursor FDR =============================
0:43:11.933042 PROGRESS: Total precursors accumulated: 1,256
0:43:11.933113 PROGRESS: Target precursors: 1,244 (99.04%)
0:43:11.933171 PROGRESS: Decoy precursors: 12 (0.96%)
0:43:11.933224 PROGRESS: 
0:43:11.933274 PROGRESS: Precursor Summary:
0:43:11.934707 PROGRESS: Channel   0:	 0.050 FDR: 1,244; 0.010 FDR: 1,244; 0.001 FDR: 1,122
0:43:11.934812 PROGRESS: 
0:43:11.934875 PROGRESS: Protein Summary:
0:43:11.937100 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR: 1,240; 0.001 FDR: 1,119
0:43:11.937201 PROGRESS: =========================================================================
0:43:11.956024 INFO: Target number of precursors reached.
0:43:12.245143 INFO: fragments_df: keeping 5000 of 3783960 [sum(precursor_idx_mask)=28945 sum(mass_error_mask)=3783960 stop_rank=5000
0:43:12.802102 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:13.019256 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:13.744769 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:13.745277 INFO: Using score_cutoff 11.610349730014802 (fac=0.99, q=1)
0:43:13.745661 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:13.745747 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:13.745804 INFO: Updating optimization_manager: score_cutoff        : 11.557284052848814 -> 11.610349730014802
0:43:13.745869 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:13.900842 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:14.252824 INFO: === checking if optimization conditions were reached ===
0:43:14.255714 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:43:14.255894 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:43:14.255985 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:43:14.256067 INFO: ==============================================
0:43:14.256151 INFO: Starting optimization step 12.
0:43:14.256225 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:43:14.256326 INFO: Using rust extraction backend
0:43:14.256410 PROGRESS: Extracting batch of 251735 precursors
0:43:14.697045 INFO: === Search parameters used ===
0:43:14.697435 INFO: rt_error       : 805.5951538085938
0:43:14.697501 INFO: mobility_error : 0.1
0:43:14.697573 INFO: num_candidates : 3
0:43:14.697618 INFO: ms1_error      : 30
0:43:14.697661 INFO: ms2_error      : 10.0
0:43:14.697704 INFO: fwhm_rt        : 3.0
0:43:14.697747 INFO: quant_window   : 3
0:43:14.697788 INFO: ==============================================
0:43:17.342121 INFO: performing precursor FDR with 40 features
0:43:17.342263 INFO: Decoy channel: -1
0:43:17.342293 INFO: competitive: True
0:43:17.543480 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:17.870194 INFO: Estimating optimal hyperparameters - samples: 601,243, batch_size: 2,462, learning_rate: 7.75e-04
0:43:17.871373 INFO: Using random state 502239 for train-test-split
0:43:30.522598 INFO: Test AUC: 0.606
0:43:30.522763 INFO: Train AUC: 0.618
0:43:30.522795 INFO: AUC difference: 1.97%
0:43:31.012352 INFO: Resetting torch num_threads to 80
0:43:31.047046 PROGRESS: === Extracted 751554 precursors and 3784173 fragments ===
0:43:31.047654 INFO: === FDR correction performed with classifier version 11 ===
0:43:31.048382 PROGRESS: ============================= Precursor FDR =============================
0:43:31.048489 PROGRESS: Total precursors accumulated: 1,234
0:43:31.048554 PROGRESS: Target precursors: 1,222 (99.03%)
0:43:31.048611 PROGRESS: Decoy precursors: 12 (0.97%)
0:43:31.048663 PROGRESS: 
0:43:31.048711 PROGRESS: Precursor Summary:
0:43:31.050133 PROGRESS: Channel   0:	 0.050 FDR: 1,222; 0.010 FDR: 1,222; 0.001 FDR: 1,101
0:43:31.050239 PROGRESS: 
0:43:31.050302 PROGRESS: Protein Summary:
0:43:31.052511 PROGRESS: Channel   0:	 0.050 FDR: 1,219; 0.010 FDR: 1,219; 0.001 FDR: 1,098
0:43:31.052621 PROGRESS: =========================================================================
0:43:31.071496 INFO: Target number of precursors reached.
0:43:31.355780 INFO: fragments_df: keeping 5000 of 3784173 [sum(precursor_idx_mask)=28229 sum(mass_error_mask)=3784173 stop_rank=5000
0:43:31.871278 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:32.084477 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:32.774231 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:32.774726 INFO: Using score_cutoff 11.343544741344452 (fac=0.99, q=1)
0:43:32.775066 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:32.775150 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:32.775210 INFO: Updating optimization_manager: score_cutoff        : 11.610349730014802 -> 11.343544741344452
0:43:32.775273 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:32.925691 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:33.266059 INFO: === checking if optimization conditions were reached ===
0:43:33.268858 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:43:33.269026 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
0:43:33.269112 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:43:33.269190 INFO: ==============================================
0:43:33.269275 PROGRESS: Optimization finished for ms2_error.
0:43:33.687326 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:33.838942 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:34.176049 INFO: Starting optimization step 0.
0:43:34.176411 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:43:34.176511 INFO: Using rust extraction backend
0:43:34.176598 PROGRESS: Extracting batch of 251735 precursors
0:43:34.611750 INFO: === Search parameters used ===
0:43:34.612080 INFO: rt_error       : 805.5951538085938
0:43:34.612143 INFO: mobility_error : 0.1
0:43:34.612195 INFO: num_candidates : 3
0:43:34.612242 INFO: ms1_error      : 30
0:43:34.612294 INFO: ms2_error      : 10.0
0:43:34.612358 INFO: fwhm_rt        : 3.0
0:43:34.612402 INFO: quant_window   : 3
0:43:34.612446 INFO: ==============================================
0:43:37.228049 INFO: performing precursor FDR with 40 features
0:43:37.228197 INFO: Decoy channel: -1
0:43:37.228227 INFO: competitive: True
0:43:37.421679 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:37.734746 INFO: Estimating optimal hyperparameters - samples: 601,233, batch_size: 2,462, learning_rate: 7.75e-04
0:43:37.735892 INFO: Using random state 794846 for train-test-split
0:43:50.431907 INFO: Test AUC: 0.608
0:43:50.432068 INFO: Train AUC: 0.620
0:43:50.432102 INFO: AUC difference: 1.94%
0:43:50.918694 INFO: Resetting torch num_threads to 80
0:43:50.950668 PROGRESS: === Extracted 751542 precursors and 3783905 fragments ===
0:43:50.951211 INFO: === FDR correction performed with classifier version 12 ===
0:43:50.951936 PROGRESS: ============================= Precursor FDR =============================
0:43:50.952043 PROGRESS: Total precursors accumulated: 1,238
0:43:50.952109 PROGRESS: Target precursors: 1,226 (99.03%)
0:43:50.952165 PROGRESS: Decoy precursors: 12 (0.97%)
0:43:50.952216 PROGRESS: 
0:43:50.952266 PROGRESS: Precursor Summary:
0:43:50.953664 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR: 1,021
0:43:50.953781 PROGRESS: 
0:43:50.953842 PROGRESS: Protein Summary:
0:43:50.956062 PROGRESS: Channel   0:	 0.050 FDR: 1,223; 0.010 FDR: 1,223; 0.001 FDR: 1,019
0:43:50.956168 PROGRESS: =========================================================================
0:43:50.974722 INFO: Target number of precursors reached.
0:43:51.265327 INFO: fragments_df: keeping 5000 of 3783905 [sum(precursor_idx_mask)=28099 sum(mass_error_mask)=3783905 stop_rank=5000
0:43:51.693777 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:51.878978 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:52.539276 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:52.539771 INFO: Using score_cutoff 10.394618332386017 (fac=0.99, q=1)
0:43:52.540101 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:52.540185 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:52.540244 INFO: Updating optimization_manager: score_cutoff        : 11.343544741344452 -> 10.394618332386017
0:43:52.540318 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:52.690717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:53.030200 INFO: === checking if optimization conditions were reached ===
0:43:53.030555 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:43:53.033625 INFO: Updating optimization_manager: rt_error            : 805.5951538085938 -> 510.80047132682887
0:43:53.033768 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 510.8005.
0:43:53.033882 INFO: ==============================================
0:43:53.033988 INFO: Starting optimization step 1.
0:43:53.034065 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:43:53.034145 INFO: Using rust extraction backend
0:43:53.034228 PROGRESS: Extracting batch of 251735 precursors
0:43:53.463974 INFO: === Search parameters used ===
0:43:53.464571 INFO: rt_error       : 510.80047132682887
0:43:53.464641 INFO: mobility_error : 0.1
0:43:53.464693 INFO: num_candidates : 3
0:43:53.464740 INFO: ms1_error      : 30
0:43:53.464786 INFO: ms2_error      : 10.0
0:43:53.464829 INFO: fwhm_rt        : 3.0
0:43:53.464873 INFO: quant_window   : 3
0:43:53.464915 INFO: ==============================================
0:43:55.969484 INFO: performing precursor FDR with 40 features
0:43:55.969637 INFO: Decoy channel: -1
0:43:55.969667 INFO: competitive: True
0:43:56.161336 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:56.470247 INFO: Estimating optimal hyperparameters - samples: 600,640, batch_size: 2,460, learning_rate: 7.75e-04
0:43:56.471395 INFO: Using random state 794846 for train-test-split
0:44:08.599437 INFO: Test AUC: 0.607
0:44:08.599619 INFO: Train AUC: 0.617
0:44:08.599652 INFO: AUC difference: 1.68%
0:44:09.087615 INFO: Resetting torch num_threads to 80
0:44:09.126057 PROGRESS: === Extracted 750801 precursors and 3742923 fragments ===
0:44:09.126652 INFO: === FDR correction performed with classifier version 12 ===
0:44:09.127400 PROGRESS: ============================= Precursor FDR =============================
0:44:09.127507 PROGRESS: Total precursors accumulated: 1,375
0:44:09.127575 PROGRESS: Target precursors: 1,362 (99.05%)
0:44:09.127632 PROGRESS: Decoy precursors: 13 (0.95%)
0:44:09.127683 PROGRESS: 
0:44:09.127739 PROGRESS: Precursor Summary:
0:44:09.129180 PROGRESS: Channel   0:	 0.050 FDR: 1,362; 0.010 FDR: 1,362; 0.001 FDR: 1,132
0:44:09.129299 PROGRESS: 
0:44:09.129360 PROGRESS: Protein Summary:
0:44:09.131706 PROGRESS: Channel   0:	 0.050 FDR: 1,358; 0.010 FDR: 1,358; 0.001 FDR: 1,129
0:44:09.131818 PROGRESS: =========================================================================
0:44:09.150418 INFO: Target number of precursors reached.
0:44:09.446141 INFO: fragments_df: keeping 5000 of 3742923 [sum(precursor_idx_mask)=31329 sum(mass_error_mask)=3742923 stop_rank=5000
0:44:09.892866 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:10.089295 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:11.404858 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:11.405352 INFO: Using score_cutoff 10.743195510578156 (fac=0.99, q=1)
0:44:11.405697 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:11.405781 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:11.405839 INFO: Updating optimization_manager: score_cutoff        : 10.394618332386017 -> 10.743195510578156
0:44:11.405912 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:11.556700 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:11.899167 INFO: === checking if optimization conditions were reached ===
0:44:11.899525 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:44:11.902956 INFO: Updating optimization_manager: rt_error            : 510.80047132682887 -> 475.85905638843667
0:44:11.903151 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 475.8591.
0:44:11.903240 INFO: ==============================================
0:44:11.903327 INFO: Starting optimization step 2.
0:44:11.903404 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:44:11.903484 INFO: Using rust extraction backend
0:44:11.903562 PROGRESS: Extracting batch of 251735 precursors
0:44:12.342689 INFO: === Search parameters used ===
0:44:12.343019 INFO: rt_error       : 475.85905638843667
0:44:12.343086 INFO: mobility_error : 0.1
0:44:12.343139 INFO: num_candidates : 3
0:44:12.343189 INFO: ms1_error      : 30
0:44:12.343236 INFO: ms2_error      : 10.0
0:44:12.343282 INFO: fwhm_rt        : 3.0
0:44:12.343328 INFO: quant_window   : 3
0:44:12.343374 INFO: ==============================================
0:44:14.864340 INFO: performing precursor FDR with 40 features
0:44:14.864494 INFO: Decoy channel: -1
0:44:14.864522 INFO: competitive: True
0:44:15.060021 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:15.369208 INFO: Estimating optimal hyperparameters - samples: 600,432, batch_size: 2,459, learning_rate: 7.75e-04
0:44:15.370437 INFO: Using random state 794846 for train-test-split
0:44:28.048994 INFO: Test AUC: 0.607
0:44:28.049161 INFO: Train AUC: 0.617
0:44:28.049192 INFO: AUC difference: 1.53%
0:44:28.535388 INFO: Resetting torch num_threads to 80
0:44:28.568029 PROGRESS: === Extracted 750541 precursors and 3722926 fragments ===
0:44:28.568595 INFO: === FDR correction performed with classifier version 12 ===
0:44:28.569363 PROGRESS: ============================= Precursor FDR =============================
0:44:28.569482 PROGRESS: Total precursors accumulated: 1,264
0:44:28.569561 PROGRESS: Target precursors: 1,252 (99.05%)
0:44:28.569645 PROGRESS: Decoy precursors: 12 (0.95%)
0:44:28.569712 PROGRESS: 
0:44:28.569771 PROGRESS: Precursor Summary:
0:44:28.571242 PROGRESS: Channel   0:	 0.050 FDR: 1,252; 0.010 FDR: 1,252; 0.001 FDR: 1,105
0:44:28.571376 PROGRESS: 
0:44:28.571447 PROGRESS: Protein Summary:
0:44:28.573749 PROGRESS: Channel   0:	 0.050 FDR: 1,249; 0.010 FDR: 1,249; 0.001 FDR: 1,103
0:44:28.573859 PROGRESS: =========================================================================
0:44:28.593003 INFO: Target number of precursors reached.
0:44:28.882584 INFO: fragments_df: keeping 5000 of 3722926 [sum(precursor_idx_mask)=28914 sum(mass_error_mask)=3722926 stop_rank=5000
0:44:29.313998 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:29.530611 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:30.256917 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:30.257462 INFO: Using score_cutoff 11.402719432353972 (fac=0.99, q=1)
0:44:30.257812 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:30.257936 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:30.258016 INFO: Updating optimization_manager: score_cutoff        : 10.743195510578156 -> 11.402719432353972
0:44:30.258094 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:30.410713 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:30.723183 INFO: === checking if optimization conditions were reached ===
0:44:30.723529 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:44:30.726476 INFO: Updating optimization_manager: rt_error            : 475.85905638843667 -> 383.4357345235688
0:44:30.726599 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 383.4357.
0:44:30.726680 INFO: ==============================================
0:44:30.726774 INFO: Starting optimization step 3.
0:44:30.726866 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:44:30.726957 INFO: Using rust extraction backend
0:44:30.727038 PROGRESS: Extracting batch of 251735 precursors
0:44:31.159072 INFO: === Search parameters used ===
0:44:31.159426 INFO: rt_error       : 383.4357345235688
0:44:31.159506 INFO: mobility_error : 0.1
0:44:31.159572 INFO: num_candidates : 3
0:44:31.159647 INFO: ms1_error      : 30
0:44:31.159707 INFO: ms2_error      : 10.0
0:44:31.159766 INFO: fwhm_rt        : 3.0
0:44:31.159828 INFO: quant_window   : 3
0:44:31.159883 INFO: ==============================================
0:44:33.593819 INFO: performing precursor FDR with 40 features
0:44:33.593990 INFO: Decoy channel: -1
0:44:33.594019 INFO: competitive: True
0:44:33.785208 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:34.096190 INFO: Estimating optimal hyperparameters - samples: 599,478, batch_size: 2,455, learning_rate: 7.74e-04
0:44:34.097410 INFO: Using random state 794846 for train-test-split
0:44:46.227735 INFO: Test AUC: 0.611
0:44:46.227897 INFO: Train AUC: 0.615
0:44:46.227929 INFO: AUC difference: 0.73%
0:44:46.713651 INFO: Resetting torch num_threads to 80
0:44:46.747582 PROGRESS: === Extracted 749348 precursors and 3625119 fragments ===
0:44:46.748154 INFO: === FDR correction performed with classifier version 12 ===
0:44:46.748910 PROGRESS: ============================= Precursor FDR =============================
0:44:46.749020 PROGRESS: Total precursors accumulated: 1,314
0:44:46.749099 PROGRESS: Target precursors: 1,301 (99.01%)
0:44:46.749158 PROGRESS: Decoy precursors: 13 (0.99%)
0:44:46.749210 PROGRESS: 
0:44:46.749259 PROGRESS: Precursor Summary:
0:44:46.750705 PROGRESS: Channel   0:	 0.050 FDR: 1,301; 0.010 FDR: 1,301; 0.001 FDR:   925
0:44:46.750810 PROGRESS: 
0:44:46.750871 PROGRESS: Protein Summary:
0:44:46.753090 PROGRESS: Channel   0:	 0.050 FDR: 1,298; 0.010 FDR: 1,298; 0.001 FDR:   922
0:44:46.753191 PROGRESS: =========================================================================
0:44:46.771774 INFO: Target number of precursors reached.
0:44:47.052941 INFO: fragments_df: keeping 5000 of 3625119 [sum(precursor_idx_mask)=29225 sum(mass_error_mask)=3625119 stop_rank=5000
0:44:47.532310 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:47.752312 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:48.482230 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:48.482757 INFO: Using score_cutoff 8.508284568786621 (fac=0.99, q=1)
0:44:48.483111 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:48.483194 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:48.483253 INFO: Updating optimization_manager: score_cutoff        : 11.402719432353972 -> 8.508284568786621
0:44:48.483325 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:48.632029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:48.966995 INFO: === checking if optimization conditions were reached ===
0:44:48.967356 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:44:48.970771 INFO: Updating optimization_manager: rt_error            : 383.4357345235688 -> 502.18879683580894
0:44:48.970907 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 502.1888.
0:44:48.970988 INFO: ==============================================
0:44:48.971075 INFO: Starting optimization step 4.
0:44:48.971165 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:44:48.971262 INFO: Using rust extraction backend
0:44:48.971350 PROGRESS: Extracting batch of 251735 precursors
0:44:49.403714 INFO: === Search parameters used ===
0:44:49.404041 INFO: rt_error       : 502.18879683580894
0:44:49.404104 INFO: mobility_error : 0.1
0:44:49.404156 INFO: num_candidates : 3
0:44:49.404203 INFO: ms1_error      : 30
0:44:49.404247 INFO: ms2_error      : 10.0
0:44:49.404295 INFO: fwhm_rt        : 3.0
0:44:49.404361 INFO: quant_window   : 3
0:44:49.404424 INFO: ==============================================
0:44:51.918978 INFO: performing precursor FDR with 40 features
0:44:51.919125 INFO: Decoy channel: -1
0:44:51.919153 INFO: competitive: True
0:44:52.109851 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:52.424752 INFO: Estimating optimal hyperparameters - samples: 600,668, batch_size: 2,460, learning_rate: 7.75e-04
0:44:52.426005 INFO: Using random state 794846 for train-test-split
0:45:04.750403 INFO: Test AUC: 0.608
0:45:04.750560 INFO: Train AUC: 0.616
0:45:04.750592 INFO: AUC difference: 1.31%
0:45:05.231877 INFO: Resetting torch num_threads to 80
0:45:05.264082 PROGRESS: === Extracted 750835 precursors and 3743305 fragments ===
0:45:05.264661 INFO: === FDR correction performed with classifier version 12 ===
0:45:05.265437 PROGRESS: ============================= Precursor FDR =============================
0:45:05.265546 PROGRESS: Total precursors accumulated: 1,256
0:45:05.265626 PROGRESS: Target precursors: 1,244 (99.04%)
0:45:05.265696 PROGRESS: Decoy precursors: 12 (0.96%)
0:45:05.265766 PROGRESS: 
0:45:05.265831 PROGRESS: Precursor Summary:
0:45:05.267375 PROGRESS: Channel   0:	 0.050 FDR: 1,244; 0.010 FDR: 1,244; 0.001 FDR: 1,103
0:45:05.267487 PROGRESS: 
0:45:05.267562 PROGRESS: Protein Summary:
0:45:05.269860 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR: 1,240; 0.001 FDR: 1,101
0:45:05.269975 PROGRESS: =========================================================================
0:45:05.288480 INFO: Target number of precursors reached.
0:45:05.581174 INFO: fragments_df: keeping 5000 of 3743305 [sum(precursor_idx_mask)=28390 sum(mass_error_mask)=3743305 stop_rank=5000
0:45:06.008431 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:06.195361 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:06.854950 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:06.855500 INFO: Using score_cutoff 9.800518518161773 (fac=0.99, q=1)
0:45:06.855864 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:06.855960 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:06.856031 INFO: Updating optimization_manager: score_cutoff        : 8.508284568786621 -> 9.800518518161773
0:45:06.856117 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:07.007460 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:07.345288 INFO: === checking if optimization conditions were reached ===
0:45:07.345634 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:45:07.348956 INFO: Updating optimization_manager: rt_error            : 502.18879683580894 -> 453.4539000094303
0:45:07.349097 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 453.4539.
0:45:07.349178 INFO: ==============================================
0:45:07.349260 INFO: Starting optimization step 5.
0:45:07.349330 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:07.349406 INFO: Using rust extraction backend
0:45:07.349480 PROGRESS: Extracting batch of 251735 precursors
0:45:07.783191 INFO: === Search parameters used ===
0:45:07.783516 INFO: rt_error       : 453.4539000094303
0:45:07.783608 INFO: mobility_error : 0.1
0:45:07.783664 INFO: num_candidates : 3
0:45:07.783712 INFO: ms1_error      : 30
0:45:07.783756 INFO: ms2_error      : 10.0
0:45:07.783799 INFO: fwhm_rt        : 3.0
0:45:07.783839 INFO: quant_window   : 3
0:45:07.783880 INFO: ==============================================
0:45:10.271977 INFO: performing precursor FDR with 40 features
0:45:10.272123 INFO: Decoy channel: -1
0:45:10.272151 INFO: competitive: True
0:45:10.470169 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:10.778176 INFO: Estimating optimal hyperparameters - samples: 600,234, batch_size: 2,458, learning_rate: 7.75e-04
0:45:10.779374 INFO: Using random state 794846 for train-test-split
0:45:23.297440 INFO: Test AUC: 0.606
0:45:23.297595 INFO: Train AUC: 0.617
0:45:23.297627 INFO: AUC difference: 1.85%
0:45:23.775065 INFO: Resetting torch num_threads to 80
0:45:23.808463 PROGRESS: === Extracted 750293 precursors and 3701520 fragments ===
0:45:23.809038 INFO: === FDR correction performed with classifier version 12 ===
0:45:23.809824 PROGRESS: ============================= Precursor FDR =============================
0:45:23.809942 PROGRESS: Total precursors accumulated: 1,429
0:45:23.810010 PROGRESS: Target precursors: 1,415 (99.02%)
0:45:23.810068 PROGRESS: Decoy precursors: 14 (0.98%)
0:45:23.810120 PROGRESS: 
0:45:23.810172 PROGRESS: Precursor Summary:
0:45:23.811635 PROGRESS: Channel   0:	 0.050 FDR: 1,415; 0.010 FDR: 1,415; 0.001 FDR: 1,099
0:45:23.811754 PROGRESS: 
0:45:23.811816 PROGRESS: Protein Summary:
0:45:23.814196 PROGRESS: Channel   0:	 0.050 FDR: 1,411; 0.010 FDR: 1,411; 0.001 FDR: 1,096
0:45:23.814317 PROGRESS: =========================================================================
0:45:23.832715 INFO: Target number of precursors reached.
0:45:24.124224 INFO: fragments_df: keeping 5000 of 3701520 [sum(precursor_idx_mask)=32210 sum(mass_error_mask)=3701520 stop_rank=5000
0:45:24.550549 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:24.754818 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:25.421955 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:25.422455 INFO: Using score_cutoff 9.965428639411927 (fac=0.99, q=1)
0:45:25.422788 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:25.422881 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:25.422942 INFO: Updating optimization_manager: score_cutoff        : 9.800518518161773 -> 9.965428639411927
0:45:25.423006 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:25.574059 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:25.914751 INFO: === checking if optimization conditions were reached ===
0:45:25.915081 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:45:25.918077 INFO: Updating optimization_manager: rt_error            : 453.4539000094303 -> 525.4539205911087
0:45:25.918199 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 525.4539.
0:45:25.918281 INFO: ==============================================
0:45:25.918367 INFO: Starting optimization step 6.
0:45:25.918444 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:25.918522 INFO: Using rust extraction backend
0:45:25.918596 PROGRESS: Extracting batch of 251735 precursors
0:45:26.349548 INFO: === Search parameters used ===
0:45:26.349888 INFO: rt_error       : 525.4539205911087
0:45:26.350000 INFO: mobility_error : 0.1
0:45:26.350075 INFO: num_candidates : 3
0:45:26.350142 INFO: ms1_error      : 30
0:45:26.350198 INFO: ms2_error      : 10.0
0:45:26.350254 INFO: fwhm_rt        : 3.0
0:45:26.350309 INFO: quant_window   : 3
0:45:26.350379 INFO: ==============================================
0:45:28.909170 INFO: performing precursor FDR with 40 features
0:45:28.909324 INFO: Decoy channel: -1
0:45:28.909356 INFO: competitive: True
0:45:29.106347 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:29.412840 INFO: Estimating optimal hyperparameters - samples: 600,620, batch_size: 2,460, learning_rate: 7.75e-04
0:45:29.414125 INFO: Using random state 794846 for train-test-split
0:45:41.482682 INFO: Test AUC: 0.607
0:45:41.482843 INFO: Train AUC: 0.618
0:45:41.482875 INFO: AUC difference: 1.79%
0:45:41.965541 INFO: Resetting torch num_threads to 80
0:45:41.998581 PROGRESS: === Extracted 750775 precursors and 3747101 fragments ===
0:45:41.999135 INFO: === FDR correction performed with classifier version 12 ===
0:45:41.999887 PROGRESS: ============================= Precursor FDR =============================
0:45:41.999997 PROGRESS: Total precursors accumulated: 1,360
0:45:42.000062 PROGRESS: Target precursors: 1,347 (99.04%)
0:45:42.000119 PROGRESS: Decoy precursors: 13 (0.96%)
0:45:42.000171 PROGRESS: 
0:45:42.000220 PROGRESS: Precursor Summary:
0:45:42.001637 PROGRESS: Channel   0:	 0.050 FDR: 1,347; 0.010 FDR: 1,347; 0.001 FDR:   961
0:45:42.001750 PROGRESS: 
0:45:42.001811 PROGRESS: Protein Summary:
0:45:42.004072 PROGRESS: Channel   0:	 0.050 FDR: 1,343; 0.010 FDR: 1,343; 0.001 FDR:   959
0:45:42.004183 PROGRESS: =========================================================================
0:45:42.023403 INFO: Target number of precursors reached.
0:45:42.318664 INFO: fragments_df: keeping 5000 of 3747101 [sum(precursor_idx_mask)=31184 sum(mass_error_mask)=3747101 stop_rank=5000
0:45:42.748845 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:42.944250 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:43.635991 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:43.636472 INFO: Using score_cutoff 11.47345792980194 (fac=0.99, q=1)
0:45:43.636805 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:43.636889 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:43.636955 INFO: Updating optimization_manager: score_cutoff        : 9.965428639411927 -> 11.47345792980194
0:45:43.637022 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:43.789447 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:44.135059 INFO: === checking if optimization conditions were reached ===
0:45:44.135411 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:45:44.138803 INFO: Updating optimization_manager: rt_error            : 525.4539205911087 -> 391.45237470535
0:45:44.138943 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 391.4524.
0:45:44.139030 INFO: ==============================================
0:45:44.139118 INFO: Starting optimization step 7.
0:45:44.139196 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:44.139276 INFO: Using rust extraction backend
0:45:44.139358 PROGRESS: Extracting batch of 251735 precursors
0:45:44.571310 INFO: === Search parameters used ===
0:45:44.571632 INFO: rt_error       : 391.45237470535
0:45:44.571693 INFO: mobility_error : 0.1
0:45:44.571743 INFO: num_candidates : 3
0:45:44.571790 INFO: ms1_error      : 30
0:45:44.571835 INFO: ms2_error      : 10.0
0:45:44.571903 INFO: fwhm_rt        : 3.0
0:45:44.571949 INFO: quant_window   : 3
0:45:44.571995 INFO: ==============================================
0:45:47.004815 INFO: performing precursor FDR with 40 features
0:45:47.004968 INFO: Decoy channel: -1
0:45:47.004996 INFO: competitive: True
0:45:47.204490 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:47.517061 INFO: Estimating optimal hyperparameters - samples: 599,612, batch_size: 2,456, learning_rate: 7.74e-04
0:45:47.518288 INFO: Using random state 794846 for train-test-split
0:45:59.728913 INFO: Test AUC: 0.606
0:45:59.729071 INFO: Train AUC: 0.616
0:45:59.729103 INFO: AUC difference: 1.60%
0:46:00.208118 INFO: Resetting torch num_threads to 80
0:46:00.240674 PROGRESS: === Extracted 749516 precursors and 3640378 fragments ===
0:46:00.241220 INFO: === FDR correction performed with classifier version 12 ===
0:46:00.242008 PROGRESS: ============================= Precursor FDR =============================
0:46:00.242116 PROGRESS: Total precursors accumulated: 1,300
0:46:00.242182 PROGRESS: Target precursors: 1,288 (99.08%)
0:46:00.242238 PROGRESS: Decoy precursors: 12 (0.92%)
0:46:00.242292 PROGRESS: 
0:46:00.242342 PROGRESS: Precursor Summary:
0:46:00.243765 PROGRESS: Channel   0:	 0.050 FDR: 1,288; 0.010 FDR: 1,288; 0.001 FDR: 1,163
0:46:00.243866 PROGRESS: 
0:46:00.243928 PROGRESS: Protein Summary:
0:46:00.246235 PROGRESS: Channel   0:	 0.050 FDR: 1,284; 0.010 FDR: 1,284; 0.001 FDR: 1,160
0:46:00.246342 PROGRESS: =========================================================================
0:46:00.264991 INFO: Target number of precursors reached.
0:46:00.549475 INFO: fragments_df: keeping 5000 of 3640378 [sum(precursor_idx_mask)=29472 sum(mass_error_mask)=3640378 stop_rank=5000
0:46:00.980396 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:01.199162 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:01.923739 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:01.924252 INFO: Using score_cutoff 10.562642474269866 (fac=0.99, q=1)
0:46:01.924591 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:01.924676 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:01.924735 INFO: Updating optimization_manager: score_cutoff        : 11.47345792980194 -> 10.562642474269866
0:46:01.924797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:02.076728 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:02.415561 INFO: === checking if optimization conditions were reached ===
0:46:02.415921 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:46:02.419239 INFO: Updating optimization_manager: rt_error            : 391.45237470535 -> 463.2093779938687
0:46:02.419370 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 463.2094.
0:46:02.419455 INFO: ==============================================
0:46:02.419540 INFO: Starting optimization step 8.
0:46:02.419612 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:02.419690 INFO: Using rust extraction backend
0:46:02.419764 PROGRESS: Extracting batch of 251735 precursors
0:46:02.851694 INFO: === Search parameters used ===
0:46:02.852016 INFO: rt_error       : 463.2093779938687
0:46:02.852079 INFO: mobility_error : 0.1
0:46:02.852130 INFO: num_candidates : 3
0:46:02.852193 INFO: ms1_error      : 30
0:46:02.852242 INFO: ms2_error      : 10.0
0:46:02.852287 INFO: fwhm_rt        : 3.0
0:46:02.852332 INFO: quant_window   : 3
0:46:02.852374 INFO: ==============================================
0:46:05.385068 INFO: performing precursor FDR with 40 features
0:46:05.385219 INFO: Decoy channel: -1
0:46:05.385247 INFO: competitive: True
0:46:05.580546 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:05.890990 INFO: Estimating optimal hyperparameters - samples: 600,383, batch_size: 2,459, learning_rate: 7.75e-04
0:46:05.891992 INFO: Using random state 794846 for train-test-split
0:46:18.498282 INFO: Test AUC: 0.605
0:46:18.498441 INFO: Train AUC: 0.617
0:46:18.498474 INFO: AUC difference: 2.05%
0:46:18.982875 INFO: Resetting torch num_threads to 80
0:46:19.015433 PROGRESS: === Extracted 750479 precursors and 3717466 fragments ===
0:46:19.016014 INFO: === FDR correction performed with classifier version 12 ===
0:46:19.016750 PROGRESS: ============================= Precursor FDR =============================
0:46:19.016860 PROGRESS: Total precursors accumulated: 1,240
0:46:19.016926 PROGRESS: Target precursors: 1,228 (99.03%)
0:46:19.016983 PROGRESS: Decoy precursors: 12 (0.97%)
0:46:19.017035 PROGRESS: 
0:46:19.017085 PROGRESS: Precursor Summary:
0:46:19.018510 PROGRESS: Channel   0:	 0.050 FDR: 1,228; 0.010 FDR: 1,228; 0.001 FDR: 1,049
0:46:19.018614 PROGRESS: 
0:46:19.018676 PROGRESS: Protein Summary:
0:46:19.020875 PROGRESS: Channel   0:	 0.050 FDR: 1,225; 0.010 FDR: 1,225; 0.001 FDR: 1,046
0:46:19.020977 PROGRESS: =========================================================================
0:46:19.039385 INFO: Target number of precursors reached.
0:46:19.323622 INFO: fragments_df: keeping 5000 of 3717466 [sum(precursor_idx_mask)=28529 sum(mass_error_mask)=3717466 stop_rank=5000
0:46:19.750034 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:19.961065 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:20.684389 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:20.684890 INFO: Using score_cutoff 11.353999799823761 (fac=0.99, q=1)
0:46:20.685217 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:20.685300 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:20.685360 INFO: Updating optimization_manager: score_cutoff        : 10.562642474269866 -> 11.353999799823761
0:46:20.685421 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:20.837079 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:21.187080 INFO: === checking if optimization conditions were reached ===
0:46:21.187449 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:46:21.190845 INFO: Updating optimization_manager: rt_error            : 463.2093779938687 -> 379.0177899581301
0:46:21.191010 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 379.0178.
0:46:21.191098 INFO: ==============================================
0:46:21.191189 INFO: Starting optimization step 9.
0:46:21.191267 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:21.191347 INFO: Using rust extraction backend
0:46:21.191424 PROGRESS: Extracting batch of 251735 precursors
0:46:21.622202 INFO: === Search parameters used ===
0:46:21.622526 INFO: rt_error       : 379.0177899581301
0:46:21.622613 INFO: mobility_error : 0.1
0:46:21.622668 INFO: num_candidates : 3
0:46:21.622718 INFO: ms1_error      : 30
0:46:21.622763 INFO: ms2_error      : 10.0
0:46:21.622808 INFO: fwhm_rt        : 3.0
0:46:21.622855 INFO: quant_window   : 3
0:46:21.622898 INFO: ==============================================
0:46:24.068382 INFO: performing precursor FDR with 40 features
0:46:24.068534 INFO: Decoy channel: -1
0:46:24.068562 INFO: competitive: True
0:46:24.265771 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:24.583371 INFO: Estimating optimal hyperparameters - samples: 599,478, batch_size: 2,455, learning_rate: 7.74e-04
0:46:24.584541 INFO: Using random state 794846 for train-test-split
0:46:37.071347 INFO: Test AUC: 0.603
0:46:37.071509 INFO: Train AUC: 0.616
0:46:37.071541 INFO: AUC difference: 2.08%
0:46:37.558652 INFO: Resetting torch num_threads to 80
0:46:37.591218 PROGRESS: === Extracted 749348 precursors and 3619631 fragments ===
0:46:37.591756 INFO: === FDR correction performed with classifier version 12 ===
0:46:37.592506 PROGRESS: ============================= Precursor FDR =============================
0:46:37.592613 PROGRESS: Total precursors accumulated: 1,325
0:46:37.592680 PROGRESS: Target precursors: 1,312 (99.02%)
0:46:37.592737 PROGRESS: Decoy precursors: 13 (0.98%)
0:46:37.592788 PROGRESS: 
0:46:37.592837 PROGRESS: Precursor Summary:
0:46:37.594325 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR: 1,082
0:46:37.594437 PROGRESS: 
0:46:37.594509 PROGRESS: Protein Summary:
0:46:37.596863 PROGRESS: Channel   0:	 0.050 FDR: 1,309; 0.010 FDR: 1,309; 0.001 FDR: 1,079
0:46:37.596970 PROGRESS: =========================================================================
0:46:37.615320 INFO: Target number of precursors reached.
0:46:37.897248 INFO: fragments_df: keeping 5000 of 3619631 [sum(precursor_idx_mask)=29979 sum(mass_error_mask)=3619631 stop_rank=5000
0:46:38.324113 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:38.518539 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:39.181010 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:39.181509 INFO: Using score_cutoff 10.263259423828126 (fac=0.99, q=1)
0:46:39.181854 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:39.181956 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:39.182031 INFO: Updating optimization_manager: score_cutoff        : 11.353999799823761 -> 10.263259423828126
0:46:39.182103 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:39.334236 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:39.672174 INFO: === checking if optimization conditions were reached ===
0:46:39.672530 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
0:46:39.675894 INFO: Updating optimization_manager: rt_error            : 379.0177899581301 -> 389.82317877367177
0:46:39.676028 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 389.8232.
0:46:39.676115 INFO: ==============================================
0:46:39.676203 INFO: Starting optimization step 10.
0:46:39.676281 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:39.676368 INFO: Using rust extraction backend
0:46:39.676451 PROGRESS: Extracting batch of 251735 precursors
0:46:40.108784 INFO: === Search parameters used ===
0:46:40.109128 INFO: rt_error       : 389.82317877367177
0:46:40.109200 INFO: mobility_error : 0.1
0:46:40.109259 INFO: num_candidates : 3
0:46:40.109314 INFO: ms1_error      : 30
0:46:40.109365 INFO: ms2_error      : 10.0
0:46:40.109416 INFO: fwhm_rt        : 3.0
0:46:40.109465 INFO: quant_window   : 3
0:46:40.109514 INFO: ==============================================
0:46:42.583485 INFO: performing precursor FDR with 40 features
0:46:42.583634 INFO: Decoy channel: -1
0:46:42.583664 INFO: competitive: True
0:46:42.782612 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:43.095690 INFO: Estimating optimal hyperparameters - samples: 599,592, batch_size: 2,455, learning_rate: 7.74e-04
0:46:43.096926 INFO: Using random state 794846 for train-test-split
0:46:55.717977 INFO: Test AUC: 0.606
0:46:55.718137 INFO: Train AUC: 0.616
0:46:55.718169 INFO: AUC difference: 1.56%
0:46:56.202412 INFO: Resetting torch num_threads to 80
0:46:56.235072 PROGRESS: === Extracted 749490 precursors and 3633856 fragments ===
0:46:56.235652 INFO: === FDR correction performed with classifier version 12 ===
0:46:56.236403 PROGRESS: ============================= Precursor FDR =============================
0:46:56.236512 PROGRESS: Total precursors accumulated: 1,334
0:46:56.236579 PROGRESS: Target precursors: 1,321 (99.03%)
0:46:56.236635 PROGRESS: Decoy precursors: 13 (0.97%)
0:46:56.236686 PROGRESS: 
0:46:56.236735 PROGRESS: Precursor Summary:
0:46:56.238184 PROGRESS: Channel   0:	 0.050 FDR: 1,321; 0.010 FDR: 1,321; 0.001 FDR: 1,099
0:46:56.238295 PROGRESS: 
0:46:56.238365 PROGRESS: Protein Summary:
0:46:56.240649 PROGRESS: Channel   0:	 0.050 FDR: 1,316; 0.010 FDR: 1,316; 0.001 FDR: 1,096
0:46:56.240756 PROGRESS: =========================================================================
0:46:56.259257 INFO: Target number of precursors reached.
0:46:56.535582 INFO: fragments_df: keeping 5000 of 3633856 [sum(precursor_idx_mask)=30311 sum(mass_error_mask)=3633856 stop_rank=5000
0:46:56.964611 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:57.151596 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:57.877154 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:57.877637 INFO: Using score_cutoff 11.442296499252318 (fac=0.99, q=1)
0:46:57.877971 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:57.878059 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:57.878117 INFO: Updating optimization_manager: score_cutoff        : 10.263259423828126 -> 11.442296499252318
0:46:57.878178 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:58.030962 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:58.369808 INFO: === checking if optimization conditions were reached ===
0:46:58.370183 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
0:46:58.371313 INFO: Updating optimization_manager: rt_error            : 389.82317877367177 -> 453.4539000094303
0:46:58.371468 INFO: Updating optimization_manager: classifier_version  : 12 -> 18
0:46:58.371590 INFO: Updating optimization_manager: score_cutoff        : 11.442296499252318 -> 9.965428639411927
0:46:58.371706 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:58.371856 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:58.372017 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 453.4539 found after 11 searches.
0:46:58.372123 INFO: ==============================================
0:46:58.372235 PROGRESS: Optimization finished for rt_error.
0:46:58.786934 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:58.939915 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:59.280053 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:46:59.280469 PROGRESS: ==============================================
0:46:59.280586 PROGRESS: ms2_error      : 10.0000
0:46:59.280686 PROGRESS: rt_error       : 453.4539
0:46:59.280770 PROGRESS: ==============================================
0:46:59.291233 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:06.963181 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:23.680843 INFO: Using rust extraction backend
0:47:23.681185 PROGRESS: Extracting batch of 12096565 precursors
0:47:41.315061 INFO: === Search parameters used ===
0:47:41.315370 INFO: rt_error       : 453.4539000094303
0:47:41.315438 INFO: mobility_error : 0.1
0:47:41.315495 INFO: num_candidates : 3
0:47:41.315546 INFO: ms1_error      : 30
0:47:41.315595 INFO: ms2_error      : 10.0
0:47:41.315655 INFO: fwhm_rt        : 3.0
0:47:41.315729 INFO: quant_window   : 3
0:47:41.315773 INFO: ==============================================
0:48:06.360610 INFO: Removed 10181871 precursors with score below cutoff 9.965428639411927
0:48:28.488851 INFO: performing precursor FDR with 40 features
0:48:28.489006 INFO: Decoy channel: -1
0:48:28.489035 INFO: competitive: True
0:48:31.677257 INFO: Setting torch num_threads to 2 for FDR classification task
0:48:42.828350 INFO: Estimating optimal hyperparameters - samples: 20,880,152, batch_size: 4,096, learning_rate: 1.00e-03
0:48:42.891747 INFO: Using random state 497906 for train-test-split
0:55:05.779303 INFO: Test AUC: 0.619
0:55:05.779592 INFO: Train AUC: 0.619
0:55:05.779639 INFO: AUC difference: 0.05%
0:55:11.933207 INFO: Resetting torch num_threads to 80
0:55:14.700448 PROGRESS: ============================= Precursor FDR =============================
0:55:14.700846 PROGRESS: Total precursors accumulated: 73,313
0:55:14.700934 PROGRESS: Target precursors: 72,589 (99.01%)
0:55:14.700994 PROGRESS: Decoy precursors: 724 (0.99%)
0:55:14.701047 PROGRESS: 
0:55:14.701106 PROGRESS: Precursor Summary:
0:55:14.725398 PROGRESS: Channel   0:	 0.050 FDR: 72,589; 0.010 FDR: 72,589; 0.001 FDR: 50,908
0:55:14.725702 PROGRESS: 
0:55:14.725784 PROGRESS: Protein Summary:
0:55:14.810611 PROGRESS: Channel   0:	 0.050 FDR: 67,342; 0.010 FDR: 67,342; 0.001 FDR: 47,485
0:55:14.810908 PROGRESS: =========================================================================
0:55:15.047525 INFO: Saving results to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/psm.parquet
0:55:15.221593 INFO: Saving results to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/frag.parquet
0:55:15.417989 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Human_02
0:55:16.394206 PROGRESS: Loading raw file 3/3: LFQ_Astral_DIA_15min_50ng_Human_03 
0:55:16.394399 INFO: Quantification results path: /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant
0:55:16.394524 INFO: Creating folder /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/figures
0:55:16.394773 INFO: Initializing TimingManager
0:55:16.395615 INFO: Initializing RawFileManager
0:55:29.234450 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.
0:55:29.242821 INFO: Determining DIA cycle
0:55:29.260890 INFO: Found cycle with start 0.00 min and length 300.
0:55:29.380213 INFO: RT (min)            : 0.0 - 26.9
0:55:29.380334 INFO: RT duration (sec)   : 1611.2
0:55:29.380364 INFO: RT duration (min)   : 26.9
0:55:29.380386 INFO: Cycle len (scans)   : 300
0:55:29.380406 INFO: Cycle len (sec)     : 1.65
0:55:29.380425 INFO: Number of cycles    : 975
0:55:29.380454 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:55:29.380492 INFO: Creating DIA data object took: 12.984739303588867
0:55:30.031276 INFO: Creating DIA data NG object took: 0.6505920886993408
0:55:31.851166 INFO: Initializing CalibrationManager
0:55:31.851527 INFO: Setting up calibration estimators ..
0:55:31.851604 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:55:31.851693 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'}' ..
0:55:31.851794 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:55:31.851855 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:55:31.851913 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}}' ..
0:55:31.851972 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:55:31.852023 INFO: Done setting up calibration estimators.
0:55:31.852254 INFO: Initializing OptimizationManager
0:55:31.852446 INFO: initial parameter: ms1_error = 30
0:55:31.852505 INFO: initial parameter: ms2_error = 30
0:55:31.852560 INFO: initial parameter: rt_error = 805.6095581054688
0:55:31.852606 INFO: initial parameter: mobility_error = 0.1
0:55:31.852650 INFO: initial parameter: num_candidates = 1
0:55:31.852692 INFO: initial parameter: fwhm_rt = 5
0:55:31.852746 INFO: initial parameter: fwhm_mobility = 0.01
0:55:31.852803 INFO: initial parameter: score_cutoff = 0
0:55:31.852854 INFO: initial parameter: classifier_version = -1
0:55:31.852937 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Human_03
0:55:31.853272 INFO: FDRManager: loading saved state not requested, will be initialized.
0:55:31.853310 INFO: Initializing FDRManager
0:55:31.853351 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
0:55:33.620787 PROGRESS: Initializing spectral library: 6,065,786 target precursors potentially observable (100,729 removed)
0:55:34.629369 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:55:34.629879 INFO: Updating optimization_manager: rt_error            : 805.6095581054688 -> 805.6095581054688
0:55:34.630025 PROGRESS: Starting initial search for precursors.
0:55:34.630150 INFO: Starting optimization step 0.
0:55:34.630233 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:55:34.630304 INFO: Using rust extraction backend
0:55:34.630394 PROGRESS: Extracting batch of 1985 precursors
0:55:34.635664 INFO: === Search parameters used ===
0:55:34.635832 INFO: rt_error       : 805.6095581054688
0:55:34.635897 INFO: mobility_error : 0.1
0:55:34.635966 INFO: num_candidates : 1
0:55:34.636026 INFO: ms1_error      : 30
0:55:34.636079 INFO: ms2_error      : 30
0:55:34.636130 INFO: fwhm_rt        : 5
0:55:34.636184 INFO: quant_window   : 3
0:55:34.636237 INFO: ==============================================
0:55:34.671288 INFO: performing precursor FDR with 40 features
0:55:34.671417 INFO: Decoy channel: -1
0:55:34.671449 INFO: competitive: True
0:55:34.673154 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:34.675786 INFO: Estimating optimal hyperparameters - samples: 1,563, batch_size: 128, learning_rate: 1.77e-04
0:55:34.676769 INFO: Using random state 157444 for train-test-split
0:55:34.834729 INFO: Test AUC: 0.532
0:55:34.834842 INFO: Train AUC: 0.574
0:55:34.834883 INFO: AUC difference: 7.25%
0:55:34.834919 WARNING: AUC difference > 5%. This may indicate overfitting.
0:55:35.093655 INFO: Resetting torch num_threads to 80
0:55:35.095520 PROGRESS: === Extracted 1954 precursors and 8844 fragments ===
0:55:35.095944 INFO: === FDR correction performed with classifier version -1 ===
0:55:35.096481 PROGRESS: ============================= Precursor FDR =============================
0:55:35.096595 PROGRESS: Total precursors accumulated: 4
0:55:35.096675 PROGRESS: Target precursors: 4 (100.00%)
0:55:35.096755 PROGRESS: Decoy precursors: 0 (0.00%)
0:55:35.096817 PROGRESS: 
0:55:35.096885 PROGRESS: Precursor Summary:
0:55:35.098056 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:55:35.098174 PROGRESS: 
0:55:35.098251 PROGRESS: Protein Summary:
0:55:35.099504 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:55:35.099620 PROGRESS: =========================================================================
0:55:35.099858 INFO: Target number of precursors not reached yet.
0:55:35.186384 INFO: Starting optimization step 1.
0:55:35.186694 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:55:35.186809 INFO: Using rust extraction backend
0:55:35.186895 PROGRESS: Extracting batch of 3969 precursors
0:55:35.195619 INFO: === Search parameters used ===
0:55:35.195765 INFO: rt_error       : 805.6095581054688
0:55:35.195834 INFO: mobility_error : 0.1
0:55:35.195898 INFO: num_candidates : 1
0:55:35.195958 INFO: ms1_error      : 30
0:55:35.196017 INFO: ms2_error      : 30
0:55:35.196074 INFO: fwhm_rt        : 5
0:55:35.196130 INFO: quant_window   : 3
0:55:35.196184 INFO: ==============================================
0:55:35.238858 INFO: performing precursor FDR with 40 features
0:55:35.238956 INFO: Decoy channel: -1
0:55:35.238988 INFO: competitive: True
0:55:35.243333 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:35.245888 INFO: Estimating optimal hyperparameters - samples: 4,681, batch_size: 128, learning_rate: 1.77e-04
0:55:35.245986 INFO: Using random state 434314 for train-test-split
0:55:35.697753 INFO: Test AUC: 0.545
0:55:35.697870 INFO: Train AUC: 0.565
0:55:35.697920 INFO: AUC difference: 3.62%
0:55:36.744903 INFO: Resetting torch num_threads to 80
0:55:36.748049 PROGRESS: === Extracted 5852 precursors and 26214 fragments ===
0:55:36.748501 INFO: === FDR correction performed with classifier version -1 ===
0:55:36.749014 PROGRESS: ============================= Precursor FDR =============================
0:55:36.749107 PROGRESS: Total precursors accumulated: 9
0:55:36.749190 PROGRESS: Target precursors: 9 (100.00%)
0:55:36.749266 PROGRESS: Decoy precursors: 0 (0.00%)
0:55:36.749339 PROGRESS: 
0:55:36.749408 PROGRESS: Precursor Summary:
0:55:36.750559 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
0:55:36.750670 PROGRESS: 
0:55:36.750754 PROGRESS: Protein Summary:
0:55:36.751978 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
0:55:36.752085 PROGRESS: =========================================================================
0:55:36.752365 INFO: Target number of precursors not reached yet.
0:55:36.845253 INFO: Starting optimization step 2.
0:55:36.845566 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:55:36.845672 INFO: Using rust extraction backend
0:55:36.845761 PROGRESS: Extracting batch of 7917 precursors
0:55:36.860883 INFO: === Search parameters used ===
0:55:36.861048 INFO: rt_error       : 805.6095581054688
0:55:36.861125 INFO: mobility_error : 0.1
0:55:36.861180 INFO: num_candidates : 1
0:55:36.861227 INFO: ms1_error      : 30
0:55:36.861283 INFO: ms2_error      : 30
0:55:36.861349 INFO: fwhm_rt        : 5
0:55:36.861410 INFO: quant_window   : 3
0:55:36.861482 INFO: ==============================================
0:55:36.945457 INFO: performing precursor FDR with 40 features
0:55:36.945580 INFO: Decoy channel: -1
0:55:36.945611 INFO: competitive: True
0:55:36.951858 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:36.956063 INFO: Estimating optimal hyperparameters - samples: 10,924, batch_size: 128, learning_rate: 1.77e-04
0:55:36.956190 INFO: Using random state 910549 for train-test-split
0:55:38.050618 INFO: Test AUC: 0.538
0:55:38.050749 INFO: Train AUC: 0.572
0:55:38.050785 INFO: AUC difference: 6.06%
0:55:38.050808 WARNING: AUC difference > 5%. This may indicate overfitting.
0:55:38.322561 INFO: Resetting torch num_threads to 80
0:55:38.327850 PROGRESS: === Extracted 13655 precursors and 60875 fragments ===
0:55:38.328361 INFO: === FDR correction performed with classifier version -1 ===
0:55:38.328954 PROGRESS: ============================= Precursor FDR =============================
0:55:38.329059 PROGRESS: Total precursors accumulated: 27
0:55:38.329140 PROGRESS: Target precursors: 27 (100.00%)
0:55:38.329206 PROGRESS: Decoy precursors: 0 (0.00%)
0:55:38.329270 PROGRESS: 
0:55:38.329341 PROGRESS: Precursor Summary:
0:55:38.330486 PROGRESS: Channel   0:	 0.050 FDR:    27; 0.010 FDR:    27; 0.001 FDR:    27
0:55:38.330594 PROGRESS: 
0:55:38.330668 PROGRESS: Protein Summary:
0:55:38.331910 PROGRESS: Channel   0:	 0.050 FDR:    27; 0.010 FDR:    27; 0.001 FDR:    27
0:55:38.332012 PROGRESS: =========================================================================
0:55:38.332380 INFO: Target number of precursors not reached yet.
0:55:38.437677 INFO: Starting optimization step 3.
0:55:38.437973 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:55:38.438076 INFO: Using rust extraction backend
0:55:38.438163 PROGRESS: Extracting batch of 15855 precursors
0:55:38.467017 INFO: === Search parameters used ===
0:55:38.467266 INFO: rt_error       : 805.6095581054688
0:55:38.467336 INFO: mobility_error : 0.1
0:55:38.467389 INFO: num_candidates : 1
0:55:38.467435 INFO: ms1_error      : 30
0:55:38.467483 INFO: ms2_error      : 30
0:55:38.467552 INFO: fwhm_rt        : 5
0:55:38.467612 INFO: quant_window   : 3
0:55:38.467673 INFO: ==============================================
0:55:38.608694 INFO: performing precursor FDR with 40 features
0:55:38.608825 INFO: Decoy channel: -1
0:55:38.608851 INFO: competitive: True
0:55:38.620161 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:38.627832 INFO: Estimating optimal hyperparameters - samples: 23,378, batch_size: 128, learning_rate: 1.77e-04
0:55:38.628043 INFO: Using random state 17575 for train-test-split
0:55:40.959698 INFO: Test AUC: 0.556
0:55:40.959860 INFO: Train AUC: 0.590
0:55:40.959891 INFO: AUC difference: 5.90%
0:55:40.959913 WARNING: AUC difference > 5%. This may indicate overfitting.
0:55:41.231540 INFO: Resetting torch num_threads to 80
0:55:41.238601 PROGRESS: === Extracted 29223 precursors and 130585 fragments ===
0:55:41.239155 INFO: === FDR correction performed with classifier version -1 ===
0:55:41.239749 PROGRESS: ============================= Precursor FDR =============================
0:55:41.239861 PROGRESS: Total precursors accumulated: 60
0:55:41.239951 PROGRESS: Target precursors: 60 (100.00%)
0:55:41.240036 PROGRESS: Decoy precursors: 0 (0.00%)
0:55:41.240112 PROGRESS: 
0:55:41.240185 PROGRESS: Precursor Summary:
0:55:41.241340 PROGRESS: Channel   0:	 0.050 FDR:    60; 0.010 FDR:    60; 0.001 FDR:    60
0:55:41.241445 PROGRESS: 
0:55:41.241512 PROGRESS: Protein Summary:
0:55:41.242818 PROGRESS: Channel   0:	 0.050 FDR:    60; 0.010 FDR:    60; 0.001 FDR:    60
0:55:41.242924 PROGRESS: =========================================================================
0:55:41.243491 INFO: Target number of precursors not reached yet.
0:55:41.384398 INFO: Starting optimization step 4.
0:55:41.384711 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:55:41.384847 INFO: Using rust extraction backend
0:55:41.384948 PROGRESS: Extracting batch of 31732 precursors
0:55:41.444589 INFO: === Search parameters used ===
0:55:41.444847 INFO: rt_error       : 805.6095581054688
0:55:41.444922 INFO: mobility_error : 0.1
0:55:41.445000 INFO: num_candidates : 1
0:55:41.445064 INFO: ms1_error      : 30
0:55:41.445127 INFO: ms2_error      : 30
0:55:41.445189 INFO: fwhm_rt        : 5
0:55:41.445255 INFO: quant_window   : 3
0:55:41.445319 INFO: ==============================================
0:55:41.686819 INFO: performing precursor FDR with 40 features
0:55:41.686961 INFO: Decoy channel: -1
0:55:41.686991 INFO: competitive: True
0:55:41.711464 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:41.726972 INFO: Estimating optimal hyperparameters - samples: 48,361, batch_size: 198, learning_rate: 2.20e-04
0:55:41.727218 INFO: Using random state 573772 for train-test-split
0:55:44.398300 INFO: Test AUC: 0.570
0:55:44.398435 INFO: Train AUC: 0.599
0:55:44.398465 INFO: AUC difference: 4.88%
0:55:44.679438 INFO: Resetting torch num_threads to 80
0:55:44.692335 PROGRESS: === Extracted 60452 precursors and 269785 fragments ===
0:55:44.692993 INFO: === FDR correction performed with classifier version -1 ===
0:55:44.693558 PROGRESS: ============================= Precursor FDR =============================
0:55:44.693655 PROGRESS: Total precursors accumulated: 152
0:55:44.693722 PROGRESS: Target precursors: 151 (99.34%)
0:55:44.693793 PROGRESS: Decoy precursors: 1 (0.66%)
0:55:44.693870 PROGRESS: 
0:55:44.693950 PROGRESS: Precursor Summary:
0:55:44.695044 PROGRESS: Channel   0:	 0.050 FDR:   151; 0.010 FDR:   151; 0.001 FDR:   144
0:55:44.695156 PROGRESS: 
0:55:44.695230 PROGRESS: Protein Summary:
0:55:44.696511 PROGRESS: Channel   0:	 0.050 FDR:   151; 0.010 FDR:   151; 0.001 FDR:   144
0:55:44.696630 PROGRESS: =========================================================================
0:55:44.697560 INFO: Target number of precursors not reached yet.
0:55:44.871050 INFO: Starting optimization step 5.
0:55:44.871413 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:55:44.871538 INFO: Using rust extraction backend
0:55:44.871636 PROGRESS: Extracting batch of 63446 precursors
0:55:44.982918 INFO: === Search parameters used ===
0:55:44.983315 INFO: rt_error       : 805.6095581054688
0:55:44.983389 INFO: mobility_error : 0.1
0:55:44.983456 INFO: num_candidates : 1
0:55:44.983518 INFO: ms1_error      : 30
0:55:44.983589 INFO: ms2_error      : 30
0:55:44.983651 INFO: fwhm_rt        : 5
0:55:44.983712 INFO: quant_window   : 3
0:55:44.983774 INFO: ==============================================
0:55:45.410270 INFO: performing precursor FDR with 40 features
0:55:45.410422 INFO: Decoy channel: -1
0:55:45.410450 INFO: competitive: True
0:55:45.460138 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:45.495374 INFO: Estimating optimal hyperparameters - samples: 98,247, batch_size: 402, learning_rate: 3.13e-04
0:55:45.495718 INFO: Using random state 156464 for train-test-split
0:55:49.855526 INFO: Test AUC: 0.576
0:55:49.855669 INFO: Train AUC: 0.606
0:55:49.855715 INFO: AUC difference: 4.86%
0:55:50.154231 INFO: Resetting torch num_threads to 80
0:55:50.183568 PROGRESS: === Extracted 122809 precursors and 548555 fragments ===
0:55:50.184224 INFO: === FDR correction performed with classifier version -1 ===
0:55:50.184886 PROGRESS: ============================= Precursor FDR =============================
0:55:50.185013 PROGRESS: Total precursors accumulated: 242
0:55:50.185093 PROGRESS: Target precursors: 240 (99.17%)
0:55:50.185164 PROGRESS: Decoy precursors: 2 (0.83%)
0:55:50.185231 PROGRESS: 
0:55:50.185307 PROGRESS: Precursor Summary:
0:55:50.186407 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:     0
0:55:50.186523 PROGRESS: 
0:55:50.186596 PROGRESS: Protein Summary:
0:55:50.187897 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:     0
0:55:50.188004 PROGRESS: =========================================================================
0:55:50.189975 INFO: Target number of precursors not reached yet.
0:55:50.446909 INFO: Starting optimization step 6.
0:55:50.447245 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:55:50.447357 INFO: Using rust extraction backend
0:55:50.447450 PROGRESS: Extracting batch of 126831 precursors
0:55:50.669060 INFO: === Search parameters used ===
0:55:50.669409 INFO: rt_error       : 805.6095581054688
0:55:50.669482 INFO: mobility_error : 0.1
0:55:50.669544 INFO: num_candidates : 1
0:55:50.669598 INFO: ms1_error      : 30
0:55:50.669646 INFO: ms2_error      : 30
0:55:50.669692 INFO: fwhm_rt        : 5
0:55:50.669738 INFO: quant_window   : 3
0:55:50.669783 INFO: ==============================================
0:55:51.493932 INFO: performing precursor FDR with 40 features
0:55:51.494076 INFO: Decoy channel: -1
0:55:51.494104 INFO: competitive: True
0:55:51.600343 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:51.686441 INFO: Estimating optimal hyperparameters - samples: 198,015, batch_size: 811, learning_rate: 4.45e-04
0:55:51.687134 INFO: Using random state 617217 for train-test-split
0:55:57.702707 INFO: Test AUC: 0.581
0:55:57.702864 INFO: Train AUC: 0.605
0:55:57.702895 INFO: AUC difference: 4.02%
0:55:58.038679 INFO: Resetting torch num_threads to 80
0:55:58.087469 PROGRESS: === Extracted 247519 precursors and 1106665 fragments ===
0:55:58.088232 INFO: === FDR correction performed with classifier version -1 ===
0:55:58.089042 PROGRESS: ============================= Precursor FDR =============================
0:55:58.089158 PROGRESS: Total precursors accumulated: 692
0:55:58.089242 PROGRESS: Target precursors: 686 (99.13%)
0:55:58.089319 PROGRESS: Decoy precursors: 6 (0.87%)
0:55:58.089393 PROGRESS: 
0:55:58.089465 PROGRESS: Precursor Summary:
0:55:58.090812 PROGRESS: Channel   0:	 0.050 FDR:   686; 0.010 FDR:   686; 0.001 FDR:   465
0:55:58.090931 PROGRESS: 
0:55:58.091014 PROGRESS: Protein Summary:
0:55:58.092807 PROGRESS: Channel   0:	 0.050 FDR:   685; 0.010 FDR:   685; 0.001 FDR:   464
0:55:58.092919 PROGRESS: =========================================================================
0:55:58.097456 INFO: Target number of precursors not reached yet.
0:55:58.522980 INFO: Starting optimization step 7.
0:55:58.523335 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:55:58.523438 INFO: Using rust extraction backend
0:55:58.523525 PROGRESS: Extracting batch of 253660 precursors
0:55:58.958240 INFO: === Search parameters used ===
0:55:58.958581 INFO: rt_error       : 805.6095581054688
0:55:58.958650 INFO: mobility_error : 0.1
0:55:58.958723 INFO: num_candidates : 1
0:55:58.958788 INFO: ms1_error      : 30
0:55:58.958883 INFO: ms2_error      : 30
0:55:58.958951 INFO: fwhm_rt        : 5
0:55:58.959010 INFO: quant_window   : 3
0:55:58.959061 INFO: ==============================================
0:56:00.515757 INFO: performing precursor FDR with 40 features
0:56:00.515911 INFO: Decoy channel: -1
0:56:00.515939 INFO: competitive: True
0:56:00.725649 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:00.929743 INFO: Estimating optimal hyperparameters - samples: 397,638, batch_size: 1,628, learning_rate: 6.30e-04
0:56:00.930491 INFO: Using random state 597400 for train-test-split
0:56:10.356736 INFO: Test AUC: 0.588
0:56:10.356893 INFO: Train AUC: 0.601
0:56:10.356925 INFO: AUC difference: 2.23%
0:56:10.758745 INFO: Resetting torch num_threads to 80
0:56:10.854905 PROGRESS: === Extracted 497048 precursors and 2223560 fragments ===
0:56:10.855714 INFO: === FDR correction performed with classifier version -1 ===
0:56:10.856684 PROGRESS: ============================= Precursor FDR =============================
0:56:10.856796 PROGRESS: Total precursors accumulated: 1,659
0:56:10.856881 PROGRESS: Target precursors: 1,643 (99.04%)
0:56:10.856954 PROGRESS: Decoy precursors: 16 (0.96%)
0:56:10.857026 PROGRESS: 
0:56:10.857087 PROGRESS: Precursor Summary:
0:56:10.858658 PROGRESS: Channel   0:	 0.050 FDR: 1,643; 0.010 FDR: 1,643; 0.001 FDR: 1,189
0:56:10.858776 PROGRESS: 
0:56:10.858850 PROGRESS: Protein Summary:
0:56:10.861379 PROGRESS: Channel   0:	 0.050 FDR: 1,639; 0.010 FDR: 1,639; 0.001 FDR: 1,185
0:56:10.861494 PROGRESS: =========================================================================
0:56:10.870373 INFO: Target number of precursors reached.
0:56:11.048413 INFO: fragments_df: keeping 5000 of 2223560 [sum(precursor_idx_mask)=17539 sum(mass_error_mask)=2223560 stop_rank=5000
0:56:11.797738 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:12.057838 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:12.778573 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:56:12.779069 INFO: Using score_cutoff 12.297034063339233 (fac=0.99, q=1)
0:56:12.779455 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:56:12.779551 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:56:12.779627 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.297034063339233
0:56:12.779711 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:13.086890 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:13.786259 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:56:13.786546 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:56:13.786656 INFO: Starting optimization step 8.
0:56:13.786727 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:56:13.786813 INFO: Using rust extraction backend
0:56:13.786887 PROGRESS: Extracting batch of 505395 precursors
0:56:14.652008 INFO: === Search parameters used ===
0:56:14.652409 INFO: rt_error       : 805.6095581054688
0:56:14.652474 INFO: mobility_error : 0.1
0:56:14.652545 INFO: num_candidates : 3
0:56:14.652611 INFO: ms1_error      : 30
0:56:14.652669 INFO: ms2_error      : 30
0:56:14.652726 INFO: fwhm_rt        : 3.0
0:56:14.652802 INFO: quant_window   : 3
0:56:14.652859 INFO: ==============================================
0:56:20.397832 INFO: performing precursor FDR with 40 features
0:56:20.398018 INFO: Decoy channel: -1
0:56:20.398047 INFO: competitive: True
0:56:20.821915 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:21.525865 INFO: Estimating optimal hyperparameters - samples: 1,192,151, batch_size: 4,096, learning_rate: 1.00e-03
0:56:21.528483 INFO: Using random state 152659 for train-test-split
0:56:42.936375 INFO: Test AUC: 0.594
0:56:42.936587 INFO: Train AUC: 0.601
0:56:42.936621 INFO: AUC difference: 1.23%
0:56:43.662557 INFO: Resetting torch num_threads to 80
0:56:43.729172 PROGRESS: === Extracted 1490189 precursors and 6492403 fragments ===
0:56:43.729838 INFO: === FDR correction performed with classifier version 7 ===
0:56:43.730959 PROGRESS: ============================= Precursor FDR =============================
0:56:43.731080 PROGRESS: Total precursors accumulated: 2,126
0:56:43.731147 PROGRESS: Target precursors: 2,105 (99.01%)
0:56:43.731223 PROGRESS: Decoy precursors: 21 (0.99%)
0:56:43.731296 PROGRESS: 
0:56:43.731370 PROGRESS: Precursor Summary:
0:56:43.733207 PROGRESS: Channel   0:	 0.050 FDR: 2,105; 0.010 FDR: 2,105; 0.001 FDR: 1,451
0:56:43.733323 PROGRESS: 
0:56:43.733394 PROGRESS: Protein Summary:
0:56:43.736432 PROGRESS: Channel   0:	 0.050 FDR: 2,099; 0.010 FDR: 2,099; 0.001 FDR: 1,447
0:56:43.736539 PROGRESS: =========================================================================
0:56:43.775722 INFO: Target number of precursors reached.
0:56:44.272049 INFO: fragments_df: keeping 5000 of 6492403 [sum(precursor_idx_mask)=45095 sum(mass_error_mask)=6492403 stop_rank=5000
0:56:44.845474 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:45.160342 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:45.887685 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:45.888193 INFO: Using score_cutoff 12.183373381805419 (fac=0.99, q=1)
0:56:45.888553 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:45.888635 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:45.888693 INFO: Updating optimization_manager: score_cutoff        : 12.297034063339233 -> 12.183373381805419
0:56:45.888753 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:46.044342 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:46.404266 INFO: === checking if optimization conditions were reached ===
0:56:46.407288 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:56:46.407543 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:56:46.407657 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:56:46.407763 INFO: ==============================================
0:56:46.407874 INFO: Starting optimization step 9.
0:56:46.407974 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:56:46.408082 INFO: Using rust extraction backend
0:56:46.408187 PROGRESS: Extracting batch of 251735 precursors
0:56:46.843677 INFO: === Search parameters used ===
0:56:46.844033 INFO: rt_error       : 805.6095581054688
0:56:46.844108 INFO: mobility_error : 0.1
0:56:46.844182 INFO: num_candidates : 3
0:56:46.844237 INFO: ms1_error      : 30
0:56:46.844298 INFO: ms2_error      : 10.0
0:56:46.844375 INFO: fwhm_rt        : 3.0
0:56:46.844442 INFO: quant_window   : 3
0:56:46.844503 INFO: ==============================================
0:56:49.670462 INFO: performing precursor FDR with 40 features
0:56:49.670614 INFO: Decoy channel: -1
0:56:49.670643 INFO: competitive: True
0:56:49.889158 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:50.208346 INFO: Estimating optimal hyperparameters - samples: 601,193, batch_size: 2,462, learning_rate: 7.75e-04
0:56:50.209440 INFO: Using random state 636181 for train-test-split
0:57:03.222399 INFO: Test AUC: 0.600
0:57:03.222568 INFO: Train AUC: 0.611
0:57:03.222607 INFO: AUC difference: 1.82%
0:57:03.720607 INFO: Resetting torch num_threads to 80
0:57:03.753542 PROGRESS: === Extracted 751492 precursors and 3770955 fragments ===
0:57:03.754102 INFO: === FDR correction performed with classifier version 8 ===
0:57:03.754876 PROGRESS: ============================= Precursor FDR =============================
0:57:03.755003 PROGRESS: Total precursors accumulated: 1,324
0:57:03.755090 PROGRESS: Target precursors: 1,311 (99.02%)
0:57:03.755166 PROGRESS: Decoy precursors: 13 (0.98%)
0:57:03.755234 PROGRESS: 
0:57:03.755307 PROGRESS: Precursor Summary:
0:57:03.756688 PROGRESS: Channel   0:	 0.050 FDR: 1,311; 0.010 FDR: 1,311; 0.001 FDR:     1
0:57:03.756803 PROGRESS: 
0:57:03.756881 PROGRESS: Protein Summary:
0:57:03.758927 PROGRESS: Channel   0:	 0.050 FDR: 1,309; 0.010 FDR: 1,309; 0.001 FDR:     1
0:57:03.759052 PROGRESS: =========================================================================
0:57:03.778029 INFO: Target number of precursors reached.
0:57:04.074885 INFO: fragments_df: keeping 5000 of 3770955 [sum(precursor_idx_mask)=30164 sum(mass_error_mask)=3770955 stop_rank=5000
0:57:04.537930 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:04.773685 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:05.500249 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:05.500770 INFO: Using score_cutoff 11.63487393951416 (fac=0.99, q=1)
0:57:05.501122 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:05.501217 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:05.501286 INFO: Updating optimization_manager: score_cutoff        : 12.183373381805419 -> 11.63487393951416
0:57:05.501369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:05.652323 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:05.986008 INFO: === checking if optimization conditions were reached ===
0:57:05.988740 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:57:05.988891 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:57:05.988997 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:57:05.989093 INFO: ==============================================
0:57:05.989197 INFO: Starting optimization step 10.
0:57:05.989290 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:57:05.989385 INFO: Using rust extraction backend
0:57:05.989480 PROGRESS: Extracting batch of 251735 precursors
0:57:06.420616 INFO: === Search parameters used ===
0:57:06.420911 INFO: rt_error       : 805.6095581054688
0:57:06.420972 INFO: mobility_error : 0.1
0:57:06.421021 INFO: num_candidates : 3
0:57:06.421080 INFO: ms1_error      : 30
0:57:06.421127 INFO: ms2_error      : 10.0
0:57:06.421178 INFO: fwhm_rt        : 3.0
0:57:06.421237 INFO: quant_window   : 3
0:57:06.421294 INFO: ==============================================
0:57:09.315426 INFO: performing precursor FDR with 40 features
0:57:09.315593 INFO: Decoy channel: -1
0:57:09.315628 INFO: competitive: True
0:57:09.523731 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:09.850235 INFO: Estimating optimal hyperparameters - samples: 601,212, batch_size: 2,462, learning_rate: 7.75e-04
0:57:09.851342 INFO: Using random state 81240 for train-test-split
0:57:22.076541 INFO: Test AUC: 0.602
0:57:22.076698 INFO: Train AUC: 0.615
0:57:22.076730 INFO: AUC difference: 2.08%
0:57:22.565917 INFO: Resetting torch num_threads to 80
0:57:22.598658 PROGRESS: === Extracted 751516 precursors and 3770694 fragments ===
0:57:22.599178 INFO: === FDR correction performed with classifier version 9 ===
0:57:22.599917 PROGRESS: ============================= Precursor FDR =============================
0:57:22.600023 PROGRESS: Total precursors accumulated: 1,325
0:57:22.600090 PROGRESS: Target precursors: 1,312 (99.02%)
0:57:22.600147 PROGRESS: Decoy precursors: 13 (0.98%)
0:57:22.600200 PROGRESS: 
0:57:22.600251 PROGRESS: Precursor Summary:
0:57:22.601691 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR:   643
0:57:22.601794 PROGRESS: 
0:57:22.601866 PROGRESS: Protein Summary:
0:57:22.604091 PROGRESS: Channel   0:	 0.050 FDR: 1,310; 0.010 FDR: 1,310; 0.001 FDR:   642
0:57:22.604195 PROGRESS: =========================================================================
0:57:22.623459 INFO: Target number of precursors reached.
0:57:22.917297 INFO: fragments_df: keeping 5000 of 3770694 [sum(precursor_idx_mask)=30244 sum(mass_error_mask)=3770694 stop_rank=5000
0:57:23.352111 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:23.581780 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:24.304612 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:24.305098 INFO: Using score_cutoff 12.250545663928985 (fac=0.99, q=1)
0:57:24.305435 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:24.305517 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:24.305574 INFO: Updating optimization_manager: score_cutoff        : 11.63487393951416 -> 12.250545663928985
0:57:24.305637 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:24.457575 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:24.817127 INFO: === checking if optimization conditions were reached ===
0:57:24.819823 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:57:24.819947 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:57:24.820032 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:57:24.820117 INFO: ==============================================
0:57:24.820199 INFO: Starting optimization step 11.
0:57:24.820275 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:57:24.820353 INFO: Using rust extraction backend
0:57:24.820428 PROGRESS: Extracting batch of 251735 precursors
0:57:25.251314 INFO: === Search parameters used ===
0:57:25.251653 INFO: rt_error       : 805.6095581054688
0:57:25.251728 INFO: mobility_error : 0.1
0:57:25.251806 INFO: num_candidates : 3
0:57:25.251868 INFO: ms1_error      : 30
0:57:25.251925 INFO: ms2_error      : 10.0
0:57:25.251979 INFO: fwhm_rt        : 3.0
0:57:25.252033 INFO: quant_window   : 3
0:57:25.252097 INFO: ==============================================
0:57:28.046106 INFO: performing precursor FDR with 40 features
0:57:28.046257 INFO: Decoy channel: -1
0:57:28.046287 INFO: competitive: True
0:57:28.253032 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:28.580269 INFO: Estimating optimal hyperparameters - samples: 601,197, batch_size: 2,462, learning_rate: 7.75e-04
0:57:28.581371 INFO: Using random state 669710 for train-test-split
0:57:40.706782 INFO: Test AUC: 0.606
0:57:40.706939 INFO: Train AUC: 0.619
0:57:40.706973 INFO: AUC difference: 2.00%
0:57:41.189928 INFO: Resetting torch num_threads to 80
0:57:41.222966 PROGRESS: === Extracted 751497 precursors and 3770813 fragments ===
0:57:41.223479 INFO: === FDR correction performed with classifier version 10 ===
0:57:41.224288 PROGRESS: ============================= Precursor FDR =============================
0:57:41.224404 PROGRESS: Total precursors accumulated: 1,393
0:57:41.224482 PROGRESS: Target precursors: 1,380 (99.07%)
0:57:41.224545 PROGRESS: Decoy precursors: 13 (0.93%)
0:57:41.224607 PROGRESS: 
0:57:41.224672 PROGRESS: Precursor Summary:
0:57:41.226078 PROGRESS: Channel   0:	 0.050 FDR: 1,380; 0.010 FDR: 1,380; 0.001 FDR:   239
0:57:41.226192 PROGRESS: 
0:57:41.226260 PROGRESS: Protein Summary:
0:57:41.228344 PROGRESS: Channel   0:	 0.050 FDR: 1,378; 0.010 FDR: 1,378; 0.001 FDR:   238
0:57:41.228446 PROGRESS: =========================================================================
0:57:41.247644 INFO: Target number of precursors reached.
0:57:41.535167 INFO: fragments_df: keeping 5000 of 3770813 [sum(precursor_idx_mask)=31573 sum(mass_error_mask)=3770813 stop_rank=5000
0:57:41.970117 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:42.203913 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:42.929208 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:42.929708 INFO: Using score_cutoff 11.691839122009277 (fac=0.99, q=1)
0:57:42.930048 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:42.930136 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:42.930203 INFO: Updating optimization_manager: score_cutoff        : 12.250545663928985 -> 11.691839122009277
0:57:42.930282 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:43.082600 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:43.430351 INFO: === checking if optimization conditions were reached ===
0:57:43.433317 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:57:43.433557 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:57:43.433712 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:57:43.433828 INFO: ==============================================
0:57:43.433953 INFO: Starting optimization step 12.
0:57:43.434066 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:57:43.434179 INFO: Using rust extraction backend
0:57:43.434286 PROGRESS: Extracting batch of 251735 precursors
0:57:43.871722 INFO: === Search parameters used ===
0:57:43.872099 INFO: rt_error       : 805.6095581054688
0:57:43.872175 INFO: mobility_error : 0.1
0:57:43.872239 INFO: num_candidates : 3
0:57:43.872298 INFO: ms1_error      : 30
0:57:43.872354 INFO: ms2_error      : 10.0
0:57:43.872407 INFO: fwhm_rt        : 3.0
0:57:43.872461 INFO: quant_window   : 3
0:57:43.872514 INFO: ==============================================
0:57:46.730803 INFO: performing precursor FDR with 40 features
0:57:46.730961 INFO: Decoy channel: -1
0:57:46.731000 INFO: competitive: True
0:57:46.941069 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:47.268029 INFO: Estimating optimal hyperparameters - samples: 601,191, batch_size: 2,462, learning_rate: 7.75e-04
0:57:47.269248 INFO: Using random state 305996 for train-test-split
0:57:59.526615 INFO: Test AUC: 0.608
0:57:59.526774 INFO: Train AUC: 0.619
0:57:59.526808 INFO: AUC difference: 1.74%
0:58:00.010130 INFO: Resetting torch num_threads to 80
0:58:00.043478 PROGRESS: === Extracted 751489 precursors and 3770102 fragments ===
0:58:00.044024 INFO: === FDR correction performed with classifier version 11 ===
0:58:00.044788 PROGRESS: ============================= Precursor FDR =============================
0:58:00.044903 PROGRESS: Total precursors accumulated: 1,411
0:58:00.044968 PROGRESS: Target precursors: 1,398 (99.08%)
0:58:00.045023 PROGRESS: Decoy precursors: 13 (0.92%)
0:58:00.045074 PROGRESS: 
0:58:00.045125 PROGRESS: Precursor Summary:
0:58:00.046515 PROGRESS: Channel   0:	 0.050 FDR: 1,398; 0.010 FDR: 1,398; 0.001 FDR:     2
0:58:00.046627 PROGRESS: 
0:58:00.046700 PROGRESS: Protein Summary:
0:58:00.048752 PROGRESS: Channel   0:	 0.050 FDR: 1,396; 0.010 FDR: 1,396; 0.001 FDR:     2
0:58:00.048858 PROGRESS: =========================================================================
0:58:00.067618 INFO: Target number of precursors reached.
0:58:00.360594 INFO: fragments_df: keeping 5000 of 3770102 [sum(precursor_idx_mask)=31991 sum(mass_error_mask)=3770102 stop_rank=5000
0:58:00.792076 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:01.029773 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:01.751820 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:01.752296 INFO: Using score_cutoff 11.51461099834442 (fac=0.99, q=1)
0:58:01.752627 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:58:01.752712 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:58:01.752776 INFO: Updating optimization_manager: score_cutoff        : 11.691839122009277 -> 11.51461099834442
0:58:01.752840 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:01.903669 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:02.249432 INFO: === checking if optimization conditions were reached ===
0:58:02.252275 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:58:02.252480 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
0:58:02.252672 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:58:02.252779 INFO: ==============================================
0:58:02.252907 PROGRESS: Optimization finished for ms2_error.
0:58:02.666689 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:02.817456 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:03.163806 INFO: Starting optimization step 0.
0:58:03.164245 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:58:03.164372 INFO: Using rust extraction backend
0:58:03.164483 PROGRESS: Extracting batch of 251735 precursors
0:58:03.597387 INFO: === Search parameters used ===
0:58:03.597705 INFO: rt_error       : 805.6095581054688
0:58:03.597768 INFO: mobility_error : 0.1
0:58:03.597817 INFO: num_candidates : 3
0:58:03.597863 INFO: ms1_error      : 30
0:58:03.597919 INFO: ms2_error      : 10.0
0:58:03.597967 INFO: fwhm_rt        : 3.0
0:58:03.598011 INFO: quant_window   : 3
0:58:03.598054 INFO: ==============================================
0:58:06.469782 INFO: performing precursor FDR with 40 features
0:58:06.469938 INFO: Decoy channel: -1
0:58:06.469968 INFO: competitive: True
0:58:06.680291 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:07.010568 INFO: Estimating optimal hyperparameters - samples: 601,193, batch_size: 2,462, learning_rate: 7.75e-04
0:58:07.011771 INFO: Using random state 238860 for train-test-split
0:58:19.306200 INFO: Test AUC: 0.610
0:58:19.306369 INFO: Train AUC: 0.622
0:58:19.306402 INFO: AUC difference: 1.84%
0:58:19.783181 INFO: Resetting torch num_threads to 80
0:58:19.816761 PROGRESS: === Extracted 751492 precursors and 3770464 fragments ===
0:58:19.817337 INFO: === FDR correction performed with classifier version 12 ===
0:58:19.818154 PROGRESS: ============================= Precursor FDR =============================
0:58:19.818280 PROGRESS: Total precursors accumulated: 1,428
0:58:19.818363 PROGRESS: Target precursors: 1,414 (99.02%)
0:58:19.818439 PROGRESS: Decoy precursors: 14 (0.98%)
0:58:19.818504 PROGRESS: 
0:58:19.818561 PROGRESS: Precursor Summary:
0:58:19.819928 PROGRESS: Channel   0:	 0.050 FDR: 1,414; 0.010 FDR: 1,414; 0.001 FDR:     1
0:58:19.820043 PROGRESS: 
0:58:19.820115 PROGRESS: Protein Summary:
0:58:19.822193 PROGRESS: Channel   0:	 0.050 FDR: 1,412; 0.010 FDR: 1,412; 0.001 FDR:     1
0:58:19.822308 PROGRESS: =========================================================================
0:58:19.840908 INFO: Target number of precursors reached.
0:58:20.137598 INFO: fragments_df: keeping 5000 of 3770464 [sum(precursor_idx_mask)=31665 sum(mass_error_mask)=3770464 stop_rank=5000
0:58:20.579841 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:20.818355 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:21.540905 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:21.541431 INFO: Using score_cutoff 9.107221331977845 (fac=0.99, q=1)
0:58:21.541783 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:58:21.541876 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:58:21.541970 INFO: Updating optimization_manager: score_cutoff        : 11.51461099834442 -> 9.107221331977845
0:58:21.542057 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:21.693248 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:22.039054 INFO: === checking if optimization conditions were reached ===
0:58:22.039412 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:58:22.042624 INFO: Updating optimization_manager: rt_error            : 805.6095581054688 -> 1003.3268683856469
0:58:22.042771 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1003.3269.
0:58:22.042880 INFO: ==============================================
0:58:22.042970 INFO: Starting optimization step 1.
0:58:22.043047 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:58:22.043129 INFO: Using rust extraction backend
0:58:22.043207 PROGRESS: Extracting batch of 251735 precursors
0:58:22.475336 INFO: === Search parameters used ===
0:58:22.475626 INFO: rt_error       : 1003.3268683856469
0:58:22.475690 INFO: mobility_error : 0.1
0:58:22.475745 INFO: num_candidates : 3
0:58:22.475793 INFO: ms1_error      : 30
0:58:22.475841 INFO: ms2_error      : 10.0
0:58:22.475887 INFO: fwhm_rt        : 3.0
0:58:22.475933 INFO: quant_window   : 3
0:58:22.475977 INFO: ==============================================
0:58:25.345910 INFO: performing precursor FDR with 40 features
0:58:25.346066 INFO: Decoy channel: -1
0:58:25.346119 INFO: competitive: True
0:58:25.552088 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:25.874193 INFO: Estimating optimal hyperparameters - samples: 601,108, batch_size: 2,462, learning_rate: 7.75e-04
0:58:25.875356 INFO: Using random state 238860 for train-test-split
0:58:37.942539 INFO: Test AUC: 0.610
0:58:37.942718 INFO: Train AUC: 0.621
0:58:37.942758 INFO: AUC difference: 1.81%
0:58:38.424878 INFO: Resetting torch num_threads to 80
0:58:38.458776 PROGRESS: === Extracted 751385 precursors and 3769718 fragments ===
0:58:38.459381 INFO: === FDR correction performed with classifier version 12 ===
0:58:38.460200 PROGRESS: ============================= Precursor FDR =============================
0:58:38.460312 PROGRESS: Total precursors accumulated: 1,462
0:58:38.460382 PROGRESS: Target precursors: 1,448 (99.04%)
0:58:38.460447 PROGRESS: Decoy precursors: 14 (0.96%)
0:58:38.460515 PROGRESS: 
0:58:38.460579 PROGRESS: Precursor Summary:
0:58:38.462079 PROGRESS: Channel   0:	 0.050 FDR: 1,448; 0.010 FDR: 1,448; 0.001 FDR:   996
0:58:38.462193 PROGRESS: 
0:58:38.462266 PROGRESS: Protein Summary:
0:58:38.464629 PROGRESS: Channel   0:	 0.050 FDR: 1,446; 0.010 FDR: 1,446; 0.001 FDR:   995
0:58:38.464745 PROGRESS: =========================================================================
0:58:38.484908 INFO: Target number of precursors reached.
0:58:38.783341 INFO: fragments_df: keeping 5000 of 3769718 [sum(precursor_idx_mask)=32956 sum(mass_error_mask)=3769718 stop_rank=5000
0:58:39.219705 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:39.456693 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:40.179186 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:40.179712 INFO: Using score_cutoff 10.552110496902465 (fac=0.99, q=1)
0:58:40.180084 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:58:40.180183 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:58:40.180271 INFO: Updating optimization_manager: score_cutoff        : 9.107221331977845 -> 10.552110496902465
0:58:40.180362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:40.332226 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:40.681947 INFO: === checking if optimization conditions were reached ===
0:58:40.682299 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:58:40.685691 INFO: Updating optimization_manager: rt_error            : 1003.3268683856469 -> 749.7249256140229
0:58:40.685830 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 749.7249.
0:58:40.685928 INFO: ==============================================
0:58:40.686024 INFO: Starting optimization step 2.
0:58:40.686104 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:58:40.686196 INFO: Using rust extraction backend
0:58:40.686277 PROGRESS: Extracting batch of 251735 precursors
0:58:41.125281 INFO: === Search parameters used ===
0:58:41.125689 INFO: rt_error       : 749.7249256140229
0:58:41.125760 INFO: mobility_error : 0.1
0:58:41.125814 INFO: num_candidates : 3
0:58:41.125863 INFO: ms1_error      : 30
0:58:41.125918 INFO: ms2_error      : 10.0
0:58:41.125965 INFO: fwhm_rt        : 3.0
0:58:41.126008 INFO: quant_window   : 3
0:58:41.126050 INFO: ==============================================
0:58:44.042003 INFO: performing precursor FDR with 40 features
0:58:44.042152 INFO: Decoy channel: -1
0:58:44.042180 INFO: competitive: True
0:58:44.277910 INFO: Setting torch num_threads to 2 for FDR classification task
0:58:44.616587 INFO: Estimating optimal hyperparameters - samples: 601,177, batch_size: 2,462, learning_rate: 7.75e-04
0:58:44.617831 INFO: Using random state 238860 for train-test-split
0:58:56.843817 INFO: Test AUC: 0.610
0:58:56.843978 INFO: Train AUC: 0.622
0:58:56.844010 INFO: AUC difference: 2.05%
0:58:58.222943 INFO: Resetting torch num_threads to 80
0:58:58.257517 PROGRESS: === Extracted 751472 precursors and 3769625 fragments ===
0:58:58.258118 INFO: === FDR correction performed with classifier version 12 ===
0:58:58.258946 PROGRESS: ============================= Precursor FDR =============================
0:58:58.259069 PROGRESS: Total precursors accumulated: 1,451
0:58:58.259161 PROGRESS: Target precursors: 1,437 (99.04%)
0:58:58.259243 PROGRESS: Decoy precursors: 14 (0.96%)
0:58:58.259306 PROGRESS: 
0:58:58.259357 PROGRESS: Precursor Summary:
0:58:58.260857 PROGRESS: Channel   0:	 0.050 FDR: 1,437; 0.010 FDR: 1,437; 0.001 FDR:   743
0:58:58.260966 PROGRESS: 
0:58:58.261025 PROGRESS: Protein Summary:
0:58:58.263350 PROGRESS: Channel   0:	 0.050 FDR: 1,435; 0.010 FDR: 1,435; 0.001 FDR:   742
0:58:58.263470 PROGRESS: =========================================================================
0:58:58.282728 INFO: Target number of precursors reached.
0:58:58.577383 INFO: fragments_df: keeping 5000 of 3769625 [sum(precursor_idx_mask)=32758 sum(mass_error_mask)=3769625 stop_rank=5000
0:58:59.049593 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:59.304523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:00.028080 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:00.028692 INFO: Using score_cutoff 11.602103679656981 (fac=0.99, q=1)
0:59:00.029067 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:00.029149 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:00.029204 INFO: Updating optimization_manager: score_cutoff        : 10.552110496902465 -> 11.602103679656981
0:59:00.029280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:00.181049 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:00.538456 INFO: === checking if optimization conditions were reached ===
0:59:00.538813 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:59:00.542141 INFO: Updating optimization_manager: rt_error            : 749.7249256140229 -> 706.6915341292972
0:59:00.542253 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 706.6915.
0:59:00.542324 INFO: ==============================================
0:59:00.542399 INFO: Starting optimization step 3.
0:59:00.542461 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:59:00.542533 INFO: Using rust extraction backend
0:59:00.542597 PROGRESS: Extracting batch of 251735 precursors
0:59:00.977559 INFO: === Search parameters used ===
0:59:00.977893 INFO: rt_error       : 706.6915341292972
0:59:00.977963 INFO: mobility_error : 0.1
0:59:00.978014 INFO: num_candidates : 3
0:59:00.978060 INFO: ms1_error      : 30
0:59:00.978104 INFO: ms2_error      : 10.0
0:59:00.978147 INFO: fwhm_rt        : 3.0
0:59:00.978189 INFO: quant_window   : 3
0:59:00.978231 INFO: ==============================================
0:59:03.843810 INFO: performing precursor FDR with 40 features
0:59:03.843954 INFO: Decoy channel: -1
0:59:03.843982 INFO: competitive: True
0:59:04.050855 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:04.388473 INFO: Estimating optimal hyperparameters - samples: 601,088, batch_size: 2,462, learning_rate: 7.75e-04
0:59:04.389551 INFO: Using random state 238860 for train-test-split
0:59:17.031028 INFO: Test AUC: 0.609
0:59:17.031200 INFO: Train AUC: 0.623
0:59:17.031235 INFO: AUC difference: 2.22%
0:59:17.521451 INFO: Resetting torch num_threads to 80
0:59:17.556102 PROGRESS: === Extracted 751360 precursors and 3766393 fragments ===
0:59:17.556674 INFO: === FDR correction performed with classifier version 12 ===
0:59:17.557502 PROGRESS: ============================= Precursor FDR =============================
0:59:17.557624 PROGRESS: Total precursors accumulated: 1,486
0:59:17.557692 PROGRESS: Target precursors: 1,472 (99.06%)
0:59:17.557750 PROGRESS: Decoy precursors: 14 (0.94%)
0:59:17.557801 PROGRESS: 
0:59:17.557849 PROGRESS: Precursor Summary:
0:59:17.559348 PROGRESS: Channel   0:	 0.050 FDR: 1,472; 0.010 FDR: 1,472; 0.001 FDR: 1,026
0:59:17.559464 PROGRESS: 
0:59:17.559526 PROGRESS: Protein Summary:
0:59:17.561921 PROGRESS: Channel   0:	 0.050 FDR: 1,470; 0.010 FDR: 1,470; 0.001 FDR: 1,025
0:59:17.562029 PROGRESS: =========================================================================
0:59:17.581287 INFO: Target number of precursors reached.
0:59:17.877441 INFO: fragments_df: keeping 5000 of 3766393 [sum(precursor_idx_mask)=33347 sum(mass_error_mask)=3766393 stop_rank=5000
0:59:18.356817 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:18.595663 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:19.319109 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:19.319605 INFO: Using score_cutoff 10.388012220668791 (fac=0.99, q=1)
0:59:19.319938 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:19.320022 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:19.320097 INFO: Updating optimization_manager: score_cutoff        : 11.602103679656981 -> 10.388012220668791
0:59:19.320179 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:19.471769 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:19.819370 INFO: === checking if optimization conditions were reached ===
0:59:19.819714 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:59:19.823251 INFO: Updating optimization_manager: rt_error            : 706.6915341292972 -> 702.4686361627175
0:59:19.823406 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 702.4686.
0:59:19.823502 INFO: ==============================================
0:59:19.823599 INFO: Starting optimization step 4.
0:59:19.823680 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:59:19.823764 INFO: Using rust extraction backend
0:59:19.823848 PROGRESS: Extracting batch of 251735 precursors
0:59:20.262228 INFO: === Search parameters used ===
0:59:20.262574 INFO: rt_error       : 702.4686361627175
0:59:20.262647 INFO: mobility_error : 0.1
0:59:20.262710 INFO: num_candidates : 3
0:59:20.262770 INFO: ms1_error      : 30
0:59:20.262831 INFO: ms2_error      : 10.0
0:59:20.262879 INFO: fwhm_rt        : 3.0
0:59:20.262938 INFO: quant_window   : 3
0:59:20.262996 INFO: ==============================================
0:59:23.129292 INFO: performing precursor FDR with 40 features
0:59:23.129441 INFO: Decoy channel: -1
0:59:23.129469 INFO: competitive: True
0:59:23.341446 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:23.669674 INFO: Estimating optimal hyperparameters - samples: 601,106, batch_size: 2,462, learning_rate: 7.75e-04
0:59:23.670858 INFO: Using random state 238860 for train-test-split
0:59:36.385797 INFO: Test AUC: 0.610
0:59:36.385982 INFO: Train AUC: 0.623
0:59:36.386015 INFO: AUC difference: 2.10%
0:59:36.861334 INFO: Resetting torch num_threads to 80
0:59:36.896407 PROGRESS: === Extracted 751383 precursors and 3767180 fragments ===
0:59:36.896962 INFO: === FDR correction performed with classifier version 12 ===
0:59:36.897757 PROGRESS: ============================= Precursor FDR =============================
0:59:36.897879 PROGRESS: Total precursors accumulated: 1,441
0:59:36.897983 PROGRESS: Target precursors: 1,427 (99.03%)
0:59:36.898054 PROGRESS: Decoy precursors: 14 (0.97%)
0:59:36.898127 PROGRESS: 
0:59:36.898188 PROGRESS: Precursor Summary:
0:59:36.899675 PROGRESS: Channel   0:	 0.050 FDR: 1,427; 0.010 FDR: 1,427; 0.001 FDR:   741
0:59:36.899785 PROGRESS: 
0:59:36.899856 PROGRESS: Protein Summary:
0:59:36.902172 PROGRESS: Channel   0:	 0.050 FDR: 1,425; 0.010 FDR: 1,425; 0.001 FDR:   740
0:59:36.902286 PROGRESS: =========================================================================
0:59:36.923542 INFO: Target number of precursors reached.
0:59:37.208612 INFO: fragments_df: keeping 5000 of 3767180 [sum(precursor_idx_mask)=32236 sum(mass_error_mask)=3767180 stop_rank=5000
0:59:37.677427 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:59:37.918122 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:59:38.659690 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:59:38.660192 INFO: Using score_cutoff 10.210312830734253 (fac=0.99, q=1)
0:59:38.660541 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:38.660630 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:38.660687 INFO: Updating optimization_manager: score_cutoff        : 10.388012220668791 -> 10.210312830734253
0:59:38.660757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:38.811482 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:39.150272 INFO: === checking if optimization conditions were reached ===
0:59:39.150613 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:59:39.151795 INFO: Updating optimization_manager: rt_error            : 702.4686361627175 -> 706.6915341292972
0:59:39.151964 INFO: Updating optimization_manager: classifier_version  : 12 -> 16
0:59:39.152102 INFO: Updating optimization_manager: score_cutoff        : 10.210312830734253 -> 10.388012220668791
0:59:39.152258 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:59:39.152401 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:59:39.152544 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 706.6915 found after 5 searches.
0:59:39.152651 INFO: ==============================================
0:59:39.152765 PROGRESS: Optimization finished for rt_error.
0:59:39.569889 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:39.721833 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:59:40.065625 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:59:40.066039 PROGRESS: ==============================================
0:59:40.066175 PROGRESS: ms2_error      : 10.0000
0:59:40.066278 PROGRESS: rt_error       : 706.6915
0:59:40.066381 PROGRESS: ==============================================
0:59:40.067378 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:59:47.764830 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:04.998877 INFO: Using rust extraction backend
1:00:04.999378 PROGRESS: Extracting batch of 12096565 precursors
1:00:22.630572 INFO: === Search parameters used ===
1:00:22.631049 INFO: rt_error       : 706.6915341292972
1:00:22.631128 INFO: mobility_error : 0.1
1:00:22.631191 INFO: num_candidates : 3
1:00:22.631250 INFO: ms1_error      : 30
1:00:22.631313 INFO: ms2_error      : 10.0
1:00:22.631377 INFO: fwhm_rt        : 3.0
1:00:22.631444 INFO: quant_window   : 3
1:00:22.631503 INFO: ==============================================
1:00:58.959860 INFO: Removed 10274218 precursors with score below cutoff 10.388012220668791
1:01:21.945574 INFO: performing precursor FDR with 40 features
1:01:21.945776 INFO: Decoy channel: -1
1:01:21.945809 INFO: competitive: True
1:01:25.176543 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:36.356939 INFO: Estimating optimal hyperparameters - samples: 20,811,468, batch_size: 4,096, learning_rate: 1.00e-03
1:01:36.420117 INFO: Using random state 763977 for train-test-split
1:09:00.527061 INFO: Test AUC: 0.620
1:09:00.527601 INFO: Train AUC: 0.620
1:09:00.527652 INFO: AUC difference: 0.03%
1:09:06.903416 INFO: Resetting torch num_threads to 80
1:09:11.106487 PROGRESS: ============================= Precursor FDR =============================
1:09:11.106979 PROGRESS: Total precursors accumulated: 72,034
1:09:11.107089 PROGRESS: Target precursors: 71,323 (99.01%)
1:09:11.107150 PROGRESS: Decoy precursors: 711 (0.99%)
1:09:11.107207 PROGRESS: 
1:09:11.107258 PROGRESS: Precursor Summary:
1:09:11.129954 PROGRESS: Channel   0:	 0.050 FDR: 71,323; 0.010 FDR: 71,323; 0.001 FDR:     1
1:09:11.130172 PROGRESS: 
1:09:11.130243 PROGRESS: Protein Summary:
1:09:11.216489 PROGRESS: Channel   0:	 0.050 FDR: 66,080; 0.010 FDR: 66,080; 0.001 FDR:     1
1:09:11.216769 PROGRESS: =========================================================================
1:09:11.567103 INFO: Saving results to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/psm.parquet
1:09:11.752878 INFO: Saving results to /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/frag.parquet
1:09:11.958832 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Human_03
1:09:44.092256 PROGRESS: Processing search outputs
1:09:44.092569 PROGRESS: === Performing protein grouping and FDR ===
1:09:44.092620 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Human_01
1:09:44.189438 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Human_02
1:09:44.276126 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Human_03
1:09:44.383733 INFO: Performing protein inference
1:09:44.647266 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1:55:59.532425 INFO: Performing protein FDR
1:56:17.866174 INFO: Normalizing q-values using 71,609 targets and 1,939 decoys
1:56:17.876521 INFO: Test AUC: 0.896
1:56:17.876609 INFO: Train AUC: 0.898
1:56:17.876639 INFO: AUC difference: 0.18%
1:56:18.416518 INFO: ================ Protein FDR =================
1:56:18.416699 INFO: Unique protein groups in output
1:56:18.416733 INFO:   1% protein FDR: 41,110
1:56:18.416754 INFO: 
1:56:18.416776 INFO: Unique precursor in output
1:56:18.416796 INFO:   1% protein FDR: 60,178
1:56:18.416815 INFO: ================================================
1:56:18.452666 PROGRESS: Building search statistics
1:56:18.514329 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/optimization_manager.pkl
1:56:18.514603 INFO: Initializing OptimizationManager
1:56:18.514920 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/calibration_manager.pkl
1:56:18.515005 INFO: Initializing CalibrationManager
1:56:18.515259 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/raw_file_manager.pkl
1:56:18.515341 INFO: Initializing RawFileManager
1:56:18.542256 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/optimization_manager.pkl
1:56:18.542454 INFO: Initializing OptimizationManager
1:56:18.542714 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/calibration_manager.pkl
1:56:18.542794 INFO: Initializing CalibrationManager
1:56:18.543001 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/raw_file_manager.pkl
1:56:18.543081 INFO: Initializing RawFileManager
1:56:18.569218 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/optimization_manager.pkl
1:56:18.569398 INFO: Initializing OptimizationManager
1:56:18.569613 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/calibration_manager.pkl
1:56:18.569691 INFO: Initializing CalibrationManager
1:56:18.569911 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/raw_file_manager.pkl
1:56:18.569993 INFO: Initializing RawFileManager
1:56:18.574175 INFO: Writing stat output to disk
1:56:18.574252 INFO: Saving /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/stat.tsv to disk
1:56:18.580969 PROGRESS: Building internal statistics
1:56:18.581223 INFO: Loaded TimingManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_01/timing_manager.pkl
1:56:18.581291 INFO: Initializing TimingManager
1:56:18.581612 INFO: Loaded TimingManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_02/timing_manager.pkl
1:56:18.581653 INFO: Initializing TimingManager
1:56:18.581872 INFO: Loaded TimingManager from /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/quant/LFQ_Astral_DIA_15min_50ng_Human_03/timing_manager.pkl
1:56:18.581918 INFO: Initializing TimingManager
1:56:18.582313 INFO: Writing internal output to disk
1:56:18.582355 INFO: Saving /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/internal.tsv to disk
1:56:18.616828 INFO: Performing label free quantification
1:56:18.616970 INFO: Accumulating fragment data
1:56:18.617033 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Human_01
1:56:18.772644 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Human_02
1:56:19.494485 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Human_03
1:56:20.327126 INFO: Performing label free quantification on the precursor level
1:56:20.327302 INFO: Filtering fragments by quality
1:56:20.491704 INFO: Performing label-free quantification with directlfq normalization
1:56:20.716904 INFO: Applying directLFQ normalization
1:56:21.482132 INFO: 60178 lfq-groups total
1:57:11.722024 INFO: using 80 processes
1:57:11.864585 INFO: lfq-object 0
1:57:11.943231 INFO: lfq-object 200
1:57:11.972049 INFO: lfq-object 100
1:57:12.030557 INFO: lfq-object 400
1:57:12.055791 INFO: lfq-object 300
1:57:12.101957 INFO: lfq-object 600
1:57:12.140472 INFO: lfq-object 500
1:57:12.192529 INFO: lfq-object 800
1:57:12.213040 INFO: lfq-object 700
1:57:12.288897 INFO: lfq-object 1000
1:57:12.293560 INFO: lfq-object 900
1:57:12.385576 INFO: lfq-object 1200
1:57:12.398029 INFO: lfq-object 1100
1:57:12.491734 INFO: lfq-object 1300
1:57:12.508363 INFO: lfq-object 1400
1:57:12.617032 INFO: lfq-object 1500
1:57:12.632735 INFO: lfq-object 1600
1:57:12.737453 INFO: lfq-object 1700
1:57:12.786317 INFO: lfq-object 1900
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1:57:12.885684 INFO: lfq-object 2100
1:57:12.891790 INFO: lfq-object 2000
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1:57:12.992887 INFO: lfq-object 2200
1:57:13.057674 INFO: lfq-object 2500
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1:57:15.831301 INFO: lfq-object 3000
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1:57:16.582796 INFO: lfq-object 4800
1:57:16.609157 INFO: lfq-object 4700
1:57:16.676718 INFO: lfq-object 5000
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1:57:59.807644 INFO: Performing label free quantification on the peptide level
1:57:59.808101 INFO: Filtering fragments by quality
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1:58:00.224910 INFO: Applying directLFQ normalization
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2:00:49.121059 INFO: lfq-object 37700
2:00:49.247496 INFO: lfq-object 37900
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2:00:49.297222 INFO: lfq-object 38000
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2:00:49.434873 INFO: lfq-object 38300
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2:00:49.559738 INFO: lfq-object 38600
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2:00:49.717771 INFO: lfq-object 38800
2:00:49.761312 INFO: lfq-object 38900
2:00:49.785299 INFO: lfq-object 39000
2:00:49.811792 INFO: lfq-object 39100
2:00:49.930768 INFO: lfq-object 39200
2:00:52.320791 INFO: lfq-object 39300
2:00:52.340874 INFO: lfq-object 39400
2:00:52.351275 INFO: lfq-object 39500
2:00:52.466967 INFO: lfq-object 39600
2:00:52.477756 INFO: lfq-object 39700
2:00:52.492535 INFO: lfq-object 39800
2:00:52.519560 INFO: lfq-object 39900
2:00:52.533114 INFO: lfq-object 40000
2:00:52.652139 INFO: lfq-object 40100
2:00:52.676299 INFO: lfq-object 40200
2:00:52.716090 INFO: lfq-object 40300
2:00:52.742609 INFO: lfq-object 40400
2:00:52.861083 INFO: lfq-object 40500
2:00:52.906855 INFO: lfq-object 40600
2:00:52.943733 INFO: lfq-object 40700
2:00:53.027488 INFO: lfq-object 40800
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2:00:53.253059 INFO: lfq-object 41000
2:00:53.286613 INFO: lfq-object 41100
2:00:56.420198 INFO: Writing psm output to disk
2:00:56.464828 INFO: Saving /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/precursors.parquet to disk
2:00:56.833799 INFO: Writing precursor output to disk
2:00:56.836304 INFO: Saving /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/precursor.matrix.parquet to disk
2:00:56.896865 INFO: Writing peptide output to disk
2:00:56.900661 INFO: Saving /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/peptide.matrix.parquet to disk
2:00:56.943256 INFO: Writing pg output to disk
2:00:56.947757 INFO: Saving /home/robbe/PB_output/results/Entrapment/Entrapment_DIA/alphadia_vlatest/pg.matrix.parquet to disk
2:00:56.999061 PROGRESS: Building MBR spectral library
2:00:56.999265 INFO: Running MbrLibraryBuilder
2:00:59.250725 INFO: MBR spectral library contains 60,178 precursors, 41,110 proteins
2:00:59.250887 INFO: Writing MBR spectral library to disk
2:00:59.740108 PROGRESS: =================== Search step 'library' finished ===================
2:01:02.437508 INFO: =================== Search Finished ===================
