0:00:00 INFO: Moved old log file Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\log.txt to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\log.1.bkp.txt
0:00:00.001007 INFO: Output directory: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA, cwd: C:\Program Files (x86)\AlphaDIA1.12.2.
0:00:00.001007 INFO: User provided config file: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\config.yaml.
0:00:00.076566 PROGRESS:           _      _         ___ ___   _   
0:00:00.076566 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.077567 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.077567 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.078572 PROGRESS:            |_|                           
0:00:00.078572 PROGRESS: 
0:00:00.079573 PROGRESS: version: 1.12.2
0:00:00.079573 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.080574 INFO: hostname: fw01c311
0:00:00.081573 INFO: date: 2025-10-30 13:34:12
0:00:00.082574 INFO: ================ AlphaX Environment ===============
0:00:00.082574 INFO: alphatims       : 1.0.9
0:00:00.083574 INFO: alpharaw        : 0.4.7
0:00:00.083574 INFO: alphabase       : 1.7.1
0:00:00.084573 INFO: alphapeptdeep   : 1.3.2
0:00:00.084573 INFO: directlfq       : 0.3.1
0:00:00.085574 INFO: ===================================================
0:00:00.086572 INFO: ================= Pip Environment =================
0:00:00.333097 INFO: alphabase==1.7.1 alphadia==1.12.2 alpharaw==0.4.7 alphatims==1.0.9 filelock==3.18.0 huggingface-hub==0.30.2 Jinja2==3.1.6 MarkupSafe==3.0.2 numpy==1.26.4 packaging==24.2 peptdeep==1.3.2 pillow==11.1.0 psutil==7.0.0 PyYAML==6.0.2 regex==2024.11.6 requests==2.32.3 safetensors==0.5.3 scikit-learn==1.6.1 scipy==1.12.0 tokenizers==0.21.1 torch==2.6.0 tqdm==4.67.1 wheel==0.45.1 importlib_metadata==8.0.0
0:00:00.334094 INFO: ===================================================
0:00:00.335095 INFO: Running step 'library'
0:00:00.338096 INFO: loading default config from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\default.yaml
0:00:00.377064 INFO: loading additional config provided via CLI
0:00:00.378064 INFO: loading additional config provided via CLI parameters
0:00:00.381054 INFO: Updating config with 'user defined'
0:00:00.382055 INFO: Updating config with 'user defined (cli)'
0:00:00.383058 INFO: updating config with user defined values: [{'workflow_name': 'PeptideCentric.v1', 'fasta_paths': ['Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\FASTA\\uniprotkb_proteome_HYE_UniversalContaminants.fasta'], 'raw_paths': ['D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff'], 'output_directory': 'Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\DATA_ANALYSIS\\AlphaDIA', 'general': {'thread_count': 10, 'transfer_step_enabled': False, 'mbr_step_enabled': True, 'reuse_quant': False, 'reuse_calibration': False, 'use_gpu': True, 'log_level': 'INFO'}, 'search': {'target_ms1_tolerance': 5, 'target_ms2_tolerance': 10, 'target_mobility_tolerance': 0, 'target_rt_tolerance': 0, 'channel_filter': '', 'exclude_shared_ions': True, 'compete_for_fragments': True, 'target_num_candidates': 3, 'quant_window': 3, 'quant_all': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [395, 905], 'fragment_mz': [140, 1750], 'nce': 25, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'SciexTOF', 'peptdeep_model_path': None, 'peptdeep_model_type': 'generic'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'channel_wise_fdr': False, 'keep_decoys': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': False}, 'search_initial': {'initial_ms1_tolerance': 30, 'initial_ms2_tolerance': 30, 'initial_mobility_tolerance': 0.1, 'initial_rt_tolerance': 0.5}, 'multiplexing': {'enabled': False, 'target_channels': '4,8', 'decoy_channel': 12, 'reference_channel': 0, 'competetive_scoring': True}, 'search_output': {'file_format': 'tsv', 'peptide_level_lfq': True, 'precursor_level_lfq': True, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3, 'normalize_lfq': False}, 'transfer_library': {'enabled': False, 'fragment_types': ['b', 'y'], 'max_charge': 2, 'top_k_samples': 3, 'norm_delta_max': True, 'precursor_correlation_cutoff': 0.5, 'fragment_correlation_ratio': 0.75}, 'transfer_learning': {'enabled': False, 'batch_size': 2000, 'max_lr': 0.0001, 'train_fraction': 0.7, 'validation_fraction': 0.2, 'test_fraction': 0.1, 'test_interval': 1, 'lr_patience': 3, 'epochs': 51, 'warmup_epochs': 5, 'nce': 25, 'instrument': 'Lumos'}}, {'raw_paths': ['D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False, 'reuse_quant': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'output_directory': 'Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\DATA_ANALYSIS\\AlphaDIA\\library'}]
0:00:00.384061 INFO: Updating config with 'user defined'
0:00:00.386057 INFO: Updating config with 'user defined (cli)'
0:00:00.387058 INFO: Updating config with 'multistep search'
0:00:00.388055 INFO: ├──version: 1
0:00:00.389054 INFO: [32;20m├──workflow_name: PeptideCentric.v1 [user defined, default: None][0m
0:00:00.391069 INFO: [32;20m├──output_directory: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library [multistep search, default: None][0m
0:00:00.392072 INFO: ├──library_path: None
0:00:00.393072 INFO: ├──raw_paths:
0:00:00.394072 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff [user defined (cli), default: None][0m
0:00:00.395070 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff [user defined (cli), default: None][0m
0:00:00.395070 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff [user defined (cli), default: None][0m
0:00:00.396070 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff [user defined (cli), default: None][0m
0:00:00.397073 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff [user defined (cli), default: None][0m
0:00:00.398072 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff [user defined (cli), default: None][0m
0:00:00.408647 INFO: ├──fasta_paths:
0:00:00.409648 INFO: │   [32;20m- Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\FASTA\uniprotkb_proteome_HYE_UniversalContaminants.fasta [user defined, default: None][0m
0:00:00.411650 INFO: ├──quant_directory: None
0:00:00.412646 INFO: ├──general
0:00:00.413647 INFO: │   ├──thread_count: 10
0:00:00.414644 INFO: │   ├──transfer_step_enabled: False
0:00:00.414644 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.415646 INFO: │   ├──reuse_calibration: False
0:00:00.416644 INFO: │   ├──reuse_quant: False
0:00:00.417644 INFO: │   ├──astral_ms1: False
0:00:00.417644 INFO: │   ├──log_level: INFO
0:00:00.418643 INFO: │   ├──mmap_detector_events: False
0:00:00.419646 INFO: │   ├──use_gpu: True
0:00:00.419646 INFO: │   ├──save_figures: True
0:00:00.420644 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.421646 INFO: │   ├──save_flat_library: False
0:00:00.422653 INFO: │   ├──input_library_type: base
0:00:00.422653 INFO: │   ├──save_mbr_library: True
0:00:00.423654 INFO: │   └──random_state: None
0:00:00.424653 INFO: ├──library_loading
0:00:00.425656 INFO: │   └──rt_heuristic: 180
0:00:00.425656 INFO: ├──library_prediction
0:00:00.426654 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.427654 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.428654 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.428654 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.429652 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.430654 INFO: │   ├──missed_cleavages: 1
0:00:00.431654 INFO: │   ├──precursor_len:
0:00:00.431654 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.432653 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.433653 INFO: │   ├──precursor_charge:
0:00:00.434652 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.434652 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.435652 INFO: │   ├──precursor_mz:
0:00:00.436653 INFO: │   │   [32;20m- 395 [user defined, default: 400][0m
0:00:00.437700 INFO: │   │   [32;20m- 905 [user defined, default: 1200][0m
0:00:00.438703 INFO: │   ├──fragment_mz:
0:00:00.439698 INFO: │   │   [32;20m- 140 [user defined, default: 200][0m
0:00:00.440699 INFO: │   │   [32;20m- 1750 [user defined, default: 2000][0m
0:00:00.441698 INFO: │   ├──nce: 25
0:00:00.442698 INFO: │   ├──fragment_types:
0:00:00.443698 INFO: │   │   - b
0:00:00.444700 INFO: │   │   - y
0:00:00.445700 INFO: │   ├──max_fragment_charge: 2
0:00:00.446700 INFO: │   [32;20m├──instrument: SciexTOF [user defined, default: Lumos][0m
0:00:00.447700 INFO: │   ├──peptdeep_model_path: None
0:00:00.448700 INFO: │   └──peptdeep_model_type: generic
0:00:00.449698 INFO: ├──custom_modifications:
0:00:00.450699 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.451699 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.452699 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.453707 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.454706 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.455706 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.456706 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.457706 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.458705 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.459705 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.459705 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.460705 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.461707 INFO: │   ├──name: Label:13C(12)@K
0:00:00.462706 INFO: │   └──composition: C(12)
0:00:00.462706 INFO: ├──search
0:00:00.463709 INFO: │   ├──extraction_backend: classic
0:00:00.464705 INFO: │   ├──target_ms1_tolerance: 5
0:00:00.465707 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.465707 INFO: │   ├──target_rt_tolerance: 0
0:00:00.466705 INFO: │   ├──target_mobility_tolerance: 0
0:00:00.466705 INFO: │   ├──quant_window: 3
0:00:00.468210 INFO: │   ├──target_num_candidates: 3
0:00:00.469216 INFO: │   ├──channel_filter: 
0:00:00.470217 INFO: │   ├──exclude_shared_ions: True
0:00:00.471218 INFO: │   ├──compete_for_fragments: True
0:00:00.472218 INFO: │   ├──quant_all: True
0:00:00.473218 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.473218 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.474217 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.475218 INFO: │   ├──experimental_xic: True
0:00:00.476216 INFO: │   └──optimized_peak_group_score: False
0:00:00.476216 INFO: ├──calibration
0:00:00.477217 INFO: │   ├──batch_size: 8000
0:00:00.478218 INFO: │   ├──optimization_lock_target: 200
0:00:00.478218 INFO: │   ├──max_steps: 20
0:00:00.479218 INFO: │   ├──min_steps: 2
0:00:00.480218 INFO: │   ├──max_skips: 1
0:00:00.481217 INFO: │   ├──max_fragments: 5000
0:00:00.481217 INFO: │   └──min_correlation: 0.7
0:00:00.482217 INFO: ├──search_initial
0:00:00.483218 INFO: │   ├──initial_num_candidates: 1
0:00:00.484218 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.484218 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.485224 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.486224 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.487224 INFO: ├──selection_config
0:00:00.487224 INFO: │   ├──peak_len_rt: 10.0
0:00:00.488225 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.489225 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.489225 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.490225 INFO: │   ├──top_k_precursors: 3
0:00:00.491225 INFO: │   ├──kernel_size: 30
0:00:00.491225 INFO: │   ├──f_mobility: 1.0
0:00:00.492226 INFO: │   ├──f_rt: 0.99
0:00:00.493224 INFO: │   ├──center_fraction: 0.5
0:00:00.494226 INFO: │   ├──min_size_mobility: 8
0:00:00.494226 INFO: │   ├──min_size_rt: 3
0:00:00.495225 INFO: │   ├──max_size_mobility: 20
0:00:00.496225 INFO: │   ├──max_size_rt: 15
0:00:00.496225 INFO: │   ├──group_channels: False
0:00:00.497225 INFO: │   ├──use_weighted_score: True
0:00:00.498225 INFO: │   ├──join_close_candidates: False
0:00:00.498225 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.499732 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.500738 INFO: ├──scoring_config
0:00:00.500738 INFO: │   ├──score_grouped: False
0:00:00.501739 INFO: │   ├──top_k_isotopes: 3
0:00:00.502741 INFO: │   ├──reference_channel: -1
0:00:00.503740 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.504740 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.505247 INFO: ├──library_multiplexing
0:00:00.506254 INFO: │   ├──enabled: False
0:00:00.506254 INFO: │   ├──input_channel: 0
0:00:00.507255 INFO: │   └──multiplex_mapping:
0:00:00.508255 INFO: ├──multiplexing
0:00:00.509254 INFO: │   ├──enabled: False
0:00:00.509254 INFO: │   ├──target_channels: 4,8
0:00:00.510256 INFO: │   ├──decoy_channel: 12
0:00:00.511256 INFO: │   ├──reference_channel: 0
0:00:00.511256 INFO: │   └──competetive_scoring: True
0:00:00.512255 INFO: ├──fdr
0:00:00.513255 INFO: │   ├──fdr: 0.01
0:00:00.514254 INFO: │   ├──group_level: proteins
0:00:00.514254 INFO: │   ├──inference_strategy: heuristic
0:00:00.515256 INFO: │   ├──competetive_scoring: True
0:00:00.516263 INFO: │   ├──keep_decoys: False
0:00:00.516263 INFO: │   ├──channel_wise_fdr: False
0:00:00.517263 INFO: │   ├──enable_two_step_classifier: False
0:00:00.518264 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.519263 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.519263 INFO: ├──search_output
0:00:00.520262 INFO: │   ├──file_format: tsv
0:00:00.521262 INFO: │   [32;20m├──peptide_level_lfq: True [user defined, default: False][0m
0:00:00.522261 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.522261 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.523262 INFO: │   ├──min_k_fragments: 12
0:00:00.524261 INFO: │   ├──min_correlation: 0.9
0:00:00.524261 INFO: │   ├──num_samples_quadratic: 50
0:00:00.525263 INFO: │   ├──min_nonnan: 3
0:00:00.526261 INFO: │   [32;20m└──normalize_lfq: False [user defined, default: True][0m
0:00:00.527261 INFO: ├──optimization
0:00:00.527261 INFO: │   ├──order_of_optimization: None
0:00:00.528261 INFO: │   ├──ms2_error
0:00:00.529263 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.529263 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.530769 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.530769 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.531775 INFO: │   │   ├──try_narrower_values: True
0:00:00.532775 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.533775 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.534776 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.535776 INFO: │   ├──ms1_error
0:00:00.535776 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.536776 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.537776 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.537776 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.538776 INFO: │   │   ├──try_narrower_values: False
0:00:00.539776 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.539776 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.540776 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.541776 INFO: │   ├──mobility_error
0:00:00.542776 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.542776 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.543775 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.544776 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.544776 INFO: │   │   ├──try_narrower_values: False
0:00:00.545776 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.546776 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.547782 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.547782 INFO: │   └──rt_error
0:00:00.548783 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.549783 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.549783 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.550782 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.551783 INFO: │       ├──try_narrower_values: True
0:00:00.551783 INFO: │       ├──maximal_decrease: 0.2
0:00:00.552783 INFO: │       ├──favour_narrower_optimum: True
0:00:00.553783 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.553783 INFO: ├──optimization_manager
0:00:00.554783 INFO: │   ├──fwhm_rt: 5
0:00:00.555783 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.556784 INFO: │   └──score_cutoff: 0
0:00:00.556784 INFO: ├──transfer_library
0:00:00.557783 INFO: │   ├──enabled: False
0:00:00.558783 INFO: │   ├──fragment_types:
0:00:00.558783 INFO: │   │   - b
0:00:00.559783 INFO: │   │   - y
0:00:00.560782 INFO: │   ├──max_charge: 2
0:00:00.560782 INFO: │   ├──top_k_samples: 3
0:00:00.562289 INFO: │   ├──norm_delta_max: True
0:00:00.562289 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.563296 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.564296 INFO: └──transfer_learning
0:00:00.564296 INFO:     ├──enabled: False
0:00:00.565302 INFO:     ├──batch_size: 2000
0:00:00.566296 INFO:     ├──max_lr: 0.0001
0:00:00.567296 INFO:     ├──train_fraction: 0.7
0:00:00.567296 INFO:     ├──validation_fraction: 0.2
0:00:00.568297 INFO:     ├──test_fraction: 0.1
0:00:00.569296 INFO:     ├──test_interval: 1
0:00:00.569296 INFO:     ├──lr_patience: 3
0:00:00.570296 INFO:     ├──epochs: 51
0:00:00.571297 INFO:     ├──warmup_epochs: 5
0:00:00.571297 INFO:     ├──nce: 25
0:00:00.572296 INFO:     └──instrument: Lumos
0:00:00.604815 INFO: Moved existing config file Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\frozen_config.yaml to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\frozen_config.1.bkp.yaml
0:00:00.605813 INFO: Registering 7 custom modifications
0:00:00.692882 INFO: Searching 6 files:
0:00:00.693881 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff
0:00:00.694881 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff
0:00:00.694881 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff
0:00:00.695881 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff
0:00:00.696879 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff
0:00:00.697881 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff
0:00:00.697881 INFO: Using 1 fasta files:
0:00:00.698882 INFO:   Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\FASTA\uniprotkb_proteome_HYE_UniversalContaminants.fasta
0:00:00.699881 INFO: Using library: None
0:00:00.699881 INFO: Saving output to: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library
0:00:00.700880 PROGRESS: Loading spectral library
0:00:00.701879 PROGRESS: No library provided. Building library from fasta files.
0:00:00.701879 INFO: Running FastaDigest
0:00:02.321807 INFO: Digesting fasta file
0:00:14.971795 INFO: Adding modifications
0:03:38.641605 INFO: Removing non-canonical amino acids
0:03:51.617339 INFO: Fasta library contains 5,681,204 precursors
0:03:51.620339 PROGRESS: Predicting library properties.
0:03:51.621339 INFO: Running PeptDeepPrediction
0:03:51.622338 INFO: Device set to cpu
0:03:53.345784 INFO: Loading PeptDeep models of type generic
0:03:54.852256 INFO: Predicting RT, MS2 and mobility
0:03:54.853256 INFO: Using multiprocessing with 10 processes ...
0:03:56.828159 INFO: Predicting rt,ms2,mobility ...
0:50:31.630516 INFO: Adding fragment mz information
0:50:32.644898 INFO: Adding fragment intensity information
0:50:33.627225 INFO: Adding precursor information
0:50:34.711607 INFO: Running PrecursorInitializer
0:50:34.762613 INFO: Running AnnotateFasta
0:50:35.374276 INFO: Dropping decoys from input library before annotation
0:51:15.119442 INFO: Running IsotopeGenerator
0:51:15.122440 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
1:01:24.919549 INFO: Running RTNormalization
1:01:24.921553 WARNING: Input library already contains normalized RT information. Skipping RT normalization
1:01:24.923552 INFO: Saving library to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\speclib.hdf
1:05:49.597800 INFO: Running DecoyGenerator
1:09:15.371312 INFO: Running FlattenLibrary
1:10:15.894873 INFO: Running InitFlatColumns
1:10:17.115516 INFO: Running LogFlatLibraryStats
1:10:17.116512 INFO: ============ Library Stats ============
1:10:17.117512 INFO: Number of precursors: 11,332,192
1:10:20.445336 INFO: 	thereof targets:5,681,204
1:10:20.447337 INFO: 	thereof decoys: 5,650,988
1:10:20.659863 INFO: Number of elution groups: 5,681,204
1:10:20.660863 INFO: 	average size: 1.99
1:10:21.389435 INFO: Number of proteins: 117,382
1:10:21.480436 INFO: Number of channels: 1 ([0])
1:10:21.481436 INFO: Isotopes Distribution for 4 isotopes
1:10:21.482436 INFO: =======================================
1:10:21.909484 PROGRESS: Starting Search Workflows
1:10:21.910484 PROGRESS: 
1:10:21.911484 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant
1:10:21.912484 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\figures
1:10:21.921486 INFO: Initializing TimingManager
1:10:21.934485 INFO: Initializing RawFileManager
1:13:43.200050 INFO: Determining DIA cycle
1:13:43.756099 INFO: Found cycle with start 0.00 min and length 86.
1:13:44.337149 INFO: RT (min)            : 0.0 - 55.4
1:13:44.338150 INFO: RT duration (sec)   : 3325.6
1:13:44.339149 INFO: RT duration (min)   : 55.4
1:13:44.340149 INFO: Cycle len (scans)   : 86
1:13:44.341149 INFO: Cycle len (sec)     : 1.90
1:13:44.342151 INFO: Number of cycles    : 1747
1:13:44.343150 INFO: MS2 range (m/z)     : 399.5 - 903.5
1:13:44.344150 INFO: Creating DIA data object took: 202.40366506576538
1:13:47.194452 INFO: Initializing CalibrationManager
1:13:47.206452 INFO: Setting up calibration estimators ..
1:13:47.211451 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:13:47.216468 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1:13:47.220452 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:13:47.225452 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1:13:47.230452 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1:13:47.235454 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:13:47.238452 INFO: Done setting up calibration estimators.
1:13:47.244453 INFO: Initializing OptimizationManager
1:13:47.258452 INFO: initial parameter: ms1_error = 30
1:13:47.266452 INFO: initial parameter: ms2_error = 30
1:13:47.273453 INFO: initial parameter: rt_error = 1662.8485107421875
1:13:47.280453 INFO: initial parameter: mobility_error = 0.1
1:13:47.287453 INFO: initial parameter: num_candidates = 1
1:13:47.294453 INFO: initial parameter: fwhm_rt = 5
1:13:47.319453 INFO: initial parameter: fwhm_mobility = 0.01
1:13:47.331454 INFO: initial parameter: score_cutoff = 0
1:13:47.341454 INFO: initial parameter: classifier_version = -1
1:13:47.354453 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
1:13:47.364455 INFO: FDRManager: loading saved state not requested, will be initialized.
1:13:47.365454 INFO: Initializing FDRManager
1:13:47.367454 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
1:13:50.397774 PROGRESS: Initializing spectral library: 5,593,630 target precursors potentially observable (87,574 removed)
1:13:53.433074 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1:13:53.441073 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 1662.8485107421875
1:13:53.448081 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1:13:53.454081 PROGRESS: Starting initial search for precursors.
1:13:53.463597 INFO: Starting optimization step 0.
1:13:53.471597 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:13:53.478598 INFO: Using classic extraction backend
1:13:53.484598 PROGRESS: Extracting batch of 15689 precursors
1:13:53.489598 INFO: === Search parameters used ===
1:13:53.494598 INFO: rt_error       : 1662.8485107421875
1:13:53.498598 INFO: mobility_error : 0.1
1:13:53.506598 INFO: num_candidates : 1
1:13:53.515598 INFO: ms1_error      : 30
1:13:53.525599 INFO: ms2_error      : 30
1:13:53.535599 INFO: fwhm_rt        : 5
1:13:53.544599 INFO: quant_window   : 3
1:13:53.550598 INFO: ==============================================
1:13:57.151947 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:13:57.153947 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:13:57.155948 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
1:13:57.156949 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:14:00.311864 INFO: Starting candidate selection
1:15:17.036846 INFO: Starting candidate scoring
1:18:37.726353 INFO: Finished candidate processing
1:18:37.727361 INFO: Collecting candidate features
1:18:38.419931 INFO: Collecting fragment features
1:18:40.818647 INFO: Finished candidate scoring
1:18:40.833648 INFO: performing precursor FDR with 47 features
1:18:40.835650 INFO: Decoy channel: -1
1:18:40.836647 INFO: Competetive: True
1:18:40.854649 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:40.873648 INFO: Using random state 146689 for train-test-split
1:18:45.399489 INFO: Test AUC: 0.519
1:18:45.400490 INFO: Train AUC: 0.535
1:18:45.401490 INFO: AUC difference: 2.88%
1:18:46.053052 INFO: Resetting torch num_threads to 10
1:18:46.059052 PROGRESS: === Extracted 15680 precursors and 144101 fragments ===
1:18:46.067053 INFO: === FDR correction performed with classifier version -1 ===
1:18:46.075053 PROGRESS: ============================= Precursor FDR =============================
1:18:46.080053 PROGRESS: Total precursors accumulated: 1
1:18:46.085052 PROGRESS: Target precursors: 1 (100.00%)
1:18:46.090054 PROGRESS: Decoy precursors: 0 (0.00%)
1:18:46.094053 PROGRESS: 
1:18:46.098053 PROGRESS: Precursor Summary:
1:18:46.106054 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:18:46.110053 PROGRESS: 
1:18:46.114066 PROGRESS: Protein Summary:
1:18:46.121052 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:18:46.126053 PROGRESS: =========================================================================
1:18:46.131054 INFO: Target number of precursors not reached yet.
1:18:46.417116 INFO: Starting optimization step 1.
1:18:46.422117 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:18:46.426115 INFO: Using classic extraction backend
1:18:46.430116 PROGRESS: Extracting batch of 31390 precursors
1:18:46.434116 INFO: === Search parameters used ===
1:18:46.438115 INFO: rt_error       : 1662.8485107421875
1:18:46.443117 INFO: mobility_error : 0.1
1:18:46.446117 INFO: num_candidates : 1
1:18:46.450117 INFO: ms1_error      : 30
1:18:46.454119 INFO: ms2_error      : 30
1:18:46.458117 INFO: fwhm_rt        : 5
1:18:46.462117 INFO: quant_window   : 3
1:18:46.466117 INFO: ==============================================
1:18:46.487117 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:18:46.489117 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:46.490117 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
1:18:46.491124 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:18:46.493117 INFO: Starting candidate selection
1:19:13.188655 INFO: Starting candidate scoring
1:19:14.370757 INFO: Finished candidate processing
1:19:14.371759 INFO: Collecting candidate features
1:19:14.564295 INFO: Collecting fragment features
1:19:14.631294 INFO: Finished candidate scoring
1:19:14.692309 INFO: performing precursor FDR with 47 features
1:19:14.693306 INFO: Decoy channel: -1
1:19:14.694306 INFO: Competetive: True
1:19:14.784827 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:14.833827 INFO: Using random state 682637 for train-test-split
1:19:17.315405 INFO: Test AUC: 0.573
1:19:17.316401 INFO: Train AUC: 0.582
1:19:17.318402 INFO: AUC difference: 1.50%
1:19:17.926473 INFO: Resetting torch num_threads to 10
1:19:17.964009 PROGRESS: === Extracted 47048 precursors and 432185 fragments ===
1:19:17.970008 INFO: === FDR correction performed with classifier version -1 ===
1:19:17.988008 PROGRESS: ============================= Precursor FDR =============================
1:19:17.994008 PROGRESS: Total precursors accumulated: 23,871
1:19:17.999008 PROGRESS: Target precursors: 14,708 (61.61%)
1:19:18.004009 PROGRESS: Decoy precursors: 9,163 (38.39%)
1:19:18.009010 PROGRESS: 
1:19:18.014008 PROGRESS: Precursor Summary:
1:19:18.027009 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1:19:18.031008 PROGRESS: 
1:19:18.036009 PROGRESS: Protein Summary:
1:19:18.043009 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1:19:18.047022 PROGRESS: =========================================================================
1:19:18.051009 INFO: Target number of precursors not reached yet.
1:19:18.433545 INFO: Starting optimization step 2.
1:19:18.440545 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:19:18.460070 INFO: Using classic extraction backend
1:19:18.467080 PROGRESS: Extracting batch of 62842 precursors
1:19:18.476082 INFO: === Search parameters used ===
1:19:18.484082 INFO: rt_error       : 1662.8485107421875
1:19:18.493081 INFO: mobility_error : 0.1
1:19:18.500081 INFO: num_candidates : 1
1:19:18.507083 INFO: ms1_error      : 30
1:19:18.538082 INFO: ms2_error      : 30
1:19:18.546082 INFO: fwhm_rt        : 5
1:19:18.567083 INFO: quant_window   : 3
1:19:18.575083 INFO: ==============================================
1:19:18.633083 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:19:18.634083 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:18.635083 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
1:19:18.636083 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:19:18.637083 INFO: Starting candidate selection
1:20:52.883498 INFO: Starting candidate scoring
1:20:54.991225 INFO: Finished candidate processing
1:20:54.992737 INFO: Collecting candidate features
1:20:55.316260 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 62802)
1:20:55.332263 INFO: Collecting fragment features
1:20:55.452781 INFO: Finished candidate scoring
1:20:55.573782 INFO: performing precursor FDR with 47 features
1:20:55.574784 INFO: Decoy channel: -1
1:20:55.575783 INFO: Competetive: True
1:20:55.731301 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:55.789303 WARNING: dropped 1 decoy PSMs due to missing features
1:20:55.877825 INFO: Using random state 521541 for train-test-split
1:20:58.364537 INFO: Test AUC: 0.575
1:20:58.366052 INFO: Train AUC: 0.599
1:20:58.367052 INFO: AUC difference: 4.04%
1:20:59.025101 INFO: Resetting torch num_threads to 10
1:20:59.101109 PROGRESS: === Extracted 109850 precursors and 1008895 fragments ===
1:20:59.107109 INFO: === FDR correction performed with classifier version -1 ===
1:20:59.112109 PROGRESS: ============================= Precursor FDR =============================
1:20:59.116614 PROGRESS: Total precursors accumulated: 392
1:20:59.121622 PROGRESS: Target precursors: 357 (91.07%)
1:20:59.126622 PROGRESS: Decoy precursors: 35 (8.93%)
1:20:59.130624 PROGRESS: 
1:20:59.134622 PROGRESS: Precursor Summary:
1:20:59.147622 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   229; 0.001 FDR:   184
1:20:59.153623 PROGRESS: 
1:20:59.157623 PROGRESS: Protein Summary:
1:20:59.171622 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:   216; 0.001 FDR:   174
1:20:59.178622 PROGRESS: =========================================================================
1:20:59.190623 INFO: Target number of precursors reached.
1:20:59.399148 INFO: fragments_df: keeping 2205 of 1008895 [sum(precursor_idx_mask)=2579 sum(mass_error_mask)=1008895 stop_rank=2205
1:20:59.922191 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:21:00.210717 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:00.553240 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:01.536333 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:21:01.541333 INFO: Using score_cutoff 54.533814793396 (fac=0.99, q=1)
1:21:01.545333 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.506518602371216
1:21:01.549333 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
1:21:01.553334 INFO: Updating optimization_manager: score_cutoff        : 0 -> 54.533814793396
1:21:01.557333 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:21:01.594333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:01.687862 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:02.129908 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
1:21:02.134910 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:21:02.138909 INFO: Starting optimization step 3.
1:21:02.142910 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:21:02.145909 INFO: Using classic extraction backend
1:21:02.150910 PROGRESS: Extracting batch of 109921 precursors
1:21:02.154910 INFO: === Search parameters used ===
1:21:02.159909 INFO: rt_error       : 1662.8485107421875
1:21:02.164909 INFO: mobility_error : 0.1
1:21:02.168909 INFO: num_candidates : 3
1:21:02.172909 INFO: ms1_error      : 30
1:21:02.179909 INFO: ms2_error      : 30
1:21:02.188910 INFO: fwhm_rt        : 2.506518602371216
1:21:02.194910 INFO: quant_window   : 3
1:21:02.201910 INFO: ==============================================
1:21:02.267910 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:21:02.268910 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:21:02.269911 INFO: FWHM in RT is 2.51 seconds, sigma is 0.28
1:21:02.270911 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:21:02.272911 INFO: Starting candidate selection
1:22:50.573606 INFO: Starting candidate scoring
1:23:00.675558 INFO: Finished candidate processing
1:23:00.677563 INFO: Collecting candidate features
1:23:01.929311 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 329532)
1:23:01.998312 INFO: Collecting fragment features
1:23:02.570952 INFO: Finished candidate scoring
1:23:02.858500 INFO: performing precursor FDR with 47 features
1:23:02.859499 INFO: Decoy channel: -1
1:23:02.860499 INFO: Competetive: True
1:23:03.113049 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:03.287050 WARNING: dropped 2 target PSMs due to missing features
1:23:03.288052 WARNING: dropped 3 decoy PSMs due to missing features
1:23:03.599114 INFO: Using random state 555862 for train-test-split
1:23:11.087813 INFO: Test AUC: 0.581
1:23:11.088814 INFO: Train AUC: 0.598
1:23:11.090814 INFO: AUC difference: 2.98%
1:23:11.889382 INFO: Resetting torch num_threads to 10
1:23:11.914382 PROGRESS: === Extracted 329532 precursors and 2922375 fragments ===
1:23:11.920382 INFO: === FDR correction performed with classifier version 2 ===
1:23:11.925382 PROGRESS: ============================= Precursor FDR =============================
1:23:11.930383 PROGRESS: Total precursors accumulated: 374
1:23:11.933384 PROGRESS: Target precursors: 341 (91.18%)
1:23:11.937382 PROGRESS: Decoy precursors: 33 (8.82%)
1:23:11.941382 PROGRESS: 
1:23:11.944382 PROGRESS: Precursor Summary:
1:23:11.951382 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   130; 0.001 FDR:    12
1:23:11.955383 PROGRESS: 
1:23:11.958383 PROGRESS: Protein Summary:
1:23:11.965384 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   124; 0.001 FDR:    12
1:23:11.969384 PROGRESS: =========================================================================
1:23:11.975383 INFO: Target number of precursors not reached yet.
1:23:12.574943 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:23:12.619951 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:12.745952 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:13.252997 INFO: === skipping optimization until target number of precursors are found ===
1:23:13.258997 INFO: Starting optimization step 4.
1:23:13.264004 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:23:13.268997 INFO: Using classic extraction backend
1:23:13.274999 PROGRESS: Extracting batch of 125627 precursors
1:23:13.279998 INFO: === Search parameters used ===
1:23:13.284997 INFO: rt_error       : 1662.8485107421875
1:23:13.288999 INFO: mobility_error : 0.1
1:23:13.293999 INFO: num_candidates : 3
1:23:13.297998 INFO: ms1_error      : 30
1:23:13.301998 INFO: ms2_error      : 30
1:23:13.306000 INFO: fwhm_rt        : 2.506518602371216
1:23:13.309998 INFO: quant_window   : 3
1:23:13.314005 INFO: ==============================================
1:23:13.386520 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:23:13.387519 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:23:13.388522 INFO: FWHM in RT is 2.51 seconds, sigma is 0.28
1:23:13.389526 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:23:13.390520 INFO: Starting candidate selection
1:25:17.455452 INFO: Starting candidate scoring
1:25:29.405387 INFO: Finished candidate processing
1:25:29.406395 INFO: Collecting candidate features
1:25:30.804528 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 376656)
1:25:30.859529 INFO: Collecting fragment features
1:25:31.501581 INFO: Finished candidate scoring
1:25:32.221228 INFO: performing precursor FDR with 47 features
1:25:32.222225 INFO: Decoy channel: -1
1:25:32.222225 INFO: Competetive: True
1:25:32.894844 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:33.235391 WARNING: dropped 4 target PSMs due to missing features
1:25:33.236391 WARNING: dropped 5 decoy PSMs due to missing features
1:25:33.965962 INFO: Using random state 555862 for train-test-split
1:25:50.657279 INFO: Test AUC: 0.585
1:25:50.658279 INFO: Train AUC: 0.595
1:25:50.659280 INFO: AUC difference: 1.65%
1:25:51.692373 INFO: Resetting torch num_threads to 10
1:25:52.033897 PROGRESS: === Extracted 706188 precursors and 6260240 fragments ===
1:25:52.041899 INFO: === FDR correction performed with classifier version 2 ===
1:25:52.050899 PROGRESS: ============================= Precursor FDR =============================
1:25:52.057898 PROGRESS: Total precursors accumulated: 982
1:25:52.063897 PROGRESS: Target precursors: 898 (91.45%)
1:25:52.071904 PROGRESS: Decoy precursors: 84 (8.55%)
1:25:52.077904 PROGRESS: 
1:25:52.084418 PROGRESS: Precursor Summary:
1:25:52.096420 PROGRESS: Channel   0:	 0.050 FDR:   659; 0.010 FDR:   431; 0.001 FDR:   249
1:25:52.106420 PROGRESS: 
1:25:52.119420 PROGRESS: Protein Summary:
1:25:52.141421 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   393; 0.001 FDR:   231
1:25:52.151420 PROGRESS: =========================================================================
1:25:52.164421 INFO: Target number of precursors reached.
1:25:53.328520 INFO: fragments_df: keeping 5000 of 6260240 [sum(precursor_idx_mask)=12892 sum(mass_error_mask)=6260240 stop_rank=5000
1:25:53.914077 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:25:54.229601 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:54.519124 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:57.858463 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:57.863463 INFO: Using score_cutoff 48.68989672851562 (fac=0.99, q=1)
1:25:57.868464 INFO: Updating optimization_manager: fwhm_rt             : 2.506518602371216 -> 2.5037665367126465
1:25:57.872467 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:25:57.876466 INFO: Updating optimization_manager: score_cutoff        : 54.533814793396 -> 48.68989672851562
1:25:57.880466 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:25:57.919463 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:58.013466 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:58.431880 INFO: === checking if optimization conditions were reached ===
1:25:58.440881 INFO: Updating optimization_manager: ms2_error           : 30 -> 19.21686704484286
1:25:58.444880 INFO: Updating optimization_manager: classifier_version  : 2 -> 4
1:25:58.448879 PROGRESS: ❌ ms2_error      : 19.2169 > 10.0000 or insufficient steps taken.
1:25:58.454881 INFO: Updating optimization_manager: ms1_error           : 30 -> 11.409031305333514
1:25:58.458881 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
1:25:58.462879 PROGRESS: ❌ ms1_error      : 11.4090 > 5.0000 or insufficient steps taken.
1:25:58.466880 INFO: ==============================================
1:25:58.470881 INFO: Starting optimization step 5.
1:25:58.474880 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:25:58.478879 INFO: Using classic extraction backend
1:25:58.482881 PROGRESS: Extracting batch of 109921 precursors
1:25:58.486882 INFO: === Search parameters used ===
1:25:58.493879 INFO: rt_error       : 1662.8485107421875
1:25:58.500882 INFO: mobility_error : 0.1
1:25:58.506881 INFO: num_candidates : 3
1:25:58.515883 INFO: ms1_error      : 11.409031305333514
1:25:58.522878 INFO: ms2_error      : 19.21686704484286
1:25:58.529880 INFO: fwhm_rt        : 2.5037665367126465
1:25:58.536881 INFO: quant_window   : 3
1:25:58.552883 INFO: ==============================================
1:25:58.634438 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:25:58.635444 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:25:58.637439 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
1:25:58.638438 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:25:58.639437 INFO: Starting candidate selection
1:27:45.774237 INFO: Starting candidate scoring
1:27:55.948517 INFO: Finished candidate processing
1:27:55.949517 INFO: Collecting candidate features
1:27:57.269140 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 329478)
1:27:57.319653 INFO: Collecting fragment features
1:27:57.857702 INFO: Finished candidate scoring
1:27:58.127224 INFO: performing precursor FDR with 47 features
1:27:58.129225 INFO: Decoy channel: -1
1:27:58.130225 INFO: Competetive: True
1:27:58.399747 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:58.553269 WARNING: dropped 3 target PSMs due to missing features
1:27:58.556269 WARNING: dropped 1 decoy PSMs due to missing features
1:27:58.852793 INFO: Using random state 276376 for train-test-split
1:28:06.336498 INFO: Test AUC: 0.582
1:28:06.337498 INFO: Train AUC: 0.601
1:28:06.338498 INFO: AUC difference: 3.23%
1:28:07.165068 INFO: Resetting torch num_threads to 10
1:28:07.203069 PROGRESS: === Extracted 329478 precursors and 2750526 fragments ===
1:28:07.209068 INFO: === FDR correction performed with classifier version 4 ===
1:28:07.217068 PROGRESS: ============================= Precursor FDR =============================
1:28:07.222069 PROGRESS: Total precursors accumulated: 688
1:28:07.226069 PROGRESS: Target precursors: 626 (90.99%)
1:28:07.231069 PROGRESS: Decoy precursors: 62 (9.01%)
1:28:07.236069 PROGRESS: 
1:28:07.240068 PROGRESS: Precursor Summary:
1:28:07.250069 PROGRESS: Channel   0:	 0.050 FDR:   457; 0.010 FDR:   343; 0.001 FDR:   248
1:28:07.255070 PROGRESS: 
1:28:07.260073 PROGRESS: Protein Summary:
1:28:07.268069 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   319; 0.001 FDR:   235
1:28:07.273069 PROGRESS: =========================================================================
1:28:07.279069 INFO: Target number of precursors reached.
1:28:07.764116 INFO: fragments_df: keeping 4734 of 2750526 [sum(precursor_idx_mask)=9982 sum(mass_error_mask)=2750526 stop_rank=4734
1:28:08.328683 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:28:08.607205 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:08.959730 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:12.043009 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:12.049010 INFO: Using score_cutoff 54.456976874542235 (fac=0.99, q=1)
1:28:12.053010 INFO: Updating optimization_manager: fwhm_rt             : 2.5037665367126465 -> 2.4971506595611572
1:28:12.056524 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:28:12.060524 INFO: Updating optimization_manager: score_cutoff        : 48.68989672851562 -> 54.456976874542235
1:28:12.064524 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:28:12.102524 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:12.204525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:12.624568 INFO: === checking if optimization conditions were reached ===
1:28:12.633569 INFO: Updating optimization_manager: ms2_error           : 19.21686704484286 -> 11.924835048072445
1:28:12.637569 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
1:28:12.641568 PROGRESS: ❌ ms2_error      : 11.9248 > 10.0000 or insufficient steps taken.
1:28:12.647568 INFO: Updating optimization_manager: ms1_error           : 11.409031305333514 -> 5.0
1:28:12.651569 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
1:28:12.655569 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
1:28:12.659569 INFO: ==============================================
1:28:12.663569 INFO: Starting optimization step 6.
1:28:12.671569 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:28:12.678569 INFO: Using classic extraction backend
1:28:12.685569 PROGRESS: Extracting batch of 109921 precursors
1:28:12.693571 INFO: === Search parameters used ===
1:28:12.701569 INFO: rt_error       : 1662.8485107421875
1:28:12.709570 INFO: mobility_error : 0.1
1:28:12.717570 INFO: num_candidates : 3
1:28:12.724570 INFO: ms1_error      : 5.0
1:28:12.734570 INFO: ms2_error      : 11.924835048072445
1:28:12.742569 INFO: fwhm_rt        : 2.4971506595611572
1:28:12.752572 INFO: quant_window   : 3
1:28:12.758587 INFO: ==============================================
1:28:12.838091 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:28:12.839091 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:12.840091 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
1:28:12.841091 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:28:12.842092 INFO: Starting candidate selection
1:29:59.868192 INFO: Starting candidate scoring
1:30:11.099022 INFO: Finished candidate processing
1:30:11.100029 INFO: Collecting candidate features
1:30:12.363653 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 329303)
1:30:12.366652 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329303)
1:30:12.414653 INFO: Collecting fragment features
1:30:12.930714 INFO: Finished candidate scoring
1:30:13.232246 INFO: performing precursor FDR with 47 features
1:30:13.233246 INFO: Decoy channel: -1
1:30:13.234247 INFO: Competetive: True
1:30:13.484771 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:13.639287 WARNING: dropped 4 target PSMs due to missing features
1:30:13.640288 WARNING: dropped 6 decoy PSMs due to missing features
1:30:13.954812 INFO: Using random state 568552 for train-test-split
1:30:21.402570 INFO: Test AUC: 0.575
1:30:21.404569 INFO: Train AUC: 0.598
1:30:21.404569 INFO: AUC difference: 3.93%
1:30:22.218142 INFO: Resetting torch num_threads to 10
1:30:22.242142 PROGRESS: === Extracted 329303 precursors and 2558861 fragments ===
1:30:22.249151 INFO: === FDR correction performed with classifier version 5 ===
1:30:22.254151 PROGRESS: ============================= Precursor FDR =============================
1:30:22.258151 PROGRESS: Total precursors accumulated: 721
1:30:22.261666 PROGRESS: Target precursors: 657 (91.12%)
1:30:22.265665 PROGRESS: Decoy precursors: 64 (8.88%)
1:30:22.269665 PROGRESS: 
1:30:22.272666 PROGRESS: Precursor Summary:
1:30:22.279665 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   335; 0.001 FDR:   245
1:30:22.283665 PROGRESS: 
1:30:22.287663 PROGRESS: Protein Summary:
1:30:22.294665 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   314; 0.001 FDR:   234
1:30:22.298665 PROGRESS: =========================================================================
1:30:22.304667 INFO: Target number of precursors reached.
1:30:22.776793 INFO: fragments_df: keeping 4586 of 2558861 [sum(precursor_idx_mask)=9336 sum(mass_error_mask)=2558861 stop_rank=4586
1:30:23.313977 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:30:23.596596 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:30:23.915210 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:30:26.812502 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:30:26.817502 INFO: Using score_cutoff 68.55150480194092 (fac=0.99, q=1)
1:30:26.821503 INFO: Updating optimization_manager: fwhm_rt             : 2.4971506595611572 -> 2.4753406047821045
1:30:26.825502 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:30:26.829502 INFO: Updating optimization_manager: score_cutoff        : 54.456976874542235 -> 68.55150480194092
1:30:26.833502 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:30:26.870502 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:30:26.963503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:30:27.383554 INFO: === checking if optimization conditions were reached ===
1:30:27.391554 INFO: Updating optimization_manager: ms2_error           : 11.924835048072445 -> 10.0
1:30:27.396555 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
1:30:27.399555 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:30:27.403555 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
1:30:27.407554 INFO: ==============================================
1:30:27.410555 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:30:27.916601 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:30:27.955602 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:30:28.049124 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:30:28.461649 INFO: Starting optimization step 0.
1:30:28.466651 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:30:28.470651 INFO: Using classic extraction backend
1:30:28.479650 PROGRESS: Extracting batch of 109921 precursors
1:30:28.486652 INFO: === Search parameters used ===
1:30:28.494650 INFO: rt_error       : 1662.8485107421875
1:30:28.503651 INFO: mobility_error : 0.1
1:30:28.511659 INFO: num_candidates : 3
1:30:28.515659 INFO: ms1_error      : 5.0
1:30:28.523166 INFO: ms2_error      : 10.0
1:30:28.530174 INFO: fwhm_rt        : 2.4753406047821045
1:30:28.539173 INFO: quant_window   : 3
1:30:28.546175 INFO: ==============================================
1:30:28.627174 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:30:28.628174 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:28.629174 INFO: FWHM in RT is 2.48 seconds, sigma is 0.28
1:30:28.630175 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:28.631175 INFO: Starting candidate selection
1:32:15.128923 INFO: Starting candidate scoring
1:32:24.874040 INFO: Finished candidate processing
1:32:24.875050 INFO: Collecting candidate features
1:32:25.926194 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 329253)
1:32:25.928194 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 329253)
1:32:25.972723 INFO: Collecting fragment features
1:32:26.427286 INFO: Finished candidate scoring
1:32:26.698362 INFO: performing precursor FDR with 47 features
1:32:26.699363 INFO: Decoy channel: -1
1:32:26.700361 INFO: Competetive: True
1:32:26.924376 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:27.060900 WARNING: dropped 3 target PSMs due to missing features
1:32:27.061900 WARNING: dropped 7 decoy PSMs due to missing features
1:32:27.324448 INFO: Using random state 797481 for train-test-split
1:32:33.877441 INFO: Test AUC: 0.583
1:32:33.879441 INFO: Train AUC: 0.606
1:32:33.880441 INFO: AUC difference: 3.72%
1:32:34.688986 INFO: Resetting torch num_threads to 10
1:32:34.728494 PROGRESS: === Extracted 329253 precursors and 2521586 fragments ===
1:32:34.735493 INFO: === FDR correction performed with classifier version 6 ===
1:32:34.743493 PROGRESS: ============================= Precursor FDR =============================
1:32:34.748495 PROGRESS: Total precursors accumulated: 881
1:32:34.753493 PROGRESS: Target precursors: 804 (91.26%)
1:32:34.757493 PROGRESS: Decoy precursors: 77 (8.74%)
1:32:34.761494 PROGRESS: 
1:32:34.765494 PROGRESS: Precursor Summary:
1:32:34.774496 PROGRESS: Channel   0:	 0.050 FDR:   573; 0.010 FDR:   348; 0.001 FDR:   223
1:32:34.778495 PROGRESS: 
1:32:34.782495 PROGRESS: Protein Summary:
1:32:34.790506 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   326; 0.001 FDR:   214
1:32:34.794493 PROGRESS: =========================================================================
1:32:34.800494 INFO: Target number of precursors reached.
1:32:35.241521 INFO: fragments_df: keeping 4678 of 2521586 [sum(precursor_idx_mask)=9574 sum(mass_error_mask)=2521586 stop_rank=4678
1:32:35.746548 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:32:36.025061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:32:36.930606 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:32:39.903774 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:32:39.908775 INFO: Using score_cutoff 54.09722983131409 (fac=0.99, q=1)
1:32:39.912775 INFO: Updating optimization_manager: fwhm_rt             : 2.4753406047821045 -> 2.5429646968841553
1:32:39.916775 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:32:39.920775 INFO: Updating optimization_manager: score_cutoff        : 68.55150480194092 -> 54.09722983131409
1:32:39.923775 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:32:39.983287 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:32:40.096288 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:32:40.499323 INFO: === checking if optimization conditions were reached ===
1:32:40.504325 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:32:40.510324 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 356.27984763781745
1:32:40.518326 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 356.2798.
1:32:40.525328 INFO: ==============================================
1:32:40.533327 INFO: Starting optimization step 1.
1:32:40.540331 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:32:40.549334 INFO: Using classic extraction backend
1:32:40.556331 PROGRESS: Extracting batch of 109921 precursors
1:32:40.563332 INFO: === Search parameters used ===
1:32:40.568329 INFO: rt_error       : 356.27984763781745
1:32:40.581333 INFO: mobility_error : 0.1
1:32:40.590332 INFO: num_candidates : 3
1:32:40.602330 INFO: ms1_error      : 5.0
1:32:40.610336 INFO: ms2_error      : 10.0
1:32:40.618331 INFO: fwhm_rt        : 2.5429646968841553
1:32:40.623331 INFO: quant_window   : 3
1:32:40.628331 INFO: ==============================================
1:32:40.698351 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:32:40.699353 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:32:40.700350 INFO: FWHM in RT is 2.54 seconds, sigma is 0.28
1:32:40.700350 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:32:40.701351 INFO: Starting candidate selection
1:33:04.499667 INFO: Starting candidate scoring
1:33:12.975266 INFO: Finished candidate processing
1:33:12.977343 INFO: Collecting candidate features
1:33:13.958093 WARNING: intensity_correlation has 14 NaNs ( 0.00 % out of 329221)
1:33:13.960662 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329221)
1:33:14.006448 INFO: Collecting fragment features
1:33:14.464745 INFO: Finished candidate scoring
1:33:14.730808 INFO: performing precursor FDR with 47 features
1:33:14.731807 INFO: Decoy channel: -1
1:33:14.732805 INFO: Competetive: True
1:33:14.954331 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:15.089863 WARNING: dropped 6 target PSMs due to missing features
1:33:15.090860 WARNING: dropped 8 decoy PSMs due to missing features
1:33:15.350393 INFO: Using random state 797481 for train-test-split
1:33:21.944611 INFO: Test AUC: 0.573
1:33:21.946612 INFO: Train AUC: 0.602
1:33:21.947611 INFO: AUC difference: 4.87%
1:33:22.719195 INFO: Resetting torch num_threads to 10
1:33:22.744195 PROGRESS: === Extracted 329221 precursors and 2500831 fragments ===
1:33:22.750196 INFO: === FDR correction performed with classifier version 6 ===
1:33:22.756197 PROGRESS: ============================= Precursor FDR =============================
1:33:22.760195 PROGRESS: Total precursors accumulated: 760
1:33:22.764203 PROGRESS: Target precursors: 692 (91.05%)
1:33:22.768203 PROGRESS: Decoy precursors: 68 (8.95%)
1:33:22.772204 PROGRESS: 
1:33:22.776204 PROGRESS: Precursor Summary:
1:33:22.782720 PROGRESS: Channel   0:	 0.050 FDR:   523; 0.010 FDR:   371; 0.001 FDR:   337
1:33:22.786721 PROGRESS: 
1:33:22.790721 PROGRESS: Protein Summary:
1:33:22.798722 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   344; 0.001 FDR:   315
1:33:22.802722 PROGRESS: =========================================================================
1:33:22.808722 INFO: Target number of precursors reached.
1:33:23.253248 INFO: fragments_df: keeping 4980 of 2500831 [sum(precursor_idx_mask)=10151 sum(mass_error_mask)=2500831 stop_rank=4980
1:33:23.790826 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:33:24.144356 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:33:24.411883 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:33:27.663747 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:33:27.668746 INFO: Using score_cutoff 64.58817531967162 (fac=0.99, q=1)
1:33:27.673747 INFO: Updating optimization_manager: fwhm_rt             : 2.5429646968841553 -> 2.5268898010253906
1:33:27.677746 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:33:27.680747 INFO: Updating optimization_manager: score_cutoff        : 54.09722983131409 -> 64.58817531967162
1:33:27.684747 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:33:27.721745 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:27.833308 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:28.251828 INFO: === checking if optimization conditions were reached ===
1:33:28.256828 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:33:28.263829 INFO: Updating optimization_manager: rt_error            : 356.27984763781745 -> 167.44852231922758
1:33:28.268829 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 167.4485.
1:33:28.271829 INFO: ==============================================
1:33:28.275838 INFO: Starting optimization step 2.
1:33:28.279837 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:33:28.283837 INFO: Using classic extraction backend
1:33:28.287836 PROGRESS: Extracting batch of 109921 precursors
1:33:28.292351 INFO: === Search parameters used ===
1:33:28.296353 INFO: rt_error       : 167.44852231922758
1:33:28.299351 INFO: mobility_error : 0.1
1:33:28.303351 INFO: num_candidates : 3
1:33:28.307353 INFO: ms1_error      : 5.0
1:33:28.311352 INFO: ms2_error      : 10.0
1:33:28.318353 INFO: fwhm_rt        : 2.5268898010253906
1:33:28.348352 INFO: quant_window   : 3
1:33:28.356353 INFO: ==============================================
1:33:28.440353 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:33:28.441353 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:33:28.442353 INFO: FWHM in RT is 2.53 seconds, sigma is 0.28
1:33:28.443353 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:33:28.444353 INFO: Starting candidate selection
1:33:41.299193 INFO: Starting candidate scoring
1:33:50.804986 INFO: Finished candidate processing
1:33:50.806997 INFO: Collecting candidate features
1:33:51.900722 WARNING: intensity_correlation has 18 NaNs ( 0.01 % out of 329155)
1:33:51.902722 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 329155)
1:33:51.952723 INFO: Collecting fragment features
1:33:52.486777 INFO: Finished candidate scoring
1:33:52.756303 INFO: performing precursor FDR with 47 features
1:33:52.757303 INFO: Decoy channel: -1
1:33:52.758303 INFO: Competetive: True
1:33:53.012839 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:53.181365 WARNING: dropped 9 target PSMs due to missing features
1:33:53.182365 WARNING: dropped 11 decoy PSMs due to missing features
1:33:53.499890 INFO: Using random state 797481 for train-test-split
1:34:00.682348 INFO: Test AUC: 0.567
1:34:00.683344 INFO: Train AUC: 0.594
1:34:00.684344 INFO: AUC difference: 4.62%
1:34:01.558108 INFO: Resetting torch num_threads to 10
1:34:01.583124 PROGRESS: === Extracted 329155 precursors and 2459284 fragments ===
1:34:01.589123 INFO: === FDR correction performed with classifier version 6 ===
1:34:01.594715 PROGRESS: ============================= Precursor FDR =============================
1:34:01.598717 PROGRESS: Total precursors accumulated: 825
1:34:01.602720 PROGRESS: Target precursors: 752 (91.15%)
1:34:01.605717 PROGRESS: Decoy precursors: 73 (8.85%)
1:34:01.609718 PROGRESS: 
1:34:01.613719 PROGRESS: Precursor Summary:
1:34:01.619717 PROGRESS: Channel   0:	 0.050 FDR:   609; 0.010 FDR:   368; 0.001 FDR:   306
1:34:01.624717 PROGRESS: 
1:34:01.627718 PROGRESS: Protein Summary:
1:34:01.635717 PROGRESS: Channel   0:	 0.050 FDR:   566; 0.010 FDR:   341; 0.001 FDR:   290
1:34:01.639716 PROGRESS: =========================================================================
1:34:01.645716 INFO: Target number of precursors reached.
1:34:02.091847 INFO: fragments_df: keeping 4870 of 2459284 [sum(precursor_idx_mask)=10101 sum(mass_error_mask)=2459284 stop_rank=4870
1:34:02.654096 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:34:03.019709 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:03.366836 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:06.611809 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:06.619810 INFO: Using score_cutoff 61.65147724227906 (fac=0.99, q=1)
1:34:06.626810 INFO: Updating optimization_manager: fwhm_rt             : 2.5268898010253906 -> 2.518996477127075
1:34:06.631810 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:34:06.636811 INFO: Updating optimization_manager: score_cutoff        : 64.58817531967162 -> 61.65147724227906
1:34:06.641809 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:34:06.679810 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:06.766810 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:07.126048 INFO: === checking if optimization conditions were reached ===
1:34:07.132048 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:34:07.142049 INFO: Updating optimization_manager: rt_error            : 167.44852231922758 -> 97.2792573902204
1:34:07.148046 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 97.2793.
1:34:07.154048 INFO: ==============================================
1:34:07.159048 INFO: Starting optimization step 3.
1:34:07.163048 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:34:07.168048 INFO: Using classic extraction backend
1:34:07.172049 PROGRESS: Extracting batch of 109921 precursors
1:34:07.177046 INFO: === Search parameters used ===
1:34:07.180048 INFO: rt_error       : 97.2792573902204
1:34:07.183048 INFO: mobility_error : 0.1
1:34:07.186046 INFO: num_candidates : 3
1:34:07.189047 INFO: ms1_error      : 5.0
1:34:07.192049 INFO: ms2_error      : 10.0
1:34:07.195048 INFO: fwhm_rt        : 2.518996477127075
1:34:07.197047 INFO: quant_window   : 3
1:34:07.200049 INFO: ==============================================
1:34:07.255053 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:34:07.256047 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:34:07.256047 INFO: FWHM in RT is 2.52 seconds, sigma is 0.28
1:34:07.257047 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:34:07.258047 INFO: Starting candidate selection
1:34:15.949721 INFO: Starting candidate scoring
1:34:25.239532 INFO: Finished candidate processing
1:34:25.241548 INFO: Collecting candidate features
1:34:26.514954 WARNING: intensity_correlation has 47 NaNs ( 0.01 % out of 329143)
1:34:26.519953 WARNING: height_correlation has 33 NaNs ( 0.01 % out of 329143)
1:34:26.588954 INFO: Collecting fragment features
1:34:27.099025 INFO: Finished candidate scoring
1:34:27.383075 INFO: performing precursor FDR with 47 features
1:34:27.384082 INFO: Decoy channel: -1
1:34:27.385083 INFO: Competetive: True
1:34:27.668610 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:27.842612 WARNING: dropped 37 target PSMs due to missing features
1:34:27.843611 WARNING: dropped 27 decoy PSMs due to missing features
1:34:28.171669 INFO: Using random state 797481 for train-test-split
1:34:34.694740 INFO: Test AUC: 0.566
1:34:34.695740 INFO: Train AUC: 0.590
1:34:34.696739 INFO: AUC difference: 4.06%
1:34:35.348963 INFO: Resetting torch num_threads to 10
1:34:35.370963 PROGRESS: === Extracted 329143 precursors and 2415138 fragments ===
1:34:35.378963 INFO: === FDR correction performed with classifier version 6 ===
1:34:35.383963 PROGRESS: ============================= Precursor FDR =============================
1:34:35.387975 PROGRESS: Total precursors accumulated: 948
1:34:35.391976 PROGRESS: Target precursors: 867 (91.46%)
1:34:35.395976 PROGRESS: Decoy precursors: 81 (8.54%)
1:34:35.399492 PROGRESS: 
1:34:35.402506 PROGRESS: Precursor Summary:
1:34:35.407505 PROGRESS: Channel   0:	 0.050 FDR:   633; 0.010 FDR:   422; 0.001 FDR:   381
1:34:35.411505 PROGRESS: 
1:34:35.413508 PROGRESS: Protein Summary:
1:34:35.419508 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   391; 0.001 FDR:   357
1:34:35.422507 PROGRESS: =========================================================================
1:34:35.427508 INFO: Target number of precursors reached.
1:34:35.782115 INFO: fragments_df: keeping 5000 of 2415138 [sum(precursor_idx_mask)=11297 sum(mass_error_mask)=2415138 stop_rank=5000
1:34:36.300275 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:34:36.645811 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:36.965863 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:40.170772 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:40.176773 INFO: Using score_cutoff 57.452126697921756 (fac=0.99, q=1)
1:34:40.181773 INFO: Updating optimization_manager: fwhm_rt             : 2.518996477127075 -> 2.5350027084350586
1:34:40.185772 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:34:40.190772 INFO: Updating optimization_manager: score_cutoff        : 61.65147724227906 -> 57.452126697921756
1:34:40.195772 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:34:40.233772 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:40.327774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:40.740834 INFO: === checking if optimization conditions were reached ===
1:34:40.747833 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:34:40.757834 INFO: Updating optimization_manager: rt_error            : 97.2792573902204 -> 85.79538019995444
1:34:40.763834 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 85.7954.
1:34:40.770834 INFO: ==============================================
1:34:40.775834 INFO: Starting optimization step 4.
1:34:40.779835 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:34:40.784834 INFO: Using classic extraction backend
1:34:40.789836 PROGRESS: Extracting batch of 109921 precursors
1:34:40.797835 INFO: === Search parameters used ===
1:34:40.805835 INFO: rt_error       : 85.79538019995444
1:34:40.814835 INFO: mobility_error : 0.1
1:34:40.824835 INFO: num_candidates : 3
1:34:40.832835 INFO: ms1_error      : 5.0
1:34:40.842835 INFO: ms2_error      : 10.0
1:34:40.848835 INFO: fwhm_rt        : 2.5350027084350586
1:34:40.855835 INFO: quant_window   : 3
1:34:40.864836 INFO: ==============================================
1:34:40.934361 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:34:40.936361 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:34:40.937361 INFO: FWHM in RT is 2.54 seconds, sigma is 0.28
1:34:40.938361 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:34:40.940361 INFO: Starting candidate selection
1:34:48.240788 INFO: Starting candidate scoring
1:34:58.546105 INFO: Finished candidate processing
1:34:58.548113 INFO: Collecting candidate features
1:34:59.788741 WARNING: intensity_correlation has 52 NaNs ( 0.02 % out of 329119)
1:34:59.790742 WARNING: height_correlation has 43 NaNs ( 0.01 % out of 329119)
1:34:59.843743 INFO: Collecting fragment features
1:35:00.356790 INFO: Finished candidate scoring
1:35:00.617314 INFO: performing precursor FDR with 47 features
1:35:00.618315 INFO: Decoy channel: -1
1:35:00.619314 INFO: Competetive: True
1:35:00.866839 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:01.022363 WARNING: dropped 42 target PSMs due to missing features
1:35:01.023363 WARNING: dropped 34 decoy PSMs due to missing features
1:35:01.352891 INFO: Using random state 797481 for train-test-split
1:35:08.625633 INFO: Test AUC: 0.563
1:35:08.627633 INFO: Train AUC: 0.590
1:35:08.627633 INFO: AUC difference: 4.67%
1:35:09.364296 INFO: Resetting torch num_threads to 10
1:35:09.389296 PROGRESS: === Extracted 329119 precursors and 2396818 fragments ===
1:35:09.397297 INFO: === FDR correction performed with classifier version 6 ===
1:35:09.404296 PROGRESS: ============================= Precursor FDR =============================
1:35:09.408295 PROGRESS: Total precursors accumulated: 868
1:35:09.413297 PROGRESS: Target precursors: 791 (91.13%)
1:35:09.418296 PROGRESS: Decoy precursors: 77 (8.87%)
1:35:09.422297 PROGRESS: 
1:35:09.426297 PROGRESS: Precursor Summary:
1:35:09.432296 PROGRESS: Channel   0:	 0.050 FDR:   594; 0.010 FDR:   480; 0.001 FDR:   360
1:35:09.436296 PROGRESS: 
1:35:09.440296 PROGRESS: Protein Summary:
1:35:09.447305 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   442; 0.001 FDR:   335
1:35:09.451306 PROGRESS: =========================================================================
1:35:09.456305 INFO: Target number of precursors reached.
1:35:09.861351 INFO: fragments_df: keeping 5000 of 2396818 [sum(precursor_idx_mask)=12907 sum(mass_error_mask)=2396818 stop_rank=5000
1:35:10.285404 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:35:10.628932 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:10.997984 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:14.317826 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:35:14.324827 INFO: Using score_cutoff 57.29970799827576 (fac=0.99, q=1)
1:35:14.331826 INFO: Updating optimization_manager: fwhm_rt             : 2.5350027084350586 -> 2.5708746910095215
1:35:14.335826 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:35:14.340826 INFO: Updating optimization_manager: score_cutoff        : 57.452126697921756 -> 57.29970799827576
1:35:14.345827 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:35:14.365826 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:14.411827 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:14.594352 INFO: === checking if optimization conditions were reached ===
1:35:14.601352 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1:35:14.610353 INFO: Updating optimization_manager: rt_error            : 85.79538019995444 -> 79.79525902344476
1:35:14.616353 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 79.7953.
1:35:14.622354 INFO: ==============================================
1:35:14.628354 INFO: Starting optimization step 5.
1:35:14.632353 PROGRESS: === Extracting elution groups 0 to 24000 ===
1:35:14.637355 INFO: Using classic extraction backend
1:35:14.641354 PROGRESS: Extracting batch of 47079 precursors
1:35:14.646354 INFO: === Search parameters used ===
1:35:14.649353 INFO: rt_error       : 79.79525902344476
1:35:14.652353 INFO: mobility_error : 0.1
1:35:14.655354 INFO: num_candidates : 3
1:35:14.658354 INFO: ms1_error      : 5.0
1:35:14.661355 INFO: ms2_error      : 10.0
1:35:14.666354 INFO: fwhm_rt        : 2.5708746910095215
1:35:14.673354 INFO: quant_window   : 3
1:35:14.679354 INFO: ==============================================
1:35:14.717364 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:35:14.717364 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:35:14.718871 INFO: FWHM in RT is 2.57 seconds, sigma is 0.29
1:35:14.719879 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:35:14.720880 INFO: Starting candidate selection
1:35:17.999765 INFO: Starting candidate scoring
1:35:21.860855 INFO: Finished candidate processing
1:35:21.862864 INFO: Collecting candidate features
1:35:22.407918 WARNING: intensity_correlation has 16 NaNs ( 0.01 % out of 140932)
1:35:22.409918 WARNING: height_correlation has 23 NaNs ( 0.02 % out of 140932)
1:35:22.435920 INFO: Collecting fragment features
1:35:22.658442 INFO: Finished candidate scoring
1:35:22.762968 INFO: performing precursor FDR with 47 features
1:35:22.763968 INFO: Decoy channel: -1
1:35:22.764968 INFO: Competetive: True
1:35:22.879969 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:22.950970 WARNING: dropped 15 target PSMs due to missing features
1:35:22.951971 WARNING: dropped 14 decoy PSMs due to missing features
1:35:23.066493 INFO: Using random state 797481 for train-test-split
1:35:26.077795 INFO: Test AUC: 0.561
1:35:26.078794 INFO: Train AUC: 0.599
1:35:26.079795 INFO: AUC difference: 6.36%
1:35:26.080795 WARNING: AUC difference > 5%. This may indicate overfitting.
1:35:26.638886 INFO: Resetting torch num_threads to 10
1:35:26.649886 PROGRESS: === Extracted 140932 precursors and 1029093 fragments ===
1:35:26.655886 INFO: === FDR correction performed with classifier version 6 ===
1:35:26.660887 PROGRESS: ============================= Precursor FDR =============================
1:35:26.665886 PROGRESS: Total precursors accumulated: 378
1:35:26.668886 PROGRESS: Target precursors: 344 (91.01%)
1:35:26.672890 PROGRESS: Decoy precursors: 34 (8.99%)
1:35:26.676891 PROGRESS: 
1:35:26.680891 PROGRESS: Precursor Summary:
1:35:26.687890 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   118; 0.001 FDR:   113
1:35:26.691891 PROGRESS: 
1:35:26.695890 PROGRESS: Protein Summary:
1:35:26.707890 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   118; 0.001 FDR:   113
1:35:26.711890 PROGRESS: =========================================================================
1:35:26.716890 INFO: Target number of precursors not reached yet.
1:35:27.105936 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:35:27.130939 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:27.189937 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:27.428462 INFO: === skipping optimization until target number of precursors are found ===
1:35:27.432462 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:35:27.436461 INFO: Starting optimization step 6.
1:35:27.439462 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:35:27.443464 INFO: Using classic extraction backend
1:35:27.447461 PROGRESS: Extracting batch of 62842 precursors
1:35:27.450462 INFO: === Search parameters used ===
1:35:27.454462 INFO: rt_error       : 79.79525902344476
1:35:27.458462 INFO: mobility_error : 0.1
1:35:27.461466 INFO: num_candidates : 3
1:35:27.465462 INFO: ms1_error      : 5.0
1:35:27.469462 INFO: ms2_error      : 10.0
1:35:27.473462 INFO: fwhm_rt        : 2.5708746910095215
1:35:27.477469 INFO: quant_window   : 3
1:35:27.480470 INFO: ==============================================
1:35:27.518985 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:35:27.519987 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:35:27.520985 INFO: FWHM in RT is 2.57 seconds, sigma is 0.29
1:35:27.521985 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:35:27.522986 INFO: Starting candidate selection
1:35:32.091127 INFO: Starting candidate scoring
1:35:38.558077 INFO: Finished candidate processing
1:35:38.559072 INFO: Collecting candidate features
1:35:39.244128 WARNING: intensity_correlation has 33 NaNs ( 0.02 % out of 188170)
1:35:39.246128 WARNING: height_correlation has 21 NaNs ( 0.01 % out of 188170)
1:35:39.278643 INFO: Collecting fragment features
1:35:39.574171 INFO: Finished candidate scoring
1:35:39.875696 INFO: performing precursor FDR with 47 features
1:35:39.876697 INFO: Decoy channel: -1
1:35:39.877698 INFO: Competetive: True
1:35:40.219223 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:40.377748 WARNING: dropped 37 target PSMs due to missing features
1:35:40.379748 WARNING: dropped 36 decoy PSMs due to missing features
1:35:40.692275 INFO: Using random state 797481 for train-test-split
1:35:48.117381 INFO: Test AUC: 0.564
1:35:48.119381 INFO: Train AUC: 0.591
1:35:48.120381 INFO: AUC difference: 4.52%
1:35:49.032493 INFO: Resetting torch num_threads to 10
1:35:49.215494 PROGRESS: === Extracted 329102 precursors and 2401515 fragments ===
1:35:49.224494 INFO: === FDR correction performed with classifier version 6 ===
1:35:49.233494 PROGRESS: ============================= Precursor FDR =============================
1:35:49.239496 PROGRESS: Total precursors accumulated: 894
1:35:49.244494 PROGRESS: Target precursors: 817 (91.39%)
1:35:49.250495 PROGRESS: Decoy precursors: 77 (8.61%)
1:35:49.255504 PROGRESS: 
1:35:49.260495 PROGRESS: Precursor Summary:
1:35:49.272502 PROGRESS: Channel   0:	 0.050 FDR:   590; 0.010 FDR:   392; 0.001 FDR:   284
1:35:49.277503 PROGRESS: 
1:35:49.282019 PROGRESS: Protein Summary:
1:35:49.291018 PROGRESS: Channel   0:	 0.050 FDR:   546; 0.010 FDR:   363; 0.001 FDR:   268
1:35:49.295018 PROGRESS: =========================================================================
1:35:49.301030 INFO: Target number of precursors reached.
1:35:49.767556 INFO: fragments_df: keeping 4985 of 2401515 [sum(precursor_idx_mask)=10619 sum(mass_error_mask)=2401515 stop_rank=4985
1:35:50.306128 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:35:50.683657 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:51.033712 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:54.195193 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:35:54.200193 INFO: Using score_cutoff 62.18273820533752 (fac=0.99, q=1)
1:35:54.204193 INFO: Updating optimization_manager: fwhm_rt             : 2.5708746910095215 -> 2.5381741523742676
1:35:54.208193 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:35:54.212193 INFO: Updating optimization_manager: score_cutoff        : 57.29970799827576 -> 62.18273820533752
1:35:54.216192 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:35:54.253192 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:54.346716 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:54.761245 INFO: === checking if optimization conditions were reached ===
1:35:54.766245 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1:35:54.773245 INFO: Updating optimization_manager: rt_error            : 79.79525902344476 -> 75.93331156814064
1:35:54.778254 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 75.9333.
1:35:54.782253 INFO: ==============================================
1:35:54.785253 INFO: Starting optimization step 7.
1:35:54.789253 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:35:54.792768 INFO: Using classic extraction backend
1:35:54.796771 PROGRESS: Extracting batch of 109921 precursors
1:35:54.800769 INFO: === Search parameters used ===
1:35:54.803769 INFO: rt_error       : 75.93331156814064
1:35:54.807769 INFO: mobility_error : 0.1
1:35:54.811769 INFO: num_candidates : 3
1:35:54.814769 INFO: ms1_error      : 5.0
1:35:54.820769 INFO: ms2_error      : 10.0
1:35:54.846769 INFO: fwhm_rt        : 2.5381741523742676
1:35:54.854769 INFO: quant_window   : 3
1:35:54.864769 INFO: ==============================================
1:35:54.950770 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:35:54.952771 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:35:54.953771 INFO: FWHM in RT is 2.54 seconds, sigma is 0.28
1:35:54.953771 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:35:54.955770 INFO: Starting candidate selection
1:36:02.416524 INFO: Starting candidate scoring
1:36:11.358281 INFO: Finished candidate processing
1:36:11.360297 INFO: Collecting candidate features
1:36:12.491430 WARNING: intensity_correlation has 44 NaNs ( 0.01 % out of 329046)
1:36:12.494429 WARNING: height_correlation has 44 NaNs ( 0.01 % out of 329046)
1:36:12.543429 INFO: Collecting fragment features
1:36:13.070004 INFO: Finished candidate scoring
1:36:13.356528 INFO: performing precursor FDR with 47 features
1:36:13.357530 INFO: Decoy channel: -1
1:36:13.358529 INFO: Competetive: True
1:36:13.607058 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:13.763059 WARNING: dropped 43 target PSMs due to missing features
1:36:13.764059 WARNING: dropped 29 decoy PSMs due to missing features
1:36:14.069594 INFO: Using random state 797481 for train-test-split
1:36:21.421849 INFO: Test AUC: 0.566
1:36:21.422850 INFO: Train AUC: 0.589
1:36:21.423850 INFO: AUC difference: 3.91%
1:36:22.270428 INFO: Resetting torch num_threads to 10
1:36:22.294428 PROGRESS: === Extracted 329046 precursors and 2384623 fragments ===
1:36:22.300429 INFO: === FDR correction performed with classifier version 6 ===
1:36:22.306428 PROGRESS: ============================= Precursor FDR =============================
1:36:22.310446 PROGRESS: Total precursors accumulated: 862
1:36:22.313431 PROGRESS: Target precursors: 786 (91.18%)
1:36:22.317428 PROGRESS: Decoy precursors: 76 (8.82%)
1:36:22.320431 PROGRESS: 
1:36:22.324437 PROGRESS: Precursor Summary:
1:36:22.330436 PROGRESS: Channel   0:	 0.050 FDR:   624; 0.010 FDR:   446; 0.001 FDR:   359
1:36:22.334437 PROGRESS: 
1:36:22.337952 PROGRESS: Protein Summary:
1:36:22.345952 PROGRESS: Channel   0:	 0.050 FDR:   577; 0.010 FDR:   414; 0.001 FDR:   337
1:36:22.349952 PROGRESS: =========================================================================
1:36:22.355952 INFO: Target number of precursors reached.
1:36:22.774481 INFO: fragments_df: keeping 5000 of 2384623 [sum(precursor_idx_mask)=12066 sum(mass_error_mask)=2384623 stop_rank=5000
1:36:23.313534 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:36:23.725690 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:24.041298 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:27.359817 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:27.364818 INFO: Using score_cutoff 56.63909909248352 (fac=0.99, q=1)
1:36:27.369817 INFO: Updating optimization_manager: fwhm_rt             : 2.5381741523742676 -> 2.5659682750701904
1:36:27.372818 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:36:27.376817 INFO: Updating optimization_manager: score_cutoff        : 62.18273820533752 -> 56.63909909248352
1:36:27.380819 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:36:27.418818 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:27.517821 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:27.928875 INFO: === checking if optimization conditions were reached ===
1:36:27.933875 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1:36:27.938875 INFO: Updating optimization_manager: rt_error            : 75.93331156814064 -> 75.93331156814064
1:36:27.942875 INFO: Updating optimization_manager: classifier_version  : 6 -> 14
1:36:27.946876 INFO: Updating optimization_manager: score_cutoff        : 56.63909909248352 -> 56.63909909248352
1:36:27.950876 INFO: Updating optimization_manager: fwhm_rt             : 2.5659682750701904 -> 2.5659682750701904
1:36:27.954875 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
1:36:27.957875 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 75.9333 found after 7 searches.
1:36:27.961875 INFO: ==============================================
1:36:27.964875 PROGRESS: Optimization finished for rt_error.
1:36:28.472930 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:36:28.510930 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:28.610456 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:29.131505 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:36:29.137511 PROGRESS: ==============================================
1:36:29.141508 PROGRESS: ms2_error      : 10.0000
1:36:29.145506 PROGRESS: ms1_error      : 5.0000
1:36:29.149506 PROGRESS: rt_error       : 75.9333
1:36:29.153507 PROGRESS: ==============================================
1:36:29.165507 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:36:32.719881 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:41.619333 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:22.700102 INFO: Using classic extraction backend
1:37:22.706101 PROGRESS: Extracting batch of 11035943 precursors
1:37:22.710102 INFO: === Search parameters used ===
1:37:22.714615 INFO: rt_error       : 75.93331156814064
1:37:22.718624 INFO: mobility_error : 0.1
1:37:22.722623 INFO: num_candidates : 3
1:37:22.726623 INFO: ms1_error      : 5.0
1:37:22.731623 INFO: ms2_error      : 10.0
1:37:22.735623 INFO: fwhm_rt        : 2.5659682750701904
1:37:22.739624 INFO: quant_window   : 3
1:37:22.743624 INFO: ==============================================
1:37:26.013470 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
1:37:26.015470 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:37:26.015470 INFO: FWHM in RT is 2.57 seconds, sigma is 0.29
1:37:26.016470 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:37:26.017470 INFO: Starting candidate selection
1:49:52.173809 INFO: Removed 18529632 precursors with score below cutoff 56.63909909248352
1:49:56.098184 INFO: Starting candidate scoring
1:57:27.900511 INFO: Finished candidate processing
1:57:27.902513 INFO: Collecting candidate features
1:58:27.051294 WARNING: intensity_correlation has 12 NaNs ( 0.00 % out of 14565381)
1:58:28.917985 INFO: Collecting fragment features
1:58:52.711269 INFO: Finished candidate scoring
1:59:17.166526 INFO: === Performing FDR correction with classifier version 14 ===
1:59:17.173527 INFO: performing precursor FDR with 47 features
1:59:17.174527 INFO: Decoy channel: -1
1:59:17.175527 INFO: Competetive: True
1:59:26.960490 INFO: Setting torch num_threads to 2 for FDR classification task
1:59:32.933301 WARNING: dropped 7 target PSMs due to missing features
1:59:32.935298 WARNING: dropped 5 decoy PSMs due to missing features
1:59:58.880066 INFO: Using random state 370927 for train-test-split
2:07:07.352039 INFO: Test AUC: 0.582
2:07:07.353040 INFO: Train AUC: 0.583
2:07:07.355039 INFO: AUC difference: 0.20%
2:07:15.588457 INFO: Resetting torch num_threads to 10
2:07:16.251071 INFO: Removing fragments below FDR threshold
2:07:20.474111 PROGRESS: ============================= Precursor FDR =============================
2:07:20.479111 PROGRESS: Total precursors accumulated: 44,640
2:07:20.484110 PROGRESS: Target precursors: 44,199 (99.01%)
2:07:20.487111 PROGRESS: Decoy precursors: 441 (0.99%)
2:07:20.491110 PROGRESS: 
2:07:20.495111 PROGRESS: Precursor Summary:
2:07:20.573113 PROGRESS: Channel   0:	 0.050 FDR: 44,199; 0.010 FDR: 44,199; 0.001 FDR: 29,365
2:07:20.578118 PROGRESS: 
2:07:20.582113 PROGRESS: Protein Summary:
2:07:20.679128 PROGRESS: Channel   0:	 0.050 FDR: 8,396; 0.010 FDR: 8,396; 0.001 FDR: 6,229
2:07:20.684723 PROGRESS: =========================================================================
2:07:21.175313 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\psm.parquet
2:07:24.013084 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\frag.parquet
2:07:25.088512 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
2:07:26.366443 PROGRESS: 
2:07:26.367440 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant
2:07:26.369441 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\figures
2:07:26.376442 INFO: Initializing TimingManager
2:07:26.391440 INFO: Initializing RawFileManager
2:11:21.732188 INFO: Determining DIA cycle
2:11:21.759189 INFO: Found cycle with start 0.00 min and length 86.
2:11:22.468767 INFO: RT (min)            : 0.0 - 55.4
2:11:22.469768 INFO: RT duration (sec)   : 3325.7
2:11:22.470769 INFO: RT duration (min)   : 55.4
2:11:22.471768 INFO: Cycle len (scans)   : 86
2:11:22.472768 INFO: Cycle len (sec)     : 1.90
2:11:22.474768 INFO: Number of cycles    : 1747
2:11:22.475769 INFO: MS2 range (m/z)     : 399.5 - 903.5
2:11:22.476768 INFO: Creating DIA data object took: 236.079327583313
2:11:25.317595 INFO: Initializing CalibrationManager
2:11:25.329594 INFO: Setting up calibration estimators ..
2:11:25.333595 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:11:25.337595 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:11:25.341594 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:11:25.345594 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:11:25.349596 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:11:25.353595 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:11:25.358596 INFO: Done setting up calibration estimators.
2:11:25.362595 INFO: Initializing OptimizationManager
2:11:25.369594 INFO: initial parameter: ms1_error = 30
2:11:25.373595 INFO: initial parameter: ms2_error = 30
2:11:25.377595 INFO: initial parameter: rt_error = 1662.873046875
2:11:25.381596 INFO: initial parameter: mobility_error = 0.1
2:11:25.384595 INFO: initial parameter: num_candidates = 1
2:11:25.389595 INFO: initial parameter: fwhm_rt = 5
2:11:25.392596 INFO: initial parameter: fwhm_mobility = 0.01
2:11:25.396595 INFO: initial parameter: score_cutoff = 0
2:11:25.400595 INFO: initial parameter: classifier_version = -1
2:11:25.407595 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
2:11:25.412595 INFO: FDRManager: loading saved state not requested, will be initialized.
2:11:25.413595 INFO: Initializing FDRManager
2:11:25.414595 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
2:11:28.351915 PROGRESS: Initializing spectral library: 5,593,630 target precursors potentially observable (87,574 removed)
2:11:30.496670 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
2:11:30.501669 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
2:11:30.505669 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
2:11:30.509669 PROGRESS: Starting initial search for precursors.
2:11:30.513669 INFO: Starting optimization step 0.
2:11:30.517669 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:11:30.523669 INFO: Using classic extraction backend
2:11:30.529669 PROGRESS: Extracting batch of 15689 precursors
2:11:30.534670 INFO: === Search parameters used ===
2:11:30.539669 INFO: rt_error       : 1662.873046875
2:11:30.545669 INFO: mobility_error : 0.1
2:11:30.550670 INFO: num_candidates : 1
2:11:30.554669 INFO: ms1_error      : 30
2:11:30.559669 INFO: ms2_error      : 30
2:11:30.564670 INFO: fwhm_rt        : 5
2:11:30.569670 INFO: quant_window   : 3
2:11:30.575670 INFO: ==============================================
2:11:30.613670 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:11:30.614671 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:11:30.615670 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
2:11:30.616670 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:11:30.617672 INFO: Starting candidate selection
2:11:44.169495 INFO: Starting candidate scoring
2:11:44.714978 INFO: Finished candidate processing
2:11:44.716147 INFO: Collecting candidate features
2:11:44.836616 INFO: Collecting fragment features
2:11:44.893716 INFO: Finished candidate scoring
2:11:44.918885 INFO: performing precursor FDR with 47 features
2:11:44.919885 INFO: Decoy channel: -1
2:11:44.920884 INFO: Competetive: True
2:11:44.948082 INFO: Setting torch num_threads to 2 for FDR classification task
2:11:44.973237 INFO: Using random state 101110 for train-test-split
2:11:45.243438 INFO: Test AUC: 0.518
2:11:45.244941 INFO: Train AUC: 0.537
2:11:45.245944 INFO: AUC difference: 3.52%
2:11:45.871778 INFO: Resetting torch num_threads to 10
2:11:45.878780 PROGRESS: === Extracted 15681 precursors and 143957 fragments ===
2:11:45.883794 INFO: === FDR correction performed with classifier version -1 ===
2:11:45.889794 PROGRESS: ============================= Precursor FDR =============================
2:11:45.893794 PROGRESS: Total precursors accumulated: 9
2:11:45.897792 PROGRESS: Target precursors: 9 (100.00%)
2:11:45.901168 PROGRESS: Decoy precursors: 0 (0.00%)
2:11:45.905167 PROGRESS: 
2:11:45.909167 PROGRESS: Precursor Summary:
2:11:45.914180 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
2:11:45.919178 PROGRESS: 
2:11:45.922176 PROGRESS: Protein Summary:
2:11:45.933697 PROGRESS: Channel   0:	 0.050 FDR:     9; 0.010 FDR:     9; 0.001 FDR:     9
2:11:45.938699 PROGRESS: =========================================================================
2:11:45.942696 INFO: Target number of precursors not reached yet.
2:11:46.253777 INFO: Starting optimization step 1.
2:11:46.260796 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:11:46.267795 INFO: Using classic extraction backend
2:11:46.276312 PROGRESS: Extracting batch of 31390 precursors
2:11:46.288311 INFO: === Search parameters used ===
2:11:46.299320 INFO: rt_error       : 1662.873046875
2:11:46.311836 INFO: mobility_error : 0.1
2:11:46.322845 INFO: num_candidates : 1
2:11:46.333845 INFO: ms1_error      : 30
2:11:46.342361 INFO: ms2_error      : 30
2:11:46.354388 INFO: fwhm_rt        : 5
2:11:46.365388 INFO: quant_window   : 3
2:11:46.376903 INFO: ==============================================
2:11:46.426433 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:11:46.428942 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:11:46.429952 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
2:11:46.431951 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:11:46.433951 INFO: Starting candidate selection
2:12:33.572948 INFO: Starting candidate scoring
2:12:34.624825 INFO: Finished candidate processing
2:12:34.625833 INFO: Collecting candidate features
2:12:34.871537 INFO: Collecting fragment features
2:12:34.974108 INFO: Finished candidate scoring
2:12:35.064695 INFO: performing precursor FDR with 47 features
2:12:35.065695 INFO: Decoy channel: -1
2:12:35.066695 INFO: Competetive: True
2:12:35.165791 INFO: Setting torch num_threads to 2 for FDR classification task
2:12:35.227840 INFO: Using random state 22243 for train-test-split
2:12:36.304845 INFO: Test AUC: 0.578
2:12:36.305860 INFO: Train AUC: 0.585
2:12:36.306873 INFO: AUC difference: 1.16%
2:12:36.998985 INFO: Resetting torch num_threads to 10
2:12:37.054506 PROGRESS: === Extracted 47050 precursors and 431759 fragments ===
2:12:37.061622 INFO: === FDR correction performed with classifier version -1 ===
2:12:37.066623 PROGRESS: ============================= Precursor FDR =============================
2:12:37.070624 PROGRESS: Total precursors accumulated: 13
2:12:37.076135 PROGRESS: Target precursors: 12 (92.31%)
2:12:37.079137 PROGRESS: Decoy precursors: 1 (7.69%)
2:12:37.082138 PROGRESS: 
2:12:37.085647 PROGRESS: Precursor Summary:
2:12:37.091657 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2:12:37.094657 PROGRESS: 
2:12:37.098659 PROGRESS: Protein Summary:
2:12:37.103674 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
2:12:37.107672 PROGRESS: =========================================================================
2:12:37.112672 INFO: Target number of precursors not reached yet.
2:12:37.536645 INFO: Starting optimization step 2.
2:12:37.540658 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:12:37.544657 INFO: Using classic extraction backend
2:12:37.548658 PROGRESS: Extracting batch of 62842 precursors
2:12:37.555732 INFO: === Search parameters used ===
2:12:37.562742 INFO: rt_error       : 1662.873046875
2:12:37.569745 INFO: mobility_error : 0.1
2:12:37.578292 INFO: num_candidates : 1
2:12:37.585867 INFO: ms1_error      : 30
2:12:37.591887 INFO: ms2_error      : 30
2:12:37.598890 INFO: fwhm_rt        : 5
2:12:37.603898 INFO: quant_window   : 3
2:12:37.610900 INFO: ==============================================
2:12:37.675740 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:12:37.676743 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:12:37.678740 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
2:12:37.678740 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:12:37.680264 INFO: Starting candidate selection
2:14:12.574222 INFO: Starting candidate scoring
2:14:14.578733 INFO: Finished candidate processing
2:14:14.580741 INFO: Collecting candidate features
2:14:14.986793 INFO: Collecting fragment features
2:14:15.152796 INFO: Finished candidate scoring
2:14:15.320320 INFO: performing precursor FDR with 47 features
2:14:15.321320 INFO: Decoy channel: -1
2:14:15.322320 INFO: Competetive: True
2:14:15.522846 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:15.678847 INFO: Using random state 550236 for train-test-split
2:14:18.296652 INFO: Test AUC: 0.574
2:14:18.297650 INFO: Train AUC: 0.601
2:14:18.298650 INFO: AUC difference: 4.50%
2:14:19.011230 INFO: Resetting torch num_threads to 10
2:14:19.123232 PROGRESS: === Extracted 109856 precursors and 1007236 fragments ===
2:14:19.130232 INFO: === FDR correction performed with classifier version -1 ===
2:14:19.138232 PROGRESS: ============================= Precursor FDR =============================
2:14:19.142232 PROGRESS: Total precursors accumulated: 326
2:14:19.147232 PROGRESS: Target precursors: 297 (91.10%)
2:14:19.151232 PROGRESS: Decoy precursors: 29 (8.90%)
2:14:19.157232 PROGRESS: 
2:14:19.162231 PROGRESS: Precursor Summary:
2:14:19.175233 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   164; 0.001 FDR:   120
2:14:19.180234 PROGRESS: 
2:14:19.185232 PROGRESS: Protein Summary:
2:14:19.198232 PROGRESS: Channel   0:	 0.050 FDR:   217; 0.010 FDR:   157; 0.001 FDR:   115
2:14:19.203242 PROGRESS: =========================================================================
2:14:19.212240 INFO: Target number of precursors not reached yet.
2:14:19.901813 INFO: Starting optimization step 3.
2:14:19.910813 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:14:19.919813 INFO: Using classic extraction backend
2:14:19.928813 PROGRESS: Extracting batch of 125627 precursors
2:14:19.936813 INFO: === Search parameters used ===
2:14:19.944813 INFO: rt_error       : 1662.873046875
2:14:19.950823 INFO: mobility_error : 0.1
2:14:19.956822 INFO: num_candidates : 1
2:14:19.962822 INFO: ms1_error      : 30
2:14:19.969339 INFO: ms2_error      : 30
2:14:19.974339 INFO: fwhm_rt        : 5
2:14:19.979339 INFO: quant_window   : 3
2:14:19.987339 INFO: ==============================================
2:14:20.092340 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:14:20.094340 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:14:20.096340 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
2:14:20.097340 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:14:20.100340 INFO: Starting candidate selection
2:16:08.948395 INFO: Starting candidate scoring
2:16:13.222563 INFO: Finished candidate processing
2:16:13.224564 INFO: Collecting candidate features
2:16:13.967145 INFO: Collecting fragment features
2:16:14.249671 INFO: Finished candidate scoring
2:16:14.543196 INFO: performing precursor FDR with 47 features
2:16:14.544196 INFO: Decoy channel: -1
2:16:14.545196 INFO: Competetive: True
2:16:14.928252 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:15.268781 INFO: Using random state 378343 for train-test-split
2:16:20.988432 INFO: Test AUC: 0.579
2:16:20.989430 INFO: Train AUC: 0.602
2:16:20.990430 INFO: AUC difference: 3.78%
2:16:21.783021 INFO: Resetting torch num_threads to 10
2:16:21.962549 PROGRESS: === Extracted 235418 precursors and 2157884 fragments ===
2:16:21.968549 INFO: === FDR correction performed with classifier version -1 ===
2:16:21.974550 PROGRESS: ============================= Precursor FDR =============================
2:16:21.978558 PROGRESS: Total precursors accumulated: 793
2:16:21.982551 PROGRESS: Target precursors: 723 (91.17%)
2:16:21.986550 PROGRESS: Decoy precursors: 70 (8.83%)
2:16:21.990550 PROGRESS: 
2:16:21.994551 PROGRESS: Precursor Summary:
2:16:22.001550 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   425; 0.001 FDR:   315
2:16:22.005550 PROGRESS: 
2:16:22.011549 PROGRESS: Protein Summary:
2:16:22.018550 PROGRESS: Channel   0:	 0.050 FDR:   521; 0.010 FDR:   378; 0.001 FDR:   280
2:16:22.023550 PROGRESS: =========================================================================
2:16:22.031551 INFO: Target number of precursors reached.
2:16:22.448603 INFO: fragments_df: keeping 4066 of 2157884 [sum(precursor_idx_mask)=4814 sum(mass_error_mask)=2157884 stop_rank=4066
2:16:23.462708 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:16:23.808235 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:24.125765 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:26.620421 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:16:26.625415 INFO: Using score_cutoff 53.85529846801758 (fac=0.99, q=1)
2:16:26.629415 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.4969210624694824
2:16:26.633415 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
2:16:26.637415 INFO: Updating optimization_manager: score_cutoff        : 0 -> 53.85529846801758
2:16:26.641415 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:16:26.739558 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:26.952076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:27.831661 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
2:16:27.836663 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:16:27.840661 INFO: Starting optimization step 4.
2:16:27.844663 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:16:27.848661 INFO: Using classic extraction backend
2:16:27.853662 PROGRESS: Extracting batch of 235548 precursors
2:16:27.857661 INFO: === Search parameters used ===
2:16:27.860662 INFO: rt_error       : 1662.873046875
2:16:27.864661 INFO: mobility_error : 0.1
2:16:27.868662 INFO: num_candidates : 3
2:16:27.871662 INFO: ms1_error      : 30
2:16:27.875662 INFO: ms2_error      : 30
2:16:27.879662 INFO: fwhm_rt        : 2.4969210624694824
2:16:27.884662 INFO: quant_window   : 3
2:16:27.892662 INFO: ==============================================
2:16:28.029189 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:16:28.030189 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:16:28.031189 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
2:16:28.032189 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:16:28.033190 INFO: Starting candidate selection
2:20:22.549546 INFO: Starting candidate scoring
2:20:44.643554 INFO: Finished candidate processing
2:20:44.645549 INFO: Collecting candidate features
2:20:47.362128 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 706203)
2:20:47.478231 INFO: Collecting fragment features
2:20:48.796765 INFO: Finished candidate scoring
2:20:49.609636 INFO: performing precursor FDR with 47 features
2:20:49.610634 INFO: Decoy channel: -1
2:20:49.611633 INFO: Competetive: True
2:20:50.200095 INFO: Setting torch num_threads to 2 for FDR classification task
2:20:50.560806 WARNING: dropped 3 target PSMs due to missing features
2:20:50.561807 WARNING: dropped 1 decoy PSMs due to missing features
2:20:51.339967 INFO: Using random state 2560 for train-test-split
2:21:08.885412 INFO: Test AUC: 0.582
2:21:08.887413 INFO: Train AUC: 0.596
2:21:08.889414 INFO: AUC difference: 2.28%
2:21:10.132294 INFO: Resetting torch num_threads to 10
2:21:10.190369 PROGRESS: === Extracted 706203 precursors and 6251368 fragments ===
2:21:10.196368 INFO: === FDR correction performed with classifier version 3 ===
2:21:10.204378 PROGRESS: ============================= Precursor FDR =============================
2:21:10.209380 PROGRESS: Total precursors accumulated: 865
2:21:10.213380 PROGRESS: Target precursors: 793 (91.68%)
2:21:10.216381 PROGRESS: Decoy precursors: 72 (8.32%)
2:21:10.219906 PROGRESS: 
2:21:10.222907 PROGRESS: Precursor Summary:
2:21:10.229907 PROGRESS: Channel   0:	 0.050 FDR:   603; 0.010 FDR:   403; 0.001 FDR:   344
2:21:10.233920 PROGRESS: 
2:21:10.236922 PROGRESS: Protein Summary:
2:21:10.244921 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   358; 0.001 FDR:   307
2:21:10.248445 PROGRESS: =========================================================================
2:21:10.258444 INFO: Target number of precursors reached.
2:21:11.396733 INFO: fragments_df: keeping 5000 of 6251368 [sum(precursor_idx_mask)=12073 sum(mass_error_mask)=6251368 stop_rank=5000
2:21:12.650645 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:21:12.994523 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:21:13.329636 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:21:16.905130 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:21:16.911129 INFO: Using score_cutoff 59.584503289031986 (fac=0.99, q=1)
2:21:16.915128 INFO: Updating optimization_manager: fwhm_rt             : 2.4969210624694824 -> 2.4665043354034424
2:21:16.919129 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:21:16.923136 INFO: Updating optimization_manager: score_cutoff        : 53.85529846801758 -> 59.584503289031986
2:21:16.926137 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:21:17.024706 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:21:17.245413 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:21:18.181467 INFO: === checking if optimization conditions were reached ===
2:21:18.192984 INFO: Updating optimization_manager: ms2_error           : 30 -> 19.172173853995155
2:21:18.197984 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:21:18.201992 PROGRESS: ❌ ms2_error      : 19.1722 > 10.0000 or insufficient steps taken.
2:21:18.208992 INFO: Updating optimization_manager: ms1_error           : 30 -> 12.932299988358352
2:21:18.214993 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
2:21:18.222511 PROGRESS: ❌ ms1_error      : 12.9323 > 5.0000 or insufficient steps taken.
2:21:18.227511 INFO: ==============================================
2:21:18.234527 INFO: Starting optimization step 5.
2:21:18.240526 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:21:18.265562 INFO: Using classic extraction backend
2:21:18.273562 PROGRESS: Extracting batch of 235548 precursors
2:21:18.284081 INFO: === Search parameters used ===
2:21:18.289082 INFO: rt_error       : 1662.873046875
2:21:18.296089 INFO: mobility_error : 0.1
2:21:18.303089 INFO: num_candidates : 3
2:21:18.310599 INFO: ms1_error      : 12.932299988358352
2:21:18.327136 INFO: ms2_error      : 19.172173853995155
2:21:18.333136 INFO: fwhm_rt        : 2.4665043354034424
2:21:18.339137 INFO: quant_window   : 3
2:21:18.343653 INFO: ==============================================
2:21:18.484763 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:21:18.486763 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:21:18.486763 INFO: FWHM in RT is 2.47 seconds, sigma is 0.28
2:21:18.487763 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:21:18.488762 INFO: Starting candidate selection
2:28:47.251361 INFO: Starting candidate scoring
2:29:08.988797 INFO: Finished candidate processing
2:29:08.990805 INFO: Collecting candidate features
2:29:11.779125 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 706004)
2:29:11.788638 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 706004)
2:29:11.921733 INFO: Collecting fragment features
2:29:13.145355 INFO: Finished candidate scoring
2:29:13.959835 INFO: performing precursor FDR with 47 features
2:29:13.960833 INFO: Decoy channel: -1
2:29:13.962836 INFO: Competetive: True
2:29:14.568551 INFO: Setting torch num_threads to 2 for FDR classification task
2:29:14.914810 WARNING: dropped 5 target PSMs due to missing features
2:29:14.916809 WARNING: dropped 5 decoy PSMs due to missing features
2:29:15.747209 INFO: Using random state 50283 for train-test-split
2:29:33.699733 INFO: Test AUC: 0.579
2:29:33.701735 INFO: Train AUC: 0.596
2:29:33.703743 INFO: AUC difference: 2.85%
2:29:34.892119 INFO: Resetting torch num_threads to 10
2:29:34.938211 PROGRESS: === Extracted 706004 precursors and 5877712 fragments ===
2:29:34.944734 INFO: === FDR correction performed with classifier version 4 ===
2:29:34.951733 PROGRESS: ============================= Precursor FDR =============================
2:29:34.956739 PROGRESS: Total precursors accumulated: 1,188
2:29:34.961740 PROGRESS: Target precursors: 1,081 (90.99%)
2:29:34.965741 PROGRESS: Decoy precursors: 107 (9.01%)
2:29:34.970257 PROGRESS: 
2:29:34.974771 PROGRESS: Precursor Summary:
2:29:34.982772 PROGRESS: Channel   0:	 0.050 FDR:   870; 0.010 FDR:   620; 0.001 FDR:   435
2:29:34.986770 PROGRESS: 
2:29:34.990777 PROGRESS: Protein Summary:
2:29:34.999775 PROGRESS: Channel   0:	 0.050 FDR:   752; 0.010 FDR:   538; 0.001 FDR:   380
2:29:35.003286 PROGRESS: =========================================================================
2:29:35.013291 INFO: Target number of precursors reached.
2:29:36.147166 INFO: fragments_df: keeping 5000 of 5877712 [sum(precursor_idx_mask)=18072 sum(mass_error_mask)=5877712 stop_rank=5000
2:29:37.046411 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:29:37.434637 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:29:37.860879 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:29:41.353727 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:29:41.358729 INFO: Using score_cutoff 77.38424126586915 (fac=0.99, q=1)
2:29:41.362729 INFO: Updating optimization_manager: fwhm_rt             : 2.4665043354034424 -> 2.501673698425293
2:29:41.365741 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:29:41.369740 INFO: Updating optimization_manager: score_cutoff        : 59.584503289031986 -> 77.38424126586915
2:29:41.373742 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:29:41.437813 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:29:41.566771 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:29:41.982668 INFO: === checking if optimization conditions were reached ===
2:29:41.990675 INFO: Updating optimization_manager: ms2_error           : 19.172173853995155 -> 10.38029676614947
2:29:41.994675 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:29:41.997677 PROGRESS: ❌ ms2_error      : 10.3803 > 10.0000 or insufficient steps taken.
2:29:42.004193 INFO: Updating optimization_manager: ms1_error           : 12.932299988358352 -> 5.0
2:29:42.008190 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
2:29:42.011191 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
2:29:42.015191 INFO: ==============================================
2:29:42.018190 INFO: Starting optimization step 6.
2:29:42.021201 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:29:42.025200 INFO: Using classic extraction backend
2:29:42.028200 PROGRESS: Extracting batch of 109921 precursors
2:29:42.032200 INFO: === Search parameters used ===
2:29:42.035714 INFO: rt_error       : 1662.873046875
2:29:42.038714 INFO: mobility_error : 0.1
2:29:42.041713 INFO: num_candidates : 3
2:29:42.049714 INFO: ms1_error      : 5.0
2:29:42.055722 INFO: ms2_error      : 10.38029676614947
2:29:42.062721 INFO: fwhm_rt        : 2.501673698425293
2:29:42.070238 INFO: quant_window   : 3
2:29:42.076238 INFO: ==============================================
2:29:42.169809 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:29:42.170807 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:29:42.171807 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
2:29:42.172808 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:29:42.174810 INFO: Starting candidate selection
2:33:54.038097 INFO: Starting candidate scoring
2:34:03.462054 INFO: Finished candidate processing
2:34:03.464067 INFO: Collecting candidate features
2:34:04.824723 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 329266)
2:34:04.829721 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329266)
2:34:04.918140 INFO: Collecting fragment features
2:34:05.481543 INFO: Finished candidate scoring
2:34:05.779766 INFO: performing precursor FDR with 47 features
2:34:05.780765 INFO: Decoy channel: -1
2:34:05.781765 INFO: Competetive: True
2:34:06.082500 INFO: Setting torch num_threads to 2 for FDR classification task
2:34:06.289701 WARNING: dropped 7 target PSMs due to missing features
2:34:06.290702 WARNING: dropped 4 decoy PSMs due to missing features
2:34:06.607437 INFO: Using random state 520801 for train-test-split
2:34:14.393858 INFO: Test AUC: 0.572
2:34:14.395858 INFO: Train AUC: 0.601
2:34:14.396858 INFO: AUC difference: 4.83%
2:34:15.253546 INFO: Resetting torch num_threads to 10
2:34:15.280071 PROGRESS: === Extracted 329266 precursors and 2521496 fragments ===
2:34:15.286073 INFO: === FDR correction performed with classifier version 5 ===
2:34:15.294590 PROGRESS: ============================= Precursor FDR =============================
2:34:15.298589 PROGRESS: Total precursors accumulated: 764
2:34:15.302589 PROGRESS: Target precursors: 698 (91.36%)
2:34:15.305597 PROGRESS: Decoy precursors: 66 (8.64%)
2:34:15.309597 PROGRESS: 
2:34:15.312600 PROGRESS: Precursor Summary:
2:34:15.319103 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   372; 0.001 FDR:   336
2:34:15.323111 PROGRESS: 
2:34:15.327111 PROGRESS: Protein Summary:
2:34:15.334111 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   341; 0.001 FDR:   310
2:34:15.337119 PROGRESS: =========================================================================
2:34:15.344120 INFO: Target number of precursors reached.
2:34:15.808010 INFO: fragments_df: keeping 4985 of 2521496 [sum(precursor_idx_mask)=10102 sum(mass_error_mask)=2521496 stop_rank=4985
2:34:16.562443 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:34:16.935911 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:34:17.310866 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:34:20.747801 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:34:20.753801 INFO: Using score_cutoff 59.51391080245972 (fac=0.99, q=1)
2:34:20.760317 INFO: Updating optimization_manager: fwhm_rt             : 2.501673698425293 -> 2.54268741607666
2:34:20.764317 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:34:20.769317 INFO: Updating optimization_manager: score_cutoff        : 77.38424126586915 -> 59.51391080245972
2:34:20.773325 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:34:20.833361 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:34:20.956963 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:34:21.383014 INFO: === checking if optimization conditions were reached ===
2:34:21.395019 INFO: Updating optimization_manager: ms2_error           : 10.38029676614947 -> 10.0
2:34:21.401030 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:34:21.408031 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:34:21.414624 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
2:34:21.421623 INFO: ==============================================
2:34:21.425623 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:34:21.996872 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:34:22.065639 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:34:22.211243 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:34:22.645772 INFO: Starting optimization step 0.
2:34:22.651780 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:34:22.655780 INFO: Using classic extraction backend
2:34:22.660780 PROGRESS: Extracting batch of 109921 precursors
2:34:22.666294 INFO: === Search parameters used ===
2:34:22.672296 INFO: rt_error       : 1662.873046875
2:34:22.677295 INFO: mobility_error : 0.1
2:34:22.681305 INFO: num_candidates : 3
2:34:22.685305 INFO: ms1_error      : 5.0
2:34:22.690306 INFO: ms2_error      : 10.0
2:34:22.694821 INFO: fwhm_rt        : 2.54268741607666
2:34:22.699822 INFO: quant_window   : 3
2:34:22.703823 INFO: ==============================================
2:34:22.790393 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:34:22.791394 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:34:22.792393 INFO: FWHM in RT is 2.54 seconds, sigma is 0.28
2:34:22.793393 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:34:22.794394 INFO: Starting candidate selection
2:36:15.399195 INFO: Starting candidate scoring
2:36:25.380911 INFO: Finished candidate processing
2:36:25.382418 INFO: Collecting candidate features
2:36:26.706446 WARNING: intensity_correlation has 14 NaNs ( 0.00 % out of 329256)
2:36:26.709446 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329256)
2:36:26.772501 INFO: Collecting fragment features
2:36:27.349456 INFO: Finished candidate scoring
2:36:27.665715 INFO: performing precursor FDR with 47 features
2:36:27.666713 INFO: Decoy channel: -1
2:36:27.668713 INFO: Competetive: True
2:36:27.978539 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:28.149002 WARNING: dropped 10 target PSMs due to missing features
2:36:28.150001 WARNING: dropped 5 decoy PSMs due to missing features
2:36:28.479515 INFO: Using random state 787432 for train-test-split
2:36:36.409235 INFO: Test AUC: 0.582
2:36:36.411234 INFO: Train AUC: 0.606
2:36:36.412235 INFO: AUC difference: 3.93%
2:36:37.262414 INFO: Resetting torch num_threads to 10
2:36:37.289446 PROGRESS: === Extracted 329256 precursors and 2522429 fragments ===
2:36:37.297453 INFO: === FDR correction performed with classifier version 6 ===
2:36:37.304454 PROGRESS: ============================= Precursor FDR =============================
2:36:37.308462 PROGRESS: Total precursors accumulated: 772
2:36:37.313462 PROGRESS: Target precursors: 706 (91.45%)
2:36:37.317461 PROGRESS: Decoy precursors: 66 (8.55%)
2:36:37.322979 PROGRESS: 
2:36:37.327979 PROGRESS: Precursor Summary:
2:36:37.339988 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   386; 0.001 FDR:   292
2:36:37.344988 PROGRESS: 
2:36:37.349989 PROGRESS: Protein Summary:
2:36:37.360506 PROGRESS: Channel   0:	 0.050 FDR:   543; 0.010 FDR:   356; 0.001 FDR:   269
2:36:37.364506 PROGRESS: =========================================================================
2:36:37.371515 INFO: Target number of precursors reached.
2:36:37.842007 INFO: fragments_df: keeping 5000 of 2522429 [sum(precursor_idx_mask)=10361 sum(mass_error_mask)=2522429 stop_rank=5000
2:36:38.615910 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:36:39.046462 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:36:39.368546 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:36:42.863527 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:36:42.869535 INFO: Using score_cutoff 49.17644027709961 (fac=0.99, q=1)
2:36:42.874535 INFO: Updating optimization_manager: fwhm_rt             : 2.54268741607666 -> 2.6053357124328613
2:36:42.878535 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:36:42.884048 INFO: Updating optimization_manager: score_cutoff        : 59.51391080245972 -> 49.17644027709961
2:36:42.889049 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:36:42.954096 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:36:43.094711 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:36:43.572098 INFO: === checking if optimization conditions were reached ===
2:36:43.581097 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:36:43.597105 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 778.9586322718669
2:36:43.605619 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 778.9586.
2:36:43.613619 INFO: ==============================================
2:36:43.621627 INFO: Starting optimization step 1.
2:36:43.627628 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:36:43.636143 INFO: Using classic extraction backend
2:36:43.649149 PROGRESS: Extracting batch of 109921 precursors
2:36:43.661149 INFO: === Search parameters used ===
2:36:43.671664 INFO: rt_error       : 778.9586322718669
2:36:43.682671 INFO: mobility_error : 0.1
2:36:43.689671 INFO: num_candidates : 3
2:36:43.700187 INFO: ms1_error      : 5.0
2:36:43.711187 INFO: ms2_error      : 10.0
2:36:43.722194 INFO: fwhm_rt        : 2.6053357124328613
2:36:43.731712 INFO: quant_window   : 3
2:36:43.743721 INFO: ==============================================
2:36:43.840807 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:36:43.842808 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:36:43.843808 INFO: FWHM in RT is 2.61 seconds, sigma is 0.29
2:36:43.844808 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:36:43.846808 INFO: Starting candidate selection
2:37:40.161402 INFO: Starting candidate scoring
2:37:49.604508 INFO: Finished candidate processing
2:37:49.606515 INFO: Collecting candidate features
2:37:50.927019 WARNING: intensity_correlation has 15 NaNs ( 0.00 % out of 329249)
2:37:50.993352 INFO: Collecting fragment features
2:37:51.540171 INFO: Finished candidate scoring
2:37:51.858543 INFO: performing precursor FDR with 47 features
2:37:51.860543 INFO: Decoy channel: -1
2:37:51.861542 INFO: Competetive: True
2:37:52.152868 INFO: Setting torch num_threads to 2 for FDR classification task
2:37:52.344070 WARNING: dropped 10 target PSMs due to missing features
2:37:52.345072 WARNING: dropped 5 decoy PSMs due to missing features
2:37:52.654055 INFO: Using random state 787432 for train-test-split
2:38:00.666071 INFO: Test AUC: 0.576
2:38:00.667072 INFO: Train AUC: 0.604
2:38:00.668072 INFO: AUC difference: 4.65%
2:38:01.538769 INFO: Resetting torch num_threads to 10
2:38:01.565293 PROGRESS: === Extracted 329249 precursors and 2521747 fragments ===
2:38:01.571295 INFO: === FDR correction performed with classifier version 6 ===
2:38:01.579812 PROGRESS: ============================= Precursor FDR =============================
2:38:01.583812 PROGRESS: Total precursors accumulated: 903
2:38:01.586811 PROGRESS: Target precursors: 821 (90.92%)
2:38:01.589818 PROGRESS: Decoy precursors: 82 (9.08%)
2:38:01.593819 PROGRESS: 
2:38:01.596818 PROGRESS: Precursor Summary:
2:38:01.604334 PROGRESS: Channel   0:	 0.050 FDR:   558; 0.010 FDR:   385; 0.001 FDR:   336
2:38:01.607333 PROGRESS: 
2:38:01.611333 PROGRESS: Protein Summary:
2:38:01.618334 PROGRESS: Channel   0:	 0.050 FDR:   512; 0.010 FDR:   351; 0.001 FDR:   310
2:38:01.621341 PROGRESS: =========================================================================
2:38:01.628341 INFO: Target number of precursors reached.
2:38:02.090666 INFO: fragments_df: keeping 5000 of 2521747 [sum(precursor_idx_mask)=10539 sum(mass_error_mask)=2521747 stop_rank=5000
2:38:02.710670 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:38:04.106307 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:04.448217 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:07.887492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:07.893500 INFO: Using score_cutoff 61.733297790527345 (fac=0.99, q=1)
2:38:07.898499 INFO: Updating optimization_manager: fwhm_rt             : 2.6053357124328613 -> 2.587515115737915
2:38:07.902499 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:38:07.906014 INFO: Updating optimization_manager: score_cutoff        : 49.17644027709961 -> 61.733297790527345
2:38:07.910015 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:38:07.974061 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:08.118672 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:08.559042 INFO: === checking if optimization conditions were reached ===
2:38:08.563042 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:38:08.571042 INFO: Updating optimization_manager: rt_error            : 778.9586322718669 -> 304.17179940027955
2:38:08.574557 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 304.1718.
2:38:08.578556 INFO: ==============================================
2:38:08.582557 INFO: Starting optimization step 2.
2:38:08.585556 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:38:08.589566 INFO: Using classic extraction backend
2:38:08.593566 PROGRESS: Extracting batch of 109921 precursors
2:38:08.597566 INFO: === Search parameters used ===
2:38:08.600566 INFO: rt_error       : 304.17179940027955
2:38:08.605079 INFO: mobility_error : 0.1
2:38:08.610079 INFO: num_candidates : 3
2:38:08.615079 INFO: ms1_error      : 5.0
2:38:08.621087 INFO: ms2_error      : 10.0
2:38:08.626087 INFO: fwhm_rt        : 2.587515115737915
2:38:08.632088 INFO: quant_window   : 3
2:38:08.636603 INFO: ==============================================
2:38:08.725174 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:38:08.726174 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:38:08.727681 INFO: FWHM in RT is 2.59 seconds, sigma is 0.29
2:38:08.728689 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:38:08.729689 INFO: Starting candidate selection
2:38:50.574602 INFO: Starting candidate scoring
2:39:00.208038 INFO: Finished candidate processing
2:39:00.209043 INFO: Collecting candidate features
2:39:01.624937 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 329230)
2:39:01.704487 INFO: Collecting fragment features
2:39:02.271212 INFO: Finished candidate scoring
2:39:02.610500 INFO: performing precursor FDR with 47 features
2:39:02.611500 INFO: Decoy channel: -1
2:39:02.612499 INFO: Competetive: True
2:39:02.928801 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:03.109139 WARNING: dropped 11 target PSMs due to missing features
2:39:03.110138 WARNING: dropped 6 decoy PSMs due to missing features
2:39:03.456046 INFO: Using random state 787432 for train-test-split
2:39:12.039165 INFO: Test AUC: 0.570
2:39:12.040672 INFO: Train AUC: 0.600
2:39:12.041679 INFO: AUC difference: 4.88%
2:39:12.938930 INFO: Resetting torch num_threads to 10
2:39:12.967452 PROGRESS: === Extracted 329230 precursors and 2495840 fragments ===
2:39:12.973452 INFO: === FDR correction performed with classifier version 6 ===
2:39:12.979968 PROGRESS: ============================= Precursor FDR =============================
2:39:12.983967 PROGRESS: Total precursors accumulated: 803
2:39:12.987967 PROGRESS: Target precursors: 735 (91.53%)
2:39:12.991484 PROGRESS: Decoy precursors: 68 (8.47%)
2:39:12.994491 PROGRESS: 
2:39:12.998492 PROGRESS: Precursor Summary:
2:39:13.004491 PROGRESS: Channel   0:	 0.050 FDR:   545; 0.010 FDR:   373; 0.001 FDR:   334
2:39:13.009492 PROGRESS: 
2:39:13.017005 PROGRESS: Protein Summary:
2:39:13.028013 PROGRESS: Channel   0:	 0.050 FDR:   506; 0.010 FDR:   342; 0.001 FDR:   308
2:39:13.035013 PROGRESS: =========================================================================
2:39:13.043530 INFO: Target number of precursors reached.
2:39:13.513278 INFO: fragments_df: keeping 5000 of 2495840 [sum(precursor_idx_mask)=10243 sum(mass_error_mask)=2495840 stop_rank=5000
2:39:14.106354 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:39:14.435889 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:14.749941 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:18.211920 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:18.217921 INFO: Using score_cutoff 66.5967857849121 (fac=0.99, q=1)
2:39:18.223921 INFO: Updating optimization_manager: fwhm_rt             : 2.587515115737915 -> 2.5391252040863037
2:39:18.227920 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:39:18.231920 INFO: Updating optimization_manager: score_cutoff        : 61.733297790527345 -> 66.5967857849121
2:39:18.235920 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:39:18.300463 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:18.445464 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:18.908536 INFO: === checking if optimization conditions were reached ===
2:39:18.915538 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:39:18.930537 INFO: Updating optimization_manager: rt_error            : 304.17179940027955 -> 106.56843594111622
2:39:18.936538 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 106.5684.
2:39:18.940538 INFO: ==============================================
2:39:18.945538 INFO: Starting optimization step 3.
2:39:18.949536 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:39:18.954538 INFO: Using classic extraction backend
2:39:18.958538 PROGRESS: Extracting batch of 109921 precursors
2:39:18.963538 INFO: === Search parameters used ===
2:39:18.967538 INFO: rt_error       : 106.56843594111622
2:39:18.970538 INFO: mobility_error : 0.1
2:39:18.974538 INFO: num_candidates : 3
2:39:18.978538 INFO: ms1_error      : 5.0
2:39:18.982538 INFO: ms2_error      : 10.0
2:39:18.985537 INFO: fwhm_rt        : 2.5391252040863037
2:39:18.989549 INFO: quant_window   : 3
2:39:18.992549 INFO: ==============================================
2:39:19.080073 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:39:19.081072 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:39:19.082073 INFO: FWHM in RT is 2.54 seconds, sigma is 0.28
2:39:19.083073 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:39:19.084074 INFO: Starting candidate selection
2:39:35.236909 INFO: Starting candidate scoring
2:39:43.970867 INFO: Finished candidate processing
2:39:43.971887 INFO: Collecting candidate features
2:39:45.281972 WARNING: intensity_correlation has 33 NaNs ( 0.01 % out of 329164)
2:39:45.284973 WARNING: height_correlation has 22 NaNs ( 0.01 % out of 329164)
2:39:45.348563 INFO: Collecting fragment features
2:39:45.889797 INFO: Finished candidate scoring
2:39:46.212407 INFO: performing precursor FDR with 47 features
2:39:46.213406 INFO: Decoy channel: -1
2:39:46.214404 INFO: Competetive: True
2:39:46.497945 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:46.681563 WARNING: dropped 22 target PSMs due to missing features
2:39:46.682564 WARNING: dropped 21 decoy PSMs due to missing features
2:39:47.013094 INFO: Using random state 787432 for train-test-split
2:39:54.969269 INFO: Test AUC: 0.566
2:39:54.971271 INFO: Train AUC: 0.593
2:39:54.972273 INFO: AUC difference: 4.50%
2:39:55.876529 INFO: Resetting torch num_threads to 10
2:39:55.902529 PROGRESS: === Extracted 329164 precursors and 2423104 fragments ===
2:39:55.908530 INFO: === FDR correction performed with classifier version 6 ===
2:39:55.914529 PROGRESS: ============================= Precursor FDR =============================
2:39:55.919528 PROGRESS: Total precursors accumulated: 755
2:39:55.923529 PROGRESS: Target precursors: 688 (91.13%)
2:39:55.926529 PROGRESS: Decoy precursors: 67 (8.87%)
2:39:55.930529 PROGRESS: 
2:39:55.934530 PROGRESS: Precursor Summary:
2:39:55.941530 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   431; 0.001 FDR:   356
2:39:55.945529 PROGRESS: 
2:39:55.949530 PROGRESS: Protein Summary:
2:39:55.957531 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   395; 0.001 FDR:   329
2:39:55.961530 PROGRESS: =========================================================================
2:39:55.969530 INFO: Target number of precursors reached.
2:39:56.414584 INFO: fragments_df: keeping 5000 of 2423104 [sum(precursor_idx_mask)=11558 sum(mass_error_mask)=2423104 stop_rank=5000
2:39:56.998637 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:39:57.445688 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:57.755217 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:01.177078 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:01.182078 INFO: Using score_cutoff 50.29191767120361 (fac=0.99, q=1)
2:40:01.186079 INFO: Updating optimization_manager: fwhm_rt             : 2.5391252040863037 -> 2.574345350265503
2:40:01.190078 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:40:01.194077 INFO: Updating optimization_manager: score_cutoff        : 66.5967857849121 -> 50.29191767120361
2:40:01.197078 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:40:01.263078 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:01.388610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:01.801152 INFO: === checking if optimization conditions were reached ===
2:40:01.806153 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:40:01.813152 INFO: Updating optimization_manager: rt_error            : 106.56843594111622 -> 101.67319914601865
2:40:01.818165 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 101.6732.
2:40:01.824163 INFO: ==============================================
2:40:01.833689 INFO: Starting optimization step 4.
2:40:01.840688 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:40:01.846688 INFO: Using classic extraction backend
2:40:01.855688 PROGRESS: Extracting batch of 109921 precursors
2:40:01.861690 INFO: === Search parameters used ===
2:40:01.869689 INFO: rt_error       : 101.67319914601865
2:40:01.875689 INFO: mobility_error : 0.1
2:40:01.880691 INFO: num_candidates : 3
2:40:01.887689 INFO: ms1_error      : 5.0
2:40:01.893692 INFO: ms2_error      : 10.0
2:40:01.903689 INFO: fwhm_rt        : 2.574345350265503
2:40:01.912690 INFO: quant_window   : 3
2:40:01.923690 INFO: ==============================================
2:40:02.015689 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:40:02.016690 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:40:02.017685 INFO: FWHM in RT is 2.57 seconds, sigma is 0.29
2:40:02.018686 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:40:02.019692 INFO: Starting candidate selection
2:40:17.284570 INFO: Starting candidate scoring
2:40:26.601712 INFO: Finished candidate processing
2:40:26.603716 INFO: Collecting candidate features
2:40:27.902231 WARNING: intensity_correlation has 30 NaNs ( 0.01 % out of 329160)
2:40:27.905229 WARNING: height_correlation has 17 NaNs ( 0.01 % out of 329160)
2:40:27.966233 INFO: Collecting fragment features
2:40:28.514470 INFO: Finished candidate scoring
2:40:28.812079 INFO: performing precursor FDR with 47 features
2:40:28.813082 INFO: Decoy channel: -1
2:40:28.815080 INFO: Competetive: True
2:40:29.108706 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:29.304299 WARNING: dropped 21 target PSMs due to missing features
2:40:29.305299 WARNING: dropped 18 decoy PSMs due to missing features
2:40:29.616933 INFO: Using random state 787432 for train-test-split
2:40:37.390985 INFO: Test AUC: 0.565
2:40:37.391985 INFO: Train AUC: 0.591
2:40:37.392984 INFO: AUC difference: 4.43%
2:40:38.231565 INFO: Resetting torch num_threads to 10
2:40:38.257565 PROGRESS: === Extracted 329160 precursors and 2414798 fragments ===
2:40:38.264565 INFO: === FDR correction performed with classifier version 6 ===
2:40:38.271565 PROGRESS: ============================= Precursor FDR =============================
2:40:38.275566 PROGRESS: Total precursors accumulated: 835
2:40:38.280566 PROGRESS: Target precursors: 760 (91.02%)
2:40:38.284566 PROGRESS: Decoy precursors: 75 (8.98%)
2:40:38.287566 PROGRESS: 
2:40:38.291568 PROGRESS: Precursor Summary:
2:40:38.298566 PROGRESS: Channel   0:	 0.050 FDR:   604; 0.010 FDR:   446; 0.001 FDR:   333
2:40:38.301566 PROGRESS: 
2:40:38.305566 PROGRESS: Protein Summary:
2:40:38.320566 PROGRESS: Channel   0:	 0.050 FDR:   550; 0.010 FDR:   406; 0.001 FDR:   309
2:40:38.327567 PROGRESS: =========================================================================
2:40:38.339567 INFO: Target number of precursors reached.
2:40:38.782616 INFO: fragments_df: keeping 5000 of 2414798 [sum(precursor_idx_mask)=11963 sum(mass_error_mask)=2414798 stop_rank=5000
2:40:39.368668 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:40:39.793720 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:40.164773 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:43.580617 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:43.588618 INFO: Using score_cutoff 61.22601984786988 (fac=0.99, q=1)
2:40:43.595616 INFO: Updating optimization_manager: fwhm_rt             : 2.574345350265503 -> 2.5425329208374023
2:40:43.600620 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:40:43.607617 INFO: Updating optimization_manager: score_cutoff        : 50.29191767120361 -> 61.22601984786988
2:40:43.613617 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:40:43.691139 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:43.820143 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:44.239194 INFO: === checking if optimization conditions were reached ===
2:40:44.244193 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:40:44.250192 INFO: Updating optimization_manager: rt_error            : 101.67319914601865 -> 101.67319914601865
2:40:44.255193 INFO: Updating optimization_manager: classifier_version  : 6 -> 11
2:40:44.260211 INFO: Updating optimization_manager: score_cutoff        : 61.22601984786988 -> 61.22601984786988
2:40:44.265194 INFO: Updating optimization_manager: fwhm_rt             : 2.5425329208374023 -> 2.5425329208374023
2:40:44.270195 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
2:40:44.274194 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 101.6732 found after 5 searches.
2:40:44.279194 INFO: ==============================================
2:40:44.284194 PROGRESS: Optimization finished for rt_error.
2:40:44.845247 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:40:44.906774 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:45.031776 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:45.507825 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:40:45.512825 PROGRESS: ==============================================
2:40:45.516825 PROGRESS: ms2_error      : 10.0000
2:40:45.520825 PROGRESS: ms1_error      : 5.0000
2:40:45.524825 PROGRESS: rt_error       : 101.6732
2:40:45.528826 PROGRESS: ==============================================
2:40:45.541825 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:40:49.174960 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:58.177852 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:39.780481 INFO: Using classic extraction backend
2:41:39.787482 PROGRESS: Extracting batch of 11035943 precursors
2:41:39.791485 INFO: === Search parameters used ===
2:41:39.795485 INFO: rt_error       : 101.67319914601865
2:41:39.799484 INFO: mobility_error : 0.1
2:41:39.802484 INFO: num_candidates : 3
2:41:39.807484 INFO: ms1_error      : 5.0
2:41:39.810484 INFO: ms2_error      : 10.0
2:41:39.814484 INFO: fwhm_rt        : 2.5425329208374023
2:41:39.819485 INFO: quant_window   : 3
2:41:39.824483 INFO: ==============================================
2:41:43.194622 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
2:41:43.196621 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:41:43.197631 INFO: FWHM in RT is 2.54 seconds, sigma is 0.28
2:41:43.198622 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:41:43.200623 INFO: Starting candidate selection
2:56:50.545252 INFO: Removed 20053063 precursors with score below cutoff 61.22601984786988
2:56:54.913007 INFO: Starting candidate scoring
3:04:09.519347 INFO: Finished candidate processing
3:04:09.521350 INFO: Collecting candidate features
3:04:56.338988 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 13042412)
3:04:58.136668 INFO: Collecting fragment features
3:05:20.591544 INFO: Finished candidate scoring
3:06:04.845504 INFO: === Performing FDR correction with classifier version 11 ===
3:06:04.852504 INFO: performing precursor FDR with 47 features
3:06:04.854504 INFO: Decoy channel: -1
3:06:04.855504 INFO: Competetive: True
3:06:13.656204 INFO: Setting torch num_threads to 2 for FDR classification task
3:06:19.541848 WARNING: dropped 6 target PSMs due to missing features
3:06:19.550858 WARNING: dropped 3 decoy PSMs due to missing features
3:06:46.021493 INFO: Using random state 551642 for train-test-split
3:13:41.356608 INFO: Test AUC: 0.582
3:13:41.357610 INFO: Train AUC: 0.583
3:13:41.358609 INFO: AUC difference: 0.11%
3:13:49.211412 INFO: Resetting torch num_threads to 10
3:13:49.834002 INFO: Removing fragments below FDR threshold
3:13:53.646667 PROGRESS: ============================= Precursor FDR =============================
3:13:53.651668 PROGRESS: Total precursors accumulated: 44,289
3:13:53.655667 PROGRESS: Target precursors: 43,851 (99.01%)
3:13:53.660183 PROGRESS: Decoy precursors: 438 (0.99%)
3:13:53.668183 PROGRESS: 
3:13:53.678190 PROGRESS: Precursor Summary:
3:13:53.795278 PROGRESS: Channel   0:	 0.050 FDR: 43,851; 0.010 FDR: 43,851; 0.001 FDR: 29,555
3:13:53.801287 PROGRESS: 
3:13:53.806284 PROGRESS: Protein Summary:
3:13:53.931012 PROGRESS: Channel   0:	 0.050 FDR: 8,088; 0.010 FDR: 8,088; 0.001 FDR: 6,144
3:13:53.936013 PROGRESS: =========================================================================
3:13:54.562227 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\psm.parquet
3:13:55.647656 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\frag.parquet
3:13:56.763994 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
3:13:57.956421 PROGRESS: 
3:13:57.958421 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant
3:13:57.960421 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\figures
3:13:57.969928 INFO: Initializing TimingManager
3:13:57.989944 INFO: Initializing RawFileManager
3:18:34.650374 INFO: Determining DIA cycle
3:18:34.676391 INFO: Found cycle with start 0.00 min and length 86.
3:18:35.319153 INFO: RT (min)            : 0.0 - 55.4
3:18:35.320153 INFO: RT duration (sec)   : 3325.7
3:18:35.321152 INFO: RT duration (min)   : 55.4
3:18:35.322152 INFO: Cycle len (scans)   : 86
3:18:35.323152 INFO: Cycle len (sec)     : 1.90
3:18:35.324152 INFO: Number of cycles    : 1747
3:18:35.325153 INFO: MS2 range (m/z)     : 399.5 - 903.5
3:18:35.326153 INFO: Creating DIA data object took: 277.3272087574005
3:18:38.743711 INFO: Initializing CalibrationManager
3:18:38.758236 INFO: Setting up calibration estimators ..
3:18:38.766236 INFO: Found 1 estimator(s) in calibration group 'fragment'
3:18:38.771249 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
3:18:38.777251 INFO: Found 3 estimator(s) in calibration group 'precursor'
3:18:38.782250 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
3:18:38.786777 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
3:18:38.791777 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
3:18:38.796779 INFO: Done setting up calibration estimators.
3:18:38.801777 INFO: Initializing OptimizationManager
3:18:38.810789 INFO: initial parameter: ms1_error = 30
3:18:38.814790 INFO: initial parameter: ms2_error = 30
3:18:38.819321 INFO: initial parameter: rt_error = 1662.873046875
3:18:38.823321 INFO: initial parameter: mobility_error = 0.1
3:18:38.828320 INFO: initial parameter: num_candidates = 1
3:18:38.832321 INFO: initial parameter: fwhm_rt = 5
3:18:38.836334 INFO: initial parameter: fwhm_mobility = 0.01
3:18:38.840334 INFO: initial parameter: score_cutoff = 0
3:18:38.844333 INFO: initial parameter: classifier_version = -1
3:18:38.851860 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
3:18:38.855861 INFO: FDRManager: loading saved state not requested, will be initialized.
3:18:38.856859 INFO: Initializing FDRManager
3:18:38.857860 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
3:18:41.862832 PROGRESS: Initializing spectral library: 5,593,630 target precursors potentially observable (87,574 removed)
3:18:43.926215 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
3:18:43.932731 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
3:18:43.938732 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
3:18:43.943248 PROGRESS: Starting initial search for precursors.
3:18:43.948248 INFO: Starting optimization step 0.
3:18:43.953246 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:18:43.958251 INFO: Using classic extraction backend
3:18:43.964251 PROGRESS: Extracting batch of 15689 precursors
3:18:43.969251 INFO: === Search parameters used ===
3:18:43.974335 INFO: rt_error       : 1662.873046875
3:18:43.978335 INFO: mobility_error : 0.1
3:18:43.983335 INFO: num_candidates : 1
3:18:43.987336 INFO: ms1_error      : 30
3:18:43.992343 INFO: ms2_error      : 30
3:18:43.996344 INFO: fwhm_rt        : 5
3:18:44.000345 INFO: quant_window   : 3
3:18:44.005465 INFO: ==============================================
3:18:44.038642 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:18:44.039644 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:18:44.040647 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
3:18:44.041646 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:18:44.043643 INFO: Starting candidate selection
3:18:57.108590 INFO: Starting candidate scoring
3:18:57.636407 INFO: Finished candidate processing
3:18:57.636924 INFO: Collecting candidate features
3:18:57.728072 INFO: Collecting fragment features
3:18:57.807232 INFO: Finished candidate scoring
3:18:57.828761 INFO: performing precursor FDR with 47 features
3:18:57.829760 INFO: Decoy channel: -1
3:18:57.830762 INFO: Competetive: True
3:18:57.853392 INFO: Setting torch num_threads to 2 for FDR classification task
3:18:57.874405 INFO: Using random state 529501 for train-test-split
3:18:58.212710 INFO: Test AUC: 0.540
3:18:58.213709 INFO: Train AUC: 0.549
3:18:58.213709 INFO: AUC difference: 1.57%
3:18:58.736548 INFO: Resetting torch num_threads to 10
3:18:58.742559 PROGRESS: === Extracted 15682 precursors and 144185 fragments ===
3:18:58.747559 INFO: === FDR correction performed with classifier version -1 ===
3:18:58.761089 PROGRESS: ============================= Precursor FDR =============================
3:18:58.764089 PROGRESS: Total precursors accumulated: 7,980
3:18:58.768089 PROGRESS: Target precursors: 4,631 (58.03%)
3:18:58.771101 PROGRESS: Decoy precursors: 3,349 (41.97%)
3:18:58.774101 PROGRESS: 
3:18:58.778100 PROGRESS: Precursor Summary:
3:18:58.783103 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
3:18:58.786692 PROGRESS: 
3:18:58.789695 PROGRESS: Protein Summary:
3:18:58.795691 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
3:18:58.798691 PROGRESS: =========================================================================
3:18:58.802705 INFO: Target number of precursors not reached yet.
3:18:59.060827 INFO: Starting optimization step 1.
3:18:59.068354 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:18:59.075353 INFO: Using classic extraction backend
3:18:59.082355 PROGRESS: Extracting batch of 31390 precursors
3:18:59.090368 INFO: === Search parameters used ===
3:18:59.097367 INFO: rt_error       : 1662.873046875
3:18:59.103900 INFO: mobility_error : 0.1
3:18:59.109896 INFO: num_candidates : 1
3:18:59.116911 INFO: ms1_error      : 30
3:18:59.119911 INFO: ms2_error      : 30
3:18:59.125910 INFO: fwhm_rt        : 5
3:18:59.133508 INFO: quant_window   : 3
3:18:59.139506 INFO: ==============================================
3:18:59.192065 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:18:59.193129 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:18:59.194127 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
3:18:59.195137 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:18:59.196128 INFO: Starting candidate selection
3:19:44.486378 INFO: Starting candidate scoring
3:19:45.550126 INFO: Finished candidate processing
3:19:45.551139 INFO: Collecting candidate features
3:19:45.801960 INFO: Collecting fragment features
3:19:45.904573 INFO: Finished candidate scoring
3:19:46.008725 INFO: performing precursor FDR with 47 features
3:19:46.009727 INFO: Decoy channel: -1
3:19:46.011719 INFO: Competetive: True
3:19:46.147933 INFO: Setting torch num_threads to 2 for FDR classification task
3:19:46.217985 INFO: Using random state 789877 for train-test-split
3:19:47.974816 INFO: Test AUC: 0.567
3:19:47.976817 INFO: Train AUC: 0.583
3:19:47.977815 INFO: AUC difference: 2.64%
3:19:48.628592 INFO: Resetting torch num_threads to 10
3:19:48.699157 PROGRESS: === Extracted 47054 precursors and 432182 fragments ===
3:19:48.706158 INFO: === FDR correction performed with classifier version -1 ===
3:19:48.735685 PROGRESS: ============================= Precursor FDR =============================
3:19:48.739684 PROGRESS: Total precursors accumulated: 23,862
3:19:48.742692 PROGRESS: Target precursors: 14,734 (61.75%)
3:19:48.747692 PROGRESS: Decoy precursors: 9,128 (38.25%)
3:19:48.751692 PROGRESS: 
3:19:48.756209 PROGRESS: Precursor Summary:
3:19:48.763216 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
3:19:48.767216 PROGRESS: 
3:19:48.770216 PROGRESS: Protein Summary:
3:19:48.778732 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
3:19:48.782732 PROGRESS: =========================================================================
3:19:48.793247 INFO: Target number of precursors not reached yet.
3:19:49.299701 INFO: Starting optimization step 2.
3:19:49.304709 PROGRESS: === Extracting elution groups 24000 to 56000 ===
3:19:49.309709 INFO: Using classic extraction backend
3:19:49.313710 PROGRESS: Extracting batch of 62842 precursors
3:19:49.317710 INFO: === Search parameters used ===
3:19:49.321226 INFO: rt_error       : 1662.873046875
3:19:49.325226 INFO: mobility_error : 0.1
3:19:49.328228 INFO: num_candidates : 1
3:19:49.331226 INFO: ms1_error      : 30
3:19:49.335235 INFO: ms2_error      : 30
3:19:49.338233 INFO: fwhm_rt        : 5
3:19:49.341234 INFO: quant_window   : 3
3:19:49.345234 INFO: ==============================================
3:19:49.407285 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:19:49.409284 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:19:49.409284 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
3:19:49.410284 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:19:49.411791 INFO: Starting candidate selection
3:20:43.453771 INFO: Starting candidate scoring
3:20:45.524291 INFO: Finished candidate processing
3:20:45.526289 INFO: Collecting candidate features
3:20:46.010282 INFO: Collecting fragment features
3:20:46.224715 INFO: Finished candidate scoring
3:20:46.430389 INFO: performing precursor FDR with 47 features
3:20:46.432389 INFO: Decoy channel: -1
3:20:46.433389 INFO: Competetive: True
3:20:46.684098 INFO: Setting torch num_threads to 2 for FDR classification task
3:20:46.845720 INFO: Using random state 14493 for train-test-split
3:20:49.631557 INFO: Test AUC: 0.576
3:20:49.632557 INFO: Train AUC: 0.594
3:20:49.633557 INFO: AUC difference: 3.01%
3:20:50.349775 INFO: Resetting torch num_threads to 10
3:20:50.492271 PROGRESS: === Extracted 109859 precursors and 1009050 fragments ===
3:20:50.498271 INFO: === FDR correction performed with classifier version -1 ===
3:20:50.504271 PROGRESS: ============================= Precursor FDR =============================
3:20:50.508789 PROGRESS: Total precursors accumulated: 1
3:20:50.513789 PROGRESS: Target precursors: 1 (100.00%)
3:20:50.518789 PROGRESS: Decoy precursors: 0 (0.00%)
3:20:50.522797 PROGRESS: 
3:20:50.526798 PROGRESS: Precursor Summary:
3:20:50.535797 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
3:20:50.540316 PROGRESS: 
3:20:50.556324 PROGRESS: Protein Summary:
3:20:50.566324 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
3:20:50.572838 PROGRESS: =========================================================================
3:20:50.591846 INFO: Target number of precursors not reached yet.
3:20:51.313970 INFO: Starting optimization step 3.
3:20:51.318477 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:20:51.322487 INFO: Using classic extraction backend
3:20:51.326485 PROGRESS: Extracting batch of 125627 precursors
3:20:51.331485 INFO: === Search parameters used ===
3:20:51.335493 INFO: rt_error       : 1662.873046875
3:20:51.339493 INFO: mobility_error : 0.1
3:20:51.343493 INFO: num_candidates : 1
3:20:51.346494 INFO: ms1_error      : 30
3:20:51.350000 INFO: ms2_error      : 30
3:20:51.354517 INFO: fwhm_rt        : 5
3:20:51.358518 INFO: quant_window   : 3
3:20:51.362517 INFO: ==============================================
3:20:51.462097 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:20:51.463096 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:20:51.464097 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
3:20:51.465096 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:20:51.466098 INFO: Starting candidate selection
3:24:10.555315 INFO: Starting candidate scoring
3:24:14.604097 INFO: Finished candidate processing
3:24:14.606105 INFO: Collecting candidate features
3:24:15.505259 INFO: Collecting fragment features
3:24:15.778495 INFO: Finished candidate scoring
3:24:16.088269 INFO: performing precursor FDR with 47 features
3:24:16.090269 INFO: Decoy channel: -1
3:24:16.091269 INFO: Competetive: True
3:24:16.586668 INFO: Setting torch num_threads to 2 for FDR classification task
3:24:16.915458 INFO: Using random state 906374 for train-test-split
3:24:22.623805 INFO: Test AUC: 0.579
3:24:22.625804 INFO: Train AUC: 0.595
3:24:22.626806 INFO: AUC difference: 2.66%
3:24:23.485158 INFO: Resetting torch num_threads to 10
3:24:23.692810 PROGRESS: === Extracted 235421 precursors and 2162099 fragments ===
3:24:23.700327 INFO: === FDR correction performed with classifier version -1 ===
3:24:23.709327 PROGRESS: ============================= Precursor FDR =============================
3:24:23.714335 PROGRESS: Total precursors accumulated: 465
3:24:23.720335 PROGRESS: Target precursors: 426 (91.61%)
3:24:23.725335 PROGRESS: Decoy precursors: 39 (8.39%)
3:24:23.729851 PROGRESS: 
3:24:23.735851 PROGRESS: Precursor Summary:
3:24:23.750859 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   180; 0.001 FDR:   149
3:24:23.756858 PROGRESS: 
3:24:23.764374 PROGRESS: Protein Summary:
3:24:23.775381 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   170; 0.001 FDR:   141
3:24:23.784382 PROGRESS: =========================================================================
3:24:23.802898 INFO: Target number of precursors not reached yet.
3:24:24.984336 INFO: Starting optimization step 4.
3:24:24.989336 PROGRESS: === Extracting elution groups 120000 to 248000 ===
3:24:24.993350 INFO: Using classic extraction backend
3:24:24.997350 PROGRESS: Extracting batch of 251335 precursors
3:24:25.001349 INFO: === Search parameters used ===
3:24:25.004351 INFO: rt_error       : 1662.873046875
3:24:25.007927 INFO: mobility_error : 0.1
3:24:25.011944 INFO: num_candidates : 1
3:24:25.015944 INFO: ms1_error      : 30
3:24:25.018943 INFO: ms2_error      : 30
3:24:25.022945 INFO: fwhm_rt        : 5
3:24:25.025960 INFO: quant_window   : 3
3:24:25.029959 INFO: ==============================================
3:24:25.174075 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:24:25.175075 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:25.176074 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
3:24:25.177075 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:25.178075 INFO: Starting candidate selection
3:28:02.766448 INFO: Starting candidate scoring
3:28:10.669825 INFO: Finished candidate processing
3:28:10.670835 INFO: Collecting candidate features
3:28:11.964874 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 251209)
3:28:12.022914 INFO: Collecting fragment features
3:28:12.508804 INFO: Finished candidate scoring
3:28:13.107293 INFO: performing precursor FDR with 47 features
3:28:13.109294 INFO: Decoy channel: -1
3:28:13.110294 INFO: Competetive: True
3:28:13.857390 INFO: Setting torch num_threads to 2 for FDR classification task
3:28:14.104105 WARNING: dropped 3 decoy PSMs due to missing features
3:28:14.606538 INFO: Using random state 918997 for train-test-split
3:28:26.416989 INFO: Test AUC: 0.583
3:28:26.418001 INFO: Train AUC: 0.594
3:28:26.419002 INFO: AUC difference: 1.88%
3:28:27.491803 INFO: Resetting torch num_threads to 10
3:28:27.802667 PROGRESS: === Extracted 486630 precursors and 4471540 fragments ===
3:28:27.808679 INFO: === FDR correction performed with classifier version -1 ===
3:28:27.817678 PROGRESS: ============================= Precursor FDR =============================
3:28:27.821679 PROGRESS: Total precursors accumulated: 1,678
3:28:27.826204 PROGRESS: Target precursors: 1,532 (91.30%)
3:28:27.829204 PROGRESS: Decoy precursors: 146 (8.70%)
3:28:27.833204 PROGRESS: 
3:28:27.837204 PROGRESS: Precursor Summary:
3:28:27.848218 PROGRESS: Channel   0:	 0.050 FDR: 1,281; 0.010 FDR:   873; 0.001 FDR:   470
3:28:27.852217 PROGRESS: 
3:28:27.856741 PROGRESS: Protein Summary:
3:28:27.868741 PROGRESS: Channel   0:	 0.050 FDR: 1,022; 0.010 FDR:   715; 0.001 FDR:   402
3:28:27.871754 PROGRESS: =========================================================================
3:28:27.883754 INFO: Target number of precursors reached.
3:28:28.799900 INFO: fragments_df: keeping 5000 of 4471540 [sum(precursor_idx_mask)=9999 sum(mass_error_mask)=4471540 stop_rank=5000
3:28:30.001835 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:28:30.463890 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:28:30.972516 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:28:34.421746 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
3:28:34.426747 INFO: Using score_cutoff 84.28796100769043 (fac=0.99, q=1)
3:28:34.431747 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.4786646366119385
3:28:34.435752 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
3:28:34.439753 INFO: Updating optimization_manager: score_cutoff        : 0 -> 84.28796100769043
3:28:34.443752 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:28:34.536367 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:28:34.760635 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:28:35.665848 INFO: Updating optimization_manager: classifier_version  : -1 -> 4
3:28:35.673365 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:28:35.680365 INFO: Starting optimization step 5.
3:28:35.685373 PROGRESS: === Extracting elution groups 0 to 120000 ===
3:28:35.688381 INFO: Using classic extraction backend
3:28:35.692382 PROGRESS: Extracting batch of 235548 precursors
3:28:35.696382 INFO: === Search parameters used ===
3:28:35.699917 INFO: rt_error       : 1662.873046875
3:28:35.702917 INFO: mobility_error : 0.1
3:28:35.708916 INFO: num_candidates : 3
3:28:35.713917 INFO: ms1_error      : 30
3:28:35.718925 INFO: ms2_error      : 30
3:28:35.723925 INFO: fwhm_rt        : 2.4786646366119385
3:28:35.729432 INFO: quant_window   : 3
3:28:35.733441 INFO: ==============================================
3:28:35.878637 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:28:35.880639 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:28:35.880639 INFO: FWHM in RT is 2.48 seconds, sigma is 0.28
3:28:35.881638 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:28:35.882638 INFO: Starting candidate selection
3:36:20.197802 INFO: Starting candidate scoring
3:36:42.552525 INFO: Finished candidate processing
3:36:42.554534 INFO: Collecting candidate features
3:36:45.448381 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 706207)
3:36:46.709026 INFO: Collecting fragment features
3:36:48.027464 INFO: Finished candidate scoring
3:36:49.074010 INFO: performing precursor FDR with 47 features
3:36:49.075010 INFO: Decoy channel: -1
3:36:49.076006 INFO: Competetive: True
3:36:49.715443 INFO: Setting torch num_threads to 2 for FDR classification task
3:36:50.065732 WARNING: dropped 3 target PSMs due to missing features
3:36:50.067733 WARNING: dropped 1 decoy PSMs due to missing features
3:36:50.845526 INFO: Using random state 765200 for train-test-split
3:37:08.935527 INFO: Test AUC: 0.584
3:37:08.936527 INFO: Train AUC: 0.594
3:37:08.938527 INFO: AUC difference: 1.71%
3:37:10.203746 INFO: Resetting torch num_threads to 10
3:37:10.258314 PROGRESS: === Extracted 706207 precursors and 6257517 fragments ===
3:37:10.264314 INFO: === FDR correction performed with classifier version 4 ===
3:37:10.270836 PROGRESS: ============================= Precursor FDR =============================
3:37:10.273835 PROGRESS: Total precursors accumulated: 976
3:37:10.277835 PROGRESS: Target precursors: 893 (91.50%)
3:37:10.280836 PROGRESS: Decoy precursors: 83 (8.50%)
3:37:10.284848 PROGRESS: 
3:37:10.287847 PROGRESS: Precursor Summary:
3:37:10.295849 PROGRESS: Channel   0:	 0.050 FDR:   752; 0.010 FDR:   484; 0.001 FDR:   313
3:37:10.299371 PROGRESS: 
3:37:10.303371 PROGRESS: Protein Summary:
3:37:10.311370 PROGRESS: Channel   0:	 0.050 FDR:   662; 0.010 FDR:   423; 0.001 FDR:   283
3:37:10.315383 PROGRESS: =========================================================================
3:37:10.335906 INFO: Target number of precursors reached.
3:37:11.458232 INFO: fragments_df: keeping 5000 of 6257517 [sum(precursor_idx_mask)=14768 sum(mass_error_mask)=6257517 stop_rank=5000
3:37:12.373578 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:37:12.777406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:37:13.143726 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:37:16.456466 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:37:16.462466 INFO: Using score_cutoff 84.00546220550537 (fac=0.99, q=1)
3:37:16.466466 INFO: Updating optimization_manager: fwhm_rt             : 2.4786646366119385 -> 2.473954916000366
3:37:16.470476 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:37:16.474476 INFO: Updating optimization_manager: score_cutoff        : 84.28796100769043 -> 84.00546220550537
3:37:16.478476 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:37:16.566046 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:37:16.717170 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:37:17.127502 INFO: === checking if optimization conditions were reached ===
3:37:17.147531 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.837204488705815
3:37:17.153531 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
3:37:17.161540 PROGRESS: ❌ ms2_error      : 17.8372 > 10.0000 or insufficient steps taken.
3:37:17.171540 INFO: Updating optimization_manager: ms1_error           : 30 -> 12.640470842423465
3:37:17.178056 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
3:37:17.185057 PROGRESS: ❌ ms1_error      : 12.6405 > 5.0000 or insufficient steps taken.
3:37:17.193066 INFO: ==============================================
3:37:17.197066 INFO: Starting optimization step 6.
3:37:17.201065 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:37:17.209583 INFO: Using classic extraction backend
3:37:17.218580 PROGRESS: Extracting batch of 109921 precursors
3:37:17.227588 INFO: === Search parameters used ===
3:37:17.236106 INFO: rt_error       : 1662.873046875
3:37:17.243104 INFO: mobility_error : 0.1
3:37:17.250105 INFO: num_candidates : 3
3:37:17.256113 INFO: ms1_error      : 12.640470842423465
3:37:17.265112 INFO: ms2_error      : 17.837204488705815
3:37:17.273628 INFO: fwhm_rt        : 2.473954916000366
3:37:17.283635 INFO: quant_window   : 3
3:37:17.291636 INFO: ==============================================
3:37:17.400245 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:37:17.401245 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:37:17.402245 INFO: FWHM in RT is 2.47 seconds, sigma is 0.28
3:37:17.403246 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:37:17.404245 INFO: Starting candidate selection
3:41:32.558074 INFO: Starting candidate scoring
3:41:42.483711 INFO: Finished candidate processing
3:41:42.485727 INFO: Collecting candidate features
3:41:43.903749 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 329435)
3:41:43.911759 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329435)
3:41:44.009326 INFO: Collecting fragment features
3:41:44.602808 INFO: Finished candidate scoring
3:41:45.010057 INFO: performing precursor FDR with 47 features
3:41:45.012058 INFO: Decoy channel: -1
3:41:45.013058 INFO: Competetive: True
3:41:45.367102 INFO: Setting torch num_threads to 2 for FDR classification task
3:41:45.541240 WARNING: dropped 5 target PSMs due to missing features
3:41:45.542241 WARNING: dropped 4 decoy PSMs due to missing features
3:41:45.890585 INFO: Using random state 927927 for train-test-split
3:41:53.889653 INFO: Test AUC: 0.580
3:41:53.890654 INFO: Train AUC: 0.599
3:41:53.891654 INFO: AUC difference: 3.20%
3:41:54.766733 INFO: Resetting torch num_threads to 10
3:41:54.794889 PROGRESS: === Extracted 329435 precursors and 2700907 fragments ===
3:41:54.801403 INFO: === FDR correction performed with classifier version 5 ===
3:41:54.807399 PROGRESS: ============================= Precursor FDR =============================
3:41:54.811399 PROGRESS: Total precursors accumulated: 654
3:41:54.815398 PROGRESS: Target precursors: 597 (91.28%)
3:41:54.819408 PROGRESS: Decoy precursors: 57 (8.72%)
3:41:54.822406 PROGRESS: 
3:41:54.826405 PROGRESS: Precursor Summary:
3:41:54.833920 PROGRESS: Channel   0:	 0.050 FDR:   484; 0.010 FDR:   324; 0.001 FDR:   260
3:41:54.838923 PROGRESS: 
3:41:54.842924 PROGRESS: Protein Summary:
3:41:54.849933 PROGRESS: Channel   0:	 0.050 FDR:   448; 0.010 FDR:   298; 0.001 FDR:   245
3:41:54.853933 PROGRESS: =========================================================================
3:41:54.861931 INFO: Target number of precursors reached.
3:41:55.358674 INFO: fragments_df: keeping 4440 of 2700907 [sum(precursor_idx_mask)=9372 sum(mass_error_mask)=2700907 stop_rank=4440
3:41:56.227547 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:41:56.565323 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:41:56.929750 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:41:59.881584 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:41:59.886584 INFO: Using score_cutoff 71.44154375152588 (fac=0.99, q=1)
3:41:59.890581 INFO: Updating optimization_manager: fwhm_rt             : 2.473954916000366 -> 2.500722646713257
3:41:59.893582 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:41:59.898101 INFO: Updating optimization_manager: score_cutoff        : 84.00546220550537 -> 71.44154375152588
3:41:59.902100 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:42:00.003706 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:42:00.188158 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:42:00.610302 INFO: === checking if optimization conditions were reached ===
3:42:00.622371 INFO: Updating optimization_manager: ms2_error           : 17.837204488705815 -> 10.378067302787112
3:42:00.627377 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
3:42:00.631396 PROGRESS: ❌ ms2_error      : 10.3781 > 10.0000 or insufficient steps taken.
3:42:00.641394 INFO: Updating optimization_manager: ms1_error           : 12.640470842423465 -> 5.0
3:42:00.645926 INFO: Updating optimization_manager: classifier_version  : 6 -> 6
3:42:00.650926 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
3:42:00.654924 INFO: ==============================================
3:42:00.659924 INFO: Starting optimization step 7.
3:42:00.664935 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:42:00.668935 INFO: Using classic extraction backend
3:42:00.672935 PROGRESS: Extracting batch of 109921 precursors
3:42:00.677461 INFO: === Search parameters used ===
3:42:00.680461 INFO: rt_error       : 1662.873046875
3:42:00.684461 INFO: mobility_error : 0.1
3:42:00.688461 INFO: num_candidates : 3
3:42:00.691462 INFO: ms1_error      : 5.0
3:42:00.694475 INFO: ms2_error      : 10.378067302787112
3:42:00.698474 INFO: fwhm_rt        : 2.500722646713257
3:42:00.701473 INFO: quant_window   : 3
3:42:00.705474 INFO: ==============================================
3:42:00.806617 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:42:00.807617 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:42:00.808616 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
3:42:00.809617 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:42:00.812616 INFO: Starting candidate selection
3:44:00.508988 INFO: Starting candidate scoring
3:44:09.920899 INFO: Finished candidate processing
3:44:09.921899 INFO: Collecting candidate features
3:44:11.338501 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 329259)
3:44:11.345502 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 329259)
3:44:11.465099 INFO: Collecting fragment features
3:44:12.068395 INFO: Finished candidate scoring
3:44:12.467682 INFO: performing precursor FDR with 47 features
3:44:12.468687 INFO: Decoy channel: -1
3:44:12.469681 INFO: Competetive: True
3:44:12.790456 INFO: Setting torch num_threads to 2 for FDR classification task
3:44:12.963103 WARNING: dropped 6 target PSMs due to missing features
3:44:12.964103 WARNING: dropped 4 decoy PSMs due to missing features
3:44:13.313660 INFO: Using random state 366583 for train-test-split
3:44:21.661147 INFO: Test AUC: 0.573
3:44:21.662148 INFO: Train AUC: 0.597
3:44:21.663160 INFO: AUC difference: 4.04%
3:44:22.632810 INFO: Resetting torch num_threads to 10
3:44:22.661323 PROGRESS: === Extracted 329259 precursors and 2522584 fragments ===
3:44:22.668331 INFO: === FDR correction performed with classifier version 6 ===
3:44:22.675329 PROGRESS: ============================= Precursor FDR =============================
3:44:22.679383 PROGRESS: Total precursors accumulated: 733
3:44:22.684383 PROGRESS: Target precursors: 668 (91.13%)
3:44:22.689382 PROGRESS: Decoy precursors: 65 (8.87%)
3:44:22.693383 PROGRESS: 
3:44:22.697388 PROGRESS: Precursor Summary:
3:44:22.703388 PROGRESS: Channel   0:	 0.050 FDR:   470; 0.010 FDR:   336; 0.001 FDR:    86
3:44:22.707388 PROGRESS: 
3:44:22.712948 PROGRESS: Protein Summary:
3:44:22.726959 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   307; 0.001 FDR:    86
3:44:22.731955 PROGRESS: =========================================================================
3:44:22.739959 INFO: Target number of precursors reached.
3:44:23.197933 INFO: fragments_df: keeping 4636 of 2522584 [sum(precursor_idx_mask)=9299 sum(mass_error_mask)=2522584 stop_rank=4636
3:44:24.045862 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:44:24.417065 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:44:24.779988 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:44:27.898656 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:44:27.903656 INFO: Using score_cutoff 67.74617765808105 (fac=0.99, q=1)
3:44:27.908656 INFO: Updating optimization_manager: fwhm_rt             : 2.500722646713257 -> 2.5891313552856445
3:44:27.912664 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:44:27.917664 INFO: Updating optimization_manager: score_cutoff        : 71.44154375152588 -> 67.74617765808105
3:44:27.923665 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:44:28.030263 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:44:28.185918 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:44:28.640836 INFO: === checking if optimization conditions were reached ===
3:44:28.650350 INFO: Updating optimization_manager: ms2_error           : 10.378067302787112 -> 10.0
3:44:28.653351 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
3:44:28.657351 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
3:44:28.661350 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
3:44:28.665361 INFO: ==============================================
3:44:28.668360 PROGRESS: Optimization finished for ms2_error, ms1_error.
3:44:29.332480 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:44:29.441148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:44:29.631969 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:44:30.071331 INFO: Starting optimization step 0.
3:44:30.076331 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:44:30.079331 INFO: Using classic extraction backend
3:44:30.083837 PROGRESS: Extracting batch of 109921 precursors
3:44:30.087846 INFO: === Search parameters used ===
3:44:30.090847 INFO: rt_error       : 1662.873046875
3:44:30.094846 INFO: mobility_error : 0.1
3:44:30.098846 INFO: num_candidates : 3
3:44:30.102854 INFO: ms1_error      : 5.0
3:44:30.106855 INFO: ms2_error      : 10.0
3:44:30.111854 INFO: fwhm_rt        : 2.5891313552856445
3:44:30.115361 INFO: quant_window   : 3
3:44:30.119369 INFO: ==============================================
3:44:30.215942 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:44:30.217943 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:44:30.217943 INFO: FWHM in RT is 2.59 seconds, sigma is 0.29
3:44:30.219452 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:44:30.220461 INFO: Starting candidate selection
3:47:41.841498 INFO: Starting candidate scoring
3:47:50.905609 INFO: Finished candidate processing
3:47:50.906624 INFO: Collecting candidate features
3:47:52.284608 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 329256)
3:47:52.288608 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 329256)
3:47:52.373177 INFO: Collecting fragment features
3:47:52.937210 INFO: Finished candidate scoring
3:47:53.317942 INFO: performing precursor FDR with 47 features
3:47:53.318943 INFO: Decoy channel: -1
3:47:53.319941 INFO: Competetive: True
3:47:53.637708 INFO: Setting torch num_threads to 2 for FDR classification task
3:47:53.833358 WARNING: dropped 5 target PSMs due to missing features
3:47:53.834358 WARNING: dropped 4 decoy PSMs due to missing features
3:47:54.120351 INFO: Using random state 91517 for train-test-split
3:48:02.144310 INFO: Test AUC: 0.578
3:48:02.145310 INFO: Train AUC: 0.603
3:48:02.146311 INFO: AUC difference: 4.18%
3:48:03.112798 INFO: Resetting torch num_threads to 10
3:48:03.141409 PROGRESS: === Extracted 329256 precursors and 2525419 fragments ===
3:48:03.147409 INFO: === FDR correction performed with classifier version 7 ===
3:48:03.154926 PROGRESS: ============================= Precursor FDR =============================
3:48:03.157925 PROGRESS: Total precursors accumulated: 807
3:48:03.165942 PROGRESS: Target precursors: 734 (90.95%)
3:48:03.171946 PROGRESS: Decoy precursors: 73 (9.05%)
3:48:03.179459 PROGRESS: 
3:48:03.186477 PROGRESS: Precursor Summary:
3:48:03.197496 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   373; 0.001 FDR:     0
3:48:03.203490 PROGRESS: 
3:48:03.211006 PROGRESS: Protein Summary:
3:48:03.227023 PROGRESS: Channel   0:	 0.050 FDR:   479; 0.010 FDR:   340; 0.001 FDR:     0
3:48:03.232035 PROGRESS: =========================================================================
3:48:03.246110 INFO: Target number of precursors reached.
3:48:03.729209 INFO: fragments_df: keeping 5000 of 2525419 [sum(precursor_idx_mask)=10326 sum(mass_error_mask)=2525419 stop_rank=5000
3:48:04.500062 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:48:04.943154 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:48:05.318059 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:48:08.854712 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:48:08.859712 INFO: Using score_cutoff 67.38779753723144 (fac=0.99, q=1)
3:48:08.863711 INFO: Updating optimization_manager: fwhm_rt             : 2.5891313552856445 -> 2.5990378856658936
3:48:08.868237 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:48:08.872234 INFO: Updating optimization_manager: score_cutoff        : 67.74617765808105 -> 67.38779753723144
3:48:08.876235 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:48:08.960797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:48:09.133972 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:48:09.568365 INFO: === checking if optimization conditions were reached ===
3:48:09.576376 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:48:09.584377 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 163.5922710672494
3:48:09.592905 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 163.5923.
3:48:09.601905 INFO: ==============================================
3:48:09.608919 INFO: Starting optimization step 1.
3:48:09.615918 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:48:09.623989 INFO: Using classic extraction backend
3:48:09.628988 PROGRESS: Extracting batch of 109921 precursors
3:48:09.636003 INFO: === Search parameters used ===
3:48:09.643004 INFO: rt_error       : 163.5922710672494
3:48:09.651608 INFO: mobility_error : 0.1
3:48:09.660605 INFO: num_candidates : 3
3:48:09.667626 INFO: ms1_error      : 5.0
3:48:09.675622 INFO: ms2_error      : 10.0
3:48:09.679620 INFO: fwhm_rt        : 2.5990378856658936
3:48:09.684760 INFO: quant_window   : 3
3:48:09.688762 INFO: ==============================================
3:48:09.798080 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:48:09.799080 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:09.799080 INFO: FWHM in RT is 2.60 seconds, sigma is 0.29
3:48:09.802080 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:48:09.803081 INFO: Starting candidate selection
3:48:41.986217 INFO: Starting candidate scoring
3:48:51.235412 INFO: Finished candidate processing
3:48:51.237420 INFO: Collecting candidate features
3:48:52.579536 WARNING: intensity_correlation has 23 NaNs ( 0.01 % out of 329162)
3:48:52.583536 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 329162)
3:48:52.664615 INFO: Collecting fragment features
3:48:53.201565 INFO: Finished candidate scoring
3:48:53.586379 INFO: performing precursor FDR with 47 features
3:48:53.588388 INFO: Decoy channel: -1
3:48:53.589388 INFO: Competetive: True
3:48:53.923143 INFO: Setting torch num_threads to 2 for FDR classification task
3:48:54.093278 WARNING: dropped 11 target PSMs due to missing features
3:48:54.094279 WARNING: dropped 14 decoy PSMs due to missing features
3:48:54.435053 INFO: Using random state 91517 for train-test-split
3:49:02.169785 INFO: Test AUC: 0.570
3:49:02.170783 INFO: Train AUC: 0.591
3:49:02.171786 INFO: AUC difference: 3.56%
3:49:03.079355 INFO: Resetting torch num_threads to 10
3:49:03.118909 PROGRESS: === Extracted 329162 precursors and 2456564 fragments ===
3:49:03.126908 INFO: === FDR correction performed with classifier version 7 ===
3:49:03.135916 PROGRESS: ============================= Precursor FDR =============================
3:49:03.141917 PROGRESS: Total precursors accumulated: 863
3:49:03.146917 PROGRESS: Target precursors: 787 (91.19%)
3:49:03.152432 PROGRESS: Decoy precursors: 76 (8.81%)
3:49:03.157431 PROGRESS: 
3:49:03.163431 PROGRESS: Precursor Summary:
3:49:03.179457 PROGRESS: Channel   0:	 0.050 FDR:   573; 0.010 FDR:   411; 0.001 FDR:   381
3:49:03.187973 PROGRESS: 
3:49:03.192973 PROGRESS: Protein Summary:
3:49:03.206980 PROGRESS: Channel   0:	 0.050 FDR:   524; 0.010 FDR:   370; 0.001 FDR:   346
3:49:03.212498 PROGRESS: =========================================================================
3:49:03.227499 INFO: Target number of precursors reached.
3:49:03.662870 INFO: fragments_df: keeping 5000 of 2456564 [sum(precursor_idx_mask)=11313 sum(mass_error_mask)=2456564 stop_rank=5000
3:49:04.288713 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:49:04.605305 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:49:04.903129 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:49:08.388313 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:49:08.393313 INFO: Using score_cutoff 63.00608323287963 (fac=0.99, q=1)
3:49:08.398822 INFO: Updating optimization_manager: fwhm_rt             : 2.5990378856658936 -> 2.6228179931640625
3:49:08.402832 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:49:08.406831 INFO: Updating optimization_manager: score_cutoff        : 67.38779753723144 -> 63.00608323287963
3:49:08.411831 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:49:08.515407 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:49:08.694058 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:49:09.166110 INFO: === checking if optimization conditions were reached ===
3:49:09.174110 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:49:09.182625 INFO: Updating optimization_manager: rt_error            : 163.5922710672494 -> 111.84219080552427
3:49:09.187625 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 111.8422.
3:49:09.193625 INFO: ==============================================
3:49:09.201635 INFO: Starting optimization step 2.
3:49:09.209634 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:49:09.218151 INFO: Using classic extraction backend
3:49:09.225149 PROGRESS: Extracting batch of 109921 precursors
3:49:09.230160 INFO: === Search parameters used ===
3:49:09.238159 INFO: rt_error       : 111.84219080552427
3:49:09.246679 INFO: mobility_error : 0.1
3:49:09.256680 INFO: num_candidates : 3
3:49:09.263688 INFO: ms1_error      : 5.0
3:49:09.270688 INFO: ms2_error      : 10.0
3:49:09.277206 INFO: fwhm_rt        : 2.6228179931640625
3:49:09.282207 INFO: quant_window   : 3
3:49:09.291216 INFO: ==============================================
3:49:09.401809 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:49:09.402809 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:09.403810 INFO: FWHM in RT is 2.62 seconds, sigma is 0.29
3:49:09.404809 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:49:09.405809 INFO: Starting candidate selection
3:49:32.527081 INFO: Starting candidate scoring
3:49:41.738564 INFO: Finished candidate processing
3:49:41.739578 INFO: Collecting candidate features
3:49:43.123926 WARNING: intensity_correlation has 34 NaNs ( 0.01 % out of 329171)
3:49:43.126925 WARNING: height_correlation has 26 NaNs ( 0.01 % out of 329171)
3:49:43.208575 INFO: Collecting fragment features
3:49:43.701921 INFO: Finished candidate scoring
3:49:44.050766 INFO: performing precursor FDR with 47 features
3:49:44.051770 INFO: Decoy channel: -1
3:49:44.052764 INFO: Competetive: True
3:49:44.406165 INFO: Setting torch num_threads to 2 for FDR classification task
3:49:44.582802 WARNING: dropped 26 target PSMs due to missing features
3:49:44.583802 WARNING: dropped 20 decoy PSMs due to missing features
3:49:44.896560 INFO: Using random state 91517 for train-test-split
3:49:53.041366 INFO: Test AUC: 0.564
3:49:53.042366 INFO: Train AUC: 0.591
3:49:53.043365 INFO: AUC difference: 4.51%
3:49:54.031865 INFO: Resetting torch num_threads to 10
3:49:54.060393 PROGRESS: === Extracted 329171 precursors and 2433483 fragments ===
3:49:54.066394 INFO: === FDR correction performed with classifier version 7 ===
3:49:54.072405 PROGRESS: ============================= Precursor FDR =============================
3:49:54.076406 PROGRESS: Total precursors accumulated: 809
3:49:54.080405 PROGRESS: Target precursors: 736 (90.98%)
3:49:54.085406 PROGRESS: Decoy precursors: 73 (9.02%)
3:49:54.089930 PROGRESS: 
3:49:54.094931 PROGRESS: Precursor Summary:
3:49:54.103945 PROGRESS: Channel   0:	 0.050 FDR:   521; 0.010 FDR:   381; 0.001 FDR:    15
3:49:54.107945 PROGRESS: 
3:49:54.113944 PROGRESS: Protein Summary:
3:49:54.124468 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   350; 0.001 FDR:    15
3:49:54.132468 PROGRESS: =========================================================================
3:49:54.142479 INFO: Target number of precursors reached.
3:49:54.603525 INFO: fragments_df: keeping 4924 of 2433483 [sum(precursor_idx_mask)=10424 sum(mass_error_mask)=2433483 stop_rank=4924
3:49:55.384809 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:49:55.727620 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:49:56.036771 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:49:59.874847 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:49:59.878845 INFO: Using score_cutoff 66.36532131958008 (fac=0.99, q=1)
3:49:59.883846 INFO: Updating optimization_manager: fwhm_rt             : 2.6228179931640625 -> 2.6412644386291504
3:49:59.887859 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:49:59.890859 INFO: Updating optimization_manager: score_cutoff        : 63.00608323287963 -> 66.36532131958008
3:49:59.933467 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:50:00.084875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:50:00.249613 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:50:00.687361 INFO: === checking if optimization conditions were reached ===
3:50:00.692362 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:50:00.699370 INFO: Updating optimization_manager: rt_error            : 111.84219080552427 -> 98.97783805111985
3:50:00.703370 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 98.9778.
3:50:00.707370 INFO: ==============================================
3:50:00.710370 INFO: Starting optimization step 3.
3:50:00.714888 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:50:00.717888 INFO: Using classic extraction backend
3:50:00.721888 PROGRESS: Extracting batch of 109921 precursors
3:50:00.726892 INFO: === Search parameters used ===
3:50:00.729896 INFO: rt_error       : 98.97783805111985
3:50:00.733896 INFO: mobility_error : 0.1
3:50:00.737895 INFO: num_candidates : 3
3:50:00.741896 INFO: ms1_error      : 5.0
3:50:00.745411 INFO: ms2_error      : 10.0
3:50:00.749411 INFO: fwhm_rt        : 2.6412644386291504
3:50:00.753410 INFO: quant_window   : 3
3:50:00.757409 INFO: ==============================================
3:50:00.851907 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:50:00.853915 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:00.853915 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
3:50:00.854915 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:00.855916 INFO: Starting candidate selection
3:50:09.436301 INFO: Starting candidate scoring
3:50:18.876748 INFO: Finished candidate processing
3:50:18.878757 INFO: Collecting candidate features
3:50:20.263881 WARNING: intensity_correlation has 42 NaNs ( 0.01 % out of 329162)
3:50:20.267882 WARNING: height_correlation has 28 NaNs ( 0.01 % out of 329162)
3:50:20.352479 INFO: Collecting fragment features
3:50:20.896847 INFO: Finished candidate scoring
3:50:21.287221 INFO: performing precursor FDR with 47 features
3:50:21.288220 INFO: Decoy channel: -1
3:50:21.289220 INFO: Competetive: True
3:50:21.605084 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:21.780790 WARNING: dropped 30 target PSMs due to missing features
3:50:21.781790 WARNING: dropped 25 decoy PSMs due to missing features
3:50:22.093665 INFO: Using random state 91517 for train-test-split
3:50:30.130723 INFO: Test AUC: 0.562
3:50:30.132723 INFO: Train AUC: 0.591
3:50:30.133723 INFO: AUC difference: 4.78%
3:50:31.060820 INFO: Resetting torch num_threads to 10
3:50:31.090363 PROGRESS: === Extracted 329162 precursors and 2422030 fragments ===
3:50:31.096364 INFO: === FDR correction performed with classifier version 7 ===
3:50:31.102363 PROGRESS: ============================= Precursor FDR =============================
3:50:31.106372 PROGRESS: Total precursors accumulated: 758
3:50:31.110371 PROGRESS: Target precursors: 691 (91.16%)
3:50:31.113372 PROGRESS: Decoy precursors: 67 (8.84%)
3:50:31.117382 PROGRESS: 
3:50:31.120898 PROGRESS: Precursor Summary:
3:50:31.127898 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   381; 0.001 FDR:   164
3:50:31.131898 PROGRESS: 
3:50:31.135908 PROGRESS: Protein Summary:
3:50:31.143906 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   347; 0.001 FDR:   158
3:50:31.148912 PROGRESS: =========================================================================
3:50:31.162420 INFO: Target number of precursors reached.
3:50:31.659482 INFO: fragments_df: keeping 4906 of 2422030 [sum(precursor_idx_mask)=10405 sum(mass_error_mask)=2422030 stop_rank=4906
3:50:32.311786 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:50:32.659133 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:50:33.038204 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:50:36.520825 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:50:36.525331 INFO: Using score_cutoff 66.6307010192871 (fac=0.99, q=1)
3:50:36.530339 INFO: Updating optimization_manager: fwhm_rt             : 2.6412644386291504 -> 2.591505289077759
3:50:36.534340 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:50:36.537340 INFO: Updating optimization_manager: score_cutoff        : 66.36532131958008 -> 66.6307010192871
3:50:36.540340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:50:36.623928 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:50:36.772542 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:50:37.191727 INFO: === checking if optimization conditions were reached ===
3:50:37.195727 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:50:37.203739 INFO: Updating optimization_manager: rt_error            : 98.97783805111985 -> 88.33815328205822
3:50:37.207739 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 88.3382.
3:50:37.210739 INFO: ==============================================
3:50:37.214264 INFO: Starting optimization step 4.
3:50:37.218800 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:50:37.222797 INFO: Using classic extraction backend
3:50:37.226798 PROGRESS: Extracting batch of 109921 precursors
3:50:37.230812 INFO: === Search parameters used ===
3:50:37.233808 INFO: rt_error       : 88.33815328205822
3:50:37.237808 INFO: mobility_error : 0.1
3:50:37.241808 INFO: num_candidates : 3
3:50:37.245345 INFO: ms1_error      : 5.0
3:50:37.248345 INFO: ms2_error      : 10.0
3:50:37.252345 INFO: fwhm_rt        : 2.591505289077759
3:50:37.255344 INFO: quant_window   : 3
3:50:37.259345 INFO: ==============================================
3:50:37.354983 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:50:37.355987 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:37.356983 INFO: FWHM in RT is 2.59 seconds, sigma is 0.29
3:50:37.357983 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:50:37.358982 INFO: Starting candidate selection
3:50:44.719465 INFO: Starting candidate scoring
3:50:53.736579 INFO: Finished candidate processing
3:50:53.738217 INFO: Collecting candidate features
3:50:55.083915 WARNING: intensity_correlation has 51 NaNs ( 0.02 % out of 329144)
3:50:55.091429 WARNING: height_correlation has 41 NaNs ( 0.01 % out of 329144)
3:50:55.189998 INFO: Collecting fragment features
3:50:55.753979 INFO: Finished candidate scoring
3:50:56.119778 INFO: performing precursor FDR with 47 features
3:50:56.120778 INFO: Decoy channel: -1
3:50:56.121778 INFO: Competetive: True
3:50:56.460557 INFO: Setting torch num_threads to 2 for FDR classification task
3:50:56.631210 WARNING: dropped 38 target PSMs due to missing features
3:50:56.632210 WARNING: dropped 32 decoy PSMs due to missing features
3:50:56.953959 INFO: Using random state 91517 for train-test-split
3:51:04.670370 INFO: Test AUC: 0.565
3:51:04.671370 INFO: Train AUC: 0.588
3:51:04.672369 INFO: AUC difference: 3.82%
3:51:05.573630 INFO: Resetting torch num_threads to 10
3:51:05.601144 PROGRESS: === Extracted 329144 precursors and 2400263 fragments ===
3:51:05.608152 INFO: === FDR correction performed with classifier version 7 ===
3:51:05.617152 PROGRESS: ============================= Precursor FDR =============================
3:51:05.621669 PROGRESS: Total precursors accumulated: 824
3:51:05.625670 PROGRESS: Target precursors: 751 (91.14%)
3:51:05.628669 PROGRESS: Decoy precursors: 73 (8.86%)
3:51:05.632669 PROGRESS: 
3:51:05.636677 PROGRESS: Precursor Summary:
3:51:05.643677 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   381; 0.001 FDR:   176
3:51:05.647677 PROGRESS: 
3:51:05.652194 PROGRESS: Protein Summary:
3:51:05.659194 PROGRESS: Channel   0:	 0.050 FDR:   534; 0.010 FDR:   349; 0.001 FDR:   168
3:51:05.663194 PROGRESS: =========================================================================
3:51:05.671202 INFO: Target number of precursors reached.
3:51:06.092562 INFO: fragments_df: keeping 4810 of 2400263 [sum(precursor_idx_mask)=10343 sum(mass_error_mask)=2400263 stop_rank=4810
3:51:06.760111 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:51:07.114396 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:51:07.471195 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:51:10.591284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:51:10.596285 INFO: Using score_cutoff 64.20630226135253 (fac=0.99, q=1)
3:51:10.601284 INFO: Updating optimization_manager: fwhm_rt             : 2.591505289077759 -> 2.6516194343566895
3:51:10.605293 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:51:10.609294 INFO: Updating optimization_manager: score_cutoff        : 66.6307010192871 -> 64.20630226135253
3:51:10.613292 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:51:10.694852 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:51:10.844991 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:51:11.268830 INFO: === checking if optimization conditions were reached ===
3:51:11.273831 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:51:11.281347 INFO: Updating optimization_manager: rt_error            : 88.33815328205822 -> 75.8568472969811
3:51:11.285347 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 75.8568.
3:51:11.289347 INFO: ==============================================
3:51:11.293356 INFO: Starting optimization step 5.
3:51:11.297356 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:51:11.301356 INFO: Using classic extraction backend
3:51:11.305356 PROGRESS: Extracting batch of 109921 precursors
3:51:11.308874 INFO: === Search parameters used ===
3:51:11.312874 INFO: rt_error       : 75.8568472969811
3:51:11.317874 INFO: mobility_error : 0.1
3:51:11.326882 INFO: num_candidates : 3
3:51:11.333882 INFO: ms1_error      : 5.0
3:51:11.342397 INFO: ms2_error      : 10.0
3:51:11.350398 INFO: fwhm_rt        : 2.6516194343566895
3:51:11.358406 INFO: quant_window   : 3
3:51:11.367407 INFO: ==============================================
3:51:11.480526 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:51:11.481525 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:11.482524 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
3:51:11.483525 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:11.484525 INFO: Starting candidate selection
3:51:25.349389 INFO: Starting candidate scoring
3:51:34.887890 INFO: Finished candidate processing
3:51:34.889899 INFO: Collecting candidate features
3:51:36.213959 WARNING: intensity_correlation has 50 NaNs ( 0.02 % out of 329088)
3:51:36.216969 WARNING: height_correlation has 38 NaNs ( 0.01 % out of 329088)
3:51:36.303024 INFO: Collecting fragment features
3:51:36.829940 INFO: Finished candidate scoring
3:51:37.180701 INFO: performing precursor FDR with 47 features
3:51:37.182209 INFO: Decoy channel: -1
3:51:37.183218 INFO: Competetive: True
3:51:37.503970 INFO: Setting torch num_threads to 2 for FDR classification task
3:51:37.674120 WARNING: dropped 33 target PSMs due to missing features
3:51:37.675120 WARNING: dropped 32 decoy PSMs due to missing features
3:51:37.991860 INFO: Using random state 91517 for train-test-split
3:51:45.723712 INFO: Test AUC: 0.566
3:51:45.724711 INFO: Train AUC: 0.588
3:51:45.725710 INFO: AUC difference: 3.76%
3:51:46.644017 INFO: Resetting torch num_threads to 10
3:51:46.673541 PROGRESS: === Extracted 329088 precursors and 2388703 fragments ===
3:51:46.679540 INFO: === FDR correction performed with classifier version 7 ===
3:51:46.688058 PROGRESS: ============================= Precursor FDR =============================
3:51:46.694057 PROGRESS: Total precursors accumulated: 800
3:51:46.700066 PROGRESS: Target precursors: 730 (91.25%)
3:51:46.705065 PROGRESS: Decoy precursors: 70 (8.75%)
3:51:46.710066 PROGRESS: 
3:51:46.715583 PROGRESS: Precursor Summary:
3:51:46.728583 PROGRESS: Channel   0:	 0.050 FDR:   529; 0.010 FDR:   427; 0.001 FDR:   317
3:51:46.734593 PROGRESS: 
3:51:46.739594 PROGRESS: Protein Summary:
3:51:46.753106 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   389; 0.001 FDR:   294
3:51:46.759106 PROGRESS: =========================================================================
3:51:46.772114 INFO: Target number of precursors reached.
3:51:47.188477 INFO: fragments_df: keeping 5000 of 2388703 [sum(precursor_idx_mask)=11595 sum(mass_error_mask)=2388703 stop_rank=5000
3:51:47.824513 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:51:48.213341 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:51:48.604172 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:51:51.927931 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:51:51.933447 INFO: Using score_cutoff 58.58020194625854 (fac=0.99, q=1)
3:51:51.937448 INFO: Updating optimization_manager: fwhm_rt             : 2.6516194343566895 -> 2.6880462169647217
3:51:51.941447 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:51:51.945448 INFO: Updating optimization_manager: score_cutoff        : 64.20630226135253 -> 58.58020194625854
3:51:51.948448 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:51:52.030016 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:51:52.180649 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:51:52.613106 INFO: === checking if optimization conditions were reached ===
3:51:52.619613 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:51:52.634622 INFO: Updating optimization_manager: rt_error            : 75.8568472969811 -> 74.25383333759842
3:51:52.640630 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 74.2538.
3:51:52.645631 INFO: ==============================================
3:51:52.651137 INFO: Starting optimization step 6.
3:51:52.656145 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:51:52.661145 INFO: Using classic extraction backend
3:51:52.665145 PROGRESS: Extracting batch of 109921 precursors
3:51:52.670154 INFO: === Search parameters used ===
3:51:52.674154 INFO: rt_error       : 74.25383333759842
3:51:52.679156 INFO: mobility_error : 0.1
3:51:52.683668 INFO: num_candidates : 3
3:51:52.687668 INFO: ms1_error      : 5.0
3:51:52.691668 INFO: ms2_error      : 10.0
3:51:52.695669 INFO: fwhm_rt        : 2.6880462169647217
3:51:52.699676 INFO: quant_window   : 3
3:51:52.704676 INFO: ==============================================
3:51:52.810763 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:51:52.811763 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:51:52.812763 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
3:51:52.813763 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:51:52.814772 INFO: Starting candidate selection
3:52:00.146939 INFO: Starting candidate scoring
3:52:09.406363 INFO: Finished candidate processing
3:52:09.408376 INFO: Collecting candidate features
3:52:10.734001 WARNING: intensity_correlation has 50 NaNs ( 0.02 % out of 329060)
3:52:10.738000 WARNING: height_correlation has 43 NaNs ( 0.01 % out of 329060)
3:52:10.817597 INFO: Collecting fragment features
3:52:11.354291 INFO: Finished candidate scoring
3:52:11.708712 INFO: performing precursor FDR with 47 features
3:52:11.709714 INFO: Decoy channel: -1
3:52:11.710714 INFO: Competetive: True
3:52:12.018579 INFO: Setting torch num_threads to 2 for FDR classification task
3:52:12.189301 WARNING: dropped 41 target PSMs due to missing features
3:52:12.190301 WARNING: dropped 32 decoy PSMs due to missing features
3:52:12.514203 INFO: Using random state 91517 for train-test-split
3:52:20.203799 INFO: Test AUC: 0.562
3:52:20.204799 INFO: Train AUC: 0.586
3:52:20.205799 INFO: AUC difference: 4.07%
3:52:21.200352 INFO: Resetting torch num_threads to 10
3:52:21.239871 PROGRESS: === Extracted 329060 precursors and 2375317 fragments ===
3:52:21.247321 INFO: === FDR correction performed with classifier version 7 ===
3:52:21.254318 PROGRESS: ============================= Precursor FDR =============================
3:52:21.257318 PROGRESS: Total precursors accumulated: 856
3:52:21.261321 PROGRESS: Target precursors: 780 (91.12%)
3:52:21.265328 PROGRESS: Decoy precursors: 76 (8.88%)
3:52:21.268328 PROGRESS: 
3:52:21.272328 PROGRESS: Precursor Summary:
3:52:21.279844 PROGRESS: Channel   0:	 0.050 FDR:   569; 0.010 FDR:   412; 0.001 FDR:   358
3:52:21.283844 PROGRESS: 
3:52:21.287846 PROGRESS: Protein Summary:
3:52:21.294851 PROGRESS: Channel   0:	 0.050 FDR:   519; 0.010 FDR:   378; 0.001 FDR:   327
3:52:21.298852 PROGRESS: =========================================================================
3:52:21.305852 INFO: Target number of precursors reached.
3:52:21.774333 INFO: fragments_df: keeping 5000 of 2375317 [sum(precursor_idx_mask)=11146 sum(mass_error_mask)=2375317 stop_rank=5000
3:52:22.443362 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
3:52:22.854808 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
3:52:23.169088 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
3:52:26.647657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
3:52:26.652171 INFO: Using score_cutoff 62.041409949874875 (fac=0.99, q=1)
3:52:26.656171 INFO: Updating optimization_manager: fwhm_rt             : 2.6880462169647217 -> 2.638853073120117
3:52:26.660171 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:52:26.664171 INFO: Updating optimization_manager: score_cutoff        : 58.58020194625854 -> 62.041409949874875
3:52:26.667173 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:52:26.746741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:52:26.900362 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:52:27.314204 INFO: === checking if optimization conditions were reached ===
3:52:27.319205 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
3:52:27.325213 INFO: Updating optimization_manager: rt_error            : 74.25383333759842 -> 74.25383333759842
3:52:27.329212 INFO: Updating optimization_manager: classifier_version  : 7 -> 14
3:52:27.337214 INFO: Updating optimization_manager: score_cutoff        : 62.041409949874875 -> 62.041409949874875
3:52:27.345730 INFO: Updating optimization_manager: fwhm_rt             : 2.638853073120117 -> 2.638853073120117
3:52:27.390778 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
3:52:27.402296 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 74.2538 found after 7 searches.
3:52:27.410296 INFO: ==============================================
3:52:27.418305 PROGRESS: Optimization finished for rt_error.
3:52:28.030799 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:52:28.114370 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:52:28.264992 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:52:28.761404 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:52:28.767412 PROGRESS: ==============================================
3:52:28.772412 PROGRESS: ms2_error      : 10.0000
3:52:28.776919 PROGRESS: ms1_error      : 5.0000
3:52:28.781927 PROGRESS: rt_error       : 74.2538
3:52:28.786927 PROGRESS: ==============================================
3:52:28.803935 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
3:52:32.554528 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
3:52:41.991921 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
3:53:25.237815 INFO: Using classic extraction backend
3:53:25.243815 PROGRESS: Extracting batch of 11035943 precursors
3:53:25.247328 INFO: === Search parameters used ===
3:53:25.251328 INFO: rt_error       : 74.25383333759842
3:53:25.255331 INFO: mobility_error : 0.1
3:53:25.259331 INFO: num_candidates : 3
3:53:25.264349 INFO: ms1_error      : 5.0
3:53:25.268350 INFO: ms2_error      : 10.0
3:53:25.272352 INFO: fwhm_rt        : 2.638853073120117
3:53:25.275350 INFO: quant_window   : 3
3:53:25.279865 INFO: ==============================================
3:53:28.837507 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
3:53:28.840012 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:28.849020 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
3:53:28.850021 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:53:28.852020 INFO: Starting candidate selection
4:06:29.154856 INFO: Removed 22367284 precursors with score below cutoff 62.041409949874875
4:06:33.722312 INFO: Starting candidate scoring
4:12:38.599922 INFO: Finished candidate processing
4:12:38.600922 INFO: Collecting candidate features
4:13:18.813871 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 10727596)
4:13:20.483377 INFO: Collecting fragment features
4:13:40.131636 INFO: Finished candidate scoring
4:14:27.269368 INFO: === Performing FDR correction with classifier version 14 ===
4:14:27.305975 INFO: performing precursor FDR with 47 features
4:14:27.306973 INFO: Decoy channel: -1
4:14:27.307985 INFO: Competetive: True
4:14:33.946610 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:37.486749 WARNING: dropped 8 target PSMs due to missing features
4:14:51.872304 INFO: Using random state 736578 for train-test-split
4:20:18.539809 INFO: Test AUC: 0.581
4:20:18.540809 INFO: Train AUC: 0.582
4:20:18.541807 INFO: AUC difference: 0.26%
4:20:27.647188 INFO: Resetting torch num_threads to 10
4:20:28.073873 INFO: Removing fragments below FDR threshold
4:20:31.546014 PROGRESS: ============================= Precursor FDR =============================
4:20:31.551025 PROGRESS: Total precursors accumulated: 44,059
4:20:31.555026 PROGRESS: Target precursors: 43,623 (99.01%)
4:20:31.559027 PROGRESS: Decoy precursors: 436 (0.99%)
4:20:31.562037 PROGRESS: 
4:20:31.566034 PROGRESS: Precursor Summary:
4:20:31.670513 PROGRESS: Channel   0:	 0.050 FDR: 43,623; 0.010 FDR: 43,623; 0.001 FDR: 30,830
4:20:31.674528 PROGRESS: 
4:20:31.678528 PROGRESS: Protein Summary:
4:20:31.811520 PROGRESS: Channel   0:	 0.050 FDR: 8,051; 0.010 FDR: 8,051; 0.001 FDR: 6,367
4:20:31.815519 PROGRESS: =========================================================================
4:20:32.248948 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\psm.parquet
4:20:33.277861 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\frag.parquet
4:20:34.372033 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
4:20:35.628495 PROGRESS: 
4:20:35.630490 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant
4:20:35.631491 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\figures
4:20:35.640012 INFO: Initializing TimingManager
4:20:35.663027 INFO: Initializing RawFileManager
4:25:22.187754 INFO: Determining DIA cycle
4:25:22.212279 INFO: Found cycle with start 0.00 min and length 86.
4:25:22.965078 INFO: RT (min)            : 0.0 - 55.5
4:25:22.966078 INFO: RT duration (sec)   : 3327.1
4:25:22.967079 INFO: RT duration (min)   : 55.5
4:25:22.968079 INFO: Cycle len (scans)   : 86
4:25:22.969078 INFO: Cycle len (sec)     : 1.90
4:25:22.970078 INFO: Number of cycles    : 1747
4:25:22.971091 INFO: MS2 range (m/z)     : 399.5 - 903.5
4:25:22.972091 INFO: Creating DIA data object took: 287.29353952407837
4:25:26.448329 INFO: Initializing CalibrationManager
4:25:26.457859 INFO: Setting up calibration estimators ..
4:25:26.462858 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:25:26.466860 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'}' ..
4:25:26.470870 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:25:26.474872 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
4:25:26.477871 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}}' ..
4:25:26.481869 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
4:25:26.485872 INFO: Done setting up calibration estimators.
4:25:26.489372 INFO: Initializing OptimizationManager
4:25:26.496372 INFO: initial parameter: ms1_error = 30
4:25:26.499370 INFO: initial parameter: ms2_error = 30
4:25:26.503384 INFO: initial parameter: rt_error = 1663.596435546875
4:25:26.506383 INFO: initial parameter: mobility_error = 0.1
4:25:26.510383 INFO: initial parameter: num_candidates = 1
4:25:26.513383 INFO: initial parameter: fwhm_rt = 5
4:25:26.516896 INFO: initial parameter: fwhm_mobility = 0.01
4:25:26.520910 INFO: initial parameter: score_cutoff = 0
4:25:26.523910 INFO: initial parameter: classifier_version = -1
4:25:26.529912 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
4:25:26.533922 INFO: FDRManager: loading saved state not requested, will be initialized.
4:25:26.534922 INFO: Initializing FDRManager
4:25:26.535924 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
4:25:29.612998 PROGRESS: Initializing spectral library: 5,593,630 target precursors potentially observable (87,574 removed)
4:25:31.921098 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
4:25:31.929613 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 1663.596435546875
4:25:31.937613 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
4:25:31.945621 PROGRESS: Starting initial search for precursors.
4:25:31.954621 INFO: Starting optimization step 0.
4:25:31.962135 PROGRESS: === Extracting elution groups 0 to 8000 ===
4:25:31.968135 INFO: Using classic extraction backend
4:25:31.974142 PROGRESS: Extracting batch of 15689 precursors
4:25:31.983148 INFO: === Search parameters used ===
4:25:31.994673 INFO: rt_error       : 1663.596435546875
4:25:32.003673 INFO: mobility_error : 0.1
4:25:32.015672 INFO: num_candidates : 1
4:25:32.027190 INFO: ms1_error      : 30
4:25:32.037199 INFO: ms2_error      : 30
4:25:32.051214 INFO: fwhm_rt        : 5
4:25:32.062214 INFO: quant_window   : 3
4:25:32.075223 INFO: ==============================================
4:25:32.130306 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:25:32.132306 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:25:32.134315 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
4:25:32.135306 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
4:25:32.137309 INFO: Starting candidate selection
4:25:46.137090 INFO: Starting candidate scoring
4:25:46.688373 INFO: Finished candidate processing
4:25:46.689885 INFO: Collecting candidate features
4:25:46.824114 INFO: Collecting fragment features
4:25:46.924641 INFO: Finished candidate scoring
4:25:46.965191 INFO: performing precursor FDR with 47 features
4:25:46.966190 INFO: Decoy channel: -1
4:25:46.967192 INFO: Competetive: True
4:25:47.005809 INFO: Setting torch num_threads to 2 for FDR classification task
4:25:47.040434 INFO: Using random state 459300 for train-test-split
4:25:47.513928 INFO: Test AUC: 0.551
4:25:47.514928 INFO: Train AUC: 0.550
4:25:47.515926 INFO: AUC difference: 0.23%
4:25:48.102911 INFO: Resetting torch num_threads to 10
4:25:48.113426 PROGRESS: === Extracted 15681 precursors and 144547 fragments ===
4:25:48.119427 INFO: === FDR correction performed with classifier version -1 ===
4:25:48.138434 PROGRESS: ============================= Precursor FDR =============================
4:25:48.142435 PROGRESS: Total precursors accumulated: 7,981
4:25:48.146455 PROGRESS: Target precursors: 4,679 (58.63%)
4:25:48.149465 PROGRESS: Decoy precursors: 3,302 (41.37%)
4:25:48.153464 PROGRESS: 
4:25:48.157464 PROGRESS: Precursor Summary:
4:25:48.166470 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
4:25:48.171471 PROGRESS: 
4:25:48.175985 PROGRESS: Protein Summary:
4:25:48.181985 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
4:25:48.186985 PROGRESS: =========================================================================
4:25:48.195993 INFO: Target number of precursors not reached yet.
4:25:48.555778 INFO: Starting optimization step 1.
4:25:48.561779 PROGRESS: === Extracting elution groups 8000 to 24000 ===
4:25:48.566786 INFO: Using classic extraction backend
4:25:48.571786 PROGRESS: Extracting batch of 31390 precursors
4:25:48.576787 INFO: === Search parameters used ===
4:25:48.579786 INFO: rt_error       : 1663.596435546875
4:25:48.583302 INFO: mobility_error : 0.1
4:25:48.586302 INFO: num_candidates : 1
4:25:48.590302 INFO: ms1_error      : 30
4:25:48.593302 INFO: ms2_error      : 30
4:25:48.600311 INFO: fwhm_rt        : 5
4:25:48.608311 INFO: quant_window   : 3
4:25:48.616826 INFO: ==============================================
4:25:48.679388 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:25:48.680388 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:25:48.681388 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
4:25:48.682388 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
4:25:48.683388 INFO: Starting candidate selection
4:26:16.186057 INFO: Starting candidate scoring
4:26:17.230216 INFO: Finished candidate processing
4:26:17.231225 INFO: Collecting candidate features
4:26:17.489503 INFO: Collecting fragment features
4:26:17.600114 INFO: Finished candidate scoring
4:26:17.714920 INFO: performing precursor FDR with 47 features
4:26:17.715921 INFO: Decoy channel: -1
4:26:17.716923 INFO: Competetive: True
4:26:17.850299 INFO: Setting torch num_threads to 2 for FDR classification task
4:26:17.923968 INFO: Using random state 459579 for train-test-split
4:26:19.073700 INFO: Test AUC: 0.564
4:26:19.074697 INFO: Train AUC: 0.588
4:26:19.075697 INFO: AUC difference: 4.07%
4:26:19.751786 INFO: Resetting torch num_threads to 10
4:26:19.832554 PROGRESS: === Extracted 47053 precursors and 433520 fragments ===
4:26:19.838555 INFO: === FDR correction performed with classifier version -1 ===
4:26:19.843556 PROGRESS: ============================= Precursor FDR =============================
4:26:19.847569 PROGRESS: Total precursors accumulated: 8
4:26:19.850568 PROGRESS: Target precursors: 8 (100.00%)
4:26:19.854568 PROGRESS: Decoy precursors: 0 (0.00%)
4:26:19.858567 PROGRESS: 
4:26:19.862091 PROGRESS: Precursor Summary:
4:26:19.868088 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
4:26:19.873090 PROGRESS: 
4:26:19.877088 PROGRESS: Protein Summary:
4:26:19.885117 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
4:26:19.889117 PROGRESS: =========================================================================
4:26:19.899629 INFO: Target number of precursors not reached yet.
4:26:20.397898 INFO: Starting optimization step 2.
4:26:20.405899 PROGRESS: === Extracting elution groups 24000 to 56000 ===
4:26:20.413905 INFO: Using classic extraction backend
4:26:20.422905 PROGRESS: Extracting batch of 62842 precursors
4:26:20.429427 INFO: === Search parameters used ===
4:26:20.436426 INFO: rt_error       : 1663.596435546875
4:26:20.441426 INFO: mobility_error : 0.1
4:26:20.449942 INFO: num_candidates : 1
4:26:20.457456 INFO: ms1_error      : 30
4:26:20.465456 INFO: ms2_error      : 30
4:26:20.473466 INFO: fwhm_rt        : 5
4:26:20.479466 INFO: quant_window   : 3
4:26:20.486972 INFO: ==============================================
4:26:20.582556 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:26:20.583556 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:26:20.584556 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
4:26:20.585556 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
4:26:20.586555 INFO: Starting candidate selection
4:27:15.465480 INFO: Starting candidate scoring
4:27:17.679166 INFO: Finished candidate processing
4:27:17.680163 INFO: Collecting candidate features
4:27:18.221911 INFO: Collecting fragment features
4:27:18.483621 INFO: Finished candidate scoring
4:27:18.708296 INFO: performing precursor FDR with 47 features
4:27:18.709297 INFO: Decoy channel: -1
4:27:18.709297 INFO: Competetive: True
4:27:18.985001 INFO: Setting torch num_threads to 2 for FDR classification task
4:27:19.150647 INFO: Using random state 103593 for train-test-split
4:27:22.010332 INFO: Test AUC: 0.570
4:27:22.012331 INFO: Train AUC: 0.609
4:27:22.013330 INFO: AUC difference: 6.37%
4:27:22.014332 WARNING: AUC difference > 5%. This may indicate overfitting.
4:27:22.732184 INFO: Resetting torch num_threads to 10
4:27:22.891387 PROGRESS: === Extracted 109861 precursors and 1011670 fragments ===
4:27:22.897907 INFO: === FDR correction performed with classifier version -1 ===
4:27:22.904906 PROGRESS: ============================= Precursor FDR =============================
4:27:22.908906 PROGRESS: Total precursors accumulated: 491
4:27:22.913917 PROGRESS: Target precursors: 449 (91.45%)
4:27:22.917917 PROGRESS: Decoy precursors: 42 (8.55%)
4:27:22.920918 PROGRESS: 
4:27:22.924431 PROGRESS: Precursor Summary:
4:27:22.936442 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   180; 0.001 FDR:   176
4:27:22.940443 PROGRESS: 
4:27:22.946455 PROGRESS: Protein Summary:
4:27:22.962979 PROGRESS: Channel   0:	 0.050 FDR:   285; 0.010 FDR:   172; 0.001 FDR:   168
4:27:22.967981 PROGRESS: =========================================================================
4:27:22.979993 INFO: Target number of precursors not reached yet.
4:27:23.687843 INFO: Starting optimization step 3.
4:27:23.695856 PROGRESS: === Extracting elution groups 56000 to 120000 ===
4:27:23.703855 INFO: Using classic extraction backend
4:27:23.712378 PROGRESS: Extracting batch of 125627 precursors
4:27:23.718379 INFO: === Search parameters used ===
4:27:23.723391 INFO: rt_error       : 1663.596435546875
4:27:23.728391 INFO: mobility_error : 0.1
4:27:23.733392 INFO: num_candidates : 1
4:27:23.737913 INFO: ms1_error      : 30
4:27:23.742914 INFO: ms2_error      : 30
4:27:23.747912 INFO: fwhm_rt        : 5
4:27:23.752913 INFO: quant_window   : 3
4:27:23.758925 INFO: ==============================================
4:27:23.877569 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:27:23.878581 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:27:23.879581 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
4:27:23.879581 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
4:27:23.881581 INFO: Starting candidate selection
4:29:16.855730 INFO: Starting candidate scoring
4:29:21.080280 INFO: Finished candidate processing
4:29:21.081803 INFO: Collecting candidate features
4:29:22.135439 INFO: Collecting fragment features
4:29:22.449247 INFO: Finished candidate scoring
4:29:22.772545 INFO: performing precursor FDR with 47 features
4:29:22.774545 INFO: Decoy channel: -1
4:29:22.775545 INFO: Competetive: True
4:29:23.304006 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:23.666428 INFO: Using random state 629437 for train-test-split
4:29:29.980038 INFO: Test AUC: 0.578
4:29:29.982038 INFO: Train AUC: 0.607
4:29:29.984039 INFO: AUC difference: 4.70%
4:29:30.965001 INFO: Resetting torch num_threads to 10
4:29:31.169141 PROGRESS: === Extracted 235428 precursors and 2166587 fragments ===
4:29:31.175655 INFO: === FDR correction performed with classifier version -1 ===
4:29:31.183671 PROGRESS: ============================= Precursor FDR =============================
4:29:31.186671 PROGRESS: Total precursors accumulated: 989
4:29:31.190671 PROGRESS: Target precursors: 903 (91.30%)
4:29:31.194179 PROGRESS: Decoy precursors: 86 (8.70%)
4:29:31.198185 PROGRESS: 
4:29:31.201187 PROGRESS: Precursor Summary:
4:29:31.208700 PROGRESS: Channel   0:	 0.050 FDR:   646; 0.010 FDR:   458; 0.001 FDR:   254
4:29:31.212699 PROGRESS: 
4:29:31.215700 PROGRESS: Protein Summary:
4:29:31.224706 PROGRESS: Channel   0:	 0.050 FDR:   570; 0.010 FDR:   406; 0.001 FDR:   234
4:29:31.229707 PROGRESS: =========================================================================
4:29:31.252226 INFO: Target number of precursors reached.
4:29:31.680170 INFO: fragments_df: keeping 4406 of 2166587 [sum(precursor_idx_mask)=5223 sum(mass_error_mask)=2166587 stop_rank=4406
4:29:32.503905 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:29:32.855327 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:29:33.246500 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:29:36.091487 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:29:36.096485 INFO: Using score_cutoff 81.43699288787842 (fac=0.99, q=1)
4:29:36.100501 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.5020179748535156
4:29:36.104505 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
4:29:36.107501 INFO: Updating optimization_manager: score_cutoff        : 0 -> 81.43699288787842
4:29:36.111501 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:29:36.209907 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:29:36.374696 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:29:36.840160 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
4:29:36.845160 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:29:36.849172 INFO: Starting optimization step 4.
4:29:36.852173 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:29:36.856173 INFO: Using classic extraction backend
4:29:36.860174 PROGRESS: Extracting batch of 109921 precursors
4:29:36.865702 INFO: === Search parameters used ===
4:29:36.871704 INFO: rt_error       : 1663.596435546875
4:29:36.878703 INFO: mobility_error : 0.1
4:29:36.886717 INFO: num_candidates : 3
4:29:36.969143 INFO: ms1_error      : 30
4:29:36.978165 INFO: ms2_error      : 30
4:29:36.987162 INFO: fwhm_rt        : 2.5020179748535156
4:29:36.992505 INFO: quant_window   : 3
4:29:37.001505 INFO: ==============================================
4:29:37.121631 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:29:37.122632 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:29:37.123631 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
4:29:37.123631 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:29:37.124631 INFO: Starting candidate selection
4:31:36.062094 INFO: Starting candidate scoring
4:31:46.214857 INFO: Finished candidate processing
4:31:46.215865 INFO: Collecting candidate features
4:31:47.702020 INFO: Collecting fragment features
4:31:48.314071 INFO: Finished candidate scoring
4:31:48.729122 INFO: performing precursor FDR with 47 features
4:31:48.730122 INFO: Decoy channel: -1
4:31:48.731122 INFO: Competetive: True
4:31:49.065646 INFO: Setting torch num_threads to 2 for FDR classification task
4:31:49.516700 INFO: Using random state 253416 for train-test-split
4:31:57.355011 INFO: Test AUC: 0.583
4:31:57.357013 INFO: Train AUC: 0.605
4:31:57.359012 INFO: AUC difference: 3.56%
4:31:58.296116 INFO: Resetting torch num_threads to 10
4:31:58.326117 PROGRESS: === Extracted 329543 precursors and 2923795 fragments ===
4:31:58.332116 INFO: === FDR correction performed with classifier version 3 ===
4:31:58.338116 PROGRESS: ============================= Precursor FDR =============================
4:31:58.342116 PROGRESS: Total precursors accumulated: 507
4:31:58.346116 PROGRESS: Target precursors: 464 (91.52%)
4:31:58.350117 PROGRESS: Decoy precursors: 43 (8.48%)
4:31:58.355116 PROGRESS: 
4:31:58.360118 PROGRESS: Precursor Summary:
4:31:58.373124 PROGRESS: Channel   0:	 0.050 FDR:   379; 0.010 FDR:   130; 0.001 FDR:    12
4:31:58.379125 PROGRESS: 
4:31:58.383633 PROGRESS: Protein Summary:
4:31:58.395643 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   127; 0.001 FDR:    12
4:31:58.400644 PROGRESS: =========================================================================
4:31:58.413643 INFO: Target number of precursors not reached yet.
4:31:59.261225 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:31:59.390748 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:31:59.584751 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:32:00.053802 INFO: === skipping optimization until target number of precursors are found ===
4:32:00.059801 INFO: Starting optimization step 5.
4:32:00.063802 PROGRESS: === Extracting elution groups 56000 to 120000 ===
4:32:00.068801 INFO: Using classic extraction backend
4:32:00.072803 PROGRESS: Extracting batch of 125627 precursors
4:32:00.076801 INFO: === Search parameters used ===
4:32:00.081801 INFO: rt_error       : 1663.596435546875
4:32:00.085801 INFO: mobility_error : 0.1
4:32:00.089800 INFO: num_candidates : 3
4:32:00.094801 INFO: ms1_error      : 30
4:32:00.099801 INFO: ms2_error      : 30
4:32:00.104803 INFO: fwhm_rt        : 2.5020179748535156
4:32:00.109802 INFO: quant_window   : 3
4:32:00.115801 INFO: ==============================================
4:32:00.251326 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:32:00.253325 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:32:00.254325 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
4:32:00.255329 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:32:00.257325 INFO: Starting candidate selection
4:36:03.763505 INFO: Starting candidate scoring
4:36:15.435100 INFO: Finished candidate processing
4:36:15.436098 INFO: Collecting candidate features
4:36:16.961239 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 376658)
4:36:17.068760 INFO: Collecting fragment features
4:36:17.779812 INFO: Finished candidate scoring
4:36:18.666920 INFO: performing precursor FDR with 47 features
4:36:18.667919 INFO: Decoy channel: -1
4:36:18.669919 INFO: Competetive: True
4:36:19.467491 INFO: Setting torch num_threads to 2 for FDR classification task
4:36:19.776015 WARNING: dropped 1 decoy PSMs due to missing features
4:36:20.530599 INFO: Using random state 253416 for train-test-split
4:36:37.583275 INFO: Test AUC: 0.583
4:36:37.584276 INFO: Train AUC: 0.598
4:36:37.585275 INFO: AUC difference: 2.53%
4:36:38.804889 INFO: Resetting torch num_threads to 10
4:36:39.176939 PROGRESS: === Extracted 706201 precursors and 6262448 fragments ===
4:36:39.182940 INFO: === FDR correction performed with classifier version 3 ===
4:36:39.189940 PROGRESS: ============================= Precursor FDR =============================
4:36:39.193940 PROGRESS: Total precursors accumulated: 1,132
4:36:39.197940 PROGRESS: Target precursors: 1,033 (91.25%)
4:36:39.201939 PROGRESS: Decoy precursors: 99 (8.75%)
4:36:39.205940 PROGRESS: 
4:36:39.208940 PROGRESS: Precursor Summary:
4:36:39.217940 PROGRESS: Channel   0:	 0.050 FDR:   828; 0.010 FDR:   555; 0.001 FDR:   303
4:36:39.221940 PROGRESS: 
4:36:39.225940 PROGRESS: Protein Summary:
4:36:39.234941 PROGRESS: Channel   0:	 0.050 FDR:   733; 0.010 FDR:   489; 0.001 FDR:   282
4:36:39.238940 PROGRESS: =========================================================================
4:36:39.246941 INFO: Target number of precursors reached.
4:36:40.440560 INFO: fragments_df: keeping 5000 of 6262448 [sum(precursor_idx_mask)=16906 sum(mass_error_mask)=6262448 stop_rank=5000
4:36:41.377653 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:36:41.689180 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:36:42.068705 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:36:45.455050 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:36:45.460051 INFO: Using score_cutoff 76.19124201965332 (fac=0.99, q=1)
4:36:45.464051 INFO: Updating optimization_manager: fwhm_rt             : 2.5020179748535156 -> 2.4927525520324707
4:36:45.469050 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:36:45.473051 INFO: Updating optimization_manager: score_cutoff        : 81.43699288787842 -> 76.19124201965332
4:36:45.476051 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:36:45.582052 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:36:45.753575 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:36:46.172622 INFO: === checking if optimization conditions were reached ===
4:36:46.181622 INFO: Updating optimization_manager: ms2_error           : 30 -> 18.041518374404426
4:36:46.186622 INFO: Updating optimization_manager: classifier_version  : 3 -> 5
4:36:46.189622 PROGRESS: ❌ ms2_error      : 18.0415 > 10.0000 or insufficient steps taken.
4:36:46.196622 INFO: Updating optimization_manager: ms1_error           : 30 -> 12.441018285194712
4:36:46.200622 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
4:36:46.204623 PROGRESS: ❌ ms1_error      : 12.4410 > 5.0000 or insufficient steps taken.
4:36:46.208622 INFO: ==============================================
4:36:46.211622 INFO: Starting optimization step 6.
4:36:46.215622 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:36:46.219623 INFO: Using classic extraction backend
4:36:46.223623 PROGRESS: Extracting batch of 109921 precursors
4:36:46.227622 INFO: === Search parameters used ===
4:36:46.231622 INFO: rt_error       : 1663.596435546875
4:36:46.238623 INFO: mobility_error : 0.1
4:36:46.244622 INFO: num_candidates : 3
4:36:46.251625 INFO: ms1_error      : 12.441018285194712
4:36:46.261623 INFO: ms2_error      : 18.041518374404426
4:36:46.268623 INFO: fwhm_rt        : 2.4927525520324707
4:36:46.276623 INFO: quant_window   : 3
4:36:46.281624 INFO: ==============================================
4:36:46.402148 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:36:46.403148 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:36:46.405165 INFO: FWHM in RT is 2.49 seconds, sigma is 0.28
4:36:46.405165 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:36:46.406147 INFO: Starting candidate selection
4:40:18.886514 INFO: Starting candidate scoring
4:40:28.531950 INFO: Finished candidate processing
4:40:28.533963 INFO: Collecting candidate features
4:40:29.898645 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 329461)
4:40:30.016180 INFO: Collecting fragment features
4:40:30.594251 INFO: Finished candidate scoring
4:40:31.000320 INFO: performing precursor FDR with 47 features
4:40:31.002319 INFO: Decoy channel: -1
4:40:31.003320 INFO: Competetive: True
4:40:31.346856 INFO: Setting torch num_threads to 2 for FDR classification task
4:40:31.497388 WARNING: dropped 3 target PSMs due to missing features
4:40:31.803928 INFO: Using random state 840840 for train-test-split
4:40:39.665420 INFO: Test AUC: 0.581
4:40:39.666421 INFO: Train AUC: 0.603
4:40:39.667421 INFO: AUC difference: 3.62%
4:40:40.658523 INFO: Resetting torch num_threads to 10
4:40:40.687523 PROGRESS: === Extracted 329461 precursors and 2725839 fragments ===
4:40:40.693524 INFO: === FDR correction performed with classifier version 5 ===
4:40:40.699523 PROGRESS: ============================= Precursor FDR =============================
4:40:40.703523 PROGRESS: Total precursors accumulated: 777
4:40:40.707524 PROGRESS: Target precursors: 709 (91.25%)
4:40:40.711524 PROGRESS: Decoy precursors: 68 (8.75%)
4:40:40.716525 PROGRESS: 
4:40:40.721524 PROGRESS: Precursor Summary:
4:40:40.728524 PROGRESS: Channel   0:	 0.050 FDR:   559; 0.010 FDR:   363; 0.001 FDR:   216
4:40:40.732524 PROGRESS: 
4:40:40.736525 PROGRESS: Protein Summary:
4:40:40.743524 PROGRESS: Channel   0:	 0.050 FDR:   520; 0.010 FDR:   338; 0.001 FDR:   204
4:40:40.748532 PROGRESS: =========================================================================
4:40:40.757532 INFO: Target number of precursors reached.
4:40:41.247579 INFO: fragments_df: keeping 4966 of 2725839 [sum(precursor_idx_mask)=10372 sum(mass_error_mask)=2725839 stop_rank=4966
4:40:41.911193 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:40:42.263255 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:40:42.656789 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:40:46.004594 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:40:46.011604 INFO: Using score_cutoff 70.367794972229 (fac=0.99, q=1)
4:40:46.019602 INFO: Updating optimization_manager: fwhm_rt             : 2.4927525520324707 -> 2.4451844692230225
4:40:46.024115 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:40:46.029117 INFO: Updating optimization_manager: score_cutoff        : 76.19124201965332 -> 70.367794972229
4:40:46.035116 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:40:46.152117 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:40:46.331640 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:40:46.747169 INFO: === checking if optimization conditions were reached ===
4:40:46.759176 INFO: Updating optimization_manager: ms2_error           : 18.041518374404426 -> 11.02094311548235
4:40:46.766174 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
4:40:46.772681 PROGRESS: ❌ ms2_error      : 11.0209 > 10.0000 or insufficient steps taken.
4:40:46.781689 INFO: Updating optimization_manager: ms1_error           : 12.441018285194712 -> 5.0
4:40:46.787689 INFO: Updating optimization_manager: classifier_version  : 6 -> 6
4:40:46.793689 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
4:40:46.798689 INFO: ==============================================
4:40:46.803689 INFO: Starting optimization step 7.
4:40:46.808690 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:40:46.812689 INFO: Using classic extraction backend
4:40:46.817689 PROGRESS: Extracting batch of 109921 precursors
4:40:46.820689 INFO: === Search parameters used ===
4:40:46.828692 INFO: rt_error       : 1663.596435546875
4:40:46.835690 INFO: mobility_error : 0.1
4:40:46.839689 INFO: num_candidates : 3
4:40:46.848691 INFO: ms1_error      : 5.0
4:40:46.856691 INFO: ms2_error      : 11.02094311548235
4:40:46.867691 INFO: fwhm_rt        : 2.4451844692230225
4:40:46.875691 INFO: quant_window   : 3
4:40:46.884691 INFO: ==============================================
4:40:47.003692 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:40:47.005692 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:40:47.007699 INFO: FWHM in RT is 2.45 seconds, sigma is 0.27
4:40:47.008699 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:40:47.010700 INFO: Starting candidate selection
4:42:42.240103 INFO: Starting candidate scoring
4:42:51.709890 INFO: Finished candidate processing
4:42:51.710898 INFO: Collecting candidate features
4:42:53.144972 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 329303)
4:42:53.258516 INFO: Collecting fragment features
4:42:53.864687 INFO: Finished candidate scoring
4:42:54.278828 INFO: performing precursor FDR with 47 features
4:42:54.279828 INFO: Decoy channel: -1
4:42:54.281827 INFO: Competetive: True
4:42:54.616446 INFO: Setting torch num_threads to 2 for FDR classification task
4:42:54.791056 WARNING: dropped 5 target PSMs due to missing features
4:42:54.792055 WARNING: dropped 3 decoy PSMs due to missing features
4:42:55.111674 INFO: Using random state 627245 for train-test-split
4:43:03.109432 INFO: Test AUC: 0.573
4:43:03.110435 INFO: Train AUC: 0.604
4:43:03.111433 INFO: AUC difference: 5.08%
4:43:03.112436 WARNING: AUC difference > 5%. This may indicate overfitting.
4:43:03.997535 INFO: Resetting torch num_threads to 10
4:43:04.026535 PROGRESS: === Extracted 329303 precursors and 2553221 fragments ===
4:43:04.032537 INFO: === FDR correction performed with classifier version 6 ===
4:43:04.038536 PROGRESS: ============================= Precursor FDR =============================
4:43:04.042538 PROGRESS: Total precursors accumulated: 710
4:43:04.046536 PROGRESS: Target precursors: 646 (90.99%)
4:43:04.050536 PROGRESS: Decoy precursors: 64 (9.01%)
4:43:04.053536 PROGRESS: 
4:43:04.057536 PROGRESS: Precursor Summary:
4:43:04.064535 PROGRESS: Channel   0:	 0.050 FDR:   470; 0.010 FDR:   378; 0.001 FDR:   347
4:43:04.068536 PROGRESS: 
4:43:04.072536 PROGRESS: Protein Summary:
4:43:04.079536 PROGRESS: Channel   0:	 0.050 FDR:   437; 0.010 FDR:   349; 0.001 FDR:   321
4:43:04.084536 PROGRESS: =========================================================================
4:43:04.092536 INFO: Target number of precursors reached.
4:43:04.566586 INFO: fragments_df: keeping 5000 of 2553221 [sum(precursor_idx_mask)=10408 sum(mass_error_mask)=2553221 stop_rank=5000
4:43:05.232168 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:43:05.577693 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:43:05.959221 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:43:09.248575 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:43:09.253575 INFO: Using score_cutoff 62.412853762435915 (fac=0.99, q=1)
4:43:09.259573 INFO: Updating optimization_manager: fwhm_rt             : 2.4451844692230225 -> 2.4819040298461914
4:43:09.263575 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:43:09.267575 INFO: Updating optimization_manager: score_cutoff        : 70.367794972229 -> 62.412853762435915
4:43:09.271575 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:43:09.369576 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:43:09.531101 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:43:09.936629 INFO: === checking if optimization conditions were reached ===
4:43:09.945628 INFO: Updating optimization_manager: ms2_error           : 11.02094311548235 -> 10.0
4:43:09.949628 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
4:43:09.954628 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
4:43:09.958628 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
4:43:09.965628 INFO: ==============================================
4:43:09.972637 PROGRESS: Optimization finished for ms2_error, ms1_error.
4:43:10.615205 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:43:10.732214 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:43:10.892734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:43:11.327787 INFO: Starting optimization step 0.
4:43:11.332787 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:43:11.336787 INFO: Using classic extraction backend
4:43:11.340786 PROGRESS: Extracting batch of 109921 precursors
4:43:11.344788 INFO: === Search parameters used ===
4:43:11.347788 INFO: rt_error       : 1663.596435546875
4:43:11.351788 INFO: mobility_error : 0.1
4:43:11.355787 INFO: num_candidates : 3
4:43:11.358787 INFO: ms1_error      : 5.0
4:43:11.362788 INFO: ms2_error      : 10.0
4:43:11.366788 INFO: fwhm_rt        : 2.4819040298461914
4:43:11.370788 INFO: quant_window   : 3
4:43:11.379788 INFO: ==============================================
4:43:11.502314 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:43:11.503314 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:43:11.504314 INFO: FWHM in RT is 2.48 seconds, sigma is 0.28
4:43:11.505314 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:43:11.506314 INFO: Starting candidate selection
4:44:59.760624 INFO: Starting candidate scoring
4:45:08.838743 INFO: Finished candidate processing
4:45:08.840747 INFO: Collecting candidate features
4:45:10.021325 WARNING: intensity_correlation has 11 NaNs ( 0.00 % out of 329244)
4:45:10.024326 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329244)
4:45:10.113327 INFO: Collecting fragment features
4:45:10.642864 INFO: Finished candidate scoring
4:45:11.020383 INFO: performing precursor FDR with 47 features
4:45:11.021388 INFO: Decoy channel: -1
4:45:11.022384 INFO: Competetive: True
4:45:11.316899 INFO: Setting torch num_threads to 2 for FDR classification task
4:45:11.475412 WARNING: dropped 7 target PSMs due to missing features
4:45:11.476413 WARNING: dropped 4 decoy PSMs due to missing features
4:45:11.736926 INFO: Using random state 376629 for train-test-split
4:45:18.875374 INFO: Test AUC: 0.581
4:45:18.876374 INFO: Train AUC: 0.611
4:45:18.877375 INFO: AUC difference: 4.84%
4:45:19.794434 INFO: Resetting torch num_threads to 10
4:45:19.818434 PROGRESS: === Extracted 329244 precursors and 2520040 fragments ===
4:45:19.867435 INFO: === FDR correction performed with classifier version 7 ===
4:45:19.874435 PROGRESS: ============================= Precursor FDR =============================
4:45:19.879435 PROGRESS: Total precursors accumulated: 864
4:45:19.884435 PROGRESS: Target precursors: 784 (90.74%)
4:45:19.888436 PROGRESS: Decoy precursors: 80 (9.26%)
4:45:19.893436 PROGRESS: 
4:45:19.898439 PROGRESS: Precursor Summary:
4:45:19.909440 PROGRESS: Channel   0:	 0.050 FDR:   462; 0.010 FDR:   329; 0.001 FDR:   244
4:45:19.913948 PROGRESS: 
4:45:19.918948 PROGRESS: Protein Summary:
4:45:19.929949 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   307; 0.001 FDR:   231
4:45:19.937948 PROGRESS: =========================================================================
4:45:19.950948 INFO: Target number of precursors reached.
4:45:20.420980 INFO: fragments_df: keeping 4552 of 2520040 [sum(precursor_idx_mask)=9051 sum(mass_error_mask)=2520040 stop_rank=4552
4:45:21.087014 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:45:21.412533 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:45:21.751557 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:45:24.658282 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:45:24.662279 INFO: Using score_cutoff 65.21982231445313 (fac=0.99, q=1)
4:45:24.666279 INFO: Updating optimization_manager: fwhm_rt             : 2.4819040298461914 -> 2.4797263145446777
4:45:24.670279 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:45:24.672815 INFO: Updating optimization_manager: score_cutoff        : 62.412853762435915 -> 65.21982231445313
4:45:24.676815 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:45:24.743817 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:45:24.862815 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:45:25.232912 INFO: === checking if optimization conditions were reached ===
4:45:25.236912 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
4:45:25.242914 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 157.5417817723574
4:45:25.245915 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 157.5418.
4:45:25.248912 INFO: ==============================================
4:45:25.251913 INFO: Starting optimization step 1.
4:45:25.254916 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:45:25.258915 INFO: Using classic extraction backend
4:45:25.261913 PROGRESS: Extracting batch of 109921 precursors
4:45:25.264912 INFO: === Search parameters used ===
4:45:25.268913 INFO: rt_error       : 157.5417817723574
4:45:25.271915 INFO: mobility_error : 0.1
4:45:25.274915 INFO: num_candidates : 3
4:45:25.277913 INFO: ms1_error      : 5.0
4:45:25.281912 INFO: ms2_error      : 10.0
4:45:25.284914 INFO: fwhm_rt        : 2.4797263145446777
4:45:25.287914 INFO: quant_window   : 3
4:45:25.290913 INFO: ==============================================
4:45:25.374915 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:45:25.375913 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:45:25.377918 INFO: FWHM in RT is 2.48 seconds, sigma is 0.28
4:45:25.378914 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:45:25.379915 INFO: Starting candidate selection
4:45:37.324295 INFO: Starting candidate scoring
4:45:45.616567 INFO: Finished candidate processing
4:45:45.617566 INFO: Collecting candidate features
4:45:46.695759 WARNING: intensity_correlation has 23 NaNs ( 0.01 % out of 329208)
4:45:46.699600 WARNING: height_correlation has 7 NaNs ( 0.00 % out of 329208)
4:45:46.784199 INFO: Collecting fragment features
4:45:47.254340 INFO: Finished candidate scoring
4:45:47.622946 INFO: performing precursor FDR with 47 features
4:45:47.623947 INFO: Decoy channel: -1
4:45:47.624946 INFO: Competetive: True
4:45:47.902489 INFO: Setting torch num_threads to 2 for FDR classification task
4:45:48.051031 WARNING: dropped 16 target PSMs due to missing features
4:45:48.052035 WARNING: dropped 12 decoy PSMs due to missing features
4:45:48.324648 INFO: Using random state 376629 for train-test-split
4:45:55.657378 INFO: Test AUC: 0.568
4:45:55.658381 INFO: Train AUC: 0.599
4:45:55.659379 INFO: AUC difference: 5.29%
4:45:55.660378 WARNING: AUC difference > 5%. This may indicate overfitting.
4:45:56.589823 INFO: Resetting torch num_threads to 10
4:45:56.618818 PROGRESS: === Extracted 329208 precursors and 2453251 fragments ===
4:45:56.624819 INFO: === FDR correction performed with classifier version 7 ===
4:45:56.631823 PROGRESS: ============================= Precursor FDR =============================
4:45:56.635822 PROGRESS: Total precursors accumulated: 820
4:45:56.638823 PROGRESS: Target precursors: 747 (91.10%)
4:45:56.642822 PROGRESS: Decoy precursors: 73 (8.90%)
4:45:56.645822 PROGRESS: 
4:45:56.649824 PROGRESS: Precursor Summary:
4:45:56.656823 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   360; 0.001 FDR:   258
4:45:56.660822 PROGRESS: 
4:45:56.663823 PROGRESS: Protein Summary:
4:45:56.670822 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   335; 0.001 FDR:   245
4:45:56.674823 PROGRESS: =========================================================================
4:45:56.683823 INFO: Target number of precursors reached.
4:45:57.121841 INFO: fragments_df: keeping 4707 of 2453251 [sum(precursor_idx_mask)=9810 sum(mass_error_mask)=2453251 stop_rank=4707
4:45:57.778482 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:45:58.109031 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:45:58.411581 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:46:01.610342 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:46:01.616340 INFO: Using score_cutoff 61.32648707542419 (fac=0.99, q=1)
4:46:01.621340 INFO: Updating optimization_manager: fwhm_rt             : 2.4797263145446777 -> 2.5230278968811035
4:46:01.626340 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:46:01.629338 INFO: Updating optimization_manager: score_cutoff        : 65.21982231445313 -> 61.32648707542419
4:46:01.633337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:46:01.737356 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:46:01.918879 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:46:02.345927 INFO: === checking if optimization conditions were reached ===
4:46:02.350926 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
4:46:02.357930 INFO: Updating optimization_manager: rt_error            : 157.5417817723574 -> 102.82685597668421
4:46:02.361930 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 102.8269.
4:46:02.365932 INFO: ==============================================
4:46:02.369932 INFO: Starting optimization step 2.
4:46:02.372932 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:46:02.376932 INFO: Using classic extraction backend
4:46:02.380934 PROGRESS: Extracting batch of 109921 precursors
4:46:02.383932 INFO: === Search parameters used ===
4:46:02.387932 INFO: rt_error       : 102.82685597668421
4:46:02.390931 INFO: mobility_error : 0.1
4:46:02.394932 INFO: num_candidates : 3
4:46:02.398933 INFO: ms1_error      : 5.0
4:46:02.401930 INFO: ms2_error      : 10.0
4:46:02.405932 INFO: fwhm_rt        : 2.5230278968811035
4:46:02.408932 INFO: quant_window   : 3
4:46:02.412933 INFO: ==============================================
4:46:02.531317 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:46:02.532315 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:46:02.533314 INFO: FWHM in RT is 2.52 seconds, sigma is 0.28
4:46:02.534314 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:46:02.535319 INFO: Starting candidate selection
4:46:10.956424 INFO: Starting candidate scoring
4:46:20.067717 INFO: Finished candidate processing
4:46:20.068732 INFO: Collecting candidate features
4:46:21.433700 WARNING: intensity_correlation has 28 NaNs ( 0.01 % out of 329173)
4:46:21.437700 WARNING: height_correlation has 30 NaNs ( 0.01 % out of 329173)
4:46:21.529241 INFO: Collecting fragment features
4:46:22.079417 INFO: Finished candidate scoring
4:46:22.466953 INFO: performing precursor FDR with 47 features
4:46:22.467956 INFO: Decoy channel: -1
4:46:22.468954 INFO: Competetive: True
4:46:22.732563 INFO: Setting torch num_threads to 2 for FDR classification task
4:46:22.902169 WARNING: dropped 27 target PSMs due to missing features
4:46:22.903171 WARNING: dropped 22 decoy PSMs due to missing features
4:46:23.219781 INFO: Using random state 376629 for train-test-split
4:46:30.856331 INFO: Test AUC: 0.566
4:46:30.857331 INFO: Train AUC: 0.595
4:46:30.858331 INFO: AUC difference: 4.85%
4:46:31.756099 INFO: Resetting torch num_threads to 10
4:46:31.785112 PROGRESS: === Extracted 329173 precursors and 2414613 fragments ===
4:46:31.793110 INFO: === FDR correction performed with classifier version 7 ===
4:46:31.802641 PROGRESS: ============================= Precursor FDR =============================
4:46:31.806642 PROGRESS: Total precursors accumulated: 951
4:46:31.811644 PROGRESS: Target precursors: 866 (91.06%)
4:46:31.815644 PROGRESS: Decoy precursors: 85 (8.94%)
4:46:31.820645 PROGRESS: 
4:46:31.825640 PROGRESS: Precursor Summary:
4:46:31.832643 PROGRESS: Channel   0:	 0.050 FDR:   605; 0.010 FDR:   410; 0.001 FDR:   368
4:46:31.835642 PROGRESS: 
4:46:31.839643 PROGRESS: Protein Summary:
4:46:31.847642 PROGRESS: Channel   0:	 0.050 FDR:   560; 0.010 FDR:   375; 0.001 FDR:   340
4:46:31.850645 PROGRESS: =========================================================================
4:46:31.859641 INFO: Target number of precursors reached.
4:46:32.291162 INFO: fragments_df: keeping 5000 of 2414613 [sum(precursor_idx_mask)=11139 sum(mass_error_mask)=2414613 stop_rank=5000
4:46:32.993800 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:46:33.392915 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:46:33.827042 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:46:37.154669 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:46:37.161668 INFO: Using score_cutoff 63.71002382354737 (fac=0.99, q=1)
4:46:37.168669 INFO: Updating optimization_manager: fwhm_rt             : 2.5230278968811035 -> 2.5140676498413086
4:46:37.173669 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:46:37.177668 INFO: Updating optimization_manager: score_cutoff        : 61.32648707542419 -> 63.71002382354737
4:46:37.182669 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:46:37.282679 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:46:37.446290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:46:37.868429 INFO: === checking if optimization conditions were reached ===
4:46:37.875430 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
4:46:37.884429 INFO: Updating optimization_manager: rt_error            : 102.82685597668421 -> 76.99272774855521
4:46:37.891429 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 76.9927.
4:46:37.898428 INFO: ==============================================
4:46:37.904430 INFO: Starting optimization step 3.
4:46:37.909429 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:46:37.914429 INFO: Using classic extraction backend
4:46:37.919429 PROGRESS: Extracting batch of 109921 precursors
4:46:37.923430 INFO: === Search parameters used ===
4:46:37.928429 INFO: rt_error       : 76.99272774855521
4:46:37.933429 INFO: mobility_error : 0.1
4:46:37.936430 INFO: num_candidates : 3
4:46:37.940430 INFO: ms1_error      : 5.0
4:46:37.943431 INFO: ms2_error      : 10.0
4:46:37.947429 INFO: fwhm_rt        : 2.5140676498413086
4:46:37.950429 INFO: quant_window   : 3
4:46:37.954430 INFO: ==============================================
4:46:38.057443 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:46:38.059445 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:46:38.059445 INFO: FWHM in RT is 2.51 seconds, sigma is 0.28
4:46:38.060444 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:46:38.061956 INFO: Starting candidate selection
4:46:45.433016 INFO: Starting candidate scoring
4:46:54.805597 INFO: Finished candidate processing
4:46:54.807615 INFO: Collecting candidate features
4:46:56.168663 WARNING: intensity_correlation has 46 NaNs ( 0.01 % out of 329121)
4:46:56.176659 WARNING: height_correlation has 35 NaNs ( 0.01 % out of 329121)
4:46:56.298659 INFO: Collecting fragment features
4:46:56.847218 INFO: Finished candidate scoring
4:46:57.262765 INFO: performing precursor FDR with 47 features
4:46:57.263763 INFO: Decoy channel: -1
4:46:57.264763 INFO: Competetive: True
4:46:57.612830 INFO: Setting torch num_threads to 2 for FDR classification task
4:46:57.785829 WARNING: dropped 35 target PSMs due to missing features
4:46:57.786829 WARNING: dropped 31 decoy PSMs due to missing features
4:46:58.118899 INFO: Using random state 376629 for train-test-split
4:47:05.615057 INFO: Test AUC: 0.562
4:47:05.616054 INFO: Train AUC: 0.594
4:47:05.618054 INFO: AUC difference: 5.32%
4:47:05.619051 WARNING: AUC difference > 5%. This may indicate overfitting.
4:47:06.626742 INFO: Resetting torch num_threads to 10
4:47:06.655743 PROGRESS: === Extracted 329121 precursors and 2397717 fragments ===
4:47:06.663744 INFO: === FDR correction performed with classifier version 7 ===
4:47:06.671743 PROGRESS: ============================= Precursor FDR =============================
4:47:06.676744 PROGRESS: Total precursors accumulated: 778
4:47:06.679742 PROGRESS: Target precursors: 708 (91.00%)
4:47:06.683743 PROGRESS: Decoy precursors: 70 (9.00%)
4:47:06.687744 PROGRESS: 
4:47:06.691744 PROGRESS: Precursor Summary:
4:47:06.698741 PROGRESS: Channel   0:	 0.050 FDR:   571; 0.010 FDR:   408; 0.001 FDR:   230
4:47:06.703741 PROGRESS: 
4:47:06.706744 PROGRESS: Protein Summary:
4:47:06.714746 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   376; 0.001 FDR:   215
4:47:06.718743 PROGRESS: =========================================================================
4:47:06.727743 INFO: Target number of precursors reached.
4:47:07.146895 INFO: fragments_df: keeping 5000 of 2397717 [sum(precursor_idx_mask)=11020 sum(mass_error_mask)=2397717 stop_rank=5000
4:47:07.848150 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:47:08.212295 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:47:10.057281 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:47:13.460441 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:47:13.466441 INFO: Using score_cutoff 67.53381400222777 (fac=0.99, q=1)
4:47:13.470443 INFO: Updating optimization_manager: fwhm_rt             : 2.5140676498413086 -> 2.4969534873962402
4:47:13.474443 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:47:13.478444 INFO: Updating optimization_manager: score_cutoff        : 63.71002382354737 -> 67.53381400222777
4:47:13.482444 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:47:13.579446 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:47:13.744026 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:47:14.161192 INFO: === checking if optimization conditions were reached ===
4:47:14.166190 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
4:47:14.174190 INFO: Updating optimization_manager: rt_error            : 76.99272774855521 -> 75.08024096322393
4:47:14.178190 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 75.0802.
4:47:14.183190 INFO: ==============================================
4:47:14.188189 INFO: Starting optimization step 4.
4:47:14.191191 PROGRESS: === Extracting elution groups 0 to 56000 ===
4:47:14.195187 INFO: Using classic extraction backend
4:47:14.200189 PROGRESS: Extracting batch of 109921 precursors
4:47:14.204189 INFO: === Search parameters used ===
4:47:14.207189 INFO: rt_error       : 75.08024096322393
4:47:14.211190 INFO: mobility_error : 0.1
4:47:14.215189 INFO: num_candidates : 3
4:47:14.219186 INFO: ms1_error      : 5.0
4:47:14.223190 INFO: ms2_error      : 10.0
4:47:14.227190 INFO: fwhm_rt        : 2.4969534873962402
4:47:14.231189 INFO: quant_window   : 3
4:47:14.237190 INFO: ==============================================
4:47:14.351187 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:47:14.352190 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:47:14.353189 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
4:47:14.354190 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:47:14.355188 INFO: Starting candidate selection
4:47:21.004051 INFO: Starting candidate scoring
4:47:29.407051 INFO: Finished candidate processing
4:47:29.409068 INFO: Collecting candidate features
4:47:30.752784 WARNING: intensity_correlation has 47 NaNs ( 0.01 % out of 329053)
4:47:30.760784 WARNING: height_correlation has 33 NaNs ( 0.01 % out of 329053)
4:47:30.840786 INFO: Collecting fragment features
4:47:31.382948 INFO: Finished candidate scoring
4:47:31.798111 INFO: performing precursor FDR with 47 features
4:47:31.799110 INFO: Decoy channel: -1
4:47:31.800110 INFO: Competetive: True
4:47:32.130656 INFO: Setting torch num_threads to 2 for FDR classification task
4:47:32.313274 WARNING: dropped 30 target PSMs due to missing features
4:47:32.314279 WARNING: dropped 34 decoy PSMs due to missing features
4:47:32.630887 INFO: Using random state 376629 for train-test-split
4:47:40.144218 INFO: Test AUC: 0.566
4:47:40.146221 INFO: Train AUC: 0.594
4:47:40.146221 INFO: AUC difference: 4.72%
4:47:41.015932 INFO: Resetting torch num_threads to 10
4:47:41.046932 PROGRESS: === Extracted 329053 precursors and 2368889 fragments ===
4:47:41.052935 INFO: === FDR correction performed with classifier version 7 ===
4:47:41.058935 PROGRESS: ============================= Precursor FDR =============================
4:47:41.062934 PROGRESS: Total precursors accumulated: 774
4:47:41.066931 PROGRESS: Target precursors: 705 (91.09%)
4:47:41.069934 PROGRESS: Decoy precursors: 69 (8.91%)
4:47:41.073934 PROGRESS: 
4:47:41.077936 PROGRESS: Precursor Summary:
4:47:41.083935 PROGRESS: Channel   0:	 0.050 FDR:   537; 0.010 FDR:   394; 0.001 FDR:    10
4:47:41.088931 PROGRESS: 
4:47:41.093935 PROGRESS: Protein Summary:
4:47:41.101936 PROGRESS: Channel   0:	 0.050 FDR:   497; 0.010 FDR:   362; 0.001 FDR:    10
4:47:41.105931 PROGRESS: =========================================================================
4:47:41.114938 INFO: Target number of precursors reached.
4:47:41.547613 INFO: fragments_df: keeping 5000 of 2368889 [sum(precursor_idx_mask)=10577 sum(mass_error_mask)=2368889 stop_rank=5000
4:47:42.197881 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:47:42.531442 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:47:42.873485 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:47:46.152091 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:47:46.157091 INFO: Using score_cutoff 66.6172637512207 (fac=0.99, q=1)
4:47:46.161093 INFO: Updating optimization_manager: fwhm_rt             : 2.4969534873962402 -> 2.4970345497131348
4:47:46.165092 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:47:46.168092 INFO: Updating optimization_manager: score_cutoff        : 67.53381400222777 -> 66.6172637512207
4:47:46.172092 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:47:46.267713 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:47:46.427733 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:47:46.844943 INFO: === checking if optimization conditions were reached ===
4:47:46.848942 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
4:47:46.859947 INFO: Updating optimization_manager: rt_error            : 75.08024096322393 -> 75.08024096322393
4:47:46.865944 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
4:47:46.870944 INFO: Updating optimization_manager: score_cutoff        : 66.6172637512207 -> 66.6172637512207
4:47:46.876943 INFO: Updating optimization_manager: fwhm_rt             : 2.4970345497131348 -> 2.4970345497131348
4:47:46.881942 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
4:47:46.886942 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 75.0802 found after 5 searches.
4:47:46.890940 INFO: ==============================================
4:47:46.899939 PROGRESS: Optimization finished for rt_error.
4:47:47.564724 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:47:47.657730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:47:47.826336 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:47:48.304374 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:47:48.307377 PROGRESS: ==============================================
4:47:48.311377 PROGRESS: ms2_error      : 10.0000
4:47:48.316375 PROGRESS: ms1_error      : 5.0000
4:47:48.321375 PROGRESS: rt_error       : 75.0802
4:47:48.325375 PROGRESS: ==============================================
4:47:48.342376 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:47:51.931837 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:48:00.861778 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:48:41.762799 INFO: Using classic extraction backend
4:48:41.768801 PROGRESS: Extracting batch of 11035943 precursors
4:48:41.772799 INFO: === Search parameters used ===
4:48:41.775800 INFO: rt_error       : 75.08024096322393
4:48:41.779802 INFO: mobility_error : 0.1
4:48:41.783799 INFO: num_candidates : 3
4:48:41.786801 INFO: ms1_error      : 5.0
4:48:41.790802 INFO: ms2_error      : 10.0
4:48:41.793799 INFO: fwhm_rt        : 2.4970345497131348
4:48:41.797801 INFO: quant_window   : 3
4:48:41.801800 INFO: ==============================================
4:48:45.159045 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
4:48:45.161046 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:48:45.162048 INFO: FWHM in RT is 2.50 seconds, sigma is 0.28
4:48:45.163047 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
4:48:45.165046 INFO: Starting candidate selection
5:01:04.660464 INFO: Removed 25086995 precursors with score below cutoff 66.6172637512207
5:01:08.628996 INFO: Starting candidate scoring
5:05:37.083212 INFO: Finished candidate processing
5:05:37.085209 INFO: Collecting candidate features
5:06:08.054054 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 8007724)
5:06:09.443799 INFO: Collecting fragment features
5:06:23.902920 INFO: Finished candidate scoring
5:07:09.737247 INFO: === Performing FDR correction with classifier version 12 ===
5:07:09.744245 INFO: performing precursor FDR with 47 features
5:07:09.745245 INFO: Decoy channel: -1
5:07:09.745245 INFO: Competetive: True
5:07:15.456554 INFO: Setting torch num_threads to 2 for FDR classification task
5:07:18.920305 WARNING: dropped 1 target PSMs due to missing features
5:07:18.921304 WARNING: dropped 1 decoy PSMs due to missing features
5:07:30.927756 INFO: Using random state 536999 for train-test-split
5:11:16.836025 INFO: Test AUC: 0.585
5:11:16.837024 INFO: Train AUC: 0.588
5:11:16.838025 INFO: AUC difference: 0.44%
5:11:22.924038 INFO: Resetting torch num_threads to 10
5:11:23.316123 INFO: Removing fragments below FDR threshold
5:11:25.927429 PROGRESS: ============================= Precursor FDR =============================
5:11:25.935431 PROGRESS: Total precursors accumulated: 44,041
5:11:25.941431 PROGRESS: Target precursors: 43,605 (99.01%)
5:11:25.946432 PROGRESS: Decoy precursors: 436 (0.99%)
5:11:25.952464 PROGRESS: 
5:11:25.957464 PROGRESS: Precursor Summary:
5:11:26.095465 PROGRESS: Channel   0:	 0.050 FDR: 43,605; 0.010 FDR: 43,605; 0.001 FDR: 31,009
5:11:26.101466 PROGRESS: 
5:11:26.106466 PROGRESS: Protein Summary:
5:11:26.259983 PROGRESS: Channel   0:	 0.050 FDR: 8,031; 0.010 FDR: 8,031; 0.001 FDR: 6,360
5:11:26.263984 PROGRESS: =========================================================================
5:11:26.504517 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\psm.parquet
5:11:27.527797 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\frag.parquet
5:11:28.632176 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
5:11:29.899999 PROGRESS: 
5:11:29.901000 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant
5:11:29.903003 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\figures
5:11:29.912003 INFO: Initializing TimingManager
5:11:29.929004 INFO: Initializing RawFileManager
5:16:18.537469 INFO: Determining DIA cycle
5:16:18.563469 INFO: Found cycle with start 0.00 min and length 86.
5:16:19.183293 INFO: RT (min)            : 0.0 - 55.4
5:16:19.184296 INFO: RT duration (sec)   : 3326.9
5:16:19.185296 INFO: RT duration (min)   : 55.4
5:16:19.186294 INFO: Cycle len (scans)   : 86
5:16:19.187295 INFO: Cycle len (sec)     : 1.90
5:16:19.188294 INFO: Number of cycles    : 1747
5:16:19.188294 INFO: MS2 range (m/z)     : 399.5 - 903.5
5:16:19.189295 INFO: Creating DIA data object took: 289.25329065322876
5:16:22.272204 INFO: Initializing CalibrationManager
5:16:22.280208 INFO: Setting up calibration estimators ..
5:16:22.283213 INFO: Found 1 estimator(s) in calibration group 'fragment'
5:16:22.287208 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'}' ..
5:16:22.290208 INFO: Found 3 estimator(s) in calibration group 'precursor'
5:16:22.294209 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
5:16:22.297206 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}}' ..
5:16:22.301203 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
5:16:22.304205 INFO: Done setting up calibration estimators.
5:16:22.308203 INFO: Initializing OptimizationManager
5:16:22.314202 INFO: initial parameter: ms1_error = 30
5:16:22.317203 INFO: initial parameter: ms2_error = 30
5:16:22.321200 INFO: initial parameter: rt_error = 1663.4844970703125
5:16:22.324201 INFO: initial parameter: mobility_error = 0.1
5:16:22.328201 INFO: initial parameter: num_candidates = 1
5:16:22.331201 INFO: initial parameter: fwhm_rt = 5
5:16:22.334200 INFO: initial parameter: fwhm_mobility = 0.01
5:16:22.338200 INFO: initial parameter: score_cutoff = 0
5:16:22.341199 INFO: initial parameter: classifier_version = -1
5:16:22.346199 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
5:16:22.350200 INFO: FDRManager: loading saved state not requested, will be initialized.
5:16:22.351199 INFO: Initializing FDRManager
5:16:22.351199 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
5:16:24.984585 PROGRESS: Initializing spectral library: 5,593,630 target precursors potentially observable (87,574 removed)
5:16:27.167767 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
5:16:27.172766 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 1663.4844970703125
5:16:27.176766 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
5:16:27.180766 PROGRESS: Starting initial search for precursors.
5:16:27.183766 INFO: Starting optimization step 0.
5:16:27.187766 PROGRESS: === Extracting elution groups 0 to 8000 ===
5:16:27.190766 INFO: Using classic extraction backend
5:16:27.194766 PROGRESS: Extracting batch of 15689 precursors
5:16:27.198766 INFO: === Search parameters used ===
5:16:27.201767 INFO: rt_error       : 1663.4844970703125
5:16:27.205767 INFO: mobility_error : 0.1
5:16:27.208768 INFO: num_candidates : 1
5:16:27.211768 INFO: ms1_error      : 30
5:16:27.215767 INFO: ms2_error      : 30
5:16:27.218767 INFO: fwhm_rt        : 5
5:16:27.221766 INFO: quant_window   : 3
5:16:27.224767 INFO: ==============================================
5:16:27.264770 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:16:27.264770 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:16:27.265769 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
5:16:27.266770 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
5:16:27.267768 INFO: Starting candidate selection
5:16:40.575211 INFO: Starting candidate scoring
5:16:41.114776 INFO: Finished candidate processing
5:16:41.115782 INFO: Collecting candidate features
5:16:41.258326 INFO: Collecting fragment features
5:16:41.375328 INFO: Finished candidate scoring
5:16:41.407342 INFO: performing precursor FDR with 47 features
5:16:41.408340 INFO: Decoy channel: -1
5:16:41.409340 INFO: Competetive: True
5:16:41.451874 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:41.486875 INFO: Using random state 595945 for train-test-split
5:16:41.763427 INFO: Test AUC: 0.508
5:16:41.764424 INFO: Train AUC: 0.502
5:16:41.765423 INFO: AUC difference: 1.19%
5:16:42.360500 INFO: Resetting torch num_threads to 10
5:16:42.369499 PROGRESS: === Extracted 15681 precursors and 144113 fragments ===
5:16:42.374500 INFO: === FDR correction performed with classifier version -1 ===
5:16:42.379500 PROGRESS: ============================= Precursor FDR =============================
5:16:42.383502 PROGRESS: Total precursors accumulated: 2
5:16:42.386500 PROGRESS: Target precursors: 2 (100.00%)
5:16:42.390501 PROGRESS: Decoy precursors: 0 (0.00%)
5:16:42.393501 PROGRESS: 
5:16:42.396502 PROGRESS: Precursor Summary:
5:16:42.402516 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
5:16:42.406515 PROGRESS: 
5:16:42.409515 PROGRESS: Protein Summary:
5:16:42.415514 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
5:16:42.419626 PROGRESS: =========================================================================
5:16:42.424628 INFO: Target number of precursors not reached yet.
5:16:42.783175 INFO: Starting optimization step 1.
5:16:42.788174 PROGRESS: === Extracting elution groups 8000 to 24000 ===
5:16:42.792173 INFO: Using classic extraction backend
5:16:42.796178 PROGRESS: Extracting batch of 31390 precursors
5:16:42.800173 INFO: === Search parameters used ===
5:16:42.803173 INFO: rt_error       : 1663.4844970703125
5:16:42.807174 INFO: mobility_error : 0.1
5:16:42.811173 INFO: num_candidates : 1
5:16:42.814174 INFO: ms1_error      : 30
5:16:42.818176 INFO: ms2_error      : 30
5:16:42.822176 INFO: fwhm_rt        : 5
5:16:42.825174 INFO: quant_window   : 3
5:16:42.829174 INFO: ==============================================
5:16:42.885174 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:16:42.886174 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:16:42.887176 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
5:16:42.888175 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
5:16:42.889174 INFO: Starting candidate selection
5:17:10.159167 INFO: Starting candidate scoring
5:17:11.210115 INFO: Finished candidate processing
5:17:11.211129 INFO: Collecting candidate features
5:17:11.482651 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 31374)
5:17:11.517655 INFO: Collecting fragment features
5:17:11.631659 INFO: Finished candidate scoring
5:17:11.748282 INFO: performing precursor FDR with 47 features
5:17:11.749282 INFO: Decoy channel: -1
5:17:11.750281 INFO: Competetive: True
5:17:11.887281 INFO: Setting torch num_threads to 2 for FDR classification task
5:17:11.933281 WARNING: dropped 1 target PSMs due to missing features
5:17:11.968896 INFO: Using random state 39034 for train-test-split
5:17:13.134259 INFO: Test AUC: 0.571
5:17:13.136260 INFO: Train AUC: 0.568
5:17:13.137262 INFO: AUC difference: 0.63%
5:17:13.808100 INFO: Resetting torch num_threads to 10
5:17:13.888098 PROGRESS: === Extracted 47055 precursors and 432425 fragments ===
5:17:13.894100 INFO: === FDR correction performed with classifier version -1 ===
5:17:13.899101 PROGRESS: ============================= Precursor FDR =============================
5:17:13.903101 PROGRESS: Total precursors accumulated: 2
5:17:13.907099 PROGRESS: Target precursors: 2 (100.00%)
5:17:13.911100 PROGRESS: Decoy precursors: 0 (0.00%)
5:17:13.915102 PROGRESS: 
5:17:13.919101 PROGRESS: Precursor Summary:
5:17:13.925099 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
5:17:13.929101 PROGRESS: 
5:17:13.933102 PROGRESS: Protein Summary:
5:17:13.945103 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
5:17:13.949101 PROGRESS: =========================================================================
5:17:13.958115 INFO: Target number of precursors not reached yet.
5:17:14.449335 INFO: Starting optimization step 2.
5:17:14.454350 PROGRESS: === Extracting elution groups 24000 to 56000 ===
5:17:14.459349 INFO: Using classic extraction backend
5:17:14.463349 PROGRESS: Extracting batch of 62842 precursors
5:17:14.467351 INFO: === Search parameters used ===
5:17:14.471883 INFO: rt_error       : 1663.4844970703125
5:17:14.475881 INFO: mobility_error : 0.1
5:17:14.479880 INFO: num_candidates : 1
5:17:14.486880 INFO: ms1_error      : 30
5:17:14.491880 INFO: ms2_error      : 30
5:17:14.498878 INFO: fwhm_rt        : 5
5:17:14.504881 INFO: quant_window   : 3
5:17:14.523880 INFO: ==============================================
5:17:14.606881 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:17:14.606881 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:17:14.607882 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
5:17:14.608881 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
5:17:14.609881 INFO: Starting candidate selection
5:18:08.741333 INFO: Starting candidate scoring
5:18:10.949716 INFO: Finished candidate processing
5:18:10.950716 INFO: Collecting candidate features
5:18:11.483959 INFO: Collecting fragment features
5:18:11.720574 INFO: Finished candidate scoring
5:18:11.943156 INFO: performing precursor FDR with 47 features
5:18:11.944157 INFO: Decoy channel: -1
5:18:11.945158 INFO: Competetive: True
5:18:12.224763 INFO: Setting torch num_threads to 2 for FDR classification task
5:18:12.309309 WARNING: dropped 1 target PSMs due to missing features
5:18:12.412311 INFO: Using random state 794014 for train-test-split
5:18:15.293776 INFO: Test AUC: 0.575
5:18:15.295779 INFO: Train AUC: 0.589
5:18:15.296774 INFO: AUC difference: 2.29%
5:18:16.079036 INFO: Resetting torch num_threads to 10
5:18:16.240035 PROGRESS: === Extracted 109862 precursors and 1009987 fragments ===
5:18:16.246035 INFO: === FDR correction performed with classifier version -1 ===
5:18:16.251034 PROGRESS: ============================= Precursor FDR =============================
5:18:16.255034 PROGRESS: Total precursors accumulated: 234
5:18:16.258034 PROGRESS: Target precursors: 215 (91.88%)
5:18:16.262034 PROGRESS: Decoy precursors: 19 (8.12%)
5:18:16.265034 PROGRESS: 
5:18:16.269034 PROGRESS: Precursor Summary:
5:18:16.281034 PROGRESS: Channel   0:	 0.050 FDR:   123; 0.010 FDR:    10; 0.001 FDR:    10
5:18:16.285034 PROGRESS: 
5:18:16.289034 PROGRESS: Protein Summary:
5:18:16.296041 PROGRESS: Channel   0:	 0.050 FDR:   122; 0.010 FDR:    10; 0.001 FDR:    10
5:18:16.300040 PROGRESS: =========================================================================
5:18:16.310546 INFO: Target number of precursors not reached yet.
5:18:17.007609 INFO: Starting optimization step 3.
5:18:17.011605 PROGRESS: === Extracting elution groups 56000 to 120000 ===
5:18:17.015606 INFO: Using classic extraction backend
5:18:17.019606 PROGRESS: Extracting batch of 125627 precursors
5:18:17.023607 INFO: === Search parameters used ===
5:18:17.027606 INFO: rt_error       : 1663.4844970703125
5:18:17.031606 INFO: mobility_error : 0.1
5:18:17.036606 INFO: num_candidates : 1
5:18:17.039607 INFO: ms1_error      : 30
5:18:17.043606 INFO: ms2_error      : 30
5:18:17.047613 INFO: fwhm_rt        : 5
5:18:17.051614 INFO: quant_window   : 3
5:18:17.055613 INFO: ==============================================
5:18:17.162138 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:18:17.163133 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:18:17.164135 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
5:18:17.164135 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
5:18:17.166137 INFO: Starting candidate selection
5:20:05.613377 INFO: Starting candidate scoring
5:20:09.802337 INFO: Finished candidate processing
5:20:09.804343 INFO: Collecting candidate features
5:20:10.761606 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 125565)
5:20:10.810605 INFO: Collecting fragment features
5:20:11.125244 INFO: Finished candidate scoring
5:20:11.465769 INFO: performing precursor FDR with 47 features
5:20:11.466770 INFO: Decoy channel: -1
5:20:11.467768 INFO: Competetive: True
5:20:11.992433 INFO: Setting torch num_threads to 2 for FDR classification task
5:20:12.127434 WARNING: dropped 3 target PSMs due to missing features
5:20:12.368968 INFO: Using random state 952345 for train-test-split
5:20:18.196398 INFO: Test AUC: 0.580
5:20:18.197398 INFO: Train AUC: 0.596
5:20:18.198399 INFO: AUC difference: 2.61%
5:20:19.015568 INFO: Resetting torch num_threads to 10
5:20:19.221569 PROGRESS: === Extracted 235427 precursors and 2163416 fragments ===
5:20:19.227582 INFO: === FDR correction performed with classifier version -1 ===
5:20:19.233584 PROGRESS: ============================= Precursor FDR =============================
5:20:19.236584 PROGRESS: Total precursors accumulated: 793
5:20:19.240580 PROGRESS: Target precursors: 725 (91.42%)
5:20:19.244761 PROGRESS: Decoy precursors: 68 (8.58%)
5:20:19.247761 PROGRESS: 
5:20:19.251760 PROGRESS: Precursor Summary:
5:20:19.258759 PROGRESS: Channel   0:	 0.050 FDR:   565; 0.010 FDR:   418; 0.001 FDR:   272
5:20:19.262759 PROGRESS: 
5:20:19.265757 PROGRESS: Protein Summary:
5:20:19.273759 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   370; 0.001 FDR:   246
5:20:19.277763 PROGRESS: =========================================================================
5:20:19.296763 INFO: Target number of precursors reached.
5:20:19.709311 INFO: fragments_df: keeping 4091 of 2163416 [sum(precursor_idx_mask)=4783 sum(mass_error_mask)=2163416 stop_rank=4091
5:20:20.711481 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:20:21.063566 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:20:21.451123 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:20:23.784348 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
5:20:23.789350 INFO: Using score_cutoff 84.56793427963257 (fac=0.99, q=1)
5:20:23.794351 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.367992401123047
5:20:23.798352 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
5:20:23.803351 INFO: Updating optimization_manager: score_cutoff        : 0 -> 84.56793427963257
5:20:23.806351 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:20:23.902352 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:20:24.115970 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:20:24.990826 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
5:20:24.994826 PROGRESS: Required number of precursors found. Starting search parameter optimization.
5:20:24.998831 INFO: Starting optimization step 4.
5:20:25.002831 PROGRESS: === Extracting elution groups 0 to 120000 ===
5:20:25.006356 INFO: Using classic extraction backend
5:20:25.010359 PROGRESS: Extracting batch of 235548 precursors
5:20:25.014360 INFO: === Search parameters used ===
5:20:25.017358 INFO: rt_error       : 1663.4844970703125
5:20:25.021359 INFO: mobility_error : 0.1
5:20:25.025361 INFO: num_candidates : 3
5:20:25.028361 INFO: ms1_error      : 30
5:20:25.033361 INFO: ms2_error      : 30
5:20:25.038358 INFO: fwhm_rt        : 2.367992401123047
5:20:25.043363 INFO: quant_window   : 3
5:20:25.049361 INFO: ==============================================
5:20:25.215355 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:20:25.216357 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:20:25.217356 INFO: FWHM in RT is 2.37 seconds, sigma is 0.26
5:20:25.217356 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:20:25.220356 INFO: Starting candidate selection
5:24:33.086355 INFO: Starting candidate scoring
5:24:55.322403 INFO: Finished candidate processing
5:24:55.324419 INFO: Collecting candidate features
5:24:58.110030 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 706201)
5:24:58.306577 INFO: Collecting fragment features
5:24:59.545302 INFO: Finished candidate scoring
5:25:00.785882 INFO: performing precursor FDR with 47 features
5:25:00.786878 INFO: Decoy channel: -1
5:25:00.787880 INFO: Competetive: True
5:25:01.425222 INFO: Setting torch num_threads to 2 for FDR classification task
5:25:01.785371 WARNING: dropped 2 target PSMs due to missing features
5:25:01.786371 WARNING: dropped 2 decoy PSMs due to missing features
5:25:02.545624 INFO: Using random state 775571 for train-test-split
5:25:19.893720 INFO: Test AUC: 0.582
5:25:19.895719 INFO: Train AUC: 0.595
5:25:19.896719 INFO: AUC difference: 2.22%
5:25:21.133442 INFO: Resetting torch num_threads to 10
5:25:21.180454 PROGRESS: === Extracted 706201 precursors and 6249524 fragments ===
5:25:21.187970 INFO: === FDR correction performed with classifier version 3 ===
5:25:21.194983 PROGRESS: ============================= Precursor FDR =============================
5:25:21.199985 PROGRESS: Total precursors accumulated: 969
5:25:21.203986 PROGRESS: Target precursors: 882 (91.02%)
5:25:21.207987 PROGRESS: Decoy precursors: 87 (8.98%)
5:25:21.211987 PROGRESS: 
5:25:21.215986 PROGRESS: Precursor Summary:
5:25:21.222994 PROGRESS: Channel   0:	 0.050 FDR:   687; 0.010 FDR:   526; 0.001 FDR:   390
5:25:21.226985 PROGRESS: 
5:25:21.230987 PROGRESS: Protein Summary:
5:25:21.238984 PROGRESS: Channel   0:	 0.050 FDR:   604; 0.010 FDR:   462; 0.001 FDR:   348
5:25:21.242985 PROGRESS: =========================================================================
5:25:21.254987 INFO: Target number of precursors reached.
5:25:22.352142 INFO: fragments_df: keeping 5000 of 6249524 [sum(precursor_idx_mask)=15869 sum(mass_error_mask)=6249524 stop_rank=5000
5:25:23.049791 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:25:23.398318 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:25:23.842406 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:25:27.234973 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:25:27.242973 INFO: Using score_cutoff 77.80987449645995 (fac=0.99, q=1)
5:25:27.248975 INFO: Updating optimization_manager: fwhm_rt             : 2.367992401123047 -> 2.4498414993286133
5:25:27.252974 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:25:27.256974 INFO: Updating optimization_manager: score_cutoff        : 84.56793427963257 -> 77.80987449645995
5:25:27.260974 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:25:27.379978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:25:27.561523 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:25:27.976552 INFO: === checking if optimization conditions were reached ===
5:25:27.989552 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.657143999158745
5:25:27.994552 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
5:25:27.998558 PROGRESS: ❌ ms2_error      : 17.6571 > 10.0000 or insufficient steps taken.
5:25:28.008551 INFO: Updating optimization_manager: ms1_error           : 30 -> 12.712595732413844
5:25:28.014556 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
5:25:28.022554 PROGRESS: ❌ ms1_error      : 12.7126 > 5.0000 or insufficient steps taken.
5:25:28.029555 INFO: ==============================================
5:25:28.037553 INFO: Starting optimization step 5.
5:25:28.043553 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:25:28.047553 INFO: Using classic extraction backend
5:25:28.054550 PROGRESS: Extracting batch of 109921 precursors
5:25:28.060551 INFO: === Search parameters used ===
5:25:28.069550 INFO: rt_error       : 1663.4844970703125
5:25:28.077550 INFO: mobility_error : 0.1
5:25:28.084548 INFO: num_candidates : 3
5:25:28.092548 INFO: ms1_error      : 12.712595732413844
5:25:28.097549 INFO: ms2_error      : 17.657143999158745
5:25:28.105549 INFO: fwhm_rt        : 2.4498414993286133
5:25:28.113551 INFO: quant_window   : 3
5:25:28.122553 INFO: ==============================================
5:25:28.242703 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:25:28.270694 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:25:28.271700 INFO: FWHM in RT is 2.45 seconds, sigma is 0.27
5:25:28.271700 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:25:28.273696 INFO: Starting candidate selection
5:27:23.227005 INFO: Starting candidate scoring
5:27:33.143034 INFO: Finished candidate processing
5:27:33.145051 INFO: Collecting candidate features
5:27:34.524781 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 329408)
5:27:34.627793 INFO: Collecting fragment features
5:27:35.207424 INFO: Finished candidate scoring
5:27:35.644523 INFO: performing precursor FDR with 47 features
5:27:35.645521 INFO: Decoy channel: -1
5:27:35.646521 INFO: Competetive: True
5:27:35.983070 INFO: Setting torch num_threads to 2 for FDR classification task
5:27:36.158146 WARNING: dropped 3 target PSMs due to missing features
5:27:36.159147 WARNING: dropped 2 decoy PSMs due to missing features
5:27:36.486760 INFO: Using random state 954972 for train-test-split
5:27:44.525017 INFO: Test AUC: 0.581
5:27:44.526016 INFO: Train AUC: 0.598
5:27:44.527018 INFO: AUC difference: 2.83%
5:27:45.480494 INFO: Resetting torch num_threads to 10
5:27:45.509497 PROGRESS: === Extracted 329408 precursors and 2698276 fragments ===
5:27:45.515496 INFO: === FDR correction performed with classifier version 4 ===
5:27:45.520496 PROGRESS: ============================= Precursor FDR =============================
5:27:45.524500 PROGRESS: Total precursors accumulated: 610
5:27:45.528496 PROGRESS: Target precursors: 555 (90.98%)
5:27:45.532494 PROGRESS: Decoy precursors: 55 (9.02%)
5:27:45.536491 PROGRESS: 
5:27:45.539495 PROGRESS: Precursor Summary:
5:27:45.546496 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   342; 0.001 FDR:   248
5:27:45.550496 PROGRESS: 
5:27:45.553494 PROGRESS: Protein Summary:
5:27:45.560496 PROGRESS: Channel   0:	 0.050 FDR:   390; 0.010 FDR:   316; 0.001 FDR:   233
5:27:45.565495 PROGRESS: =========================================================================
5:27:45.576494 INFO: Target number of precursors reached.
5:27:46.052565 INFO: fragments_df: keeping 4716 of 2698276 [sum(precursor_idx_mask)=9809 sum(mass_error_mask)=2698276 stop_rank=4716
5:27:46.737319 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:27:47.022871 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:27:47.423002 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:27:50.403288 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:27:50.408286 INFO: Using score_cutoff 68.86451261672974 (fac=0.99, q=1)
5:27:50.413302 INFO: Updating optimization_manager: fwhm_rt             : 2.4498414993286133 -> 2.470248222351074
5:27:50.417300 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:27:50.421301 INFO: Updating optimization_manager: score_cutoff        : 77.80987449645995 -> 68.86451261672974
5:27:50.424810 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:27:50.524828 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:27:50.698366 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:27:51.117981 INFO: === checking if optimization conditions were reached ===
5:27:51.127983 INFO: Updating optimization_manager: ms2_error           : 17.657143999158745 -> 10.448024580912065
5:27:51.131984 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
5:27:51.135983 PROGRESS: ❌ ms2_error      : 10.4480 > 10.0000 or insufficient steps taken.
5:27:51.142982 INFO: Updating optimization_manager: ms1_error           : 12.712595732413844 -> 5.0
5:27:51.146981 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
5:27:51.150984 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
5:27:51.154984 INFO: ==============================================
5:27:51.158983 INFO: Starting optimization step 6.
5:27:51.162999 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:27:51.167000 INFO: Using classic extraction backend
5:27:51.171001 PROGRESS: Extracting batch of 109921 precursors
5:27:51.174997 INFO: === Search parameters used ===
5:27:51.178524 INFO: rt_error       : 1663.4844970703125
5:27:51.181524 INFO: mobility_error : 0.1
5:27:51.185524 INFO: num_candidates : 3
5:27:51.188524 INFO: ms1_error      : 5.0
5:27:51.192525 INFO: ms2_error      : 10.448024580912065
5:27:51.195524 INFO: fwhm_rt        : 2.470248222351074
5:27:51.199527 INFO: quant_window   : 3
5:27:51.202524 INFO: ==============================================
5:27:51.309524 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:27:51.310523 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:27:51.311521 INFO: FWHM in RT is 2.47 seconds, sigma is 0.28
5:27:51.312526 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:27:51.313522 INFO: Starting candidate selection
5:29:45.247211 INFO: Starting candidate scoring
5:29:57.201693 INFO: Finished candidate processing
5:29:57.203699 INFO: Collecting candidate features
5:29:58.580419 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 329237)
5:29:58.584419 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329237)
5:29:58.708985 INFO: Collecting fragment features
5:29:59.282078 INFO: Finished candidate scoring
5:29:59.724146 INFO: performing precursor FDR with 47 features
5:29:59.725144 INFO: Decoy channel: -1
5:29:59.726144 INFO: Competetive: True
5:30:00.058692 INFO: Setting torch num_threads to 2 for FDR classification task
5:30:00.234247 WARNING: dropped 11 target PSMs due to missing features
5:30:00.236248 WARNING: dropped 7 decoy PSMs due to missing features
5:30:00.548796 INFO: Using random state 221214 for train-test-split
5:30:08.507432 INFO: Test AUC: 0.576
5:30:08.508428 INFO: Train AUC: 0.599
5:30:08.509430 INFO: AUC difference: 3.92%
5:30:09.396776 INFO: Resetting torch num_threads to 10
5:30:09.424775 PROGRESS: === Extracted 329237 precursors and 2518431 fragments ===
5:30:09.430776 INFO: === FDR correction performed with classifier version 5 ===
5:30:09.436775 PROGRESS: ============================= Precursor FDR =============================
5:30:09.440778 PROGRESS: Total precursors accumulated: 568
5:30:09.444776 PROGRESS: Target precursors: 521 (91.73%)
5:30:09.449775 PROGRESS: Decoy precursors: 47 (8.27%)
5:30:09.452777 PROGRESS: 
5:30:09.456777 PROGRESS: Precursor Summary:
5:30:09.463777 PROGRESS: Channel   0:	 0.050 FDR:   422; 0.010 FDR:   325; 0.001 FDR:   230
5:30:09.468776 PROGRESS: 
5:30:09.471776 PROGRESS: Protein Summary:
5:30:09.479776 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   299; 0.001 FDR:   215
5:30:09.483777 PROGRESS: =========================================================================
5:30:09.492777 INFO: Target number of precursors reached.
5:30:09.941931 INFO: fragments_df: keeping 4484 of 2518431 [sum(precursor_idx_mask)=9059 sum(mass_error_mask)=2518431 stop_rank=4484
5:30:10.601166 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:30:10.947318 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:30:11.301844 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:30:14.089278 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:30:14.094277 INFO: Using score_cutoff 65.80045181579591 (fac=0.99, q=1)
5:30:14.099278 INFO: Updating optimization_manager: fwhm_rt             : 2.470248222351074 -> 2.400047779083252
5:30:14.102278 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:30:14.106277 INFO: Updating optimization_manager: score_cutoff        : 68.86451261672974 -> 65.80045181579591
5:30:14.110278 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:30:14.211896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:30:14.378893 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:30:14.829036 INFO: === checking if optimization conditions were reached ===
5:30:14.839033 INFO: Updating optimization_manager: ms2_error           : 10.448024580912065 -> 10.0
5:30:14.843036 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
5:30:14.846034 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
5:30:14.850036 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
5:30:14.854038 INFO: ==============================================
5:30:14.858033 PROGRESS: Optimization finished for ms2_error, ms1_error.
5:30:15.514606 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:30:15.631613 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:30:15.830149 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:30:16.243358 INFO: Starting optimization step 0.
5:30:16.247359 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:30:16.251359 INFO: Using classic extraction backend
5:30:16.255359 PROGRESS: Extracting batch of 109921 precursors
5:30:16.259358 INFO: === Search parameters used ===
5:30:16.263371 INFO: rt_error       : 1663.4844970703125
5:30:16.267359 INFO: mobility_error : 0.1
5:30:16.271359 INFO: num_candidates : 3
5:30:16.274358 INFO: ms1_error      : 5.0
5:30:16.278358 INFO: ms2_error      : 10.0
5:30:16.282363 INFO: fwhm_rt        : 2.400047779083252
5:30:16.286361 INFO: quant_window   : 3
5:30:16.290361 INFO: ==============================================
5:30:16.395376 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:30:16.396374 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:30:16.397376 INFO: FWHM in RT is 2.40 seconds, sigma is 0.27
5:30:16.398376 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:30:16.399376 INFO: Starting candidate selection
5:32:10.908112 INFO: Starting candidate scoring
5:32:20.406741 INFO: Finished candidate processing
5:32:20.408755 INFO: Collecting candidate features
5:32:21.806761 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 329221)
5:32:21.814761 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329221)
5:32:21.919291 INFO: Collecting fragment features
5:32:22.500429 INFO: Finished candidate scoring
5:32:22.925658 INFO: performing precursor FDR with 47 features
5:32:22.927659 INFO: Decoy channel: -1
5:32:22.928659 INFO: Competetive: True
5:32:23.283284 INFO: Setting torch num_threads to 2 for FDR classification task
5:32:23.470815 WARNING: dropped 11 target PSMs due to missing features
5:32:23.471816 WARNING: dropped 7 decoy PSMs due to missing features
5:32:23.777419 INFO: Using random state 374404 for train-test-split
5:32:31.711299 INFO: Test AUC: 0.579
5:32:31.712300 INFO: Train AUC: 0.606
5:32:31.713300 INFO: AUC difference: 4.43%
5:32:32.655636 INFO: Resetting torch num_threads to 10
5:32:32.685648 PROGRESS: === Extracted 329221 precursors and 2515067 fragments ===
5:32:32.693638 INFO: === FDR correction performed with classifier version 6 ===
5:32:32.701637 PROGRESS: ============================= Precursor FDR =============================
5:32:32.707640 PROGRESS: Total precursors accumulated: 624
5:32:32.711638 PROGRESS: Target precursors: 568 (91.03%)
5:32:32.716636 PROGRESS: Decoy precursors: 56 (8.97%)
5:32:32.720634 PROGRESS: 
5:32:32.726638 PROGRESS: Precursor Summary:
5:32:32.740642 PROGRESS: Channel   0:	 0.050 FDR:   443; 0.010 FDR:   342; 0.001 FDR:   211
5:32:32.745635 PROGRESS: 
5:32:32.750636 PROGRESS: Protein Summary:
5:32:32.757635 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   314; 0.001 FDR:   198
5:32:32.761634 PROGRESS: =========================================================================
5:32:32.769636 INFO: Target number of precursors reached.
5:32:33.225729 INFO: fragments_df: keeping 4711 of 2515067 [sum(precursor_idx_mask)=9451 sum(mass_error_mask)=2515067 stop_rank=4711
5:32:33.886469 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:32:34.245095 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:32:34.573631 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:32:37.589638 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:32:37.594636 INFO: Using score_cutoff 65.36794601898193 (fac=0.99, q=1)
5:32:37.598637 INFO: Updating optimization_manager: fwhm_rt             : 2.400047779083252 -> 2.4026434421539307
5:32:37.602636 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:32:37.606650 INFO: Updating optimization_manager: score_cutoff        : 65.80045181579591 -> 65.36794601898193
5:32:37.610651 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:32:37.712179 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:32:37.882729 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:32:38.301342 INFO: === checking if optimization conditions were reached ===
5:32:38.305342 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
5:32:38.312336 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 170.38867043076425
5:32:38.317337 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 170.3887.
5:32:38.320336 INFO: ==============================================
5:32:38.326337 INFO: Starting optimization step 1.
5:32:38.335338 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:32:38.342340 INFO: Using classic extraction backend
5:32:38.350337 PROGRESS: Extracting batch of 109921 precursors
5:32:38.357354 INFO: === Search parameters used ===
5:32:38.364354 INFO: rt_error       : 170.38867043076425
5:32:38.370872 INFO: mobility_error : 0.1
5:32:38.377884 INFO: num_candidates : 3
5:32:38.383889 INFO: ms1_error      : 5.0
5:32:38.392893 INFO: ms2_error      : 10.0
5:32:38.401891 INFO: fwhm_rt        : 2.4026434421539307
5:32:38.409888 INFO: quant_window   : 3
5:32:38.417886 INFO: ==============================================
5:32:38.532889 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:32:38.533891 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:32:38.535890 INFO: FWHM in RT is 2.40 seconds, sigma is 0.27
5:32:38.535890 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:32:38.536890 INFO: Starting candidate selection
5:32:51.907062 INFO: Starting candidate scoring
5:33:01.197330 INFO: Finished candidate processing
5:33:01.199344 INFO: Collecting candidate features
5:33:02.588972 WARNING: intensity_correlation has 21 NaNs ( 0.01 % out of 329166)
5:33:02.597971 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 329166)
5:33:02.717495 INFO: Collecting fragment features
5:33:03.293549 INFO: Finished candidate scoring
5:33:03.733627 INFO: performing precursor FDR with 47 features
5:33:03.734625 INFO: Decoy channel: -1
5:33:03.735626 INFO: Competetive: True
5:33:04.064178 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:04.238724 WARNING: dropped 14 target PSMs due to missing features
5:33:04.239724 WARNING: dropped 11 decoy PSMs due to missing features
5:33:04.558073 INFO: Using random state 374404 for train-test-split
5:33:12.364879 INFO: Test AUC: 0.566
5:33:12.365878 INFO: Train AUC: 0.596
5:33:12.366880 INFO: AUC difference: 4.99%
5:33:13.260288 INFO: Resetting torch num_threads to 10
5:33:13.290293 PROGRESS: === Extracted 329166 precursors and 2454727 fragments ===
5:33:13.296294 INFO: === FDR correction performed with classifier version 6 ===
5:33:13.303293 PROGRESS: ============================= Precursor FDR =============================
5:33:13.307288 PROGRESS: Total precursors accumulated: 725
5:33:13.311284 PROGRESS: Target precursors: 663 (91.45%)
5:33:13.315288 PROGRESS: Decoy precursors: 62 (8.55%)
5:33:13.318287 PROGRESS: 
5:33:13.322289 PROGRESS: Precursor Summary:
5:33:13.329288 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   350; 0.001 FDR:   237
5:33:13.333289 PROGRESS: 
5:33:13.337291 PROGRESS: Protein Summary:
5:33:13.345287 PROGRESS: Channel   0:	 0.050 FDR:   483; 0.010 FDR:   323; 0.001 FDR:   223
5:33:13.349286 PROGRESS: =========================================================================
5:33:13.357290 INFO: Target number of precursors reached.
5:33:13.797504 INFO: fragments_df: keeping 4712 of 2454727 [sum(precursor_idx_mask)=9621 sum(mass_error_mask)=2454727 stop_rank=4712
5:33:14.469337 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:33:14.825865 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:33:15.110471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:33:18.137504 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:33:18.142504 INFO: Using score_cutoff 64.50914186553955 (fac=0.99, q=1)
5:33:18.146505 INFO: Updating optimization_manager: fwhm_rt             : 2.4026434421539307 -> 2.413872241973877
5:33:18.150505 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:33:18.154505 INFO: Updating optimization_manager: score_cutoff        : 65.36794601898193 -> 64.50914186553955
5:33:18.158504 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:33:18.261108 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:33:18.426121 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:33:18.844189 INFO: === checking if optimization conditions were reached ===
5:33:18.849190 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
5:33:18.857189 INFO: Updating optimization_manager: rt_error            : 170.38867043076425 -> 93.96502911481184
5:33:18.861189 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 93.9650.
5:33:18.865192 INFO: ==============================================
5:33:18.869192 INFO: Starting optimization step 2.
5:33:18.873190 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:33:18.876191 INFO: Using classic extraction backend
5:33:18.880190 PROGRESS: Extracting batch of 109921 precursors
5:33:18.884191 INFO: === Search parameters used ===
5:33:18.888191 INFO: rt_error       : 93.96502911481184
5:33:18.891191 INFO: mobility_error : 0.1
5:33:18.895192 INFO: num_candidates : 3
5:33:18.899190 INFO: ms1_error      : 5.0
5:33:18.903191 INFO: ms2_error      : 10.0
5:33:18.907191 INFO: fwhm_rt        : 2.413872241973877
5:33:18.911192 INFO: quant_window   : 3
5:33:18.914192 INFO: ==============================================
5:33:19.016802 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:33:19.017801 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:33:19.018802 INFO: FWHM in RT is 2.41 seconds, sigma is 0.27
5:33:19.019803 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:33:19.020802 INFO: Starting candidate selection
5:33:27.842962 INFO: Starting candidate scoring
5:33:37.214328 INFO: Finished candidate processing
5:33:37.216333 INFO: Collecting candidate features
5:33:38.593796 WARNING: intensity_correlation has 28 NaNs ( 0.01 % out of 329144)
5:33:38.598796 WARNING: height_correlation has 13 NaNs ( 0.00 % out of 329144)
5:33:38.696795 INFO: Collecting fragment features
5:33:39.241659 INFO: Finished candidate scoring
5:33:39.662270 INFO: performing precursor FDR with 47 features
5:33:39.663269 INFO: Decoy channel: -1
5:33:39.664268 INFO: Competetive: True
5:33:39.996504 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:40.187504 WARNING: dropped 20 target PSMs due to missing features
5:33:40.189504 WARNING: dropped 16 decoy PSMs due to missing features
5:33:40.502719 INFO: Using random state 374404 for train-test-split
5:33:48.290203 INFO: Test AUC: 0.562
5:33:48.292195 INFO: Train AUC: 0.591
5:33:48.293200 INFO: AUC difference: 4.86%
5:33:49.306506 INFO: Resetting torch num_threads to 10
5:33:49.335496 PROGRESS: === Extracted 329144 precursors and 2408764 fragments ===
5:33:49.341498 INFO: === FDR correction performed with classifier version 6 ===
5:33:49.347497 PROGRESS: ============================= Precursor FDR =============================
5:33:49.352499 PROGRESS: Total precursors accumulated: 703
5:33:49.356499 PROGRESS: Target precursors: 642 (91.32%)
5:33:49.360499 PROGRESS: Decoy precursors: 61 (8.68%)
5:33:49.364500 PROGRESS: 
5:33:49.368502 PROGRESS: Precursor Summary:
5:33:49.375501 PROGRESS: Channel   0:	 0.050 FDR:   529; 0.010 FDR:   315; 0.001 FDR:     0
5:33:49.379504 PROGRESS: 
5:33:49.383504 PROGRESS: Protein Summary:
5:33:49.390503 PROGRESS: Channel   0:	 0.050 FDR:   484; 0.010 FDR:   291; 0.001 FDR:     0
5:33:49.395506 PROGRESS: =========================================================================
5:33:49.404504 INFO: Target number of precursors reached.
5:33:49.834672 INFO: fragments_df: keeping 4214 of 2408764 [sum(precursor_idx_mask)=8564 sum(mass_error_mask)=2408764 stop_rank=4214
5:33:50.494848 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:33:50.805990 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:33:51.099604 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:33:53.645956 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:33:53.650956 INFO: Using score_cutoff 68.70462352294922 (fac=0.99, q=1)
5:33:53.655955 INFO: Updating optimization_manager: fwhm_rt             : 2.413872241973877 -> 2.3729684352874756
5:33:53.659956 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:33:53.662956 INFO: Updating optimization_manager: score_cutoff        : 64.50914186553955 -> 68.70462352294922
5:33:53.666955 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:33:53.764568 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:33:53.927565 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:33:54.348700 INFO: === checking if optimization conditions were reached ===
5:33:54.352702 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
5:33:54.359703 INFO: Updating optimization_manager: rt_error            : 93.96502911481184 -> 77.11760489887887
5:33:54.363703 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 77.1176.
5:33:54.366706 INFO: ==============================================
5:33:54.370706 INFO: Starting optimization step 3.
5:33:54.373705 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:33:54.377702 INFO: Using classic extraction backend
5:33:54.381702 PROGRESS: Extracting batch of 109921 precursors
5:33:54.384707 INFO: === Search parameters used ===
5:33:54.388707 INFO: rt_error       : 77.11760489887887
5:33:54.391705 INFO: mobility_error : 0.1
5:33:54.395706 INFO: num_candidates : 3
5:33:54.398707 INFO: ms1_error      : 5.0
5:33:54.402706 INFO: ms2_error      : 10.0
5:33:54.407714 INFO: fwhm_rt        : 2.3729684352874756
5:33:54.412707 INFO: quant_window   : 3
5:33:54.418708 INFO: ==============================================
5:33:54.531251 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:33:54.532249 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:33:54.533250 INFO: FWHM in RT is 2.37 seconds, sigma is 0.26
5:33:54.534249 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:33:54.536252 INFO: Starting candidate selection
5:34:02.203093 INFO: Starting candidate scoring
5:34:11.476123 INFO: Finished candidate processing
5:34:11.478131 INFO: Collecting candidate features
5:34:12.847486 WARNING: intensity_correlation has 45 NaNs ( 0.01 % out of 329113)
5:34:12.851489 WARNING: height_correlation has 29 NaNs ( 0.01 % out of 329113)
5:34:12.950482 INFO: Collecting fragment features
5:34:13.493644 INFO: Finished candidate scoring
5:34:13.909872 INFO: performing precursor FDR with 47 features
5:34:13.910871 INFO: Decoy channel: -1
5:34:13.911873 INFO: Competetive: True
5:34:14.244420 INFO: Setting torch num_threads to 2 for FDR classification task
5:34:14.427974 WARNING: dropped 34 target PSMs due to missing features
5:34:14.428970 WARNING: dropped 26 decoy PSMs due to missing features
5:34:14.745586 INFO: Using random state 374404 for train-test-split
5:34:22.612057 INFO: Test AUC: 0.566
5:34:22.614051 INFO: Train AUC: 0.591
5:34:22.615052 INFO: AUC difference: 4.11%
5:34:23.604171 INFO: Resetting torch num_threads to 10
5:34:23.633173 PROGRESS: === Extracted 329113 precursors and 2392333 fragments ===
5:34:23.639170 INFO: === FDR correction performed with classifier version 6 ===
5:34:23.645169 PROGRESS: ============================= Precursor FDR =============================
5:34:23.649171 PROGRESS: Total precursors accumulated: 687
5:34:23.653171 PROGRESS: Target precursors: 626 (91.12%)
5:34:23.657167 PROGRESS: Decoy precursors: 61 (8.88%)
5:34:23.661172 PROGRESS: 
5:34:23.665173 PROGRESS: Precursor Summary:
5:34:23.671170 PROGRESS: Channel   0:	 0.050 FDR:   528; 0.010 FDR:   394; 0.001 FDR:   280
5:34:23.676168 PROGRESS: 
5:34:23.679170 PROGRESS: Protein Summary:
5:34:23.687170 PROGRESS: Channel   0:	 0.050 FDR:   483; 0.010 FDR:   359; 0.001 FDR:   262
5:34:23.691173 PROGRESS: =========================================================================
5:34:23.700171 INFO: Target number of precursors reached.
5:34:24.138326 INFO: fragments_df: keeping 5000 of 2392333 [sum(precursor_idx_mask)=10649 sum(mass_error_mask)=2392333 stop_rank=5000
5:34:24.797459 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:34:26.906670 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:34:27.213292 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:34:30.606448 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:34:30.611451 INFO: Using score_cutoff 64.63363033218384 (fac=0.99, q=1)
5:34:30.616451 INFO: Updating optimization_manager: fwhm_rt             : 2.3729684352874756 -> 2.4723825454711914
5:34:30.619453 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:34:30.623453 INFO: Updating optimization_manager: score_cutoff        : 68.70462352294922 -> 64.63363033218384
5:34:30.627452 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:34:30.724452 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:34:30.886067 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:34:31.304679 INFO: === checking if optimization conditions were reached ===
5:34:31.308675 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
5:34:31.316683 INFO: Updating optimization_manager: rt_error            : 77.11760489887887 -> 74.98983726617391
5:34:31.320679 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 74.9898.
5:34:31.324678 INFO: ==============================================
5:34:31.327678 INFO: Starting optimization step 4.
5:34:31.332193 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:34:31.336193 INFO: Using classic extraction backend
5:34:31.340193 PROGRESS: Extracting batch of 109921 precursors
5:34:31.344193 INFO: === Search parameters used ===
5:34:31.350193 INFO: rt_error       : 74.98983726617391
5:34:31.358193 INFO: mobility_error : 0.1
5:34:31.365196 INFO: num_candidates : 3
5:34:31.374198 INFO: ms1_error      : 5.0
5:34:31.381199 INFO: ms2_error      : 10.0
5:34:31.410201 INFO: fwhm_rt        : 2.4723825454711914
5:34:31.417199 INFO: quant_window   : 3
5:34:31.426200 INFO: ==============================================
5:34:31.547202 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:34:31.549202 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:34:31.550202 INFO: FWHM in RT is 2.47 seconds, sigma is 0.28
5:34:31.550202 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:34:31.552201 INFO: Starting candidate selection
5:34:39.139850 INFO: Starting candidate scoring
5:34:48.489811 INFO: Finished candidate processing
5:34:48.491819 INFO: Collecting candidate features
5:34:49.864115 WARNING: intensity_correlation has 48 NaNs ( 0.01 % out of 329058)
5:34:49.869114 WARNING: height_correlation has 44 NaNs ( 0.01 % out of 329058)
5:34:49.968118 INFO: Collecting fragment features
5:34:50.518312 INFO: Finished candidate scoring
5:34:50.954472 INFO: performing precursor FDR with 47 features
5:34:50.956469 INFO: Decoy channel: -1
5:34:50.957468 INFO: Competetive: True
5:34:51.294062 INFO: Setting torch num_threads to 2 for FDR classification task
5:34:51.476573 WARNING: dropped 34 target PSMs due to missing features
5:34:51.478575 WARNING: dropped 39 decoy PSMs due to missing features
5:34:51.791116 INFO: Using random state 374404 for train-test-split
5:34:59.569131 INFO: Test AUC: 0.563
5:34:59.571129 INFO: Train AUC: 0.590
5:34:59.572127 INFO: AUC difference: 4.61%
5:35:00.555284 INFO: Resetting torch num_threads to 10
5:35:00.584283 PROGRESS: === Extracted 329058 precursors and 2361513 fragments ===
5:35:00.590286 INFO: === FDR correction performed with classifier version 6 ===
5:35:00.597289 PROGRESS: ============================= Precursor FDR =============================
5:35:00.602288 PROGRESS: Total precursors accumulated: 708
5:35:00.606288 PROGRESS: Target precursors: 647 (91.38%)
5:35:00.610290 PROGRESS: Decoy precursors: 61 (8.62%)
5:35:00.614290 PROGRESS: 
5:35:00.618303 PROGRESS: Precursor Summary:
5:35:00.625303 PROGRESS: Channel   0:	 0.050 FDR:   546; 0.010 FDR:   359; 0.001 FDR:   232
5:35:00.629304 PROGRESS: 
5:35:00.633390 PROGRESS: Protein Summary:
5:35:00.640391 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   329; 0.001 FDR:   219
5:35:00.645392 PROGRESS: =========================================================================
5:35:00.653391 INFO: Target number of precursors reached.
5:35:01.064996 INFO: fragments_df: keeping 4645 of 2361513 [sum(precursor_idx_mask)=9708 sum(mass_error_mask)=2361513 stop_rank=4645
5:35:01.763565 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:35:02.124091 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:35:02.462131 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:35:05.575700 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:35:05.583695 INFO: Using score_cutoff 67.39663587341308 (fac=0.99, q=1)
5:35:05.590696 INFO: Updating optimization_manager: fwhm_rt             : 2.4723825454711914 -> 2.4083688259124756
5:35:05.596696 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:35:05.600696 INFO: Updating optimization_manager: score_cutoff        : 64.63363033218384 -> 67.39663587341308
5:35:05.605695 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:35:05.706313 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:35:05.867314 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:35:06.282548 INFO: === checking if optimization conditions were reached ===
5:35:06.287553 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
5:35:06.296553 INFO: Updating optimization_manager: rt_error            : 74.98983726617391 -> 74.98983726617391
5:35:06.303552 INFO: Updating optimization_manager: classifier_version  : 6 -> 11
5:35:06.310552 INFO: Updating optimization_manager: score_cutoff        : 67.39663587341308 -> 67.39663587341308
5:35:06.318544 INFO: Updating optimization_manager: fwhm_rt             : 2.4083688259124756 -> 2.4083688259124756
5:35:06.322547 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
5:35:06.330544 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 74.9898 found after 5 searches.
5:35:06.334544 INFO: ==============================================
5:35:06.338545 PROGRESS: Optimization finished for rt_error.
5:35:06.988184 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:35:07.106185 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:35:07.300791 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:35:07.828022 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:35:07.834021 PROGRESS: ==============================================
5:35:07.838021 PROGRESS: ms2_error      : 10.0000
5:35:07.844021 PROGRESS: ms1_error      : 5.0000
5:35:07.849021 PROGRESS: rt_error       : 74.9898
5:35:07.854020 PROGRESS: ==============================================
5:35:07.870021 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:35:11.477036 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:35:20.454439 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:36:01.940717 INFO: Using classic extraction backend
5:36:01.946709 PROGRESS: Extracting batch of 11035943 precursors
5:36:01.950707 INFO: === Search parameters used ===
5:36:01.954708 INFO: rt_error       : 74.98983726617391
5:36:01.957706 INFO: mobility_error : 0.1
5:36:01.961706 INFO: num_candidates : 3
5:36:01.965709 INFO: ms1_error      : 5.0
5:36:01.970709 INFO: ms2_error      : 10.0
5:36:01.975708 INFO: fwhm_rt        : 2.4083688259124756
5:36:01.980705 INFO: quant_window   : 3
5:36:01.985706 INFO: ==============================================
5:36:05.294794 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
5:36:05.296794 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:36:05.297793 INFO: FWHM in RT is 2.41 seconds, sigma is 0.27
5:36:05.298794 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:36:05.299794 INFO: Starting candidate selection
5:47:25.775818 INFO: Removed 25461255 precursors with score below cutoff 67.39663587341308
5:47:29.718354 INFO: Starting candidate scoring
5:51:45.501220 INFO: Finished candidate processing
5:51:45.502221 INFO: Collecting candidate features
5:52:14.623897 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 7633392)
5:52:15.933712 INFO: Collecting fragment features
5:52:29.667712 INFO: Finished candidate scoring
5:53:12.292729 INFO: === Performing FDR correction with classifier version 11 ===
5:53:12.303730 INFO: performing precursor FDR with 47 features
5:53:12.305733 INFO: Decoy channel: -1
5:53:12.307732 INFO: Competetive: True
5:53:17.706159 INFO: Setting torch num_threads to 2 for FDR classification task
5:53:20.541304 WARNING: dropped 1 decoy PSMs due to missing features
5:53:31.349374 INFO: Using random state 686829 for train-test-split
5:57:07.432865 INFO: Test AUC: 0.586
5:57:07.433866 INFO: Train AUC: 0.588
5:57:07.434866 INFO: AUC difference: 0.47%
5:57:13.079886 INFO: Resetting torch num_threads to 10
5:57:13.511413 INFO: Removing fragments below FDR threshold
5:57:15.858137 PROGRESS: ============================= Precursor FDR =============================
5:57:15.865139 PROGRESS: Total precursors accumulated: 43,647
5:57:15.871140 PROGRESS: Target precursors: 43,215 (99.01%)
5:57:15.877139 PROGRESS: Decoy precursors: 432 (0.99%)
5:57:15.883141 PROGRESS: 
5:57:15.889138 PROGRESS: Precursor Summary:
5:57:15.995140 PROGRESS: Channel   0:	 0.050 FDR: 43,215; 0.010 FDR: 43,215; 0.001 FDR: 31,836
5:57:16.000140 PROGRESS: 
5:57:16.005141 PROGRESS: Protein Summary:
5:57:16.143749 PROGRESS: Channel   0:	 0.050 FDR: 7,943; 0.010 FDR: 7,943; 0.001 FDR: 6,416
5:57:16.148746 PROGRESS: =========================================================================
5:57:16.552888 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\psm.parquet
5:57:17.670200 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\frag.parquet
5:57:18.754517 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
5:57:20.038422 PROGRESS: 
5:57:20.039423 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant
5:57:20.040425 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\figures
5:57:20.048424 INFO: Initializing TimingManager
5:57:20.062958 INFO: Initializing RawFileManager
6:02:34.509249 INFO: Determining DIA cycle
6:02:34.536767 INFO: Found cycle with start 0.00 min and length 86.
6:02:35.155928 INFO: RT (min)            : 0.0 - 55.5
6:02:35.156929 INFO: RT duration (sec)   : 3327.2
6:02:35.157927 INFO: RT duration (min)   : 55.5
6:02:35.158929 INFO: Cycle len (scans)   : 86
6:02:35.159928 INFO: Cycle len (sec)     : 1.90
6:02:35.160931 INFO: Number of cycles    : 1747
6:02:35.160931 INFO: MS2 range (m/z)     : 399.5 - 903.5
6:02:35.161927 INFO: Creating DIA data object took: 315.0929641723633
6:02:37.999314 INFO: Initializing CalibrationManager
6:02:38.006313 INFO: Setting up calibration estimators ..
6:02:38.010313 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:02:38.014312 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'}' ..
6:02:38.018315 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:02:38.022314 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
6:02:38.026328 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}}' ..
6:02:38.029329 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:02:38.033329 INFO: Done setting up calibration estimators.
6:02:38.037330 INFO: Initializing OptimizationManager
6:02:38.043858 INFO: initial parameter: ms1_error = 30
6:02:38.046856 INFO: initial parameter: ms2_error = 30
6:02:38.050858 INFO: initial parameter: rt_error = 1663.6044921875
6:02:38.053857 INFO: initial parameter: mobility_error = 0.1
6:02:38.057856 INFO: initial parameter: num_candidates = 1
6:02:38.061858 INFO: initial parameter: fwhm_rt = 5
6:02:38.064859 INFO: initial parameter: fwhm_mobility = 0.01
6:02:38.068854 INFO: initial parameter: score_cutoff = 0
6:02:38.072861 INFO: initial parameter: classifier_version = -1
6:02:38.079856 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
6:02:38.083857 INFO: FDRManager: loading saved state not requested, will be initialized.
6:02:38.084853 INFO: Initializing FDRManager
6:02:38.085856 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
6:02:41.062701 PROGRESS: Initializing spectral library: 5,593,630 target precursors potentially observable (87,574 removed)
6:02:43.254371 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
6:02:43.259370 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 1663.6044921875
6:02:43.263370 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
6:02:43.267376 PROGRESS: Starting initial search for precursors.
6:02:43.271371 INFO: Starting optimization step 0.
6:02:43.274370 PROGRESS: === Extracting elution groups 0 to 8000 ===
6:02:43.277370 INFO: Using classic extraction backend
6:02:43.281371 PROGRESS: Extracting batch of 15689 precursors
6:02:43.288377 INFO: === Search parameters used ===
6:02:43.294377 INFO: rt_error       : 1663.6044921875
6:02:43.303887 INFO: mobility_error : 0.1
6:02:43.313889 INFO: num_candidates : 1
6:02:43.319889 INFO: ms1_error      : 30
6:02:43.327889 INFO: ms2_error      : 30
6:02:43.333888 INFO: fwhm_rt        : 5
6:02:43.341889 INFO: quant_window   : 3
6:02:43.350889 INFO: ==============================================
6:02:43.400888 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:02:43.400888 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:02:43.401888 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
6:02:43.402889 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:02:43.404890 INFO: Starting candidate selection
6:02:57.081508 INFO: Starting candidate scoring
6:02:57.662810 INFO: Finished candidate processing
6:02:57.664824 INFO: Collecting candidate features
6:02:57.809836 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15683)
6:02:57.821837 INFO: Collecting fragment features
6:02:57.927433 INFO: Finished candidate scoring
6:02:57.963434 INFO: performing precursor FDR with 47 features
6:02:57.964432 INFO: Decoy channel: -1
6:02:57.965430 INFO: Competetive: True
6:02:58.008433 INFO: Setting torch num_threads to 2 for FDR classification task
6:02:58.034430 WARNING: dropped 1 decoy PSMs due to missing features
6:02:58.047429 INFO: Using random state 999713 for train-test-split
6:02:58.323035 INFO: Test AUC: 0.543
6:02:58.324548 INFO: Train AUC: 0.529
6:02:58.325566 INFO: AUC difference: 2.60%
6:02:58.931794 INFO: Resetting torch num_threads to 10
6:02:58.941792 PROGRESS: === Extracted 15683 precursors and 144472 fragments ===
6:02:58.946793 INFO: === FDR correction performed with classifier version -1 ===
6:02:58.952794 PROGRESS: ============================= Precursor FDR =============================
6:02:58.956793 PROGRESS: Total precursors accumulated: 1
6:02:58.959790 PROGRESS: Target precursors: 1 (100.00%)
6:02:58.963794 PROGRESS: Decoy precursors: 0 (0.00%)
6:02:58.967794 PROGRESS: 
6:02:58.971793 PROGRESS: Precursor Summary:
6:02:58.976794 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
6:02:58.981795 PROGRESS: 
6:02:58.984793 PROGRESS: Protein Summary:
6:02:58.991792 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
6:02:58.995794 PROGRESS: =========================================================================
6:02:59.001794 INFO: Target number of precursors not reached yet.
6:02:59.356946 INFO: Starting optimization step 1.
6:02:59.361948 PROGRESS: === Extracting elution groups 8000 to 24000 ===
6:02:59.369946 INFO: Using classic extraction backend
6:02:59.376951 PROGRESS: Extracting batch of 31390 precursors
6:02:59.383947 INFO: === Search parameters used ===
6:02:59.390949 INFO: rt_error       : 1663.6044921875
6:02:59.396946 INFO: mobility_error : 0.1
6:02:59.403946 INFO: num_candidates : 1
6:02:59.408949 INFO: ms1_error      : 30
6:02:59.414947 INFO: ms2_error      : 30
6:02:59.420943 INFO: fwhm_rt        : 5
6:02:59.427949 INFO: quant_window   : 3
6:02:59.435947 INFO: ==============================================
6:02:59.505947 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:02:59.507948 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:02:59.508945 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
6:02:59.509951 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:02:59.510954 INFO: Starting candidate selection
6:03:27.182031 INFO: Starting candidate scoring
6:03:28.300090 INFO: Finished candidate processing
6:03:28.300090 INFO: Collecting candidate features
6:03:28.572125 INFO: Collecting fragment features
6:03:28.687675 INFO: Finished candidate scoring
6:03:28.802672 INFO: performing precursor FDR with 47 features
6:03:28.804676 INFO: Decoy channel: -1
6:03:28.806674 INFO: Competetive: True
6:03:28.945219 INFO: Setting torch num_threads to 2 for FDR classification task
6:03:28.993221 WARNING: dropped 1 decoy PSMs due to missing features
6:03:29.028220 INFO: Using random state 708851 for train-test-split
6:03:30.215659 INFO: Test AUC: 0.573
6:03:30.217659 INFO: Train AUC: 0.574
6:03:30.218659 INFO: AUC difference: 0.06%
6:03:30.936279 INFO: Resetting torch num_threads to 10
6:03:31.017281 PROGRESS: === Extracted 47054 precursors and 433161 fragments ===
6:03:31.024281 INFO: === FDR correction performed with classifier version -1 ===
6:03:31.029282 PROGRESS: ============================= Precursor FDR =============================
6:03:31.033281 PROGRESS: Total precursors accumulated: 24
6:03:31.036283 PROGRESS: Target precursors: 22 (91.67%)
6:03:31.040281 PROGRESS: Decoy precursors: 2 (8.33%)
6:03:31.045283 PROGRESS: 
6:03:31.048280 PROGRESS: Precursor Summary:
6:03:31.054280 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:     9; 0.001 FDR:     9
6:03:31.058282 PROGRESS: 
6:03:31.063281 PROGRESS: Protein Summary:
6:03:31.070281 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:     9; 0.001 FDR:     9
6:03:31.075281 PROGRESS: =========================================================================
6:03:31.089281 INFO: Target number of precursors not reached yet.
6:03:31.594001 INFO: Starting optimization step 2.
6:03:31.598999 PROGRESS: === Extracting elution groups 24000 to 56000 ===
6:03:31.602997 INFO: Using classic extraction backend
6:03:31.610019 PROGRESS: Extracting batch of 62842 precursors
6:03:31.616014 INFO: === Search parameters used ===
6:03:31.624548 INFO: rt_error       : 1663.6044921875
6:03:31.631547 INFO: mobility_error : 0.1
6:03:31.636547 INFO: num_candidates : 1
6:03:31.643551 INFO: ms1_error      : 30
6:03:31.649544 INFO: ms2_error      : 30
6:03:31.655547 INFO: fwhm_rt        : 5
6:03:31.663547 INFO: quant_window   : 3
6:03:31.671547 INFO: ==============================================
6:03:31.756547 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:03:31.757547 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:03:31.758544 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
6:03:31.759546 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:03:31.760548 INFO: Starting candidate selection
6:04:26.342942 INFO: Starting candidate scoring
6:04:28.447765 INFO: Finished candidate processing
6:04:28.449777 INFO: Collecting candidate features
6:04:28.981448 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 62806)
6:04:29.000449 INFO: Collecting fragment features
6:04:29.239074 INFO: Finished candidate scoring
6:04:29.463683 INFO: performing precursor FDR with 47 features
6:04:29.464687 INFO: Decoy channel: -1
6:04:29.465686 INFO: Competetive: True
6:04:29.751299 INFO: Setting torch num_threads to 2 for FDR classification task
6:04:29.865296 WARNING: dropped 1 target PSMs due to missing features
6:04:29.867295 WARNING: dropped 1 decoy PSMs due to missing features
6:04:29.988915 INFO: Using random state 97509 for train-test-split
6:04:32.908332 INFO: Test AUC: 0.577
6:04:32.909332 INFO: Train AUC: 0.593
6:04:32.910333 INFO: AUC difference: 2.66%
6:04:33.649069 INFO: Resetting torch num_threads to 10
6:04:33.812678 PROGRESS: === Extracted 109860 precursors and 1011324 fragments ===
6:04:33.818679 INFO: === FDR correction performed with classifier version -1 ===
6:04:33.823681 PROGRESS: ============================= Precursor FDR =============================
6:04:33.827679 PROGRESS: Total precursors accumulated: 314
6:04:33.831681 PROGRESS: Target precursors: 286 (91.08%)
6:04:33.835679 PROGRESS: Decoy precursors: 28 (8.92%)
6:04:33.838679 PROGRESS: 
6:04:33.842680 PROGRESS: Precursor Summary:
6:04:33.848680 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   145; 0.001 FDR:   135
6:04:33.853680 PROGRESS: 
6:04:33.856681 PROGRESS: Protein Summary:
6:04:33.863679 PROGRESS: Channel   0:	 0.050 FDR:   221; 0.010 FDR:   141; 0.001 FDR:   131
6:04:33.868680 PROGRESS: =========================================================================
6:04:33.878679 INFO: Target number of precursors not reached yet.
6:04:34.579520 INFO: Starting optimization step 3.
6:04:34.586520 PROGRESS: === Extracting elution groups 56000 to 120000 ===
6:04:34.593520 INFO: Using classic extraction backend
6:04:34.600518 PROGRESS: Extracting batch of 125627 precursors
6:04:34.608521 INFO: === Search parameters used ===
6:04:34.614521 INFO: rt_error       : 1663.6044921875
6:04:34.621521 INFO: mobility_error : 0.1
6:04:34.628520 INFO: num_candidates : 1
6:04:34.632522 INFO: ms1_error      : 30
6:04:34.639521 INFO: ms2_error      : 30
6:04:34.646520 INFO: fwhm_rt        : 5
6:04:34.655521 INFO: quant_window   : 3
6:04:34.663521 INFO: ==============================================
6:04:34.790068 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:04:34.791070 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:04:34.792069 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
6:04:34.794067 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:04:34.795068 INFO: Starting candidate selection
6:06:24.513927 INFO: Starting candidate scoring
6:06:28.538123 INFO: Finished candidate processing
6:06:28.539141 INFO: Collecting candidate features
6:06:29.507307 INFO: Collecting fragment features
6:06:29.794858 INFO: Finished candidate scoring
6:06:30.104403 INFO: performing precursor FDR with 47 features
6:06:30.106405 INFO: Decoy channel: -1
6:06:30.106405 INFO: Competetive: True
6:06:30.647023 INFO: Setting torch num_threads to 2 for FDR classification task
6:06:30.806029 WARNING: dropped 1 target PSMs due to missing features
6:06:30.807024 WARNING: dropped 1 decoy PSMs due to missing features
6:06:31.041546 INFO: Using random state 624429 for train-test-split
6:06:36.877924 INFO: Test AUC: 0.583
6:06:36.879924 INFO: Train AUC: 0.598
6:06:36.880925 INFO: AUC difference: 2.57%
6:06:37.709101 INFO: Resetting torch num_threads to 10
6:06:37.915649 PROGRESS: === Extracted 235423 precursors and 2165242 fragments ===
6:06:37.921650 INFO: === FDR correction performed with classifier version -1 ===
6:06:37.928651 PROGRESS: ============================= Precursor FDR =============================
6:06:37.932650 PROGRESS: Total precursors accumulated: 866
6:06:37.935647 PROGRESS: Target precursors: 788 (90.99%)
6:06:37.939646 PROGRESS: Decoy precursors: 78 (9.01%)
6:06:37.942652 PROGRESS: 
6:06:37.946649 PROGRESS: Precursor Summary:
6:06:37.952650 PROGRESS: Channel   0:	 0.050 FDR:   606; 0.010 FDR:   438; 0.001 FDR:   256
6:06:37.957651 PROGRESS: 
6:06:37.960649 PROGRESS: Protein Summary:
6:06:37.967649 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   383; 0.001 FDR:   232
6:06:37.971651 PROGRESS: =========================================================================
6:06:37.989651 INFO: Target number of precursors reached.
6:06:38.434668 INFO: fragments_df: keeping 4264 of 2165242 [sum(precursor_idx_mask)=5043 sum(mass_error_mask)=2165242 stop_rank=4264
6:06:39.165292 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:06:39.523818 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:06:39.868344 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:06:42.433606 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:06:42.438607 INFO: Using score_cutoff 82.86711175689696 (fac=0.99, q=1)
6:06:42.442606 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.4311771392822266
6:06:42.446606 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
6:06:42.450607 INFO: Updating optimization_manager: score_cutoff        : 0 -> 82.86711175689696
6:06:42.454607 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:06:42.557607 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:06:42.725150 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:06:43.156711 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
6:06:43.161702 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:06:43.165928 INFO: Starting optimization step 4.
6:06:43.169929 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:06:43.176927 INFO: Using classic extraction backend
6:06:43.191928 PROGRESS: Extracting batch of 109921 precursors
6:06:43.200930 INFO: === Search parameters used ===
6:06:43.209932 INFO: rt_error       : 1663.6044921875
6:06:43.216934 INFO: mobility_error : 0.1
6:06:43.225935 INFO: num_candidates : 3
6:06:43.233936 INFO: ms1_error      : 30
6:06:43.255934 INFO: ms2_error      : 30
6:06:43.264932 INFO: fwhm_rt        : 2.4311771392822266
6:06:43.272935 INFO: quant_window   : 3
6:06:43.281933 INFO: ==============================================
6:06:43.408947 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:06:43.409949 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:06:43.410950 INFO: FWHM in RT is 2.43 seconds, sigma is 0.27
6:06:43.411947 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:06:43.411947 INFO: Starting candidate selection
6:08:40.669185 INFO: Starting candidate scoring
6:08:50.717949 INFO: Finished candidate processing
6:08:50.718963 INFO: Collecting candidate features
6:08:52.111215 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 329544)
6:08:52.255214 INFO: Collecting fragment features
6:08:52.873797 INFO: Finished candidate scoring
6:08:53.305340 INFO: performing precursor FDR with 47 features
6:08:53.306341 INFO: Decoy channel: -1
6:08:53.307341 INFO: Competetive: True
6:08:53.655401 INFO: Setting torch num_threads to 2 for FDR classification task
6:08:53.828403 WARNING: dropped 2 target PSMs due to missing features
6:08:53.829401 WARNING: dropped 1 decoy PSMs due to missing features
6:08:54.145451 INFO: Using random state 903232 for train-test-split
6:09:01.906071 INFO: Test AUC: 0.582
6:09:01.907071 INFO: Train AUC: 0.600
6:09:01.908070 INFO: AUC difference: 2.92%
6:09:02.857906 INFO: Resetting torch num_threads to 10
6:09:02.886510 PROGRESS: === Extracted 329544 precursors and 2921630 fragments ===
6:09:02.892513 INFO: === FDR correction performed with classifier version 3 ===
6:09:02.898511 PROGRESS: ============================= Precursor FDR =============================
6:09:02.902512 PROGRESS: Total precursors accumulated: 497
6:09:02.906510 PROGRESS: Target precursors: 454 (91.35%)
6:09:02.910507 PROGRESS: Decoy precursors: 43 (8.65%)
6:09:02.914512 PROGRESS: 
6:09:02.918512 PROGRESS: Precursor Summary:
6:09:02.925511 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   268; 0.001 FDR:   244
6:09:02.929511 PROGRESS: 
6:09:02.933512 PROGRESS: Protein Summary:
6:09:02.940510 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   247; 0.001 FDR:   226
6:09:02.945512 PROGRESS: =========================================================================
6:09:02.955511 INFO: Target number of precursors reached.
6:09:03.459702 INFO: fragments_df: keeping 3851 of 2921630 [sum(precursor_idx_mask)=8052 sum(mass_error_mask)=2921630 stop_rank=3851
6:09:04.127478 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:09:04.438995 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:09:04.798536 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:09:07.050119 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:09:07.055115 INFO: Using score_cutoff 76.9486226852417 (fac=0.99, q=1)
6:09:07.060118 INFO: Updating optimization_manager: fwhm_rt             : 2.4311771392822266 -> 2.421354293823242
6:09:07.063120 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:09:07.067119 INFO: Updating optimization_manager: score_cutoff        : 82.86711175689696 -> 76.9486226852417
6:09:07.071118 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:09:07.172727 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:09:07.377729 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:09:07.793860 INFO: === checking if optimization conditions were reached ===
6:09:07.803862 INFO: Updating optimization_manager: ms2_error           : 30 -> 19.957370886402174
6:09:07.810861 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:09:07.819860 PROGRESS: ❌ ms2_error      : 19.9574 > 10.0000 or insufficient steps taken.
6:09:07.835859 INFO: Updating optimization_manager: ms1_error           : 30 -> 13.836708829658697
6:09:07.841861 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
6:09:07.846860 PROGRESS: ❌ ms1_error      : 13.8367 > 5.0000 or insufficient steps taken.
6:09:07.851861 INFO: ==============================================
6:09:07.856860 INFO: Starting optimization step 5.
6:09:07.862862 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:09:07.867860 INFO: Using classic extraction backend
6:09:07.873873 PROGRESS: Extracting batch of 109921 precursors
6:09:07.878874 INFO: === Search parameters used ===
6:09:07.883874 INFO: rt_error       : 1663.6044921875
6:09:07.888402 INFO: mobility_error : 0.1
6:09:07.893404 INFO: num_candidates : 3
6:09:07.898403 INFO: ms1_error      : 13.836708829658697
6:09:07.902404 INFO: ms2_error      : 19.957370886402174
6:09:07.907403 INFO: fwhm_rt        : 2.421354293823242
6:09:07.911404 INFO: quant_window   : 3
6:09:07.915404 INFO: ==============================================
6:09:08.041398 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:09:08.043398 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:09:08.044398 INFO: FWHM in RT is 2.42 seconds, sigma is 0.27
6:09:08.045399 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:09:08.047399 INFO: Starting candidate selection
6:11:03.292057 INFO: Starting candidate scoring
6:11:12.807003 INFO: Finished candidate processing
6:11:12.808325 INFO: Collecting candidate features
6:11:14.209948 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 329458)
6:11:14.319443 INFO: Collecting fragment features
6:11:14.938530 INFO: Finished candidate scoring
6:11:15.403576 INFO: performing precursor FDR with 47 features
6:11:15.404577 INFO: Decoy channel: -1
6:11:15.405576 INFO: Competetive: True
6:11:15.739103 INFO: Setting torch num_threads to 2 for FDR classification task
6:11:15.913645 WARNING: dropped 1 target PSMs due to missing features
6:11:15.915644 WARNING: dropped 3 decoy PSMs due to missing features
6:11:16.222170 INFO: Using random state 529075 for train-test-split
6:11:23.936404 INFO: Test AUC: 0.582
6:11:23.938402 INFO: Train AUC: 0.599
6:11:23.939402 INFO: AUC difference: 2.68%
6:11:24.898497 INFO: Resetting torch num_threads to 10
6:11:24.927496 PROGRESS: === Extracted 329458 precursors and 2742838 fragments ===
6:11:24.933498 INFO: === FDR correction performed with classifier version 4 ===
6:11:24.941497 PROGRESS: ============================= Precursor FDR =============================
6:11:24.947498 PROGRESS: Total precursors accumulated: 647
6:11:24.952497 PROGRESS: Target precursors: 592 (91.50%)
6:11:24.956499 PROGRESS: Decoy precursors: 55 (8.50%)
6:11:24.960498 PROGRESS: 
6:11:24.964498 PROGRESS: Precursor Summary:
6:11:24.971501 PROGRESS: Channel   0:	 0.050 FDR:   448; 0.010 FDR:   348; 0.001 FDR:   265
6:11:24.975499 PROGRESS: 
6:11:24.979497 PROGRESS: Protein Summary:
6:11:24.986501 PROGRESS: Channel   0:	 0.050 FDR:   414; 0.010 FDR:   323; 0.001 FDR:   247
6:11:24.991498 PROGRESS: =========================================================================
6:11:25.003499 INFO: Target number of precursors reached.
6:11:25.529568 INFO: fragments_df: keeping 4774 of 2742838 [sum(precursor_idx_mask)=9981 sum(mass_error_mask)=2742838 stop_rank=4774
6:11:26.196208 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:11:26.554760 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:11:26.893851 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:11:30.035056 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:11:30.040056 INFO: Using score_cutoff 57.46892536010743 (fac=0.99, q=1)
6:11:30.045057 INFO: Updating optimization_manager: fwhm_rt             : 2.421354293823242 -> 2.45176100730896
6:11:30.049055 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:11:30.053060 INFO: Updating optimization_manager: score_cutoff        : 76.9486226852417 -> 57.46892536010743
6:11:30.056057 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:11:30.156604 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:11:30.331621 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:11:30.756708 INFO: === checking if optimization conditions were reached ===
6:11:30.765708 INFO: Updating optimization_manager: ms2_error           : 19.957370886402174 -> 12.162152097911157
6:11:30.771704 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:11:30.777705 PROGRESS: ❌ ms2_error      : 12.1622 > 10.0000 or insufficient steps taken.
6:11:30.788705 INFO: Updating optimization_manager: ms1_error           : 13.836708829658697 -> 5.0
6:11:30.793705 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
6:11:30.802703 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
6:11:30.809704 INFO: ==============================================
6:11:30.818703 INFO: Starting optimization step 6.
6:11:30.824703 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:11:30.833708 INFO: Using classic extraction backend
6:11:30.839709 PROGRESS: Extracting batch of 109921 precursors
6:11:30.847220 INFO: === Search parameters used ===
6:11:30.856221 INFO: rt_error       : 1663.6044921875
6:11:30.864221 INFO: mobility_error : 0.1
6:11:30.872221 INFO: num_candidates : 3
6:11:30.878222 INFO: ms1_error      : 5.0
6:11:30.886222 INFO: ms2_error      : 12.162152097911157
6:11:30.893221 INFO: fwhm_rt        : 2.45176100730896
6:11:30.901222 INFO: quant_window   : 3
6:11:30.907222 INFO: ==============================================
6:11:31.031228 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:11:31.032228 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:11:31.034228 INFO: FWHM in RT is 2.45 seconds, sigma is 0.27
6:11:31.035234 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:11:31.037229 INFO: Starting candidate selection
6:13:19.230743 INFO: Starting candidate scoring
6:13:28.360724 INFO: Finished candidate processing
6:13:28.361738 INFO: Collecting candidate features
6:13:29.452167 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 329336)
6:13:29.456167 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329336)
6:13:29.543772 INFO: Collecting fragment features
6:13:30.033980 INFO: Finished candidate scoring
6:13:30.418495 INFO: performing precursor FDR with 47 features
6:13:30.419497 INFO: Decoy channel: -1
6:13:30.420497 INFO: Competetive: True
6:13:30.685101 INFO: Setting torch num_threads to 2 for FDR classification task
6:13:30.830711 WARNING: dropped 3 target PSMs due to missing features
6:13:30.832713 WARNING: dropped 5 decoy PSMs due to missing features
6:13:31.076259 INFO: Using random state 300790 for train-test-split
6:13:38.283280 INFO: Test AUC: 0.576
6:13:38.284280 INFO: Train AUC: 0.598
6:13:38.285281 INFO: AUC difference: 3.62%
6:13:38.998403 INFO: Resetting torch num_threads to 10
6:13:39.022405 PROGRESS: === Extracted 329336 precursors and 2583444 fragments ===
6:13:39.028406 INFO: === FDR correction performed with classifier version 5 ===
6:13:39.032404 PROGRESS: ============================= Precursor FDR =============================
6:13:39.037418 PROGRESS: Total precursors accumulated: 680
6:13:39.041419 PROGRESS: Target precursors: 620 (91.18%)
6:13:39.046419 PROGRESS: Decoy precursors: 60 (8.82%)
6:13:39.049952 PROGRESS: 
6:13:39.052952 PROGRESS: Precursor Summary:
6:13:39.058954 PROGRESS: Channel   0:	 0.050 FDR:   472; 0.010 FDR:   321; 0.001 FDR:   255
6:13:39.062952 PROGRESS: 
6:13:39.066952 PROGRESS: Protein Summary:
6:13:39.072953 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   297; 0.001 FDR:   237
6:13:39.076951 PROGRESS: =========================================================================
6:13:39.083951 INFO: Target number of precursors reached.
6:13:39.471498 INFO: fragments_df: keeping 4446 of 2583444 [sum(precursor_idx_mask)=8934 sum(mass_error_mask)=2583444 stop_rank=4446
6:13:40.017589 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:13:40.272135 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:13:40.556226 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:13:42.908089 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:13:42.912088 INFO: Using score_cutoff 68.22848844909667 (fac=0.99, q=1)
6:13:42.917087 INFO: Updating optimization_manager: fwhm_rt             : 2.45176100730896 -> 2.424961566925049
6:13:42.920085 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:13:42.924089 INFO: Updating optimization_manager: score_cutoff        : 57.46892536010743 -> 68.22848844909667
6:13:42.928087 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:13:43.001090 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:13:43.132614 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:13:43.546810 INFO: === checking if optimization conditions were reached ===
6:13:43.555812 INFO: Updating optimization_manager: ms2_error           : 12.162152097911157 -> 10.0
6:13:43.559329 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:13:43.563329 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:13:43.566329 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
6:13:43.570331 INFO: ==============================================
6:13:43.573332 PROGRESS: Optimization finished for ms2_error, ms1_error.
6:13:44.130553 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:13:44.207557 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:13:44.347091 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:13:44.783702 INFO: Starting optimization step 0.
6:13:44.789705 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:13:44.795724 INFO: Using classic extraction backend
6:13:44.800723 PROGRESS: Extracting batch of 109921 precursors
6:13:44.808721 INFO: === Search parameters used ===
6:13:44.819248 INFO: rt_error       : 1663.6044921875
6:13:44.828246 INFO: mobility_error : 0.1
6:13:44.847247 INFO: num_candidates : 3
6:13:44.854248 INFO: ms1_error      : 5.0
6:13:44.860247 INFO: ms2_error      : 10.0
6:13:44.868247 INFO: fwhm_rt        : 2.424961566925049
6:13:44.876247 INFO: quant_window   : 3
6:13:44.885249 INFO: ==============================================
6:13:44.981249 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:13:44.982249 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:13:44.983248 INFO: FWHM in RT is 2.42 seconds, sigma is 0.27
6:13:44.984249 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:13:44.985249 INFO: Starting candidate selection
6:15:33.244553 INFO: Starting candidate scoring
6:15:41.933753 INFO: Finished candidate processing
6:15:41.934763 INFO: Collecting candidate features
6:15:43.051735 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 329255)
6:15:43.055735 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 329255)
6:15:43.141737 INFO: Collecting fragment features
6:15:43.624854 INFO: Finished candidate scoring
6:15:44.032056 INFO: performing precursor FDR with 47 features
6:15:44.034057 INFO: Decoy channel: -1
6:15:44.035058 INFO: Competetive: True
6:15:44.345677 INFO: Setting torch num_threads to 2 for FDR classification task
6:15:44.495288 WARNING: dropped 7 target PSMs due to missing features
6:15:44.496287 WARNING: dropped 4 decoy PSMs due to missing features
6:15:44.745829 INFO: Using random state 79930 for train-test-split
6:15:52.254616 INFO: Test AUC: 0.579
6:15:52.255616 INFO: Train AUC: 0.603
6:15:52.257613 INFO: AUC difference: 4.05%
6:15:53.201395 INFO: Resetting torch num_threads to 10
6:15:53.230391 PROGRESS: === Extracted 329255 precursors and 2517706 fragments ===
6:15:53.236405 INFO: === FDR correction performed with classifier version 6 ===
6:15:53.243404 PROGRESS: ============================= Precursor FDR =============================
6:15:53.247404 PROGRESS: Total precursors accumulated: 809
6:15:53.250912 PROGRESS: Target precursors: 740 (91.47%)
6:15:53.254923 PROGRESS: Decoy precursors: 69 (8.53%)
6:15:53.258920 PROGRESS: 
6:15:53.262921 PROGRESS: Precursor Summary:
6:15:53.269921 PROGRESS: Channel   0:	 0.050 FDR:   533; 0.010 FDR:   332; 0.001 FDR:   241
6:15:53.273922 PROGRESS: 
6:15:53.277920 PROGRESS: Protein Summary:
6:15:53.285921 PROGRESS: Channel   0:	 0.050 FDR:   495; 0.010 FDR:   311; 0.001 FDR:   227
6:15:53.289921 PROGRESS: =========================================================================
6:15:53.297920 INFO: Target number of precursors reached.
6:15:53.739484 INFO: fragments_df: keeping 4515 of 2517706 [sum(precursor_idx_mask)=9029 sum(mass_error_mask)=2517706 stop_rank=4515
6:15:54.379280 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:15:54.681898 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:15:54.978519 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:15:57.770857 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:15:57.775859 INFO: Using score_cutoff 65.64631674957275 (fac=0.99, q=1)
6:15:57.780859 INFO: Updating optimization_manager: fwhm_rt             : 2.424961566925049 -> 2.433293342590332
6:15:57.784859 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:15:57.787858 INFO: Updating optimization_manager: score_cutoff        : 68.22848844909667 -> 65.64631674957275
6:15:57.791857 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:15:57.892862 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:15:58.059470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:15:58.484010 INFO: === checking if optimization conditions were reached ===
6:15:58.489010 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
6:15:58.496011 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 121.16042572921498
6:15:58.500025 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 121.1604.
6:15:58.504030 INFO: ==============================================
6:15:58.508026 INFO: Starting optimization step 1.
6:15:58.512025 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:15:58.515561 INFO: Using classic extraction backend
6:15:58.519557 PROGRESS: Extracting batch of 109921 precursors
6:15:58.522554 INFO: === Search parameters used ===
6:15:58.526558 INFO: rt_error       : 121.16042572921498
6:15:58.530558 INFO: mobility_error : 0.1
6:15:58.533557 INFO: num_candidates : 3
6:15:58.537555 INFO: ms1_error      : 5.0
6:15:58.541557 INFO: ms2_error      : 10.0
6:15:58.544558 INFO: fwhm_rt        : 2.433293342590332
6:15:58.548559 INFO: quant_window   : 3
6:15:58.551555 INFO: ==============================================
6:15:58.658557 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:15:58.660559 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:15:58.660559 INFO: FWHM in RT is 2.43 seconds, sigma is 0.27
6:15:58.661559 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:15:58.662558 INFO: Starting candidate selection
6:16:08.493187 INFO: Starting candidate scoring
6:16:17.676664 INFO: Finished candidate processing
6:16:17.677669 INFO: Collecting candidate features
6:16:19.074600 WARNING: intensity_correlation has 28 NaNs ( 0.01 % out of 329145)
6:16:19.078598 WARNING: height_correlation has 13 NaNs ( 0.00 % out of 329145)
6:16:19.178599 INFO: Collecting fragment features
6:16:19.731605 INFO: Finished candidate scoring
6:16:20.157699 INFO: performing precursor FDR with 47 features
6:16:20.159699 INFO: Decoy channel: -1
6:16:20.160701 INFO: Competetive: True
6:16:20.510250 INFO: Setting torch num_threads to 2 for FDR classification task
6:16:20.684800 WARNING: dropped 16 target PSMs due to missing features
6:16:20.685800 WARNING: dropped 17 decoy PSMs due to missing features
6:16:21.000350 INFO: Using random state 79930 for train-test-split
6:16:28.598422 INFO: Test AUC: 0.567
6:16:28.600424 INFO: Train AUC: 0.592
6:16:28.600424 INFO: AUC difference: 4.19%
6:16:29.552141 INFO: Resetting torch num_threads to 10
6:16:29.580668 PROGRESS: === Extracted 329145 precursors and 2427610 fragments ===
6:16:29.587669 INFO: === FDR correction performed with classifier version 6 ===
6:16:29.593667 PROGRESS: ============================= Precursor FDR =============================
6:16:29.597669 PROGRESS: Total precursors accumulated: 910
6:16:29.601670 PROGRESS: Target precursors: 830 (91.21%)
6:16:29.604669 PROGRESS: Decoy precursors: 80 (8.79%)
6:16:29.608669 PROGRESS: 
6:16:29.611670 PROGRESS: Precursor Summary:
6:16:29.618667 PROGRESS: Channel   0:	 0.050 FDR:   644; 0.010 FDR:   359; 0.001 FDR:   291
6:16:29.622669 PROGRESS: 
6:16:29.626670 PROGRESS: Protein Summary:
6:16:29.633669 PROGRESS: Channel   0:	 0.050 FDR:   593; 0.010 FDR:   328; 0.001 FDR:   271
6:16:29.637666 PROGRESS: =========================================================================
6:16:29.646670 INFO: Target number of precursors reached.
6:16:30.074842 INFO: fragments_df: keeping 4772 of 2427610 [sum(precursor_idx_mask)=9823 sum(mass_error_mask)=2427610 stop_rank=4772
6:16:30.755013 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:16:31.113168 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:16:31.463696 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:16:34.480864 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:16:34.485862 INFO: Using score_cutoff 64.11491208572389 (fac=0.99, q=1)
6:16:34.489863 INFO: Updating optimization_manager: fwhm_rt             : 2.433293342590332 -> 2.405501365661621
6:16:34.493862 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:16:34.497864 INFO: Updating optimization_manager: score_cutoff        : 65.64631674957275 -> 64.11491208572389
6:16:34.501862 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:16:34.602484 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:16:34.767483 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:16:35.181699 INFO: === checking if optimization conditions were reached ===
6:16:35.189699 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
6:16:35.201699 INFO: Updating optimization_manager: rt_error            : 121.16042572921498 -> 106.21048433034709
6:16:35.206700 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 106.2105.
6:16:35.211699 INFO: ==============================================
6:16:35.218700 INFO: Starting optimization step 2.
6:16:35.226701 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:16:35.233701 INFO: Using classic extraction backend
6:16:35.242703 PROGRESS: Extracting batch of 109921 precursors
6:16:35.250701 INFO: === Search parameters used ===
6:16:35.256706 INFO: rt_error       : 106.21048433034709
6:16:35.263706 INFO: mobility_error : 0.1
6:16:35.270708 INFO: num_candidates : 3
6:16:35.279706 INFO: ms1_error      : 5.0
6:16:35.288704 INFO: ms2_error      : 10.0
6:16:35.298704 INFO: fwhm_rt        : 2.405501365661621
6:16:35.304702 INFO: quant_window   : 3
6:16:35.313703 INFO: ==============================================
6:16:35.443231 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:16:35.444232 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:16:35.445230 INFO: FWHM in RT is 2.41 seconds, sigma is 0.27
6:16:35.446244 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:16:35.447231 INFO: Starting candidate selection
6:16:44.455751 INFO: Starting candidate scoring
6:16:53.622994 INFO: Finished candidate processing
6:16:53.624507 INFO: Collecting candidate features
6:16:55.000417 WARNING: intensity_correlation has 32 NaNs ( 0.01 % out of 329120)
6:16:55.004417 WARNING: height_correlation has 18 NaNs ( 0.01 % out of 329120)
6:16:55.107430 INFO: Collecting fragment features
6:16:55.666040 INFO: Finished candidate scoring
6:16:56.114172 INFO: performing precursor FDR with 47 features
6:16:56.115170 INFO: Decoy channel: -1
6:16:56.117169 INFO: Competetive: True
6:16:56.483775 INFO: Setting torch num_threads to 2 for FDR classification task
6:16:56.653315 WARNING: dropped 21 target PSMs due to missing features
6:16:56.655317 WARNING: dropped 18 decoy PSMs due to missing features
6:16:56.907841 INFO: Using random state 79930 for train-test-split
6:17:04.305726 INFO: Test AUC: 0.562
6:17:04.307725 INFO: Train AUC: 0.589
6:17:04.308723 INFO: AUC difference: 4.66%
6:17:05.314878 INFO: Resetting torch num_threads to 10
6:17:05.345871 PROGRESS: === Extracted 329120 precursors and 2415886 fragments ===
6:17:05.351870 INFO: === FDR correction performed with classifier version 6 ===
6:17:05.358867 PROGRESS: ============================= Precursor FDR =============================
6:17:05.362868 PROGRESS: Total precursors accumulated: 860
6:17:05.365868 PROGRESS: Target precursors: 782 (90.93%)
6:17:05.369871 PROGRESS: Decoy precursors: 78 (9.07%)
6:17:05.373873 PROGRESS: 
6:17:05.376873 PROGRESS: Precursor Summary:
6:17:05.384392 PROGRESS: Channel   0:	 0.050 FDR:   588; 0.010 FDR:   401; 0.001 FDR:   297
6:17:05.388391 PROGRESS: 
6:17:05.392391 PROGRESS: Protein Summary:
6:17:05.399392 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   370; 0.001 FDR:   275
6:17:05.403393 PROGRESS: =========================================================================
6:17:05.412398 INFO: Target number of precursors reached.
6:17:05.833944 INFO: fragments_df: keeping 5000 of 2415886 [sum(precursor_idx_mask)=10829 sum(mass_error_mask)=2415886 stop_rank=5000
6:17:06.495990 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:17:06.872526 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:17:07.251282 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:17:10.590310 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:17:10.595311 INFO: Using score_cutoff 55.6065043258667 (fac=0.99, q=1)
6:17:10.600310 INFO: Updating optimization_manager: fwhm_rt             : 2.405501365661621 -> 2.4362192153930664
6:17:10.604314 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:17:10.608310 INFO: Updating optimization_manager: score_cutoff        : 64.11491208572389 -> 55.6065043258667
6:17:10.611310 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:17:10.711494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:17:10.876495 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:17:11.296127 INFO: === checking if optimization conditions were reached ===
6:17:11.300126 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
6:17:11.308125 INFO: Updating optimization_manager: rt_error            : 106.21048433034709 -> 79.19914845401772
6:17:11.312125 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 79.1991.
6:17:11.316126 INFO: ==============================================
6:17:11.320127 INFO: Starting optimization step 3.
6:17:11.324125 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:17:11.327126 INFO: Using classic extraction backend
6:17:11.331125 PROGRESS: Extracting batch of 109921 precursors
6:17:11.335125 INFO: === Search parameters used ===
6:17:11.339125 INFO: rt_error       : 79.19914845401772
6:17:11.343126 INFO: mobility_error : 0.1
6:17:11.346126 INFO: num_candidates : 3
6:17:11.350127 INFO: ms1_error      : 5.0
6:17:11.354127 INFO: ms2_error      : 10.0
6:17:11.357127 INFO: fwhm_rt        : 2.4362192153930664
6:17:11.361127 INFO: quant_window   : 3
6:17:11.364128 INFO: ==============================================
6:17:11.473653 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:17:11.474651 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:17:11.475658 INFO: FWHM in RT is 2.44 seconds, sigma is 0.27
6:17:11.476653 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:17:11.477652 INFO: Starting candidate selection
6:17:19.183652 INFO: Starting candidate scoring
6:17:28.636743 INFO: Finished candidate processing
6:17:28.637754 INFO: Collecting candidate features
6:17:30.057768 WARNING: intensity_correlation has 30 NaNs ( 0.01 % out of 329079)
6:17:30.061769 WARNING: height_correlation has 17 NaNs ( 0.01 % out of 329079)
6:17:30.162785 INFO: Collecting fragment features
6:17:30.710417 INFO: Finished candidate scoring
6:17:31.128608 INFO: performing precursor FDR with 47 features
6:17:31.129606 INFO: Decoy channel: -1
6:17:31.130606 INFO: Competetive: True
6:17:31.479704 INFO: Setting torch num_threads to 2 for FDR classification task
6:17:31.653705 WARNING: dropped 18 target PSMs due to missing features
6:17:31.655706 WARNING: dropped 23 decoy PSMs due to missing features
6:17:31.973791 INFO: Using random state 79930 for train-test-split
6:17:39.800798 INFO: Test AUC: 0.565
6:17:39.801802 INFO: Train AUC: 0.589
6:17:39.802795 INFO: AUC difference: 4.03%
6:17:40.750942 INFO: Resetting torch num_threads to 10
6:17:40.779943 PROGRESS: === Extracted 329079 precursors and 2396493 fragments ===
6:17:40.784945 INFO: === FDR correction performed with classifier version 6 ===
6:17:40.791945 PROGRESS: ============================= Precursor FDR =============================
6:17:40.795943 PROGRESS: Total precursors accumulated: 1,001
6:17:40.799943 PROGRESS: Target precursors: 914 (91.31%)
6:17:40.803944 PROGRESS: Decoy precursors: 87 (8.69%)
6:17:40.807946 PROGRESS: 
6:17:40.810944 PROGRESS: Precursor Summary:
6:17:40.818945 PROGRESS: Channel   0:	 0.050 FDR:   650; 0.010 FDR:   415; 0.001 FDR:   324
6:17:40.822944 PROGRESS: 
6:17:40.825944 PROGRESS: Protein Summary:
6:17:40.833944 PROGRESS: Channel   0:	 0.050 FDR:   600; 0.010 FDR:   383; 0.001 FDR:   299
6:17:40.838943 PROGRESS: =========================================================================
6:17:40.846943 INFO: Target number of precursors reached.
6:17:41.269037 INFO: fragments_df: keeping 5000 of 2396493 [sum(precursor_idx_mask)=11170 sum(mass_error_mask)=2396493 stop_rank=5000
6:17:41.940146 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:17:42.288878 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:17:42.613426 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:17:45.968460 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:17:45.973461 INFO: Using score_cutoff 59.275918418884274 (fac=0.99, q=1)
6:17:45.978461 INFO: Updating optimization_manager: fwhm_rt             : 2.4362192153930664 -> 2.4350597858428955
6:17:45.982460 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:17:45.985462 INFO: Updating optimization_manager: score_cutoff        : 55.6065043258667 -> 59.275918418884274
6:17:45.989462 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:17:46.089461 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:17:46.255003 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:17:46.678401 INFO: === checking if optimization conditions were reached ===
6:17:46.683401 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
6:17:46.690413 INFO: Updating optimization_manager: rt_error            : 79.19914845401772 -> 77.44981927871177
6:17:46.694414 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 77.4498.
6:17:46.698414 INFO: ==============================================
6:17:46.701416 INFO: Starting optimization step 4.
6:17:46.705578 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:17:46.709578 INFO: Using classic extraction backend
6:17:46.713579 PROGRESS: Extracting batch of 109921 precursors
6:17:46.716578 INFO: === Search parameters used ===
6:17:46.720580 INFO: rt_error       : 77.44981927871177
6:17:46.723578 INFO: mobility_error : 0.1
6:17:46.727579 INFO: num_candidates : 3
6:17:46.731579 INFO: ms1_error      : 5.0
6:17:46.734579 INFO: ms2_error      : 10.0
6:17:46.738579 INFO: fwhm_rt        : 2.4350597858428955
6:17:46.741579 INFO: quant_window   : 3
6:17:46.748576 INFO: ==============================================
6:17:46.858582 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:17:46.860582 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:17:46.861582 INFO: FWHM in RT is 2.44 seconds, sigma is 0.27
6:17:46.861582 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:17:46.862581 INFO: Starting candidate selection
6:17:54.500274 INFO: Starting candidate scoring
6:18:04.042989 INFO: Finished candidate processing
6:18:04.044994 INFO: Collecting candidate features
6:18:05.165429 WARNING: intensity_correlation has 36 NaNs ( 0.01 % out of 329071)
6:18:05.169430 WARNING: height_correlation has 21 NaNs ( 0.01 % out of 329071)
6:18:05.255934 INFO: Collecting fragment features
6:18:05.740139 INFO: Finished candidate scoring
6:18:06.145756 INFO: performing precursor FDR with 47 features
6:18:06.146755 INFO: Decoy channel: -1
6:18:06.147759 INFO: Competetive: True
6:18:06.422365 INFO: Setting torch num_threads to 2 for FDR classification task
6:18:06.566974 WARNING: dropped 21 target PSMs due to missing features
6:18:06.567977 WARNING: dropped 27 decoy PSMs due to missing features
6:18:06.818508 INFO: Using random state 79930 for train-test-split
6:18:14.533017 INFO: Test AUC: 0.559
6:18:14.535016 INFO: Train AUC: 0.590
6:18:14.536017 INFO: AUC difference: 5.23%
6:18:14.537018 WARNING: AUC difference > 5%. This may indicate overfitting.
6:18:15.482637 INFO: Resetting torch num_threads to 10
6:18:15.511178 PROGRESS: === Extracted 329071 precursors and 2398313 fragments ===
6:18:15.517181 INFO: === FDR correction performed with classifier version 6 ===
6:18:15.525179 PROGRESS: ============================= Precursor FDR =============================
6:18:15.529179 PROGRESS: Total precursors accumulated: 1,007
6:18:15.534181 PROGRESS: Target precursors: 920 (91.36%)
6:18:15.538180 PROGRESS: Decoy precursors: 87 (8.64%)
6:18:15.541179 PROGRESS: 
6:18:15.545181 PROGRESS: Precursor Summary:
6:18:15.552180 PROGRESS: Channel   0:	 0.050 FDR:   631; 0.010 FDR:   410; 0.001 FDR:   226
6:18:15.556182 PROGRESS: 
6:18:15.560182 PROGRESS: Protein Summary:
6:18:15.569182 PROGRESS: Channel   0:	 0.050 FDR:   582; 0.010 FDR:   375; 0.001 FDR:   213
6:18:15.573181 PROGRESS: =========================================================================
6:18:15.582181 INFO: Target number of precursors reached.
6:18:16.004555 INFO: fragments_df: keeping 5000 of 2398313 [sum(precursor_idx_mask)=11033 sum(mass_error_mask)=2398313 stop_rank=5000
6:18:16.691154 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:18:18.849075 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:18:19.222630 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:18:22.731407 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:18:22.736407 INFO: Using score_cutoff 59.98935491867066 (fac=0.99, q=1)
6:18:22.740407 INFO: Updating optimization_manager: fwhm_rt             : 2.4350597858428955 -> 2.4744269847869873
6:18:22.744409 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:18:22.747408 INFO: Updating optimization_manager: score_cutoff        : 59.275918418884274 -> 59.98935491867066
6:18:22.751409 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:18:22.848952 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:18:23.010973 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:18:23.486018 INFO: === checking if optimization conditions were reached ===
6:18:23.490015 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
6:18:23.496016 INFO: Updating optimization_manager: rt_error            : 77.44981927871177 -> 77.44981927871177
6:18:23.500017 INFO: Updating optimization_manager: classifier_version  : 6 -> 11
6:18:23.504017 INFO: Updating optimization_manager: score_cutoff        : 59.98935491867066 -> 59.98935491867066
6:18:23.508036 INFO: Updating optimization_manager: fwhm_rt             : 2.4744269847869873 -> 2.4744269847869873
6:18:23.512035 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
6:18:23.516037 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 77.4498 found after 5 searches.
6:18:23.520033 INFO: ==============================================
6:18:23.524107 PROGRESS: Optimization finished for rt_error.
6:18:24.195201 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:18:24.295816 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:18:24.462815 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:18:24.931042 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:18:24.936043 PROGRESS: ==============================================
6:18:24.940041 PROGRESS: ms2_error      : 10.0000
6:18:24.944041 PROGRESS: ms1_error      : 5.0000
6:18:24.948042 PROGRESS: rt_error       : 77.4498
6:18:24.951042 PROGRESS: ==============================================
6:18:24.967042 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:18:28.620601 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:18:37.614415 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:19:18.985406 INFO: Using classic extraction backend
6:19:18.992405 PROGRESS: Extracting batch of 11035943 precursors
6:19:18.996407 INFO: === Search parameters used ===
6:19:19.000406 INFO: rt_error       : 77.44981927871177
6:19:19.004407 INFO: mobility_error : 0.1
6:19:19.008407 INFO: num_candidates : 3
6:19:19.012403 INFO: ms1_error      : 5.0
6:19:19.017406 INFO: ms2_error      : 10.0
6:19:19.026407 INFO: fwhm_rt        : 2.4744269847869873
6:19:19.035405 INFO: quant_window   : 3
6:19:19.044403 INFO: ==============================================
6:19:22.428384 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
6:19:22.430384 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:19:22.431384 INFO: FWHM in RT is 2.47 seconds, sigma is 0.28
6:19:22.431384 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:19:22.432393 INFO: Starting candidate selection
6:32:02.548683 INFO: Removed 20430255 precursors with score below cutoff 59.98935491867066
6:32:06.561008 INFO: Starting candidate scoring
6:39:09.188107 INFO: Finished candidate processing
6:39:09.190112 INFO: Collecting candidate features
6:39:53.995739 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 12665184)
6:39:55.936984 INFO: Collecting fragment features
6:40:17.285233 INFO: Finished candidate scoring
6:41:30.301152 INFO: === Performing FDR correction with classifier version 11 ===
6:41:30.309155 INFO: performing precursor FDR with 47 features
6:41:30.310153 INFO: Decoy channel: -1
6:41:30.310153 INFO: Competetive: True
6:41:38.127444 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:43.279732 WARNING: dropped 2 target PSMs due to missing features
6:41:43.280730 WARNING: dropped 2 decoy PSMs due to missing features
6:41:59.938533 INFO: Using random state 719961 for train-test-split
6:48:23.444327 INFO: Test AUC: 0.580
6:48:23.445329 INFO: Train AUC: 0.582
6:48:23.447329 INFO: AUC difference: 0.29%
6:48:31.998893 INFO: Resetting torch num_threads to 10
6:48:32.721555 INFO: Removing fragments below FDR threshold
6:48:36.531757 PROGRESS: ============================= Precursor FDR =============================
6:48:36.539757 PROGRESS: Total precursors accumulated: 43,716
6:48:36.544759 PROGRESS: Target precursors: 43,284 (99.01%)
6:48:36.550756 PROGRESS: Decoy precursors: 432 (0.99%)
6:48:36.558756 PROGRESS: 
6:48:36.569757 PROGRESS: Precursor Summary:
6:48:36.717280 PROGRESS: Channel   0:	 0.050 FDR: 43,284; 0.010 FDR: 43,284; 0.001 FDR: 30,335
6:48:36.725280 PROGRESS: 
6:48:36.732279 PROGRESS: Protein Summary:
6:48:36.914799 PROGRESS: Channel   0:	 0.050 FDR: 7,994; 0.010 FDR: 7,994; 0.001 FDR: 6,243
6:48:36.921809 PROGRESS: =========================================================================
6:48:37.566885 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\psm.parquet
6:48:38.595989 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\frag.parquet
6:48:39.719631 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
6:50:53.125345 PROGRESS: Processing search outputs
6:50:53.126344 PROGRESS: Performing protein grouping and FDR
6:50:53.127344 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
6:50:55.228433 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
6:50:55.653975 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
6:50:56.002131 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
6:50:56.298651 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
6:50:56.603177 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
6:50:56.923711 INFO: Building combined output
6:50:56.991245 INFO: Performing protein inference
6:50:57.713325 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
6:51:35.479912 INFO: Performing protein FDR
6:51:54.206228 INFO: Normalizing q-values using 10,904 targets and 1,891 decoys
6:51:54.213229 INFO: Test AUC: 0.869
6:51:54.214226 INFO: Train AUC: 0.874
6:51:54.215230 INFO: AUC difference: 0.60%
6:51:55.919907 PROGRESS: ================ Protein FDR =================
6:51:55.920908 PROGRESS: Unique protein groups in output
6:51:55.921906 PROGRESS:   1% protein FDR: 6,543
6:51:55.922909 PROGRESS: 
6:51:55.923908 PROGRESS: Unique precursor in output
6:51:55.924910 PROGRESS:   1% protein FDR: 61,104
6:51:55.925911 PROGRESS: ================================================
6:51:56.152431 PROGRESS: Building search statistics
6:51:56.511958 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\optimization_manager.pkl
6:51:56.573966 INFO: Initializing OptimizationManager
6:51:56.623552 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\calibration_manager.pkl
6:51:56.627551 INFO: Initializing CalibrationManager
6:51:56.685554 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\raw_file_manager.pkl
6:51:56.690552 INFO: Initializing RawFileManager
6:51:56.830555 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\optimization_manager.pkl
6:51:56.844571 INFO: Initializing OptimizationManager
6:51:56.914094 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\calibration_manager.pkl
6:51:56.922093 INFO: Initializing CalibrationManager
6:51:56.979093 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\raw_file_manager.pkl
6:51:56.987092 INFO: Initializing RawFileManager
6:51:57.132706 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\optimization_manager.pkl
6:51:57.147707 INFO: Initializing OptimizationManager
6:51:57.205705 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\calibration_manager.pkl
6:51:57.212702 INFO: Initializing CalibrationManager
6:51:57.276702 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\raw_file_manager.pkl
6:51:57.284701 INFO: Initializing RawFileManager
6:51:57.458219 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\optimization_manager.pkl
6:51:57.476221 INFO: Initializing OptimizationManager
6:51:57.513218 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\calibration_manager.pkl
6:51:57.519221 INFO: Initializing CalibrationManager
6:51:57.561220 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\raw_file_manager.pkl
6:51:57.565221 INFO: Initializing RawFileManager
6:51:57.699746 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\optimization_manager.pkl
6:51:57.704746 INFO: Initializing OptimizationManager
6:51:57.736747 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\calibration_manager.pkl
6:51:57.740745 INFO: Initializing CalibrationManager
6:51:57.772749 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\raw_file_manager.pkl
6:51:57.781745 INFO: Initializing RawFileManager
6:51:57.918355 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\optimization_manager.pkl
6:51:57.923354 INFO: Initializing OptimizationManager
6:51:57.956351 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\calibration_manager.pkl
6:51:57.961351 INFO: Initializing CalibrationManager
6:51:58.006352 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\raw_file_manager.pkl
6:51:58.010352 INFO: Initializing RawFileManager
6:51:58.053358 INFO: Writing stat output to disk
6:51:58.054359 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\stat.tsv to disk
6:51:58.091374 PROGRESS: Building internal statistics
6:51:58.123967 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\timing_manager.pkl
6:51:58.124965 INFO: Initializing TimingManager
6:51:58.186963 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\timing_manager.pkl
6:51:58.187963 INFO: Initializing TimingManager
6:51:58.214962 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\timing_manager.pkl
6:51:58.215962 INFO: Initializing TimingManager
6:51:58.243963 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\timing_manager.pkl
6:51:58.244964 INFO: Initializing TimingManager
6:51:58.269967 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\timing_manager.pkl
6:51:58.270967 INFO: Initializing TimingManager
6:51:58.293962 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\timing_manager.pkl
6:51:58.295963 INFO: Initializing TimingManager
6:51:58.297963 INFO: Writing internal output to disk
6:51:58.298963 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\internal.tsv to disk
6:51:58.305962 PROGRESS: Performing label free quantification
6:51:58.535488 INFO: Accumulating fragment data
6:51:58.538487 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
6:51:59.338067 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
6:52:01.459767 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
6:52:03.562101 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
6:52:05.654202 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
6:52:07.717713 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
6:52:10.468603 PROGRESS: Performing label free quantification on the precursor level
6:52:10.469603 INFO: Filtering fragments by quality
6:52:11.129862 INFO: Performing label-free quantification using directLFQ
6:52:11.895073 INFO: 61104 lfq-groups total
6:52:37.271158 INFO: using 10 processes
6:54:07.402861 INFO: Writing precursor output to disk
6:54:07.403860 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\precursor.matrix.tsv to disk
6:54:08.846532 PROGRESS: Performing label free quantification on the peptide level
6:54:08.847529 INFO: Filtering fragments by quality
6:54:09.663744 INFO: Performing label-free quantification using directLFQ
6:54:10.368913 INFO: 53328 lfq-groups total
6:54:33.133610 INFO: using 10 processes
6:55:53.593906 INFO: Writing peptide output to disk
6:55:53.594904 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\peptide.matrix.tsv to disk
6:55:54.976061 PROGRESS: Performing label free quantification on the pg level
6:55:54.977060 INFO: Filtering fragments by quality
6:55:55.684854 INFO: Performing label-free quantification using directLFQ
6:55:56.182890 INFO: 6543 lfq-groups total
6:55:59.156480 INFO: using 10 processes
6:56:28.875317 INFO: Writing pg output to disk
6:56:28.877317 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\pg.matrix.tsv to disk
6:56:29.401546 INFO: Writing psm output to disk
6:56:29.402546 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\precursors.tsv to disk
6:57:32.924194 PROGRESS: Building MBR spectral library
6:57:33.125733 INFO: Running MbrLibraryBuilder
6:57:35.810586 INFO: MBR spectral library contains 61,104 precursors, 6,543 proteins
6:57:35.812587 INFO: Writing MBR spectral library to disk
6:57:56.224803 PROGRESS: =================== Search Finished ===================
6:57:57.859962 INFO: Running step 'mbr'
6:57:57.906495 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 5.0, 'target_ms2_tolerance': 10.0}})
6:57:57.913511 INFO: loading default config from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\default.yaml
6:57:57.996509 INFO: loading additional config provided via CLI
6:57:57.997507 INFO: loading additional config provided via CLI parameters
6:57:58.000506 INFO: Updating config with 'user defined'
6:57:58.001506 INFO: Updating config with 'user defined (cli)'
6:57:58.002507 INFO: updating config with user defined values: [{'workflow_name': 'PeptideCentric.v1', 'fasta_paths': ['Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\FASTA\\uniprotkb_proteome_HYE_UniversalContaminants.fasta'], 'raw_paths': ['D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff'], 'output_directory': 'Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\DATA_ANALYSIS\\AlphaDIA', 'general': {'thread_count': 10, 'transfer_step_enabled': False, 'mbr_step_enabled': True, 'reuse_quant': False, 'reuse_calibration': False, 'use_gpu': True, 'log_level': 'INFO'}, 'search': {'target_ms1_tolerance': 5, 'target_ms2_tolerance': 10, 'target_mobility_tolerance': 0, 'target_rt_tolerance': 0, 'channel_filter': '', 'exclude_shared_ions': True, 'compete_for_fragments': True, 'target_num_candidates': 3, 'quant_window': 3, 'quant_all': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [395, 905], 'fragment_mz': [140, 1750], 'nce': 25, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'SciexTOF', 'peptdeep_model_path': None, 'peptdeep_model_type': 'generic'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'channel_wise_fdr': False, 'keep_decoys': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': False}, 'search_initial': {'initial_ms1_tolerance': 30, 'initial_ms2_tolerance': 30, 'initial_mobility_tolerance': 0.1, 'initial_rt_tolerance': 0.5}, 'multiplexing': {'enabled': False, 'target_channels': '4,8', 'decoy_channel': 12, 'reference_channel': 0, 'competetive_scoring': True}, 'search_output': {'file_format': 'tsv', 'peptide_level_lfq': True, 'precursor_level_lfq': True, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3, 'normalize_lfq': False}, 'transfer_library': {'enabled': False, 'fragment_types': ['b', 'y'], 'max_charge': 2, 'top_k_samples': 3, 'norm_delta_max': True, 'precursor_correlation_cutoff': 0.5, 'fragment_correlation_ratio': 0.75}, 'transfer_learning': {'enabled': False, 'batch_size': 2000, 'max_lr': 0.0001, 'train_fraction': 0.7, 'validation_fraction': 0.2, 'test_fraction': 0.1, 'test_interval': 1, 'lr_patience': 3, 'epochs': 51, 'warmup_epochs': 5, 'nce': 25, 'instrument': 'Lumos'}}, {'raw_paths': ['D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff', 'D:\\LFQ\\8600_Nano_Data\\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 5.0, 'target_ms2_tolerance': 10.0}, 'quant_directory': None, 'general': {'reuse_quant': False}, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': 'Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\DATA_ANALYSIS\\AlphaDIA\\library\\speclib.mbr.hdf', 'output_directory': 'Q:\\ACTIVE\\2024\\LFQbenchmark_2ndgeneration\\DATA_ANALYSIS\\AlphaDIA'}]
6:57:58.004506 INFO: Updating config with 'user defined'
6:57:58.005506 INFO: Updating config with 'user defined (cli)'
6:57:58.005506 INFO: Updating config with 'multistep search'
6:57:58.006507 INFO: ├──version: 1
6:57:58.007507 INFO: [32;20m├──workflow_name: PeptideCentric.v1 [user defined, default: None][0m
6:57:58.008508 INFO: [32;20m├──output_directory: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA [multistep search, default: None][0m
6:57:58.009507 INFO: [32;20m├──library_path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\speclib.mbr.hdf [multistep search, default: None][0m
6:57:58.010508 INFO: ├──raw_paths:
6:57:58.010508 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff [user defined (cli), default: None][0m
6:57:58.011507 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff [user defined (cli), default: None][0m
6:57:58.012506 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff [user defined (cli), default: None][0m
6:57:58.013508 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff [user defined (cli), default: None][0m
6:57:58.013508 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff [user defined (cli), default: None][0m
6:57:58.014506 INFO: │   [32;20m- D:\LFQ\8600_Nano_Data\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff [user defined (cli), default: None][0m
6:57:58.015508 INFO: ├──fasta_paths:
6:57:58.016507 INFO: ├──quant_directory: None
6:57:58.017507 INFO: ├──general
6:57:58.017507 INFO: │   ├──thread_count: 10
6:57:58.018508 INFO: │   ├──transfer_step_enabled: False
6:57:58.019508 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
6:57:58.020507 INFO: │   ├──reuse_calibration: False
6:57:58.020507 INFO: │   ├──reuse_quant: False
6:57:58.021507 INFO: │   ├──astral_ms1: False
6:57:58.022508 INFO: │   ├──log_level: INFO
6:57:58.023508 INFO: │   ├──mmap_detector_events: False
6:57:58.024507 INFO: │   ├──use_gpu: True
6:57:58.026506 INFO: │   ├──save_figures: True
6:57:58.027507 INFO: │   ├──save_library: True
6:57:58.028508 INFO: │   ├──save_flat_library: False
6:57:58.029507 INFO: │   ├──input_library_type: base
6:57:58.030507 INFO: │   ├──save_mbr_library: True
6:57:58.031507 INFO: │   └──random_state: None
6:57:58.032507 INFO: ├──library_loading
6:57:58.033507 INFO: │   └──rt_heuristic: 180
6:57:58.034507 INFO: ├──library_prediction
6:57:58.035507 INFO: │   ├──enabled: False
6:57:58.036507 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
6:57:58.037507 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
6:57:58.038508 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
6:57:58.039507 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
6:57:58.040508 INFO: │   ├──missed_cleavages: 1
6:57:58.041507 INFO: │   ├──precursor_len:
6:57:58.041507 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
6:57:58.042508 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
6:57:58.043508 INFO: │   ├──precursor_charge:
6:57:58.043508 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
6:57:58.044507 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
6:57:58.045507 INFO: │   ├──precursor_mz:
6:57:58.046508 INFO: │   │   [32;20m- 395 [user defined, default: 400][0m
6:57:58.046508 INFO: │   │   [32;20m- 905 [user defined, default: 1200][0m
6:57:58.047507 INFO: │   ├──fragment_mz:
6:57:58.048508 INFO: │   │   [32;20m- 140 [user defined, default: 200][0m
6:57:58.049507 INFO: │   │   [32;20m- 1750 [user defined, default: 2000][0m
6:57:58.049507 INFO: │   ├──nce: 25
6:57:58.050509 INFO: │   ├──fragment_types:
6:57:58.051509 INFO: │   │   - b
6:57:58.051509 INFO: │   │   - y
6:57:58.052510 INFO: │   ├──max_fragment_charge: 2
6:57:58.053509 INFO: │   [32;20m├──instrument: SciexTOF [user defined, default: Lumos][0m
6:57:58.054507 INFO: │   ├──peptdeep_model_path: None
6:57:58.054507 INFO: │   └──peptdeep_model_type: generic
6:57:58.055509 INFO: ├──custom_modifications:
6:57:58.056509 INFO: │   ├──name: Dimethyl:d12@K
6:57:58.056509 INFO: │   └──composition: H(-2)2H(8)13C(2)
6:57:58.057508 INFO: │   ├──name: Dimethyl:d12@Any_N-term
6:57:58.058509 INFO: │   └──composition: H(-2)2H(8)13C(2)
6:57:58.059508 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
6:57:58.059508 INFO: │   └──composition: H(-2)2H(8)13C(2)
6:57:58.060508 INFO: │   ├──name: mTRAQ:d12@K
6:57:58.061507 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
6:57:58.062510 INFO: │   ├──name: mTRAQ:d12@Any_N-term
6:57:58.062510 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
6:57:58.063508 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
6:57:58.064508 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
6:57:58.064508 INFO: │   ├──name: Label:13C(12)@K
6:57:58.065510 INFO: │   └──composition: C(12)
6:57:58.066507 INFO: ├──search
6:57:58.066507 INFO: │   ├──extraction_backend: classic
6:57:58.067508 INFO: │   ├──target_ms1_tolerance: 5.0
6:57:58.068508 INFO: │   ├──target_ms2_tolerance: 10.0
6:57:58.069509 INFO: │   ├──target_rt_tolerance: 0
6:57:58.069509 INFO: │   ├──target_mobility_tolerance: 0
6:57:58.070509 INFO: │   ├──quant_window: 3
6:57:58.071509 INFO: │   ├──target_num_candidates: 3
6:57:58.072509 INFO: │   ├──channel_filter: 
6:57:58.073509 INFO: │   ├──exclude_shared_ions: True
6:57:58.074508 INFO: │   ├──compete_for_fragments: True
6:57:58.075508 INFO: │   ├──quant_all: True
6:57:58.076509 INFO: │   ├──top_k_fragments_selection: 12
6:57:58.077508 INFO: │   ├──top_k_fragments_scoring: 12
6:57:58.078510 INFO: │   ├──min_fragment_intensity: 0.01
6:57:58.079509 INFO: │   ├──experimental_xic: True
6:57:58.080508 INFO: │   └──optimized_peak_group_score: False
6:57:58.081509 INFO: ├──calibration
6:57:58.082509 INFO: │   ├──batch_size: 8000
6:57:58.083508 INFO: │   ├──optimization_lock_target: 200
6:57:58.084508 INFO: │   ├──max_steps: 20
6:57:58.085509 INFO: │   ├──min_steps: 2
6:57:58.086508 INFO: │   ├──max_skips: 1
6:57:58.087508 INFO: │   ├──max_fragments: 5000
6:57:58.087508 INFO: │   └──min_correlation: 0.7
6:57:58.088508 INFO: ├──search_initial
6:57:58.089510 INFO: │   ├──initial_num_candidates: 1
6:57:58.090511 INFO: │   ├──initial_ms1_tolerance: 30
6:57:58.091510 INFO: │   ├──initial_ms2_tolerance: 30
6:57:58.092511 INFO: │   ├──initial_mobility_tolerance: 0.1
6:57:58.093510 INFO: │   └──initial_rt_tolerance: 0.5
6:57:58.094510 INFO: ├──selection_config
6:57:58.095509 INFO: │   ├──peak_len_rt: 10.0
6:57:58.096511 INFO: │   ├──sigma_scale_rt: 0.5
6:57:58.097511 INFO: │   ├──peak_len_mobility: 0.01
6:57:58.098510 INFO: │   ├──sigma_scale_mobility: 1.0
6:57:58.099513 INFO: │   ├──top_k_precursors: 3
6:57:58.100513 INFO: │   ├──kernel_size: 30
6:57:58.101511 INFO: │   ├──f_mobility: 1.0
6:57:58.102513 INFO: │   ├──f_rt: 0.99
6:57:58.103513 INFO: │   ├──center_fraction: 0.5
6:57:58.104513 INFO: │   ├──min_size_mobility: 8
6:57:58.105511 INFO: │   ├──min_size_rt: 3
6:57:58.106513 INFO: │   ├──max_size_mobility: 20
6:57:58.107514 INFO: │   ├──max_size_rt: 15
6:57:58.108513 INFO: │   ├──group_channels: False
6:57:58.109512 INFO: │   ├──use_weighted_score: True
6:57:58.110517 INFO: │   ├──join_close_candidates: False
6:57:58.111515 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
6:57:58.112515 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
6:57:58.113515 INFO: ├──scoring_config
6:57:58.114515 INFO: │   ├──score_grouped: False
6:57:58.114515 INFO: │   ├──top_k_isotopes: 3
6:57:58.115513 INFO: │   ├──reference_channel: -1
6:57:58.116514 INFO: │   ├──precursor_mz_tolerance: 10
6:57:58.117515 INFO: │   └──fragment_mz_tolerance: 15
6:57:58.118510 INFO: ├──library_multiplexing
6:57:58.119511 INFO: │   ├──enabled: False
6:57:58.120510 INFO: │   ├──input_channel: 0
6:57:58.121514 INFO: │   └──multiplex_mapping:
6:57:58.122517 INFO: ├──multiplexing
6:57:58.123514 INFO: │   ├──enabled: False
6:57:58.124512 INFO: │   ├──target_channels: 4,8
6:57:58.125514 INFO: │   ├──decoy_channel: 12
6:57:58.126514 INFO: │   ├──reference_channel: 0
6:57:58.127511 INFO: │   └──competetive_scoring: True
6:57:58.128515 INFO: ├──fdr
6:57:58.128515 INFO: │   ├──fdr: 0.01
6:57:58.129514 INFO: │   ├──group_level: proteins
6:57:58.130514 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
6:57:58.131514 INFO: │   ├──competetive_scoring: True
6:57:58.132512 INFO: │   ├──keep_decoys: False
6:57:58.133511 INFO: │   ├──channel_wise_fdr: False
6:57:58.134513 INFO: │   ├──enable_two_step_classifier: False
6:57:58.135516 INFO: │   ├──two_step_classifier_max_iterations: 5
6:57:58.136516 INFO: │   └──enable_nn_hyperparameter_tuning: False
6:57:58.137513 INFO: ├──search_output
6:57:58.138520 INFO: │   ├──file_format: tsv
6:57:58.139525 INFO: │   [32;20m├──peptide_level_lfq: True [user defined, default: False][0m
6:57:58.140515 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
6:57:58.141514 INFO: │   ├──save_fragment_quant_matrix: False
6:57:58.142528 INFO: │   ├──min_k_fragments: 12
6:57:58.143527 INFO: │   ├──min_correlation: 0.9
6:57:58.144527 INFO: │   ├──num_samples_quadratic: 50
6:57:58.145528 INFO: │   ├──min_nonnan: 3
6:57:58.147527 INFO: │   [32;20m└──normalize_lfq: False [user defined, default: True][0m
6:57:58.148526 INFO: ├──optimization
6:57:58.149532 INFO: │   ├──order_of_optimization: None
6:57:58.150533 INFO: │   ├──ms2_error
6:57:58.151527 INFO: │   │   ├──targeted_update_percentile_range: 0.95
6:57:58.152529 INFO: │   │   ├──targeted_update_factor: 1.0
6:57:58.153530 INFO: │   │   ├──automatic_update_percentile_range: 0.99
6:57:58.154531 INFO: │   │   ├──automatic_update_factor: 1.1
6:57:58.155531 INFO: │   │   ├──try_narrower_values: True
6:57:58.155531 INFO: │   │   ├──maximal_decrease: 0.5
6:57:58.158064 INFO: │   │   ├──favour_narrower_optimum: False
6:57:58.159064 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
6:57:58.160064 INFO: │   ├──ms1_error
6:57:58.161063 INFO: │   │   ├──targeted_update_percentile_range: 0.95
6:57:58.162063 INFO: │   │   ├──targeted_update_factor: 1.0
6:57:58.162063 INFO: │   │   ├──automatic_update_percentile_range: 0.99
6:57:58.163064 INFO: │   │   ├──automatic_update_factor: 1.1
6:57:58.164063 INFO: │   │   ├──try_narrower_values: False
6:57:58.165066 INFO: │   │   ├──maximal_decrease: 0.2
6:57:58.166063 INFO: │   │   ├──favour_narrower_optimum: False
6:57:58.167064 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
6:57:58.168064 INFO: │   ├──mobility_error
6:57:58.169069 INFO: │   │   ├──targeted_update_percentile_range: 0.95
6:57:58.170063 INFO: │   │   ├──targeted_update_factor: 1.0
6:57:58.171067 INFO: │   │   ├──automatic_update_percentile_range: 0.99
6:57:58.172064 INFO: │   │   ├──automatic_update_factor: 1.1
6:57:58.173064 INFO: │   │   ├──try_narrower_values: False
6:57:58.174062 INFO: │   │   ├──maximal_decrease: 0.2
6:57:58.175065 INFO: │   │   ├──favour_narrower_optimum: False
6:57:58.176064 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
6:57:58.177062 INFO: │   └──rt_error
6:57:58.177062 INFO: │       ├──targeted_update_percentile_range: 0.95
6:57:58.178063 INFO: │       ├──targeted_update_factor: 1.0
6:57:58.179062 INFO: │       ├──automatic_update_percentile_range: 0.99
6:57:58.180062 INFO: │       ├──automatic_update_factor: 1.1
6:57:58.181062 INFO: │       ├──try_narrower_values: True
6:57:58.182062 INFO: │       ├──maximal_decrease: 0.2
6:57:58.183064 INFO: │       ├──favour_narrower_optimum: True
6:57:58.184063 INFO: │       └──maximum_decrease_from_maximum: 0.1
6:57:58.185059 INFO: ├──optimization_manager
6:57:58.186061 INFO: │   ├──fwhm_rt: 5
6:57:58.187061 INFO: │   ├──fwhm_mobility: 0.01
6:57:58.188061 INFO: │   └──score_cutoff: 0
6:57:58.189060 INFO: ├──transfer_library
6:57:58.190060 INFO: │   ├──enabled: False
6:57:58.191061 INFO: │   ├──fragment_types:
6:57:58.192062 INFO: │   │   - b
6:57:58.193061 INFO: │   │   - y
6:57:58.194062 INFO: │   ├──max_charge: 2
6:57:58.195061 INFO: │   ├──top_k_samples: 3
6:57:58.196062 INFO: │   ├──norm_delta_max: True
6:57:58.197062 INFO: │   ├──precursor_correlation_cutoff: 0.5
6:57:58.198062 INFO: │   └──fragment_correlation_ratio: 0.75
6:57:58.199064 INFO: └──transfer_learning
6:57:58.200062 INFO:     ├──enabled: False
6:57:58.200062 INFO:     ├──batch_size: 2000
6:57:58.201063 INFO:     ├──max_lr: 0.0001
6:57:58.202063 INFO:     ├──train_fraction: 0.7
6:57:58.203063 INFO:     ├──validation_fraction: 0.2
6:57:58.203063 INFO:     ├──test_fraction: 0.1
6:57:58.204061 INFO:     ├──test_interval: 1
6:57:58.205061 INFO:     ├──lr_patience: 3
6:57:58.206063 INFO:     ├──epochs: 51
6:57:58.206063 INFO:     ├──warmup_epochs: 5
6:57:58.207062 INFO:     ├──nce: 25
6:57:58.208064 INFO:     └──instrument: Lumos
6:57:58.284064 INFO: Moved existing config file Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\frozen_config.yaml to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\frozen_config.0.bkp.yaml
6:57:58.286064 INFO: Registering 7 custom modifications
6:57:58.323063 INFO: Searching 6 files:
6:57:58.324061 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3.wiff
6:57:58.325061 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2.wiff
6:57:58.325061 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1.wiff
6:57:58.327060 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3.wiff
6:57:58.328060 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2.wiff
6:57:58.329060 INFO:   LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1.wiff
6:57:58.330060 INFO: Using 0 fasta files:
6:57:58.331060 INFO: Using library: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\speclib.mbr.hdf
6:57:58.332061 INFO: Saving output to: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA
6:57:58.333061 PROGRESS: Loading spectral library
6:57:58.334061 PROGRESS: Loading library (type: base) from disk..
6:57:58.335061 INFO: Running DynamicLoader
6:57:58.337061 INFO: Loading .hdf library from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\library\speclib.mbr.hdf
6:58:01.157903 INFO: Running PrecursorInitializer
6:58:01.158903 INFO: Running AnnotateFasta
6:58:01.160905 INFO: Dropping decoys from input library before annotation
6:58:01.214498 INFO: Running IsotopeGenerator
6:58:01.215497 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
6:58:01.216498 INFO: Running RTNormalization
6:58:01.247499 INFO: Saving library to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\speclib.hdf
6:58:20.619907 INFO: Running DecoyGenerator
6:58:34.469640 INFO: Running FlattenLibrary
6:58:36.342349 INFO: Running InitFlatColumns
6:58:36.402348 INFO: Running LogFlatLibraryStats
6:58:36.403348 INFO: ============ Library Stats ============
6:58:36.404347 INFO: Number of precursors: 122,195
6:58:36.585961 INFO: 	thereof targets:61,104
6:58:36.587963 INFO: 	thereof decoys: 61,091
6:58:36.601962 INFO: Number of elution groups: 61,104
6:58:36.603961 INFO: 	average size: 2.00
6:58:36.636962 INFO: Number of proteins: 6,543
6:58:36.639964 INFO: Number of channels: 1 ([0])
6:58:36.640966 INFO: Isotopes Distribution for 4 isotopes
6:58:36.641963 INFO: =======================================
6:58:36.645965 PROGRESS: Starting Search Workflows
6:58:36.646965 PROGRESS: 
6:58:36.647964 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant
6:58:36.649961 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\figures
6:58:36.657959 INFO: Initializing TimingManager
6:58:36.672962 INFO: Initializing RawFileManager
7:04:05.111403 INFO: Determining DIA cycle
7:04:05.137400 INFO: Found cycle with start 0.00 min and length 86.
7:04:05.795092 INFO: RT (min)            : 0.0 - 55.4
7:04:05.796095 INFO: RT duration (sec)   : 3325.6
7:04:05.796095 INFO: RT duration (min)   : 55.4
7:04:05.797092 INFO: Cycle len (scans)   : 86
7:04:05.798093 INFO: Cycle len (sec)     : 1.90
7:04:05.799095 INFO: Number of cycles    : 1747
7:04:05.800092 INFO: MS2 range (m/z)     : 399.5 - 903.5
7:04:05.800092 INFO: Creating DIA data object took: 329.1211314201355
7:04:05.887093 INFO: Initializing CalibrationManager
7:04:05.901093 INFO: Setting up calibration estimators ..
7:04:05.908099 INFO: Found 1 estimator(s) in calibration group 'fragment'
7:04:05.914092 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'}' ..
7:04:05.922093 INFO: Found 3 estimator(s) in calibration group 'precursor'
7:04:05.928091 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
7:04:05.937093 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}}' ..
7:04:05.941094 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
7:04:05.948095 INFO: Done setting up calibration estimators.
7:04:05.955095 INFO: Initializing OptimizationManager
7:04:05.970095 INFO: initial parameter: ms1_error = 30
7:04:05.977096 INFO: initial parameter: ms2_error = 30
7:04:05.985096 INFO: initial parameter: rt_error = 1662.8485107421875
7:04:05.990092 INFO: initial parameter: mobility_error = 0.1
7:04:05.996096 INFO: initial parameter: num_candidates = 1
7:04:06.001092 INFO: initial parameter: fwhm_rt = 5
7:04:06.006092 INFO: initial parameter: fwhm_mobility = 0.01
7:04:06.010092 INFO: initial parameter: score_cutoff = 0
7:04:06.016090 INFO: initial parameter: classifier_version = -1
7:04:06.026089 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
7:04:06.036093 INFO: FDRManager: loading saved state not requested, will be initialized.
7:04:06.037093 INFO: Initializing FDRManager
7:04:06.038093 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
7:04:06.159604 PROGRESS: Initializing spectral library: 61,104 target precursors potentially observable (0 removed)
7:04:06.275604 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
7:04:06.280607 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 1662.8485107421875
7:04:06.286608 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
7:04:06.291609 PROGRESS: Starting initial search for precursors.
7:04:06.301121 INFO: Starting optimization step 0.
7:04:06.306119 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:04:06.312119 INFO: Using classic extraction backend
7:04:06.320119 PROGRESS: Extracting batch of 15870 precursors
7:04:06.326119 INFO: === Search parameters used ===
7:04:06.332120 INFO: rt_error       : 1662.8485107421875
7:04:06.339120 INFO: mobility_error : 0.1
7:04:06.345119 INFO: num_candidates : 1
7:04:06.355121 INFO: ms1_error      : 30
7:04:06.364121 INFO: ms2_error      : 30
7:04:06.370122 INFO: fwhm_rt        : 5
7:04:06.378121 INFO: quant_window   : 3
7:04:06.386122 INFO: ==============================================
7:04:06.437124 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:04:06.437124 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:04:06.439124 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
7:04:06.440126 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
7:04:06.442128 INFO: Starting candidate selection
7:04:20.615372 INFO: Starting candidate scoring
7:04:21.221741 INFO: Finished candidate processing
7:04:21.223275 INFO: Collecting candidate features
7:04:21.320787 INFO: Collecting fragment features
7:04:21.413786 INFO: Finished candidate scoring
7:04:21.440789 INFO: performing precursor FDR with 47 features
7:04:21.441789 INFO: Decoy channel: -1
7:04:21.443791 INFO: Competetive: True
7:04:21.471793 INFO: Setting torch num_threads to 2 for FDR classification task
7:04:21.497795 INFO: Using random state 254865 for train-test-split
7:04:21.801884 INFO: Test AUC: 0.795
7:04:21.803885 INFO: Train AUC: 0.791
7:04:21.804885 INFO: AUC difference: 0.41%
7:04:22.298026 INFO: Resetting torch num_threads to 10
7:04:22.305038 PROGRESS: === Extracted 15870 precursors and 162009 fragments ===
7:04:22.311041 INFO: === FDR correction performed with classifier version -1 ===
7:04:22.321567 PROGRESS: ============================= Precursor FDR =============================
7:04:22.325567 PROGRESS: Total precursors accumulated: 3,852
7:04:22.328568 PROGRESS: Target precursors: 3,658 (94.96%)
7:04:22.332568 PROGRESS: Decoy precursors: 194 (5.04%)
7:04:22.336566 PROGRESS: 
7:04:22.344567 PROGRESS: Precursor Summary:
7:04:22.357568 PROGRESS: Channel   0:	 0.050 FDR: 3,550; 0.010 FDR:   827; 0.001 FDR:    20
7:04:22.361569 PROGRESS: 
7:04:22.365567 PROGRESS: Protein Summary:
7:04:22.377567 PROGRESS: Channel   0:	 0.050 FDR: 2,111; 0.010 FDR:   688; 0.001 FDR:    20
7:04:22.380566 PROGRESS: =========================================================================
7:04:22.385566 INFO: Target number of precursors reached.
7:04:22.423568 INFO: fragments_df: keeping 5000 of 162009 [sum(precursor_idx_mask)=9663 sum(mass_error_mask)=162009 stop_rank=5000
7:04:22.494567 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:04:22.911723 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:04:23.289330 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:04:26.240307 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
7:04:26.247308 INFO: Using score_cutoff 78.57672599487304 (fac=0.99, q=1)
7:04:26.251308 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.956484317779541
7:04:26.255310 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
7:04:26.259312 INFO: Updating optimization_manager: score_cutoff        : 0 -> 78.57672599487304
7:04:26.263310 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:04:26.279308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:04:26.322314 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:04:26.392831 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
7:04:26.401833 PROGRESS: Required number of precursors found. Starting search parameter optimization.
7:04:26.411833 INFO: Starting optimization step 1.
7:04:26.419832 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:04:26.427833 INFO: Using classic extraction backend
7:04:26.435833 PROGRESS: Extracting batch of 15870 precursors
7:04:26.442833 INFO: === Search parameters used ===
7:04:26.453832 INFO: rt_error       : 1662.8485107421875
7:04:26.463833 INFO: mobility_error : 0.1
7:04:26.470834 INFO: num_candidates : 3
7:04:26.479833 INFO: ms1_error      : 30
7:04:26.488835 INFO: ms2_error      : 30
7:04:26.498837 INFO: fwhm_rt        : 2.956484317779541
7:04:26.505840 INFO: quant_window   : 3
7:04:26.517837 INFO: ==============================================
7:04:26.572840 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:04:26.573840 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:04:26.576352 INFO: FWHM in RT is 2.96 seconds, sigma is 0.33
7:04:26.577353 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:04:26.579352 INFO: Starting candidate selection
7:04:42.640248 INFO: Starting candidate scoring
7:04:44.086319 INFO: Finished candidate processing
7:04:44.088333 INFO: Collecting candidate features
7:04:44.360370 INFO: Collecting fragment features
7:04:44.496379 INFO: Finished candidate scoring
7:04:44.543379 INFO: performing precursor FDR with 47 features
7:04:44.545380 INFO: Decoy channel: -1
7:04:44.546381 INFO: Competetive: True
7:04:44.610926 INFO: Setting torch num_threads to 2 for FDR classification task
7:04:44.659924 INFO: Using random state 72635 for train-test-split
7:04:45.882333 INFO: Test AUC: 0.698
7:04:45.883328 INFO: Train AUC: 0.694
7:04:45.884329 INFO: AUC difference: 0.62%
7:04:46.528515 INFO: Resetting torch num_threads to 10
7:04:46.544516 PROGRESS: === Extracted 47607 precursors and 460044 fragments ===
7:04:46.550513 INFO: === FDR correction performed with classifier version 0 ===
7:04:46.565513 PROGRESS: ============================= Precursor FDR =============================
7:04:46.570514 PROGRESS: Total precursors accumulated: 6,385
7:04:46.574513 PROGRESS: Target precursors: 6,205 (97.18%)
7:04:46.577513 PROGRESS: Decoy precursors: 180 (2.82%)
7:04:46.581514 PROGRESS: 
7:04:46.585515 PROGRESS: Precursor Summary:
7:04:46.616063 PROGRESS: Channel   0:	 0.050 FDR: 6,205; 0.010 FDR: 5,372; 0.001 FDR: 3,360
7:04:46.621061 PROGRESS: 
7:04:46.625061 PROGRESS: Protein Summary:
7:04:46.654061 PROGRESS: Channel   0:	 0.050 FDR: 3,123; 0.010 FDR: 2,799; 0.001 FDR: 1,995
7:04:46.663062 PROGRESS: =========================================================================
7:04:46.679063 INFO: Target number of precursors reached.
7:04:46.981617 INFO: fragments_df: keeping 5000 of 460044 [sum(precursor_idx_mask)=162261 sum(mass_error_mask)=460044 stop_rank=5000
7:04:47.114249 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:04:50.449760 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:04:53.983536 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:04:56.958534 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:04:56.966535 INFO: Using score_cutoff 74.92121557388306 (fac=0.99, q=1)
7:04:56.972537 INFO: Updating optimization_manager: fwhm_rt             : 2.956484317779541 -> 2.691636085510254
7:04:56.979538 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:04:56.986538 INFO: Updating optimization_manager: score_cutoff        : 78.57672599487304 -> 74.92121557388306
7:04:56.993539 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:04:57.011542 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:04:57.054541 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:04:57.118558 INFO: === checking if optimization conditions were reached ===
7:04:57.128169 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.799918177289392
7:04:57.133165 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
7:04:57.139165 PROGRESS: ❌ ms2_error      : 23.7999 > 10.0000 or insufficient steps taken.
7:04:57.148163 INFO: Updating optimization_manager: ms1_error           : 30 -> 14.24515510890778
7:04:57.152165 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
7:04:57.156165 PROGRESS: ❌ ms1_error      : 14.2452 > 5.0000 or insufficient steps taken.
7:04:57.160165 INFO: ==============================================
7:04:57.164165 INFO: Starting optimization step 2.
7:04:57.168165 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:04:57.171165 INFO: Using classic extraction backend
7:04:57.174168 PROGRESS: Extracting batch of 15870 precursors
7:04:57.177166 INFO: === Search parameters used ===
7:04:57.180165 INFO: rt_error       : 1662.8485107421875
7:04:57.183168 INFO: mobility_error : 0.1
7:04:57.186166 INFO: num_candidates : 3
7:04:57.189166 INFO: ms1_error      : 14.24515510890778
7:04:57.196166 INFO: ms2_error      : 23.799918177289392
7:04:57.202166 INFO: fwhm_rt        : 2.691636085510254
7:04:57.210167 INFO: quant_window   : 3
7:04:57.216167 INFO: ==============================================
7:04:57.266170 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:04:57.266170 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:04:57.268167 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:04:57.269166 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:04:57.270168 INFO: Starting candidate selection
7:05:13.675825 INFO: Starting candidate scoring
7:05:15.158824 INFO: Finished candidate processing
7:05:15.159847 INFO: Collecting candidate features
7:05:15.547360 INFO: Collecting fragment features
7:05:15.735880 INFO: Finished candidate scoring
7:05:15.797880 INFO: performing precursor FDR with 47 features
7:05:15.799880 INFO: Decoy channel: -1
7:05:15.799880 INFO: Competetive: True
7:05:15.895886 INFO: Setting torch num_threads to 2 for FDR classification task
7:05:15.982403 INFO: Using random state 929372 for train-test-split
7:05:17.310555 INFO: Test AUC: 0.695
7:05:17.311555 INFO: Train AUC: 0.704
7:05:17.312555 INFO: AUC difference: 1.23%
7:05:17.908152 INFO: Resetting torch num_threads to 10
7:05:17.922153 PROGRESS: === Extracted 47609 precursors and 446485 fragments ===
7:05:17.928153 INFO: === FDR correction performed with classifier version 1 ===
7:05:17.942153 PROGRESS: ============================= Precursor FDR =============================
7:05:17.946153 PROGRESS: Total precursors accumulated: 6,783
7:05:17.950153 PROGRESS: Target precursors: 6,618 (97.57%)
7:05:17.953153 PROGRESS: Decoy precursors: 165 (2.43%)
7:05:17.957153 PROGRESS: 
7:05:17.960153 PROGRESS: Precursor Summary:
7:05:17.988153 PROGRESS: Channel   0:	 0.050 FDR: 6,618; 0.010 FDR: 6,167; 0.001 FDR: 4,590
7:05:17.992153 PROGRESS: 
7:05:17.996153 PROGRESS: Protein Summary:
7:05:18.027154 PROGRESS: Channel   0:	 0.050 FDR: 3,288; 0.010 FDR: 3,106; 0.001 FDR: 2,510
7:05:18.031154 PROGRESS: =========================================================================
7:05:18.044155 INFO: Target number of precursors reached.
7:05:18.338680 INFO: fragments_df: keeping 5000 of 446485 [sum(precursor_idx_mask)=181219 sum(mass_error_mask)=446485 stop_rank=5000
7:05:18.458206 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:05:24.868398 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:05:29.960469 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:05:33.255347 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:05:33.260346 INFO: Using score_cutoff 70.38054959106445 (fac=0.99, q=1)
7:05:33.264347 INFO: Updating optimization_manager: fwhm_rt             : 2.691636085510254 -> 2.680887222290039
7:05:33.268347 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:05:33.272347 INFO: Updating optimization_manager: score_cutoff        : 74.92121557388306 -> 70.38054959106445
7:05:33.276347 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:05:33.294347 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:05:33.354347 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:05:33.429372 INFO: === checking if optimization conditions were reached ===
7:05:33.438863 INFO: Updating optimization_manager: ms2_error           : 23.799918177289392 -> 18.73140938191937
7:05:33.442872 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
7:05:33.446871 PROGRESS: ❌ ms2_error      : 18.7314 > 10.0000 or insufficient steps taken.
7:05:33.456871 INFO: Updating optimization_manager: ms1_error           : 14.24515510890778 -> 5.223362194984406
7:05:33.460871 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
7:05:33.464873 PROGRESS: ❌ ms1_error      : 5.2234 > 5.0000 or insufficient steps taken.
7:05:33.468871 INFO: ==============================================
7:05:33.472873 INFO: Starting optimization step 3.
7:05:33.476871 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:05:33.480871 INFO: Using classic extraction backend
7:05:33.484871 PROGRESS: Extracting batch of 15870 precursors
7:05:33.488872 INFO: === Search parameters used ===
7:05:33.492872 INFO: rt_error       : 1662.8485107421875
7:05:33.496871 INFO: mobility_error : 0.1
7:05:33.500872 INFO: num_candidates : 3
7:05:33.504872 INFO: ms1_error      : 5.223362194984406
7:05:33.508872 INFO: ms2_error      : 18.73140938191937
7:05:33.511872 INFO: fwhm_rt        : 2.680887222290039
7:05:33.515872 INFO: quant_window   : 3
7:05:33.519872 INFO: ==============================================
7:05:33.572872 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:05:33.573874 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:05:33.574872 INFO: FWHM in RT is 2.68 seconds, sigma is 0.30
7:05:33.575873 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:05:33.576873 INFO: Starting candidate selection
7:05:50.510156 INFO: Starting candidate scoring
7:05:51.894049 INFO: Finished candidate processing
7:05:51.895058 INFO: Collecting candidate features
7:05:52.257130 INFO: Collecting fragment features
7:05:52.437131 INFO: Finished candidate scoring
7:05:52.497669 INFO: performing precursor FDR with 47 features
7:05:52.498665 INFO: Decoy channel: -1
7:05:52.499667 INFO: Competetive: True
7:05:52.589671 INFO: Setting torch num_threads to 2 for FDR classification task
7:05:52.660671 INFO: Using random state 329364 for train-test-split
7:05:53.945884 INFO: Test AUC: 0.703
7:05:53.946879 INFO: Train AUC: 0.711
7:05:53.947879 INFO: AUC difference: 1.11%
7:05:54.615494 INFO: Resetting torch num_threads to 10
7:05:54.629494 PROGRESS: === Extracted 47608 precursors and 435696 fragments ===
7:05:54.634495 INFO: === FDR correction performed with classifier version 2 ===
7:05:54.649495 PROGRESS: ============================= Precursor FDR =============================
7:05:54.653495 PROGRESS: Total precursors accumulated: 7,011
7:05:54.656495 PROGRESS: Target precursors: 6,880 (98.13%)
7:05:54.660496 PROGRESS: Decoy precursors: 131 (1.87%)
7:05:54.664495 PROGRESS: 
7:05:54.668496 PROGRESS: Precursor Summary:
7:05:54.698500 PROGRESS: Channel   0:	 0.050 FDR: 6,880; 0.010 FDR: 6,571; 0.001 FDR: 5,307
7:05:54.702500 PROGRESS: 
7:05:54.707505 PROGRESS: Protein Summary:
7:05:54.748048 PROGRESS: Channel   0:	 0.050 FDR: 3,364; 0.010 FDR: 3,260; 0.001 FDR: 2,805
7:05:54.752051 PROGRESS: =========================================================================
7:05:54.774050 INFO: Target number of precursors reached.
7:05:55.080158 INFO: fragments_df: keeping 5000 of 435696 [sum(precursor_idx_mask)=189137 sum(mass_error_mask)=435696 stop_rank=5000
7:05:55.211158 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:06:00.887938 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:06:05.920786 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:06:09.202424 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:06:09.207422 INFO: Using score_cutoff 66.6698381652832 (fac=0.99, q=1)
7:06:09.211421 INFO: Updating optimization_manager: fwhm_rt             : 2.680887222290039 -> 2.6678969860076904
7:06:09.215420 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:06:09.218420 INFO: Updating optimization_manager: score_cutoff        : 70.38054959106445 -> 66.6698381652832
7:06:09.222420 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:06:09.237419 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:06:09.280941 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:06:09.341941 INFO: === checking if optimization conditions were reached ===
7:06:09.349943 INFO: Updating optimization_manager: ms2_error           : 18.73140938191937 -> 14.573426890834575
7:06:09.353941 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
7:06:09.356941 PROGRESS: ❌ ms2_error      : 14.5734 > 10.0000 or insufficient steps taken.
7:06:09.366940 INFO: Updating optimization_manager: ms1_error           : 5.223362194984406 -> 5.0
7:06:09.369940 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
7:06:09.373940 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:06:09.376940 INFO: ==============================================
7:06:09.380940 INFO: Starting optimization step 4.
7:06:09.383940 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:06:09.386939 INFO: Using classic extraction backend
7:06:09.390940 PROGRESS: Extracting batch of 15870 precursors
7:06:09.393940 INFO: === Search parameters used ===
7:06:09.396939 INFO: rt_error       : 1662.8485107421875
7:06:09.400941 INFO: mobility_error : 0.1
7:06:09.403942 INFO: num_candidates : 3
7:06:09.407940 INFO: ms1_error      : 5.0
7:06:09.410941 INFO: ms2_error      : 14.573426890834575
7:06:09.414940 INFO: fwhm_rt        : 2.6678969860076904
7:06:09.418942 INFO: quant_window   : 3
7:06:09.422942 INFO: ==============================================
7:06:09.482943 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:06:09.483942 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:06:09.484944 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:06:09.485942 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:06:09.487943 INFO: Starting candidate selection
7:06:25.899779 INFO: Starting candidate scoring
7:06:27.515178 INFO: Finished candidate processing
7:06:27.516176 INFO: Collecting candidate features
7:06:27.885226 INFO: Collecting fragment features
7:06:28.063749 INFO: Finished candidate scoring
7:06:28.125749 INFO: performing precursor FDR with 47 features
7:06:28.126747 INFO: Decoy channel: -1
7:06:28.127748 INFO: Competetive: True
7:06:28.218750 INFO: Setting torch num_threads to 2 for FDR classification task
7:06:28.291270 INFO: Using random state 704833 for train-test-split
7:06:29.587577 INFO: Test AUC: 0.716
7:06:29.588574 INFO: Train AUC: 0.711
7:06:29.589577 INFO: AUC difference: 0.74%
7:06:30.284713 INFO: Resetting torch num_threads to 10
7:06:30.298222 PROGRESS: === Extracted 47605 precursors and 423783 fragments ===
7:06:30.303220 INFO: === FDR correction performed with classifier version 3 ===
7:06:30.318219 PROGRESS: ============================= Precursor FDR =============================
7:06:30.322220 PROGRESS: Total precursors accumulated: 7,081
7:06:30.325219 PROGRESS: Target precursors: 6,972 (98.46%)
7:06:30.329221 PROGRESS: Decoy precursors: 109 (1.54%)
7:06:30.332219 PROGRESS: 
7:06:30.335220 PROGRESS: Precursor Summary:
7:06:30.367225 PROGRESS: Channel   0:	 0.050 FDR: 6,972; 0.010 FDR: 6,850; 0.001 FDR: 5,690
7:06:30.371223 PROGRESS: 
7:06:30.375228 PROGRESS: Protein Summary:
7:06:30.410226 PROGRESS: Channel   0:	 0.050 FDR: 3,422; 0.010 FDR: 3,365; 0.001 FDR: 2,947
7:06:30.414226 PROGRESS: =========================================================================
7:06:30.428230 INFO: Target number of precursors reached.
7:06:30.730772 INFO: fragments_df: keeping 5000 of 423783 [sum(precursor_idx_mask)=192896 sum(mass_error_mask)=423783 stop_rank=5000
7:06:30.844385 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:06:36.686488 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:06:42.862101 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:06:46.284860 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:06:46.290859 INFO: Using score_cutoff 62.51668676490784 (fac=0.99, q=1)
7:06:46.295859 INFO: Updating optimization_manager: fwhm_rt             : 2.6678969860076904 -> 2.633206605911255
7:06:46.299860 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:06:46.304860 INFO: Updating optimization_manager: score_cutoff        : 66.6698381652832 -> 62.51668676490784
7:06:46.307861 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:06:46.325875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:06:46.384403 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:06:46.460404 INFO: === checking if optimization conditions were reached ===
7:06:46.469406 INFO: Updating optimization_manager: ms2_error           : 14.573426890834575 -> 11.251002457685535
7:06:46.473401 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
7:06:46.477407 PROGRESS: ❌ ms2_error      : 11.2510 > 10.0000 or insufficient steps taken.
7:06:46.481404 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:06:46.485404 INFO: ==============================================
7:06:46.489403 INFO: Starting optimization step 5.
7:06:46.493400 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:06:46.497404 INFO: Using classic extraction backend
7:06:46.501405 PROGRESS: Extracting batch of 15870 precursors
7:06:46.504402 INFO: === Search parameters used ===
7:06:46.508404 INFO: rt_error       : 1662.8485107421875
7:06:46.512406 INFO: mobility_error : 0.1
7:06:46.516404 INFO: num_candidates : 3
7:06:46.520406 INFO: ms1_error      : 5.0
7:06:46.524401 INFO: ms2_error      : 11.251002457685535
7:06:46.528404 INFO: fwhm_rt        : 2.633206605911255
7:06:46.532404 INFO: quant_window   : 3
7:06:46.541405 INFO: ==============================================
7:06:46.609924 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:06:46.610926 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:06:46.612925 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:06:46.613923 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:06:46.614925 INFO: Starting candidate selection
7:07:03.262272 INFO: Starting candidate scoring
7:07:04.772705 INFO: Finished candidate processing
7:07:04.773714 INFO: Collecting candidate features
7:07:05.130762 INFO: Collecting fragment features
7:07:05.292763 INFO: Finished candidate scoring
7:07:05.365288 INFO: performing precursor FDR with 47 features
7:07:05.367289 INFO: Decoy channel: -1
7:07:05.367289 INFO: Competetive: True
7:07:05.439286 INFO: Setting torch num_threads to 2 for FDR classification task
7:07:05.487288 INFO: Using random state 67780 for train-test-split
7:07:06.621455 INFO: Test AUC: 0.708
7:07:06.623459 INFO: Train AUC: 0.714
7:07:06.624458 INFO: AUC difference: 0.80%
7:07:07.312557 INFO: Resetting torch num_threads to 10
7:07:07.326552 PROGRESS: === Extracted 47600 precursors and 412048 fragments ===
7:07:07.331551 INFO: === FDR correction performed with classifier version 4 ===
7:07:07.346555 PROGRESS: ============================= Precursor FDR =============================
7:07:07.350555 PROGRESS: Total precursors accumulated: 7,071
7:07:07.353556 PROGRESS: Target precursors: 6,962 (98.46%)
7:07:07.357554 PROGRESS: Decoy precursors: 109 (1.54%)
7:07:07.360659 PROGRESS: 
7:07:07.364659 PROGRESS: Precursor Summary:
7:07:07.395662 PROGRESS: Channel   0:	 0.050 FDR: 6,962; 0.010 FDR: 6,848; 0.001 FDR: 6,003
7:07:07.400664 PROGRESS: 
7:07:07.407660 PROGRESS: Protein Summary:
7:07:07.457663 PROGRESS: Channel   0:	 0.050 FDR: 3,416; 0.010 FDR: 3,360; 0.001 FDR: 3,062
7:07:07.469658 PROGRESS: =========================================================================
7:07:07.487659 INFO: Target number of precursors reached.
7:07:07.788216 INFO: fragments_df: keeping 5000 of 412048 [sum(precursor_idx_mask)=188636 sum(mass_error_mask)=412048 stop_rank=5000
7:07:07.899824 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:07:13.835808 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:07:19.889733 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:07:23.325563 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:07:23.330562 INFO: Using score_cutoff 59.64796829223633 (fac=0.99, q=1)
7:07:23.335562 INFO: Updating optimization_manager: fwhm_rt             : 2.633206605911255 -> 2.6296749114990234
7:07:23.338563 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:07:23.342563 INFO: Updating optimization_manager: score_cutoff        : 62.51668676490784 -> 59.64796829223633
7:07:23.346563 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:07:23.364563 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:07:23.424176 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:07:23.499178 INFO: === checking if optimization conditions were reached ===
7:07:23.508176 INFO: Updating optimization_manager: ms2_error           : 11.251002457685535 -> 10.0
7:07:23.512179 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
7:07:23.515177 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
7:07:23.519179 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:07:23.523177 INFO: ==============================================
7:07:23.527179 PROGRESS: Optimization finished for ms2_error, ms1_error.
7:07:23.623177 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:07:23.659711 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:07:23.722713 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:07:23.829709 INFO: Starting optimization step 0.
7:07:23.837710 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:07:23.844710 INFO: Using classic extraction backend
7:07:23.849711 PROGRESS: Extracting batch of 15870 precursors
7:07:23.854712 INFO: === Search parameters used ===
7:07:23.859712 INFO: rt_error       : 1662.8485107421875
7:07:23.867713 INFO: mobility_error : 0.1
7:07:23.876714 INFO: num_candidates : 3
7:07:23.883725 INFO: ms1_error      : 5.0
7:07:23.890727 INFO: ms2_error      : 10.0
7:07:23.923258 INFO: fwhm_rt        : 2.6296749114990234
7:07:23.933258 INFO: quant_window   : 3
7:07:23.941258 INFO: ==============================================
7:07:24.007255 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:07:24.008256 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:07:24.009256 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:07:24.010255 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:07:24.011255 INFO: Starting candidate selection
7:07:40.374205 INFO: Starting candidate scoring
7:07:41.881166 INFO: Finished candidate processing
7:07:41.882174 INFO: Collecting candidate features
7:07:42.203264 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 47599)
7:07:42.242264 INFO: Collecting fragment features
7:07:42.412279 INFO: Finished candidate scoring
7:07:42.472805 INFO: performing precursor FDR with 47 features
7:07:42.473802 INFO: Decoy channel: -1
7:07:42.474802 INFO: Competetive: True
7:07:42.564806 INFO: Setting torch num_threads to 2 for FDR classification task
7:07:42.606806 WARNING: dropped 1 decoy PSMs due to missing features
7:07:42.641807 INFO: Using random state 800479 for train-test-split
7:07:43.980564 INFO: Test AUC: 0.707
7:07:43.981563 INFO: Train AUC: 0.718
7:07:43.982561 INFO: AUC difference: 1.44%
7:07:44.724176 INFO: Resetting torch num_threads to 10
7:07:44.739176 PROGRESS: === Extracted 47599 precursors and 407821 fragments ===
7:07:44.744173 INFO: === FDR correction performed with classifier version 5 ===
7:07:44.759177 PROGRESS: ============================= Precursor FDR =============================
7:07:44.763173 PROGRESS: Total precursors accumulated: 7,075
7:07:44.767174 PROGRESS: Target precursors: 6,958 (98.35%)
7:07:44.770174 PROGRESS: Decoy precursors: 117 (1.65%)
7:07:44.774173 PROGRESS: 
7:07:44.777175 PROGRESS: Precursor Summary:
7:07:44.808178 PROGRESS: Channel   0:	 0.050 FDR: 6,958; 0.010 FDR: 6,838; 0.001 FDR: 5,770
7:07:44.811181 PROGRESS: 
7:07:44.815174 PROGRESS: Protein Summary:
7:07:44.851178 PROGRESS: Channel   0:	 0.050 FDR: 3,419; 0.010 FDR: 3,367; 0.001 FDR: 2,989
7:07:44.856174 PROGRESS: =========================================================================
7:07:44.873174 INFO: Target number of precursors reached.
7:07:45.214245 INFO: fragments_df: keeping 5000 of 407821 [sum(precursor_idx_mask)=186634 sum(mass_error_mask)=407821 stop_rank=5000
7:07:45.332243 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:07:51.395052 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:07:57.607445 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:08:01.185802 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:08:01.190804 INFO: Using score_cutoff 58.17190058898925 (fac=0.99, q=1)
7:08:01.195803 INFO: Updating optimization_manager: fwhm_rt             : 2.6296749114990234 -> 2.6250216960906982
7:08:01.199800 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:08:01.202813 INFO: Updating optimization_manager: score_cutoff        : 59.64796829223633 -> 58.17190058898925
7:08:01.206816 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:08:01.224409 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:08:01.282408 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:08:01.358410 INFO: === checking if optimization conditions were reached ===
7:08:01.362413 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
7:08:01.389410 INFO: Updating optimization_manager: rt_error            : 1662.8485107421875 -> 109.28142039418519
7:08:01.393412 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 109.2814.
7:08:01.397413 INFO: ==============================================
7:08:01.401412 INFO: Starting optimization step 1.
7:08:01.404411 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:08:01.408409 INFO: Using classic extraction backend
7:08:01.412413 PROGRESS: Extracting batch of 15870 precursors
7:08:01.416408 INFO: === Search parameters used ===
7:08:01.419410 INFO: rt_error       : 109.28142039418519
7:08:01.423408 INFO: mobility_error : 0.1
7:08:01.427408 INFO: num_candidates : 3
7:08:01.430412 INFO: ms1_error      : 5.0
7:08:01.434413 INFO: ms2_error      : 10.0
7:08:01.437411 INFO: fwhm_rt        : 2.6250216960906982
7:08:01.441411 INFO: quant_window   : 3
7:08:01.446409 INFO: ==============================================
7:08:01.504950 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:08:01.505948 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:08:01.505948 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:08:01.506953 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:08:01.508948 INFO: Starting candidate selection
7:08:03.074353 INFO: Starting candidate scoring
7:08:04.568971 INFO: Finished candidate processing
7:08:04.569978 INFO: Collecting candidate features
7:08:04.909505 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 47594)
7:08:04.926504 INFO: Collecting fragment features
7:08:05.087028 INFO: Finished candidate scoring
7:08:05.164028 INFO: performing precursor FDR with 47 features
7:08:05.165029 INFO: Decoy channel: -1
7:08:05.166028 INFO: Competetive: True
7:08:05.272553 INFO: Setting torch num_threads to 2 for FDR classification task
7:08:05.320554 WARNING: dropped 1 target PSMs due to missing features
7:08:05.321553 WARNING: dropped 2 decoy PSMs due to missing features
7:08:05.358554 INFO: Using random state 800479 for train-test-split
7:08:06.652811 INFO: Test AUC: 0.712
7:08:06.653809 INFO: Train AUC: 0.720
7:08:06.654814 INFO: AUC difference: 1.06%
7:08:07.331459 INFO: Resetting torch num_threads to 10
7:08:07.345455 PROGRESS: === Extracted 47594 precursors and 400597 fragments ===
7:08:07.350461 INFO: === FDR correction performed with classifier version 5 ===
7:08:07.367463 PROGRESS: ============================= Precursor FDR =============================
7:08:07.372463 PROGRESS: Total precursors accumulated: 7,431
7:08:07.377460 PROGRESS: Target precursors: 7,357 (99.00%)
7:08:07.382462 PROGRESS: Decoy precursors: 74 (1.00%)
7:08:07.387467 PROGRESS: 
7:08:07.392458 PROGRESS: Precursor Summary:
7:08:07.434461 PROGRESS: Channel   0:	 0.050 FDR: 7,357; 0.010 FDR: 7,354; 0.001 FDR: 6,235
7:08:07.439464 PROGRESS: 
7:08:07.443460 PROGRESS: Protein Summary:
7:08:07.492012 PROGRESS: Channel   0:	 0.050 FDR: 3,562; 0.010 FDR: 3,560; 0.001 FDR: 3,162
7:08:07.499007 PROGRESS: =========================================================================
7:08:07.514008 INFO: Target number of precursors reached.
7:08:07.800551 INFO: fragments_df: keeping 5000 of 400597 [sum(precursor_idx_mask)=198488 sum(mass_error_mask)=400597 stop_rank=5000
7:08:07.928551 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:08:14.715125 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:08:21.644592 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:08:25.189606 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:08:25.195607 INFO: Using score_cutoff 53.23931127891541 (fac=0.99, q=1)
7:08:25.202607 INFO: Updating optimization_manager: fwhm_rt             : 2.6250216960906982 -> 2.6396989822387695
7:08:25.208606 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:08:25.213606 INFO: Updating optimization_manager: score_cutoff        : 58.17190058898925 -> 53.23931127891541
7:08:25.218606 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:08:25.248612 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:08:25.308233 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:08:25.391233 INFO: === checking if optimization conditions were reached ===
7:08:25.395235 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
7:08:25.422236 INFO: Updating optimization_manager: rt_error            : 109.28142039418519 -> 49.81590107839909
7:08:25.427236 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 49.8159.
7:08:25.431244 INFO: ==============================================
7:08:25.435233 INFO: Starting optimization step 2.
7:08:25.439237 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:08:25.443237 INFO: Using classic extraction backend
7:08:25.449239 PROGRESS: Extracting batch of 15870 precursors
7:08:25.466238 INFO: === Search parameters used ===
7:08:25.473237 INFO: rt_error       : 49.81590107839909
7:08:25.481239 INFO: mobility_error : 0.1
7:08:25.488238 INFO: num_candidates : 3
7:08:25.497237 INFO: ms1_error      : 5.0
7:08:25.502239 INFO: ms2_error      : 10.0
7:08:25.507255 INFO: fwhm_rt        : 2.6396989822387695
7:08:25.515253 INFO: quant_window   : 3
7:08:25.523783 INFO: ==============================================
7:08:25.585785 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:08:25.586783 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:08:25.587782 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:08:25.588782 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:08:25.590786 INFO: Starting candidate selection
7:08:26.648726 INFO: Starting candidate scoring
7:08:28.134366 INFO: Finished candidate processing
7:08:28.135386 INFO: Collecting candidate features
7:08:28.466931 WARNING: intensity_correlation has 7 NaNs ( 0.01 % out of 47578)
7:08:28.486930 INFO: Collecting fragment features
7:08:28.649478 INFO: Finished candidate scoring
7:08:28.708476 INFO: performing precursor FDR with 47 features
7:08:28.710479 INFO: Decoy channel: -1
7:08:28.710479 INFO: Competetive: True
7:08:28.800696 INFO: Setting torch num_threads to 2 for FDR classification task
7:08:28.849697 WARNING: dropped 3 target PSMs due to missing features
7:08:28.850697 WARNING: dropped 4 decoy PSMs due to missing features
7:08:28.886697 INFO: Using random state 800479 for train-test-split
7:08:30.184554 INFO: Test AUC: 0.715
7:08:30.185553 INFO: Train AUC: 0.726
7:08:30.185553 INFO: AUC difference: 1.54%
7:08:30.891262 INFO: Resetting torch num_threads to 10
7:08:30.904260 PROGRESS: === Extracted 47578 precursors and 391337 fragments ===
7:08:30.909265 INFO: === FDR correction performed with classifier version 5 ===
7:08:30.925261 PROGRESS: ============================= Precursor FDR =============================
7:08:30.929260 PROGRESS: Total precursors accumulated: 7,549
7:08:30.933264 PROGRESS: Target precursors: 7,473 (98.99%)
7:08:30.936264 PROGRESS: Decoy precursors: 76 (1.01%)
7:08:30.940263 PROGRESS: 
7:08:30.944259 PROGRESS: Precursor Summary:
7:08:30.976264 PROGRESS: Channel   0:	 0.050 FDR: 7,473; 0.010 FDR: 7,464; 0.001 FDR: 6,509
7:08:30.980264 PROGRESS: 
7:08:30.984260 PROGRESS: Protein Summary:
7:08:31.021281 PROGRESS: Channel   0:	 0.050 FDR: 3,593; 0.010 FDR: 3,592; 0.001 FDR: 3,247
7:08:31.025283 PROGRESS: =========================================================================
7:08:31.038817 INFO: Target number of precursors reached.
7:08:31.323345 INFO: fragments_df: keeping 5000 of 391337 [sum(precursor_idx_mask)=197998 sum(mass_error_mask)=391337 stop_rank=5000
7:08:31.435335 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:08:38.351096 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:08:45.399131 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:08:48.917479 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:08:48.922478 INFO: Using score_cutoff 52.15252951126098 (fac=0.99, q=1)
7:08:48.927480 INFO: Updating optimization_manager: fwhm_rt             : 2.6396989822387695 -> 2.6431291103363037
7:08:48.931478 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:08:48.934479 INFO: Updating optimization_manager: score_cutoff        : 53.23931127891541 -> 52.15252951126098
7:08:48.938478 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:08:48.954479 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:08:49.011480 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:08:49.085003 INFO: === checking if optimization conditions were reached ===
7:08:49.092002 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
7:08:49.124002 INFO: Updating optimization_manager: rt_error            : 49.81590107839909 -> 18.821790325697958
7:08:49.129002 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 18.8218.
7:08:49.134015 INFO: ==============================================
7:08:49.141002 INFO: Starting optimization step 3.
7:08:49.145002 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:08:49.151003 INFO: Using classic extraction backend
7:08:49.159003 PROGRESS: Extracting batch of 15870 precursors
7:08:49.165002 INFO: === Search parameters used ===
7:08:49.176000 INFO: rt_error       : 18.821790325697958
7:08:49.183001 INFO: mobility_error : 0.1
7:08:49.201004 INFO: num_candidates : 3
7:08:49.209005 INFO: ms1_error      : 5.0
7:08:49.214004 INFO: ms2_error      : 10.0
7:08:49.222002 INFO: fwhm_rt        : 2.6431291103363037
7:08:49.231003 INFO: quant_window   : 3
7:08:49.241001 INFO: ==============================================
7:08:49.302002 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:08:49.303002 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:08:49.304008 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:08:49.305008 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:08:49.306008 INFO: Starting candidate selection
7:08:49.999007 INFO: Starting candidate scoring
7:08:51.386794 INFO: Finished candidate processing
7:08:51.388297 INFO: Collecting candidate features
7:08:51.704911 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 43123)
7:08:51.742913 INFO: Collecting fragment features
7:08:51.909518 INFO: Finished candidate scoring
7:08:51.965518 INFO: performing precursor FDR with 47 features
7:08:51.966519 INFO: Decoy channel: -1
7:08:51.967518 INFO: Competetive: True
7:08:52.069534 INFO: Setting torch num_threads to 2 for FDR classification task
7:08:52.134130 WARNING: dropped 3 target PSMs due to missing features
7:08:52.135129 WARNING: dropped 5 decoy PSMs due to missing features
7:08:52.167126 INFO: Using random state 800479 for train-test-split
7:08:53.346195 INFO: Test AUC: 0.764
7:08:53.347195 INFO: Train AUC: 0.776
7:08:53.348198 INFO: AUC difference: 1.52%
7:08:54.064404 INFO: Resetting torch num_threads to 10
7:08:54.076408 PROGRESS: === Extracted 43123 precursors and 340019 fragments ===
7:08:54.081935 INFO: === FDR correction performed with classifier version 5 ===
7:08:54.096935 PROGRESS: ============================= Precursor FDR =============================
7:08:54.101938 PROGRESS: Total precursors accumulated: 7,560
7:08:54.105936 PROGRESS: Target precursors: 7,497 (99.17%)
7:08:54.109932 PROGRESS: Decoy precursors: 63 (0.83%)
7:08:54.112938 PROGRESS: 
7:08:54.117936 PROGRESS: Precursor Summary:
7:08:54.151934 PROGRESS: Channel   0:	 0.050 FDR: 7,497; 0.010 FDR: 7,497; 0.001 FDR: 7,034
7:08:54.157932 PROGRESS: 
7:08:54.163937 PROGRESS: Protein Summary:
7:08:54.221930 PROGRESS: Channel   0:	 0.050 FDR: 3,599; 0.010 FDR: 3,599; 0.001 FDR: 3,439
7:08:54.227929 PROGRESS: =========================================================================
7:08:54.250930 INFO: Target number of precursors reached.
7:08:54.518483 INFO: fragments_df: keeping 5000 of 340019 [sum(precursor_idx_mask)=174973 sum(mass_error_mask)=340019 stop_rank=5000
7:08:54.627091 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:09:00.936868 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:09:07.895579 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:09:11.420460 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:09:11.426461 INFO: Using score_cutoff 51.9490537399292 (fac=0.99, q=1)
7:09:11.431460 INFO: Updating optimization_manager: fwhm_rt             : 2.6431291103363037 -> 2.643305778503418
7:09:11.435457 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:09:11.439458 INFO: Updating optimization_manager: score_cutoff        : 52.15252951126098 -> 51.9490537399292
7:09:11.443460 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:09:11.461461 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:09:11.519462 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:09:11.592462 INFO: === checking if optimization conditions were reached ===
7:09:11.596459 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
7:09:11.625010 INFO: Updating optimization_manager: rt_error            : 18.821790325697958 -> 16.533492706496276
7:09:11.629013 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.5335.
7:09:11.633013 INFO: ==============================================
7:09:11.637012 INFO: Starting optimization step 4.
7:09:11.640014 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:09:11.644014 INFO: Using classic extraction backend
7:09:11.648012 PROGRESS: Extracting batch of 15870 precursors
7:09:11.652012 INFO: === Search parameters used ===
7:09:11.655008 INFO: rt_error       : 16.533492706496276
7:09:11.659009 INFO: mobility_error : 0.1
7:09:11.663012 INFO: num_candidates : 3
7:09:11.667014 INFO: ms1_error      : 5.0
7:09:11.670012 INFO: ms2_error      : 10.0
7:09:11.674011 INFO: fwhm_rt        : 2.643305778503418
7:09:11.677012 INFO: quant_window   : 3
7:09:11.683013 INFO: ==============================================
7:09:11.744011 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:09:11.746011 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:09:11.747015 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:09:11.748011 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:09:11.750014 INFO: Starting candidate selection
7:09:12.460119 INFO: Starting candidate scoring
7:09:13.869480 INFO: Finished candidate processing
7:09:13.871009 INFO: Collecting candidate features
7:09:14.184617 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 43276)
7:09:14.186617 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43276)
7:09:14.203613 INFO: Collecting fragment features
7:09:14.348614 INFO: Finished candidate scoring
7:09:14.409168 INFO: performing precursor FDR with 47 features
7:09:14.410165 INFO: Decoy channel: -1
7:09:14.412166 INFO: Competetive: True
7:09:14.518167 INFO: Setting torch num_threads to 2 for FDR classification task
7:09:14.582170 WARNING: dropped 4 target PSMs due to missing features
7:09:14.583172 WARNING: dropped 4 decoy PSMs due to missing features
7:09:14.614182 INFO: Using random state 800479 for train-test-split
7:09:15.799647 INFO: Test AUC: 0.772
7:09:15.800642 INFO: Train AUC: 0.781
7:09:15.801648 INFO: AUC difference: 1.17%
7:09:16.475255 INFO: Resetting torch num_threads to 10
7:09:16.488261 PROGRESS: === Extracted 43276 precursors and 341365 fragments ===
7:09:16.493260 INFO: === FDR correction performed with classifier version 5 ===
7:09:16.508259 PROGRESS: ============================= Precursor FDR =============================
7:09:16.512256 PROGRESS: Total precursors accumulated: 7,553
7:09:16.517257 PROGRESS: Target precursors: 7,493 (99.21%)
7:09:16.522260 PROGRESS: Decoy precursors: 60 (0.79%)
7:09:16.528261 PROGRESS: 
7:09:16.533258 PROGRESS: Precursor Summary:
7:09:16.578261 PROGRESS: Channel   0:	 0.050 FDR: 7,493; 0.010 FDR: 7,493; 0.001 FDR: 7,099
7:09:16.582260 PROGRESS: 
7:09:16.587257 PROGRESS: Protein Summary:
7:09:16.645784 PROGRESS: Channel   0:	 0.050 FDR: 3,592; 0.010 FDR: 3,592; 0.001 FDR: 3,462
7:09:16.655784 PROGRESS: =========================================================================
7:09:16.676785 INFO: Target number of precursors reached.
7:09:16.956338 INFO: fragments_df: keeping 5000 of 341365 [sum(precursor_idx_mask)=175816 sum(mass_error_mask)=341365 stop_rank=5000
7:09:17.065343 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:09:24.188449 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:09:31.310971 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:09:34.866301 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:09:34.872302 INFO: Using score_cutoff 51.67276947784424 (fac=0.99, q=1)
7:09:34.877302 INFO: Updating optimization_manager: fwhm_rt             : 2.643305778503418 -> 2.6549110412597656
7:09:34.880301 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:09:34.884302 INFO: Updating optimization_manager: score_cutoff        : 51.9490537399292 -> 51.67276947784424
7:09:34.888302 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:09:34.904316 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:09:34.987907 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:09:35.064912 INFO: === checking if optimization conditions were reached ===
7:09:35.068906 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
7:09:35.096913 INFO: Updating optimization_manager: rt_error            : 16.533492706496276 -> 14.461329743194776
7:09:35.100909 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 14.4613.
7:09:35.104911 INFO: ==============================================
7:09:35.109908 INFO: Starting optimization step 5.
7:09:35.114910 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:09:35.120908 INFO: Using classic extraction backend
7:09:35.125911 PROGRESS: Extracting batch of 15870 precursors
7:09:35.129910 INFO: === Search parameters used ===
7:09:35.133911 INFO: rt_error       : 14.461329743194776
7:09:35.138910 INFO: mobility_error : 0.1
7:09:35.142911 INFO: num_candidates : 3
7:09:35.149908 INFO: ms1_error      : 5.0
7:09:35.155927 INFO: ms2_error      : 10.0
7:09:35.163928 INFO: fwhm_rt        : 2.6549110412597656
7:09:35.171452 INFO: quant_window   : 3
7:09:35.180447 INFO: ==============================================
7:09:35.243450 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:09:35.244450 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:09:35.245452 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:09:35.246450 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:09:35.247452 INFO: Starting candidate selection
7:09:35.937243 INFO: Starting candidate scoring
7:09:37.329181 INFO: Finished candidate processing
7:09:37.330191 INFO: Collecting candidate features
7:09:37.631715 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 43362)
7:09:37.632713 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 43362)
7:09:37.649715 INFO: Collecting fragment features
7:09:37.790239 INFO: Finished candidate scoring
7:09:37.846238 INFO: performing precursor FDR with 47 features
7:09:37.847237 INFO: Decoy channel: -1
7:09:37.847237 INFO: Competetive: True
7:09:37.937762 INFO: Setting torch num_threads to 2 for FDR classification task
7:09:38.001761 WARNING: dropped 3 target PSMs due to missing features
7:09:38.002760 WARNING: dropped 6 decoy PSMs due to missing features
7:09:38.032763 INFO: Using random state 800479 for train-test-split
7:09:39.179905 INFO: Test AUC: 0.774
7:09:39.181906 INFO: Train AUC: 0.784
7:09:39.182904 INFO: AUC difference: 1.28%
7:09:39.884956 INFO: Resetting torch num_threads to 10
7:09:39.901955 PROGRESS: === Extracted 43362 precursors and 342278 fragments ===
7:09:39.906954 INFO: === FDR correction performed with classifier version 5 ===
7:09:39.921963 PROGRESS: ============================= Precursor FDR =============================
7:09:39.925962 PROGRESS: Total precursors accumulated: 7,549
7:09:39.929476 PROGRESS: Target precursors: 7,488 (99.19%)
7:09:39.933477 PROGRESS: Decoy precursors: 61 (0.81%)
7:09:39.936476 PROGRESS: 
7:09:39.939476 PROGRESS: Precursor Summary:
7:09:39.972478 PROGRESS: Channel   0:	 0.050 FDR: 7,488; 0.010 FDR: 7,488; 0.001 FDR: 7,055
7:09:39.976476 PROGRESS: 
7:09:39.979476 PROGRESS: Protein Summary:
7:09:40.017478 PROGRESS: Channel   0:	 0.050 FDR: 3,596; 0.010 FDR: 3,596; 0.001 FDR: 3,450
7:09:40.022477 PROGRESS: =========================================================================
7:09:40.037478 INFO: Target number of precursors reached.
7:09:40.317003 INFO: fragments_df: keeping 5000 of 342278 [sum(precursor_idx_mask)=176563 sum(mass_error_mask)=342278 stop_rank=5000
7:09:40.442524 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:09:47.535210 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:09:54.636264 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:09:58.164589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:09:58.170590 INFO: Using score_cutoff 51.46211051902771 (fac=0.99, q=1)
7:09:58.174589 INFO: Updating optimization_manager: fwhm_rt             : 2.6549110412597656 -> 2.651197671890259
7:09:58.178588 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:09:58.181587 INFO: Updating optimization_manager: score_cutoff        : 51.67276947784424 -> 51.46211051902771
7:09:58.185588 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:09:58.202596 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:09:58.260110 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:09:58.334111 INFO: === checking if optimization conditions were reached ===
7:09:58.338111 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
7:09:58.366113 INFO: Updating optimization_manager: rt_error            : 14.461329743194776 -> 16.582419158014766
7:09:58.370111 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 16.5824.
7:09:58.374111 INFO: ==============================================
7:09:58.378112 INFO: Starting optimization step 6.
7:09:58.381112 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:09:58.385111 INFO: Using classic extraction backend
7:09:58.389112 PROGRESS: Extracting batch of 15870 precursors
7:09:58.394113 INFO: === Search parameters used ===
7:09:58.400111 INFO: rt_error       : 16.582419158014766
7:09:58.408111 INFO: mobility_error : 0.1
7:09:58.414112 INFO: num_candidates : 3
7:09:58.420112 INFO: ms1_error      : 5.0
7:09:58.427113 INFO: ms2_error      : 10.0
7:09:58.434112 INFO: fwhm_rt        : 2.651197671890259
7:09:58.440113 INFO: quant_window   : 3
7:09:58.445112 INFO: ==============================================
7:09:58.503632 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:09:58.505632 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:09:58.505632 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:09:58.506633 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:09:58.508632 INFO: Starting candidate selection
7:09:59.164785 INFO: Starting candidate scoring
7:10:00.534848 INFO: Finished candidate processing
7:10:00.535856 INFO: Collecting candidate features
7:10:00.854382 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 43276)
7:10:00.856381 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43276)
7:10:00.874384 INFO: Collecting fragment features
7:10:01.018908 INFO: Finished candidate scoring
7:10:01.073908 INFO: performing precursor FDR with 47 features
7:10:01.074908 INFO: Decoy channel: -1
7:10:01.074908 INFO: Competetive: True
7:10:01.165909 INFO: Setting torch num_threads to 2 for FDR classification task
7:10:01.231433 WARNING: dropped 3 target PSMs due to missing features
7:10:01.232432 WARNING: dropped 4 decoy PSMs due to missing features
7:10:01.264432 INFO: Using random state 800479 for train-test-split
7:10:02.478574 INFO: Test AUC: 0.777
7:10:02.479573 INFO: Train AUC: 0.781
7:10:02.480573 INFO: AUC difference: 0.47%
7:10:03.214630 INFO: Resetting torch num_threads to 10
7:10:03.227143 PROGRESS: === Extracted 43276 precursors and 341436 fragments ===
7:10:03.232143 INFO: === FDR correction performed with classifier version 5 ===
7:10:03.247144 PROGRESS: ============================= Precursor FDR =============================
7:10:03.251143 PROGRESS: Total precursors accumulated: 7,586
7:10:03.255144 PROGRESS: Target precursors: 7,519 (99.12%)
7:10:03.259143 PROGRESS: Decoy precursors: 67 (0.88%)
7:10:03.263144 PROGRESS: 
7:10:03.266143 PROGRESS: Precursor Summary:
7:10:03.299145 PROGRESS: Channel   0:	 0.050 FDR: 7,519; 0.010 FDR: 7,519; 0.001 FDR: 7,095
7:10:03.303145 PROGRESS: 
7:10:03.306144 PROGRESS: Protein Summary:
7:10:03.345145 PROGRESS: Channel   0:	 0.050 FDR: 3,604; 0.010 FDR: 3,604; 0.001 FDR: 3,457
7:10:03.349144 PROGRESS: =========================================================================
7:10:03.362146 INFO: Target number of precursors reached.
7:10:03.614671 INFO: fragments_df: keeping 5000 of 341436 [sum(precursor_idx_mask)=176326 sum(mass_error_mask)=341436 stop_rank=5000
7:10:03.720680 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:10:10.724991 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:10:17.867827 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:10:21.551657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:10:21.560658 INFO: Using score_cutoff 51.3410119972229 (fac=0.99, q=1)
7:10:21.566657 INFO: Updating optimization_manager: fwhm_rt             : 2.651197671890259 -> 2.6524059772491455
7:10:21.570657 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:10:21.575654 INFO: Updating optimization_manager: score_cutoff        : 51.46211051902771 -> 51.3410119972229
7:10:21.580657 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:10:21.597657 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:10:21.659659 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:10:21.748657 INFO: === checking if optimization conditions were reached ===
7:10:21.754671 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
7:10:21.783262 INFO: Updating optimization_manager: rt_error            : 16.582419158014766 -> 16.084150481645377
7:10:21.787263 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 16.0842.
7:10:21.791263 INFO: ==============================================
7:10:21.795267 INFO: Starting optimization step 7.
7:10:21.799263 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:10:21.803261 INFO: Using classic extraction backend
7:10:21.807265 PROGRESS: Extracting batch of 15870 precursors
7:10:21.811265 INFO: === Search parameters used ===
7:10:21.815265 INFO: rt_error       : 16.084150481645377
7:10:21.820264 INFO: mobility_error : 0.1
7:10:21.824265 INFO: num_candidates : 3
7:10:21.828266 INFO: ms1_error      : 5.0
7:10:21.832264 INFO: ms2_error      : 10.0
7:10:21.835268 INFO: fwhm_rt        : 2.6524059772491455
7:10:21.843263 INFO: quant_window   : 3
7:10:21.850263 INFO: ==============================================
7:10:21.919258 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:10:21.920260 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:10:21.922258 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:10:21.923259 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:10:21.924260 INFO: Starting candidate selection
7:10:22.638307 INFO: Starting candidate scoring
7:10:24.025584 INFO: Finished candidate processing
7:10:24.026590 INFO: Collecting candidate features
7:10:24.353117 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 43326)
7:10:24.374117 INFO: Collecting fragment features
7:10:24.534639 INFO: Finished candidate scoring
7:10:24.607641 INFO: performing precursor FDR with 47 features
7:10:24.608639 INFO: Decoy channel: -1
7:10:24.609639 INFO: Competetive: True
7:10:24.700642 INFO: Setting torch num_threads to 2 for FDR classification task
7:10:24.766649 WARNING: dropped 3 target PSMs due to missing features
7:10:24.767649 WARNING: dropped 4 decoy PSMs due to missing features
7:10:24.798164 INFO: Using random state 800479 for train-test-split
7:10:26.005779 INFO: Test AUC: 0.772
7:10:26.006778 INFO: Train AUC: 0.781
7:10:26.007785 INFO: AUC difference: 1.23%
7:10:26.725352 INFO: Resetting torch num_threads to 10
7:10:26.742353 PROGRESS: === Extracted 43326 precursors and 341810 fragments ===
7:10:26.748351 INFO: === FDR correction performed with classifier version 5 ===
7:10:26.763361 PROGRESS: ============================= Precursor FDR =============================
7:10:26.768360 PROGRESS: Total precursors accumulated: 7,560
7:10:26.771360 PROGRESS: Target precursors: 7,505 (99.27%)
7:10:26.775874 PROGRESS: Decoy precursors: 55 (0.73%)
7:10:26.779876 PROGRESS: 
7:10:26.782876 PROGRESS: Precursor Summary:
7:10:26.816876 PROGRESS: Channel   0:	 0.050 FDR: 7,505; 0.010 FDR: 7,505; 0.001 FDR: 7,171
7:10:26.820875 PROGRESS: 
7:10:26.824874 PROGRESS: Protein Summary:
7:10:26.862876 PROGRESS: Channel   0:	 0.050 FDR: 3,600; 0.010 FDR: 3,600; 0.001 FDR: 3,490
7:10:26.866875 PROGRESS: =========================================================================
7:10:26.880876 INFO: Target number of precursors reached.
7:10:27.145421 INFO: fragments_df: keeping 5000 of 341810 [sum(precursor_idx_mask)=176230 sum(mass_error_mask)=341810 stop_rank=5000
7:10:27.259421 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:10:34.297993 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:10:41.396500 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:10:44.979013 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:10:44.985013 INFO: Using score_cutoff 51.95889860229492 (fac=0.99, q=1)
7:10:44.990014 INFO: Updating optimization_manager: fwhm_rt             : 2.6524059772491455 -> 2.651137351989746
7:10:44.994011 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:10:44.997010 INFO: Updating optimization_manager: score_cutoff        : 51.3410119972229 -> 51.95889860229492
7:10:45.002014 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:10:45.019007 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:10:45.077540 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:10:45.162537 INFO: === checking if optimization conditions were reached ===
7:10:45.166534 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
7:10:45.172537 INFO: Updating optimization_manager: rt_error            : 16.084150481645377 -> 14.461329743194776
7:10:45.176537 INFO: Updating optimization_manager: classifier_version  : 5 -> 11
7:10:45.181540 INFO: Updating optimization_manager: score_cutoff        : 51.95889860229492 -> 51.46211051902771
7:10:45.185540 INFO: Updating optimization_manager: fwhm_rt             : 2.651137351989746 -> 2.651197671890259
7:10:45.189540 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:10:45.193536 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 14.4613 found after 8 searches.
7:10:45.197539 INFO: ==============================================
7:10:45.202540 PROGRESS: Optimization finished for rt_error.
7:10:45.302559 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:10:45.338083 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:10:45.423082 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:10:45.576606 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
7:10:45.580609 PROGRESS: ==============================================
7:10:45.584608 PROGRESS: ms2_error      : 10.0000
7:10:45.588608 PROGRESS: ms1_error      : 5.0000
7:10:45.592611 PROGRESS: rt_error       : 14.4613
7:10:45.596611 PROGRESS: ==============================================
7:10:45.619612 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:10:45.751612 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:10:45.956223 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:10:46.440332 INFO: Using classic extraction backend
7:10:46.447335 PROGRESS: Extracting batch of 121155 precursors
7:10:46.453335 INFO: === Search parameters used ===
7:10:46.460336 INFO: rt_error       : 14.461329743194776
7:10:46.467333 INFO: mobility_error : 0.1
7:10:46.473337 INFO: num_candidates : 3
7:10:46.479335 INFO: ms1_error      : 5.0
7:10:46.483334 INFO: ms2_error      : 10.0
7:10:46.488336 INFO: fwhm_rt        : 2.651197671890259
7:10:46.493331 INFO: quant_window   : 3
7:10:46.497336 INFO: ==============================================
7:10:46.597941 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:10:46.598941 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:10:46.599945 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:10:46.600943 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:10:46.601943 INFO: Starting candidate selection
7:10:50.794387 INFO: Removed 121283 precursors with score below cutoff 51.46211051902771
7:10:50.931990 INFO: Starting candidate scoring
7:10:57.368658 INFO: Finished candidate processing
7:10:57.370664 INFO: Collecting candidate features
7:10:58.275315 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 209837)
7:10:58.344864 INFO: Collecting fragment features
7:10:58.769424 INFO: Finished candidate scoring
7:10:58.977974 INFO: === Performing FDR correction with classifier version 11 ===
7:10:58.984977 INFO: performing precursor FDR with 47 features
7:10:58.985976 INFO: Decoy channel: -1
7:10:58.986977 INFO: Competetive: True
7:10:59.302528 INFO: Setting torch num_threads to 2 for FDR classification task
7:10:59.433067 WARNING: dropped 1 target PSMs due to missing features
7:10:59.435067 WARNING: FDR calculation for 119534 target and 90302 decoy PSMs
7:10:59.435067 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
7:10:59.652386 INFO: Using random state 799143 for train-test-split
7:11:06.089197 INFO: Test AUC: 0.854
7:11:06.090197 INFO: Train AUC: 0.856
7:11:06.091198 INFO: AUC difference: 0.22%
7:11:07.024489 INFO: Resetting torch num_threads to 10
7:11:07.083491 INFO: Removing fragments below FDR threshold
7:11:07.343126 PROGRESS: ============================= Precursor FDR =============================
7:11:07.348127 PROGRESS: Total precursors accumulated: 57,326
7:11:07.353127 PROGRESS: Target precursors: 56,942 (99.33%)
7:11:07.359654 PROGRESS: Decoy precursors: 384 (0.67%)
7:11:07.364651 PROGRESS: 
7:11:07.368652 PROGRESS: Precursor Summary:
7:11:07.540654 PROGRESS: Channel   0:	 0.050 FDR: 56,942; 0.010 FDR: 56,942; 0.001 FDR: 54,812
7:11:07.544657 PROGRESS: 
7:11:07.548653 PROGRESS: Protein Summary:
7:11:07.768197 PROGRESS: Channel   0:	 0.050 FDR: 6,523; 0.010 FDR: 6,523; 0.001 FDR: 6,498
7:11:07.778198 PROGRESS: =========================================================================
7:11:07.822198 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\psm.parquet
7:11:09.136509 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\frag.parquet
7:11:10.490368 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
7:11:10.782980 PROGRESS: 
7:11:10.783980 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant
7:11:10.785981 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\figures
7:11:10.795982 INFO: Initializing TimingManager
7:11:10.815981 INFO: Initializing RawFileManager
7:16:31.682043 INFO: Determining DIA cycle
7:16:31.721043 INFO: Found cycle with start 0.00 min and length 86.
7:16:32.349231 INFO: RT (min)            : 0.0 - 55.4
7:16:32.350223 INFO: RT duration (sec)   : 3325.7
7:16:32.351232 INFO: RT duration (min)   : 55.4
7:16:32.352224 INFO: Cycle len (scans)   : 86
7:16:32.353222 INFO: Cycle len (sec)     : 1.90
7:16:32.354220 INFO: Number of cycles    : 1747
7:16:32.355225 INFO: MS2 range (m/z)     : 399.5 - 903.5
7:16:32.355225 INFO: Creating DIA data object took: 321.53024220466614
7:16:32.534750 INFO: Initializing CalibrationManager
7:16:32.544749 INFO: Setting up calibration estimators ..
7:16:32.549748 INFO: Found 1 estimator(s) in calibration group 'fragment'
7:16:32.557748 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'}' ..
7:16:32.564748 INFO: Found 3 estimator(s) in calibration group 'precursor'
7:16:32.570749 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
7:16:32.576748 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}}' ..
7:16:32.580748 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
7:16:32.584749 INFO: Done setting up calibration estimators.
7:16:32.587749 INFO: Initializing OptimizationManager
7:16:32.593755 INFO: initial parameter: ms1_error = 30
7:16:32.597754 INFO: initial parameter: ms2_error = 30
7:16:32.600754 INFO: initial parameter: rt_error = 1662.873046875
7:16:32.604756 INFO: initial parameter: mobility_error = 0.1
7:16:32.611268 INFO: initial parameter: num_candidates = 1
7:16:32.616270 INFO: initial parameter: fwhm_rt = 5
7:16:32.623268 INFO: initial parameter: fwhm_mobility = 0.01
7:16:32.630267 INFO: initial parameter: score_cutoff = 0
7:16:32.637269 INFO: initial parameter: classifier_version = -1
7:16:32.646269 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
7:16:32.653270 INFO: FDRManager: loading saved state not requested, will be initialized.
7:16:32.654271 INFO: Initializing FDRManager
7:16:32.655269 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
7:16:32.776270 PROGRESS: Initializing spectral library: 61,104 target precursors potentially observable (0 removed)
7:16:32.922793 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
7:16:32.930793 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
7:16:32.937792 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
7:16:32.944793 PROGRESS: Starting initial search for precursors.
7:16:32.952793 INFO: Starting optimization step 0.
7:16:32.956792 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:16:32.963794 INFO: Using classic extraction backend
7:16:32.971793 PROGRESS: Extracting batch of 15870 precursors
7:16:32.980791 INFO: === Search parameters used ===
7:16:32.986793 INFO: rt_error       : 1662.873046875
7:16:32.995792 INFO: mobility_error : 0.1
7:16:33.003791 INFO: num_candidates : 1
7:16:33.012794 INFO: ms1_error      : 30
7:16:33.020794 INFO: ms2_error      : 30
7:16:33.025793 INFO: fwhm_rt        : 5
7:16:33.032794 INFO: quant_window   : 3
7:16:33.040794 INFO: ==============================================
7:16:33.106805 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:16:33.107805 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:16:33.107805 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
7:16:33.109316 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
7:16:33.111338 INFO: Starting candidate selection
7:16:48.349358 INFO: Starting candidate scoring
7:16:48.947444 INFO: Finished candidate processing
7:16:48.948451 INFO: Collecting candidate features
7:16:49.088460 INFO: Collecting fragment features
7:16:49.223069 INFO: Finished candidate scoring
7:16:49.261069 INFO: performing precursor FDR with 47 features
7:16:49.262066 INFO: Decoy channel: -1
7:16:49.263067 INFO: Competetive: True
7:16:49.327070 INFO: Setting torch num_threads to 2 for FDR classification task
7:16:49.380091 INFO: Using random state 805424 for train-test-split
7:16:49.787949 INFO: Test AUC: 0.770
7:16:49.788949 INFO: Train AUC: 0.772
7:16:49.789948 INFO: AUC difference: 0.32%
7:16:50.439609 INFO: Resetting torch num_threads to 10
7:16:50.450607 PROGRESS: === Extracted 15870 precursors and 162043 fragments ===
7:16:50.456607 INFO: === FDR correction performed with classifier version -1 ===
7:16:50.469607 PROGRESS: ============================= Precursor FDR =============================
7:16:50.473606 PROGRESS: Total precursors accumulated: 3,286
7:16:50.477607 PROGRESS: Target precursors: 3,084 (93.85%)
7:16:50.481607 PROGRESS: Decoy precursors: 202 (6.15%)
7:16:50.484607 PROGRESS: 
7:16:50.488606 PROGRESS: Precursor Summary:
7:16:50.502608 PROGRESS: Channel   0:	 0.050 FDR: 2,646; 0.010 FDR:   513; 0.001 FDR:    33
7:16:50.506606 PROGRESS: 
7:16:50.509606 PROGRESS: Protein Summary:
7:16:50.524608 PROGRESS: Channel   0:	 0.050 FDR: 1,621; 0.010 FDR:   420; 0.001 FDR:    31
7:16:50.528607 PROGRESS: =========================================================================
7:16:50.534608 INFO: Target number of precursors reached.
7:16:50.578608 INFO: fragments_df: keeping 5000 of 162043 [sum(precursor_idx_mask)=5879 sum(mass_error_mask)=162043 stop_rank=5000
7:16:50.681130 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:16:51.038655 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:16:51.478699 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:16:55.102861 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
7:16:55.107861 INFO: Using score_cutoff 85.39445610351564 (fac=0.99, q=1)
7:16:55.111860 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.8991506099700928
7:16:55.115861 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
7:16:55.119861 INFO: Updating optimization_manager: score_cutoff        : 0 -> 85.39445610351564
7:16:55.122860 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:16:55.140874 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:16:55.201404 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:16:55.278412 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
7:16:55.282409 PROGRESS: Required number of precursors found. Starting search parameter optimization.
7:16:55.286403 INFO: Starting optimization step 1.
7:16:55.290406 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:16:55.294406 INFO: Using classic extraction backend
7:16:55.298403 PROGRESS: Extracting batch of 15870 precursors
7:16:55.302400 INFO: === Search parameters used ===
7:16:55.305403 INFO: rt_error       : 1662.873046875
7:16:55.309401 INFO: mobility_error : 0.1
7:16:55.312401 INFO: num_candidates : 3
7:16:55.316402 INFO: ms1_error      : 30
7:16:55.319401 INFO: ms2_error      : 30
7:16:55.323402 INFO: fwhm_rt        : 2.8991506099700928
7:16:55.326401 INFO: quant_window   : 3
7:16:55.330402 INFO: ==============================================
7:16:55.382399 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:16:55.383407 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:16:55.384408 INFO: FWHM in RT is 2.90 seconds, sigma is 0.32
7:16:55.385408 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:16:55.386409 INFO: Starting candidate selection
7:17:12.784981 INFO: Starting candidate scoring
7:17:14.422058 INFO: Finished candidate processing
7:17:14.423068 INFO: Collecting candidate features
7:17:14.769523 INFO: Collecting fragment features
7:17:14.972070 INFO: Finished candidate scoring
7:17:15.032078 INFO: performing precursor FDR with 47 features
7:17:15.033071 INFO: Decoy channel: -1
7:17:15.034073 INFO: Competetive: True
7:17:15.129073 INFO: Setting torch num_threads to 2 for FDR classification task
7:17:15.202627 INFO: Using random state 657558 for train-test-split
7:17:16.529546 INFO: Test AUC: 0.694
7:17:16.530549 INFO: Train AUC: 0.696
7:17:16.531549 INFO: AUC difference: 0.35%
7:17:17.189329 INFO: Resetting torch num_threads to 10
7:17:17.202329 PROGRESS: === Extracted 47609 precursors and 459756 fragments ===
7:17:17.208331 INFO: === FDR correction performed with classifier version 0 ===
7:17:17.222332 PROGRESS: ============================= Precursor FDR =============================
7:17:17.226332 PROGRESS: Total precursors accumulated: 6,446
7:17:17.230332 PROGRESS: Target precursors: 6,262 (97.15%)
7:17:17.233332 PROGRESS: Decoy precursors: 184 (2.85%)
7:17:17.237329 PROGRESS: 
7:17:17.241331 PROGRESS: Precursor Summary:
7:17:17.268335 PROGRESS: Channel   0:	 0.050 FDR: 6,262; 0.010 FDR: 5,403; 0.001 FDR: 3,201
7:17:17.272331 PROGRESS: 
7:17:17.276331 PROGRESS: Protein Summary:
7:17:17.322334 PROGRESS: Channel   0:	 0.050 FDR: 3,150; 0.010 FDR: 2,834; 0.001 FDR: 1,930
7:17:17.327330 PROGRESS: =========================================================================
7:17:17.340334 INFO: Target number of precursors reached.
7:17:17.648957 INFO: fragments_df: keeping 5000 of 459756 [sum(precursor_idx_mask)=163006 sum(mass_error_mask)=459756 stop_rank=5000
7:17:17.775575 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:17:21.823062 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:17:25.955161 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:17:29.645983 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:17:29.652987 INFO: Using score_cutoff 73.98231675567627 (fac=0.99, q=1)
7:17:29.656988 INFO: Updating optimization_manager: fwhm_rt             : 2.8991506099700928 -> 2.7122139930725098
7:17:29.660983 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:17:29.663986 INFO: Updating optimization_manager: score_cutoff        : 85.39445610351564 -> 73.98231675567627
7:17:29.667987 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:17:29.684985 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:17:29.744534 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:17:29.817538 INFO: === checking if optimization conditions were reached ===
7:17:29.826533 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.81203774269622
7:17:29.830533 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
7:17:29.834534 PROGRESS: ❌ ms2_error      : 23.8120 > 10.0000 or insufficient steps taken.
7:17:29.843534 INFO: Updating optimization_manager: ms1_error           : 30 -> 14.10108957359516
7:17:29.847531 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
7:17:29.850533 PROGRESS: ❌ ms1_error      : 14.1011 > 5.0000 or insufficient steps taken.
7:17:29.854533 INFO: ==============================================
7:17:29.857536 INFO: Starting optimization step 2.
7:17:29.860533 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:17:29.864531 INFO: Using classic extraction backend
7:17:29.867532 PROGRESS: Extracting batch of 15870 precursors
7:17:29.871531 INFO: === Search parameters used ===
7:17:29.875529 INFO: rt_error       : 1662.873046875
7:17:29.878530 INFO: mobility_error : 0.1
7:17:29.883530 INFO: num_candidates : 3
7:17:29.887528 INFO: ms1_error      : 14.10108957359516
7:17:29.892529 INFO: ms2_error      : 23.81203774269622
7:17:29.899529 INFO: fwhm_rt        : 2.7122139930725098
7:17:29.904529 INFO: quant_window   : 3
7:17:29.912529 INFO: ==============================================
7:17:29.971053 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:17:29.972051 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:17:29.973051 INFO: FWHM in RT is 2.71 seconds, sigma is 0.30
7:17:29.974051 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:17:29.975052 INFO: Starting candidate selection
7:17:47.351094 INFO: Starting candidate scoring
7:17:48.984879 INFO: Finished candidate processing
7:17:48.985898 INFO: Collecting candidate features
7:17:49.337973 INFO: Collecting fragment features
7:17:49.516571 INFO: Finished candidate scoring
7:17:49.575570 INFO: performing precursor FDR with 47 features
7:17:49.576572 INFO: Decoy channel: -1
7:17:49.577573 INFO: Competetive: True
7:17:49.667571 INFO: Setting torch num_threads to 2 for FDR classification task
7:17:49.740182 INFO: Using random state 404833 for train-test-split
7:17:51.054635 INFO: Test AUC: 0.699
7:17:51.056634 INFO: Train AUC: 0.708
7:17:51.057638 INFO: AUC difference: 1.33%
7:17:53.982605 INFO: Resetting torch num_threads to 10
7:17:53.995620 PROGRESS: === Extracted 47607 precursors and 446508 fragments ===
7:17:54.001742 INFO: === FDR correction performed with classifier version 1 ===
7:17:54.016741 PROGRESS: ============================= Precursor FDR =============================
7:17:54.020739 PROGRESS: Total precursors accumulated: 6,850
7:17:54.024739 PROGRESS: Target precursors: 6,676 (97.46%)
7:17:54.028741 PROGRESS: Decoy precursors: 174 (2.54%)
7:17:54.032742 PROGRESS: 
7:17:54.036741 PROGRESS: Precursor Summary:
7:17:54.063744 PROGRESS: Channel   0:	 0.050 FDR: 6,676; 0.010 FDR: 6,099; 0.001 FDR: 4,777
7:17:54.068742 PROGRESS: 
7:17:54.072742 PROGRESS: Protein Summary:
7:17:54.104741 PROGRESS: Channel   0:	 0.050 FDR: 3,302; 0.010 FDR: 3,091; 0.001 FDR: 2,604
7:17:54.108743 PROGRESS: =========================================================================
7:17:54.121740 INFO: Target number of precursors reached.
7:17:54.443286 INFO: fragments_df: keeping 5000 of 446508 [sum(precursor_idx_mask)=179526 sum(mass_error_mask)=446508 stop_rank=5000
7:17:54.579808 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:17:59.458666 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:18:04.616519 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:18:08.097682 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:18:08.103683 INFO: Using score_cutoff 69.20330883178711 (fac=0.99, q=1)
7:18:08.108684 INFO: Updating optimization_manager: fwhm_rt             : 2.7122139930725098 -> 2.6922173500061035
7:18:08.112683 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:18:08.115683 INFO: Updating optimization_manager: score_cutoff        : 73.98231675567627 -> 69.20330883178711
7:18:08.119683 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:18:08.137686 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:18:08.199684 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:18:08.278197 INFO: === checking if optimization conditions were reached ===
7:18:08.290205 INFO: Updating optimization_manager: ms2_error           : 23.81203774269622 -> 18.513536216244958
7:18:08.298204 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
7:18:08.304205 PROGRESS: ❌ ms2_error      : 18.5135 > 10.0000 or insufficient steps taken.
7:18:08.317204 INFO: Updating optimization_manager: ms1_error           : 14.10108957359516 -> 5.309522205302816
7:18:08.324204 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
7:18:08.333205 PROGRESS: ❌ ms1_error      : 5.3095 > 5.0000 or insufficient steps taken.
7:18:08.341204 INFO: ==============================================
7:18:08.344205 INFO: Starting optimization step 3.
7:18:08.351205 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:18:08.378206 INFO: Using classic extraction backend
7:18:08.386205 PROGRESS: Extracting batch of 15870 precursors
7:18:08.396205 INFO: === Search parameters used ===
7:18:08.402205 INFO: rt_error       : 1662.873046875
7:18:08.410205 INFO: mobility_error : 0.1
7:18:08.416207 INFO: num_candidates : 3
7:18:08.425205 INFO: ms1_error      : 5.309522205302816
7:18:08.433207 INFO: ms2_error      : 18.513536216244958
7:18:08.441209 INFO: fwhm_rt        : 2.6922173500061035
7:18:08.448206 INFO: quant_window   : 3
7:18:08.456210 INFO: ==============================================
7:18:08.511213 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:18:08.512211 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:18:08.513227 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:18:08.514227 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:18:08.515226 INFO: Starting candidate selection
7:18:25.612368 INFO: Starting candidate scoring
7:18:27.244208 INFO: Finished candidate processing
7:18:27.245206 INFO: Collecting candidate features
7:18:27.610271 INFO: Collecting fragment features
7:18:27.787280 INFO: Finished candidate scoring
7:18:27.845885 INFO: performing precursor FDR with 47 features
7:18:27.846884 INFO: Decoy channel: -1
7:18:27.847889 INFO: Competetive: True
7:18:27.940888 INFO: Setting torch num_threads to 2 for FDR classification task
7:18:28.013888 INFO: Using random state 742693 for train-test-split
7:18:29.352991 INFO: Test AUC: 0.705
7:18:29.353988 INFO: Train AUC: 0.715
7:18:29.355988 INFO: AUC difference: 1.45%
7:18:30.047106 INFO: Resetting torch num_threads to 10
7:18:30.064640 PROGRESS: === Extracted 47604 precursors and 435646 fragments ===
7:18:30.070640 INFO: === FDR correction performed with classifier version 2 ===
7:18:30.085641 PROGRESS: ============================= Precursor FDR =============================
7:18:30.089642 PROGRESS: Total precursors accumulated: 7,063
7:18:30.093641 PROGRESS: Target precursors: 6,935 (98.19%)
7:18:30.097641 PROGRESS: Decoy precursors: 128 (1.81%)
7:18:30.100642 PROGRESS: 
7:18:30.104639 PROGRESS: Precursor Summary:
7:18:30.133640 PROGRESS: Channel   0:	 0.050 FDR: 6,935; 0.010 FDR: 6,557; 0.001 FDR: 5,324
7:18:30.137642 PROGRESS: 
7:18:30.141642 PROGRESS: Protein Summary:
7:18:30.175642 PROGRESS: Channel   0:	 0.050 FDR: 3,400; 0.010 FDR: 3,263; 0.001 FDR: 2,808
7:18:30.179641 PROGRESS: =========================================================================
7:18:30.193642 INFO: Target number of precursors reached.
7:18:30.513195 INFO: fragments_df: keeping 5000 of 435646 [sum(precursor_idx_mask)=188839 sum(mass_error_mask)=435646 stop_rank=5000
7:18:30.643732 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:18:36.417834 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:18:42.288459 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:18:45.816823 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:18:45.822823 INFO: Using score_cutoff 65.55778640441893 (fac=0.99, q=1)
7:18:45.828823 INFO: Updating optimization_manager: fwhm_rt             : 2.6922173500061035 -> 2.6818127632141113
7:18:45.833831 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:18:45.838829 INFO: Updating optimization_manager: score_cutoff        : 69.20330883178711 -> 65.55778640441893
7:18:45.843829 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:18:45.871345 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:18:45.931346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:18:46.005346 INFO: === checking if optimization conditions were reached ===
7:18:46.015347 INFO: Updating optimization_manager: ms2_error           : 18.513536216244958 -> 14.610276862276116
7:18:46.019345 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
7:18:46.023346 PROGRESS: ❌ ms2_error      : 14.6103 > 10.0000 or insufficient steps taken.
7:18:46.033347 INFO: Updating optimization_manager: ms1_error           : 5.309522205302816 -> 5.0
7:18:46.037346 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
7:18:46.041346 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:18:46.045346 INFO: ==============================================
7:18:46.049346 INFO: Starting optimization step 4.
7:18:46.052346 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:18:46.056346 INFO: Using classic extraction backend
7:18:46.060346 PROGRESS: Extracting batch of 15870 precursors
7:18:46.064346 INFO: === Search parameters used ===
7:18:46.068348 INFO: rt_error       : 1662.873046875
7:18:46.072346 INFO: mobility_error : 0.1
7:18:46.076347 INFO: num_candidates : 3
7:18:46.081354 INFO: ms1_error      : 5.0
7:18:46.087355 INFO: ms2_error      : 14.610276862276116
7:18:46.094355 INFO: fwhm_rt        : 2.6818127632141113
7:18:46.100868 INFO: quant_window   : 3
7:18:46.108870 INFO: ==============================================
7:18:46.171870 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:18:46.172869 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:18:46.173870 INFO: FWHM in RT is 2.68 seconds, sigma is 0.30
7:18:46.174868 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:18:46.176870 INFO: Starting candidate selection
7:19:03.280427 INFO: Starting candidate scoring
7:19:04.848991 INFO: Finished candidate processing
7:19:04.849988 INFO: Collecting candidate features
7:19:05.210041 INFO: Collecting fragment features
7:19:05.404565 INFO: Finished candidate scoring
7:19:05.464564 INFO: performing precursor FDR with 47 features
7:19:05.465564 INFO: Decoy channel: -1
7:19:05.466563 INFO: Competetive: True
7:19:05.559566 INFO: Setting torch num_threads to 2 for FDR classification task
7:19:05.632087 INFO: Using random state 192084 for train-test-split
7:19:06.983096 INFO: Test AUC: 0.709
7:19:06.984095 INFO: Train AUC: 0.718
7:19:06.985094 INFO: AUC difference: 1.28%
7:19:07.721767 INFO: Resetting torch num_threads to 10
7:19:07.734770 PROGRESS: === Extracted 47604 precursors and 424045 fragments ===
7:19:07.740769 INFO: === FDR correction performed with classifier version 3 ===
7:19:07.755767 PROGRESS: ============================= Precursor FDR =============================
7:19:07.760769 PROGRESS: Total precursors accumulated: 7,106
7:19:07.764767 PROGRESS: Target precursors: 6,985 (98.30%)
7:19:07.771767 PROGRESS: Decoy precursors: 121 (1.70%)
7:19:07.777768 PROGRESS: 
7:19:07.784767 PROGRESS: Precursor Summary:
7:19:07.815768 PROGRESS: Channel   0:	 0.050 FDR: 6,985; 0.010 FDR: 6,759; 0.001 FDR: 5,263
7:19:07.819768 PROGRESS: 
7:19:07.823770 PROGRESS: Protein Summary:
7:19:07.857768 PROGRESS: Channel   0:	 0.050 FDR: 3,415; 0.010 FDR: 3,323; 0.001 FDR: 2,795
7:19:07.862770 PROGRESS: =========================================================================
7:19:07.875787 INFO: Target number of precursors reached.
7:19:08.163925 INFO: fragments_df: keeping 5000 of 424045 [sum(precursor_idx_mask)=190262 sum(mass_error_mask)=424045 stop_rank=5000
7:19:08.280925 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:19:14.165132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:19:20.167350 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:19:23.669702 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:19:23.675699 INFO: Using score_cutoff 63.041455233764644 (fac=0.99, q=1)
7:19:23.680700 INFO: Updating optimization_manager: fwhm_rt             : 2.6818127632141113 -> 2.661766290664673
7:19:23.684700 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:19:23.687699 INFO: Updating optimization_manager: score_cutoff        : 65.55778640441893 -> 63.041455233764644
7:19:23.692700 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:19:23.709699 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:19:23.770700 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:19:23.845704 INFO: === checking if optimization conditions were reached ===
7:19:23.854705 INFO: Updating optimization_manager: ms2_error           : 14.610276862276116 -> 10.976965727728683
7:19:23.858703 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
7:19:23.862703 PROGRESS: ❌ ms2_error      : 10.9770 > 10.0000 or insufficient steps taken.
7:19:23.866703 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:19:23.870703 INFO: ==============================================
7:19:23.874703 INFO: Starting optimization step 5.
7:19:23.878706 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:19:23.882703 INFO: Using classic extraction backend
7:19:23.886703 PROGRESS: Extracting batch of 15870 precursors
7:19:23.890703 INFO: === Search parameters used ===
7:19:23.895704 INFO: rt_error       : 1662.873046875
7:19:23.899703 INFO: mobility_error : 0.1
7:19:23.903701 INFO: num_candidates : 3
7:19:23.907717 INFO: ms1_error      : 5.0
7:19:23.911716 INFO: ms2_error      : 10.976965727728683
7:19:23.916715 INFO: fwhm_rt        : 2.661766290664673
7:19:23.921244 INFO: quant_window   : 3
7:19:23.929245 INFO: ==============================================
7:19:23.998239 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:19:23.999239 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:19:24.001240 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:19:24.002240 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:19:24.003238 INFO: Starting candidate selection
7:19:40.980906 INFO: Starting candidate scoring
7:19:42.524176 INFO: Finished candidate processing
7:19:42.525183 INFO: Collecting candidate features
7:19:42.878796 INFO: Collecting fragment features
7:19:43.045342 INFO: Finished candidate scoring
7:19:43.105335 INFO: performing precursor FDR with 47 features
7:19:43.106334 INFO: Decoy channel: -1
7:19:43.107333 INFO: Competetive: True
7:19:43.200858 INFO: Setting torch num_threads to 2 for FDR classification task
7:19:43.274858 INFO: Using random state 844110 for train-test-split
7:19:44.599167 INFO: Test AUC: 0.708
7:19:44.600164 INFO: Train AUC: 0.717
7:19:44.601166 INFO: AUC difference: 1.31%
7:19:45.252014 INFO: Resetting torch num_threads to 10
7:19:45.265018 PROGRESS: === Extracted 47601 precursors and 408025 fragments ===
7:19:45.271013 INFO: === FDR correction performed with classifier version 4 ===
7:19:45.287013 PROGRESS: ============================= Precursor FDR =============================
7:19:45.291013 PROGRESS: Total precursors accumulated: 7,149
7:19:45.295016 PROGRESS: Target precursors: 7,025 (98.27%)
7:19:45.299014 PROGRESS: Decoy precursors: 124 (1.73%)
7:19:45.303013 PROGRESS: 
7:19:45.307015 PROGRESS: Precursor Summary:
7:19:45.338015 PROGRESS: Channel   0:	 0.050 FDR: 7,025; 0.010 FDR: 6,837; 0.001 FDR: 5,658
7:19:45.342011 PROGRESS: 
7:19:45.346015 PROGRESS: Protein Summary:
7:19:45.382016 PROGRESS: Channel   0:	 0.050 FDR: 3,439; 0.010 FDR: 3,369; 0.001 FDR: 2,956
7:19:45.386018 PROGRESS: =========================================================================
7:19:45.400011 INFO: Target number of precursors reached.
7:19:45.685565 INFO: fragments_df: keeping 5000 of 408025 [sum(precursor_idx_mask)=186707 sum(mass_error_mask)=408025 stop_rank=5000
7:19:45.805106 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:19:51.772274 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:19:58.147237 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:20:01.646722 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:20:01.652721 INFO: Using score_cutoff 59.14025627288819 (fac=0.99, q=1)
7:20:01.656718 INFO: Updating optimization_manager: fwhm_rt             : 2.661766290664673 -> 2.6656103134155273
7:20:01.660719 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:20:01.664720 INFO: Updating optimization_manager: score_cutoff        : 63.041455233764644 -> 59.14025627288819
7:20:01.668717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:20:01.685721 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:20:01.747332 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:20:01.834335 INFO: === checking if optimization conditions were reached ===
7:20:01.848335 INFO: Updating optimization_manager: ms2_error           : 10.976965727728683 -> 10.0
7:20:01.854335 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
7:20:01.858333 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
7:20:01.862335 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:20:01.866335 INFO: ==============================================
7:20:01.870337 PROGRESS: Optimization finished for ms2_error, ms1_error.
7:20:01.967335 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:20:02.008870 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:20:02.088874 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:20:02.196872 INFO: Starting optimization step 0.
7:20:02.202876 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:20:02.209875 INFO: Using classic extraction backend
7:20:02.216876 PROGRESS: Extracting batch of 15870 precursors
7:20:02.225878 INFO: === Search parameters used ===
7:20:02.231896 INFO: rt_error       : 1662.873046875
7:20:02.238895 INFO: mobility_error : 0.1
7:20:02.247417 INFO: num_candidates : 3
7:20:02.252422 INFO: ms1_error      : 5.0
7:20:02.256418 INFO: ms2_error      : 10.0
7:20:02.260418 INFO: fwhm_rt        : 2.6656103134155273
7:20:02.264419 INFO: quant_window   : 3
7:20:02.269419 INFO: ==============================================
7:20:02.319420 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:20:02.320418 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:20:02.321419 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:20:02.322418 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:20:02.323424 INFO: Starting candidate selection
7:20:19.272028 INFO: Starting candidate scoring
7:20:20.825234 INFO: Finished candidate processing
7:20:20.826700 INFO: Collecting candidate features
7:20:21.178315 INFO: Collecting fragment features
7:20:21.348943 INFO: Finished candidate scoring
7:20:21.413941 INFO: performing precursor FDR with 47 features
7:20:21.414938 INFO: Decoy channel: -1
7:20:21.415941 INFO: Competetive: True
7:20:21.509962 INFO: Setting torch num_threads to 2 for FDR classification task
7:20:21.583562 INFO: Using random state 804472 for train-test-split
7:20:22.940031 INFO: Test AUC: 0.706
7:20:22.941031 INFO: Train AUC: 0.724
7:20:22.943027 INFO: AUC difference: 2.42%
7:20:23.656681 INFO: Resetting torch num_threads to 10
7:20:23.676679 PROGRESS: === Extracted 47602 precursors and 408009 fragments ===
7:20:23.682680 INFO: === FDR correction performed with classifier version 5 ===
7:20:23.697681 PROGRESS: ============================= Precursor FDR =============================
7:20:23.701679 PROGRESS: Total precursors accumulated: 7,155
7:20:23.705680 PROGRESS: Target precursors: 7,018 (98.09%)
7:20:23.711681 PROGRESS: Decoy precursors: 137 (1.91%)
7:20:23.716681 PROGRESS: 
7:20:23.721680 PROGRESS: Precursor Summary:
7:20:23.763694 PROGRESS: Channel   0:	 0.050 FDR: 7,018; 0.010 FDR: 6,858; 0.001 FDR: 5,747
7:20:23.767694 PROGRESS: 
7:20:23.771694 PROGRESS: Protein Summary:
7:20:23.805902 PROGRESS: Channel   0:	 0.050 FDR: 3,442; 0.010 FDR: 3,373; 0.001 FDR: 2,987
7:20:23.810898 PROGRESS: =========================================================================
7:20:23.823898 INFO: Target number of precursors reached.
7:20:24.102452 INFO: fragments_df: keeping 5000 of 408009 [sum(precursor_idx_mask)=187153 sum(mass_error_mask)=408009 stop_rank=5000
7:20:24.214452 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:20:30.331864 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:20:36.576023 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:20:40.066446 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:20:40.071447 INFO: Using score_cutoff 57.42129648971558 (fac=0.99, q=1)
7:20:40.075446 INFO: Updating optimization_manager: fwhm_rt             : 2.6656103134155273 -> 2.6641733646392822
7:20:40.079446 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:20:40.083446 INFO: Updating optimization_manager: score_cutoff        : 59.14025627288819 -> 57.42129648971558
7:20:40.087447 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:20:40.104449 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:20:40.178447 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:20:40.262448 INFO: === checking if optimization conditions were reached ===
7:20:40.268449 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
7:20:40.299457 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 114.75766149826507
7:20:40.303456 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 114.7577.
7:20:40.307455 INFO: ==============================================
7:20:40.311970 INFO: Starting optimization step 1.
7:20:40.314969 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:20:40.318969 INFO: Using classic extraction backend
7:20:40.322969 PROGRESS: Extracting batch of 15870 precursors
7:20:40.326970 INFO: === Search parameters used ===
7:20:40.330970 INFO: rt_error       : 114.75766149826507
7:20:40.333969 INFO: mobility_error : 0.1
7:20:40.337970 INFO: num_candidates : 3
7:20:40.341970 INFO: ms1_error      : 5.0
7:20:40.345970 INFO: ms2_error      : 10.0
7:20:40.348981 INFO: fwhm_rt        : 2.6641733646392822
7:20:40.352969 INFO: quant_window   : 3
7:20:40.356970 INFO: ==============================================
7:20:40.410971 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:20:40.411971 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:20:40.412970 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:20:40.413970 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:20:40.414970 INFO: Starting candidate selection
7:20:42.022028 INFO: Starting candidate scoring
7:20:43.578351 INFO: Finished candidate processing
7:20:43.579353 INFO: Collecting candidate features
7:20:43.926964 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 47600)
7:20:43.944964 INFO: Collecting fragment features
7:20:44.108577 INFO: Finished candidate scoring
7:20:44.168578 INFO: performing precursor FDR with 47 features
7:20:44.169577 INFO: Decoy channel: -1
7:20:44.170582 INFO: Competetive: True
7:20:44.265579 INFO: Setting torch num_threads to 2 for FDR classification task
7:20:44.315595 WARNING: dropped 2 target PSMs due to missing features
7:20:44.317110 WARNING: dropped 1 decoy PSMs due to missing features
7:20:44.355127 INFO: Using random state 804472 for train-test-split
7:20:45.678406 INFO: Test AUC: 0.717
7:20:45.680403 INFO: Train AUC: 0.728
7:20:45.681405 INFO: AUC difference: 1.55%
7:20:46.387057 INFO: Resetting torch num_threads to 10
7:20:46.401052 PROGRESS: === Extracted 47600 precursors and 400081 fragments ===
7:20:46.406051 INFO: === FDR correction performed with classifier version 5 ===
7:20:46.422052 PROGRESS: ============================= Precursor FDR =============================
7:20:46.426055 PROGRESS: Total precursors accumulated: 7,502
7:20:46.430054 PROGRESS: Target precursors: 7,415 (98.84%)
7:20:46.434056 PROGRESS: Decoy precursors: 87 (1.16%)
7:20:46.438055 PROGRESS: 
7:20:46.443055 PROGRESS: Precursor Summary:
7:20:46.474062 PROGRESS: Channel   0:	 0.050 FDR: 7,415; 0.010 FDR: 7,368; 0.001 FDR: 5,122
7:20:46.479053 PROGRESS: 
7:20:46.483057 PROGRESS: Protein Summary:
7:20:46.520057 PROGRESS: Channel   0:	 0.050 FDR: 3,590; 0.010 FDR: 3,573; 0.001 FDR: 2,783
7:20:46.524058 PROGRESS: =========================================================================
7:20:46.537058 INFO: Target number of precursors reached.
7:20:46.838155 INFO: fragments_df: keeping 5000 of 400081 [sum(precursor_idx_mask)=198633 sum(mass_error_mask)=400081 stop_rank=5000
7:20:46.959153 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:20:53.885086 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:21:00.821815 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:21:04.336354 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:21:04.341354 INFO: Using score_cutoff 53.807621899795535 (fac=0.99, q=1)
7:21:04.346361 INFO: Updating optimization_manager: fwhm_rt             : 2.6641733646392822 -> 2.6812832355499268
7:21:04.350359 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:21:04.354360 INFO: Updating optimization_manager: score_cutoff        : 57.42129648971558 -> 53.807621899795535
7:21:04.358360 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:21:04.374876 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:21:04.435875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:21:04.509877 INFO: === checking if optimization conditions were reached ===
7:21:04.513876 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
7:21:04.541882 INFO: Updating optimization_manager: rt_error            : 114.75766149826507 -> 36.16417835054195
7:21:04.545876 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 36.1642.
7:21:04.549876 INFO: ==============================================
7:21:04.552876 INFO: Starting optimization step 2.
7:21:04.556877 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:21:04.560876 INFO: Using classic extraction backend
7:21:04.564877 PROGRESS: Extracting batch of 15870 precursors
7:21:04.568876 INFO: === Search parameters used ===
7:21:04.571876 INFO: rt_error       : 36.16417835054195
7:21:04.575877 INFO: mobility_error : 0.1
7:21:04.579877 INFO: num_candidates : 3
7:21:04.583876 INFO: ms1_error      : 5.0
7:21:04.586877 INFO: ms2_error      : 10.0
7:21:04.591877 INFO: fwhm_rt        : 2.6812832355499268
7:21:04.594877 INFO: quant_window   : 3
7:21:04.598883 INFO: ==============================================
7:21:04.659401 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:21:04.661398 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:21:04.662400 INFO: FWHM in RT is 2.68 seconds, sigma is 0.30
7:21:04.663399 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:21:04.664399 INFO: Starting candidate selection
7:21:05.479777 INFO: Starting candidate scoring
7:21:06.937006 INFO: Finished candidate processing
7:21:06.938015 INFO: Collecting candidate features
7:21:07.265538 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 47349)
7:21:07.283538 INFO: Collecting fragment features
7:21:07.455062 INFO: Finished candidate scoring
7:21:07.514063 INFO: performing precursor FDR with 47 features
7:21:07.515062 INFO: Decoy channel: -1
7:21:07.516062 INFO: Competetive: True
7:21:07.611071 INFO: Setting torch num_threads to 2 for FDR classification task
7:21:07.660589 WARNING: dropped 1 target PSMs due to missing features
7:21:07.662587 WARNING: dropped 2 decoy PSMs due to missing features
7:21:07.699588 INFO: Using random state 804472 for train-test-split
7:21:09.038632 INFO: Test AUC: 0.716
7:21:09.039636 INFO: Train AUC: 0.743
7:21:09.040631 INFO: AUC difference: 3.63%
7:21:09.750258 INFO: Resetting torch num_threads to 10
7:21:09.763256 PROGRESS: === Extracted 47349 precursors and 382416 fragments ===
7:21:09.769258 INFO: === FDR correction performed with classifier version 5 ===
7:21:09.785258 PROGRESS: ============================= Precursor FDR =============================
7:21:09.789258 PROGRESS: Total precursors accumulated: 7,576
7:21:09.793257 PROGRESS: Target precursors: 7,513 (99.17%)
7:21:09.796260 PROGRESS: Decoy precursors: 63 (0.83%)
7:21:09.800259 PROGRESS: 
7:21:09.804256 PROGRESS: Precursor Summary:
7:21:09.851269 PROGRESS: Channel   0:	 0.050 FDR: 7,513; 0.010 FDR: 7,513; 0.001 FDR: 6,418
7:21:09.856275 PROGRESS: 
7:21:09.864277 PROGRESS: Protein Summary:
7:21:09.921444 PROGRESS: Channel   0:	 0.050 FDR: 3,617; 0.010 FDR: 3,617; 0.001 FDR: 3,226
7:21:09.934444 PROGRESS: =========================================================================
7:21:09.954445 INFO: Target number of precursors reached.
7:21:10.261734 INFO: fragments_df: keeping 5000 of 382416 [sum(precursor_idx_mask)=195783 sum(mass_error_mask)=382416 stop_rank=5000
7:21:10.378283 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:21:17.452238 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:21:24.537048 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:21:28.074042 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:21:28.080043 INFO: Using score_cutoff 52.077447839355465 (fac=0.99, q=1)
7:21:28.085042 INFO: Updating optimization_manager: fwhm_rt             : 2.6812832355499268 -> 2.689422130584717
7:21:28.089042 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:21:28.093045 INFO: Updating optimization_manager: score_cutoff        : 53.807621899795535 -> 52.077447839355465
7:21:28.096043 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:21:28.113043 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:21:28.173663 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:21:28.249657 INFO: === checking if optimization conditions were reached ===
7:21:28.253657 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
7:21:28.288657 INFO: Updating optimization_manager: rt_error            : 36.16417835054195 -> 21.23515805948822
7:21:28.294656 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 21.2352.
7:21:28.301657 INFO: ==============================================
7:21:28.308656 INFO: Starting optimization step 3.
7:21:28.317657 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:21:28.325657 INFO: Using classic extraction backend
7:21:28.332658 PROGRESS: Extracting batch of 15870 precursors
7:21:28.338659 INFO: === Search parameters used ===
7:21:28.343657 INFO: rt_error       : 21.23515805948822
7:21:28.349658 INFO: mobility_error : 0.1
7:21:28.356658 INFO: num_candidates : 3
7:21:28.363658 INFO: ms1_error      : 5.0
7:21:28.372666 INFO: ms2_error      : 10.0
7:21:28.380660 INFO: fwhm_rt        : 2.689422130584717
7:21:28.388658 INFO: quant_window   : 3
7:21:28.393660 INFO: ==============================================
7:21:28.456186 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:21:28.458187 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:21:28.459187 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:21:28.459187 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:21:28.461185 INFO: Starting candidate selection
7:21:29.151039 INFO: Starting candidate scoring
7:21:30.483268 INFO: Finished candidate processing
7:21:30.484760 INFO: Collecting candidate features
7:21:30.792318 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 43198)
7:21:30.809317 INFO: Collecting fragment features
7:21:30.954874 INFO: Finished candidate scoring
7:21:31.008867 INFO: performing precursor FDR with 47 features
7:21:31.009867 INFO: Decoy channel: -1
7:21:31.010867 INFO: Competetive: True
7:21:31.102867 INFO: Setting torch num_threads to 2 for FDR classification task
7:21:31.164262 WARNING: dropped 2 decoy PSMs due to missing features
7:21:31.194263 INFO: Using random state 804472 for train-test-split
7:21:32.408842 INFO: Test AUC: 0.765
7:21:32.409841 INFO: Train AUC: 0.778
7:21:32.410839 INFO: AUC difference: 1.63%
7:21:33.129416 INFO: Resetting torch num_threads to 10
7:21:33.145418 PROGRESS: === Extracted 43198 precursors and 339830 fragments ===
7:21:33.150417 INFO: === FDR correction performed with classifier version 5 ===
7:21:33.176029 PROGRESS: ============================= Precursor FDR =============================
7:21:33.181026 PROGRESS: Total precursors accumulated: 7,615
7:21:33.185031 PROGRESS: Target precursors: 7,558 (99.25%)
7:21:33.190032 PROGRESS: Decoy precursors: 57 (0.75%)
7:21:33.194030 PROGRESS: 
7:21:33.198030 PROGRESS: Precursor Summary:
7:21:33.231029 PROGRESS: Channel   0:	 0.050 FDR: 7,558; 0.010 FDR: 7,558; 0.001 FDR: 6,701
7:21:33.279032 PROGRESS: 
7:21:33.285031 PROGRESS: Protein Summary:
7:21:33.337026 PROGRESS: Channel   0:	 0.050 FDR: 3,643; 0.010 FDR: 3,643; 0.001 FDR: 3,329
7:21:33.341027 PROGRESS: =========================================================================
7:21:33.356027 INFO: Target number of precursors reached.
7:21:33.632575 INFO: fragments_df: keeping 5000 of 339830 [sum(precursor_idx_mask)=176531 sum(mass_error_mask)=339830 stop_rank=5000
7:21:33.755198 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:21:41.126318 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:21:48.316850 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:21:51.900155 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:21:51.906152 INFO: Using score_cutoff 49.97592139663696 (fac=0.99, q=1)
7:21:51.910153 INFO: Updating optimization_manager: fwhm_rt             : 2.689422130584717 -> 2.692659854888916
7:21:51.914153 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:21:51.918153 INFO: Updating optimization_manager: score_cutoff        : 52.077447839355465 -> 49.97592139663696
7:21:51.922153 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:21:51.939154 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:21:51.999762 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:21:52.074762 INFO: === checking if optimization conditions were reached ===
7:21:52.079761 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
7:21:52.109760 INFO: Updating optimization_manager: rt_error            : 21.23515805948822 -> 17.235610398101567
7:21:52.119761 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 17.2356.
7:21:52.128763 INFO: ==============================================
7:21:52.139760 INFO: Starting optimization step 4.
7:21:52.152764 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:21:52.164762 INFO: Using classic extraction backend
7:21:52.171770 PROGRESS: Extracting batch of 15870 precursors
7:21:52.181763 INFO: === Search parameters used ===
7:21:52.189763 INFO: rt_error       : 17.235610398101567
7:21:52.215371 INFO: mobility_error : 0.1
7:21:52.227371 INFO: num_candidates : 3
7:21:52.238371 INFO: ms1_error      : 5.0
7:21:52.248372 INFO: ms2_error      : 10.0
7:21:52.260371 INFO: fwhm_rt        : 2.692659854888916
7:21:52.270373 INFO: quant_window   : 3
7:21:52.283372 INFO: ==============================================
7:21:52.371375 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:21:52.373378 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:21:52.375377 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:21:52.377376 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:21:52.379371 INFO: Starting candidate selection
7:21:53.056595 INFO: Starting candidate scoring
7:21:54.417390 INFO: Finished candidate processing
7:21:54.418899 INFO: Collecting candidate features
7:21:54.740984 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 43173)
7:21:54.742985 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43173)
7:21:54.759982 INFO: Collecting fragment features
7:21:54.906980 INFO: Finished candidate scoring
7:21:54.963000 INFO: performing precursor FDR with 47 features
7:21:54.965004 INFO: Decoy channel: -1
7:21:54.966520 INFO: Competetive: True
7:21:55.071535 INFO: Setting torch num_threads to 2 for FDR classification task
7:21:55.139536 WARNING: dropped 2 target PSMs due to missing features
7:21:55.141538 WARNING: dropped 1 decoy PSMs due to missing features
7:21:55.173538 INFO: Using random state 804472 for train-test-split
7:21:56.408653 INFO: Test AUC: 0.773
7:21:56.410654 INFO: Train AUC: 0.782
7:21:56.411652 INFO: AUC difference: 1.15%
7:21:57.132226 INFO: Resetting torch num_threads to 10
7:21:57.146226 PROGRESS: === Extracted 43173 precursors and 340251 fragments ===
7:21:57.152227 INFO: === FDR correction performed with classifier version 5 ===
7:21:57.168226 PROGRESS: ============================= Precursor FDR =============================
7:21:57.173225 PROGRESS: Total precursors accumulated: 7,609
7:21:57.178226 PROGRESS: Target precursors: 7,549 (99.21%)
7:21:57.182227 PROGRESS: Decoy precursors: 60 (0.79%)
7:21:57.187227 PROGRESS: 
7:21:57.192226 PROGRESS: Precursor Summary:
7:21:57.226750 PROGRESS: Channel   0:	 0.050 FDR: 7,549; 0.010 FDR: 7,549; 0.001 FDR: 6,593
7:21:57.234750 PROGRESS: 
7:21:57.242749 PROGRESS: Protein Summary:
7:21:57.282751 PROGRESS: Channel   0:	 0.050 FDR: 3,634; 0.010 FDR: 3,634; 0.001 FDR: 3,289
7:21:57.287749 PROGRESS: =========================================================================
7:21:57.300751 INFO: Target number of precursors reached.
7:21:57.595279 INFO: fragments_df: keeping 5000 of 340251 [sum(precursor_idx_mask)=176340 sum(mass_error_mask)=340251 stop_rank=5000
7:21:57.715286 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:22:04.762529 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:22:11.968187 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:22:15.538028 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:22:15.546027 INFO: Using score_cutoff 50.46316609954834 (fac=0.99, q=1)
7:22:15.552029 INFO: Updating optimization_manager: fwhm_rt             : 2.692659854888916 -> 2.688490152359009
7:22:15.556028 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:22:15.561024 INFO: Updating optimization_manager: score_cutoff        : 49.97592139663696 -> 50.46316609954834
7:22:15.565027 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:22:15.583028 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:22:15.643028 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:22:15.718028 INFO: === checking if optimization conditions were reached ===
7:22:15.726027 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
7:22:15.761555 INFO: Updating optimization_manager: rt_error            : 17.235610398101567 -> 16.213523585436505
7:22:15.769571 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.2135.
7:22:15.777570 INFO: ==============================================
7:22:15.785571 INFO: Starting optimization step 5.
7:22:15.794572 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:22:15.803570 INFO: Using classic extraction backend
7:22:15.811570 PROGRESS: Extracting batch of 15870 precursors
7:22:15.822571 INFO: === Search parameters used ===
7:22:15.831572 INFO: rt_error       : 16.213523585436505
7:22:15.842571 INFO: mobility_error : 0.1
7:22:15.853571 INFO: num_candidates : 3
7:22:15.866572 INFO: ms1_error      : 5.0
7:22:15.878574 INFO: ms2_error      : 10.0
7:22:15.889570 INFO: fwhm_rt        : 2.688490152359009
7:22:15.900574 INFO: quant_window   : 3
7:22:15.912573 INFO: ==============================================
7:22:15.979573 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:22:15.980577 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:22:15.982576 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:22:15.983577 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:22:15.985575 INFO: Starting candidate selection
7:22:16.672456 INFO: Starting candidate scoring
7:22:18.060020 INFO: Finished candidate processing
7:22:18.062026 INFO: Collecting candidate features
7:22:18.391580 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 43296)
7:22:18.393581 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43296)
7:22:18.409578 INFO: Collecting fragment features
7:22:18.556128 INFO: Finished candidate scoring
7:22:18.628130 INFO: performing precursor FDR with 47 features
7:22:18.630127 INFO: Decoy channel: -1
7:22:18.631129 INFO: Competetive: True
7:22:18.740122 INFO: Setting torch num_threads to 2 for FDR classification task
7:22:18.808642 WARNING: dropped 2 target PSMs due to missing features
7:22:18.809643 WARNING: dropped 3 decoy PSMs due to missing features
7:22:18.841642 INFO: Using random state 804472 for train-test-split
7:22:20.029937 INFO: Test AUC: 0.775
7:22:20.030935 INFO: Train AUC: 0.784
7:22:20.031935 INFO: AUC difference: 1.08%
7:22:20.729094 INFO: Resetting torch num_threads to 10
7:22:20.741093 PROGRESS: === Extracted 43296 precursors and 341311 fragments ===
7:22:20.747094 INFO: === FDR correction performed with classifier version 5 ===
7:22:20.763112 PROGRESS: ============================= Precursor FDR =============================
7:22:20.767112 PROGRESS: Total precursors accumulated: 7,597
7:22:20.770631 PROGRESS: Target precursors: 7,544 (99.30%)
7:22:20.774648 PROGRESS: Decoy precursors: 53 (0.70%)
7:22:20.778643 PROGRESS: 
7:22:20.782646 PROGRESS: Precursor Summary:
7:22:20.814647 PROGRESS: Channel   0:	 0.050 FDR: 7,544; 0.010 FDR: 7,544; 0.001 FDR: 6,741
7:22:20.819647 PROGRESS: 
7:22:20.824646 PROGRESS: Protein Summary:
7:22:20.863648 PROGRESS: Channel   0:	 0.050 FDR: 3,633; 0.010 FDR: 3,633; 0.001 FDR: 3,336
7:22:20.872647 PROGRESS: =========================================================================
7:22:20.887646 INFO: Target number of precursors reached.
7:22:21.155194 INFO: fragments_df: keeping 5000 of 341311 [sum(precursor_idx_mask)=177013 sum(mass_error_mask)=341311 stop_rank=5000
7:22:21.270211 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:22:28.528143 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:22:35.711167 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:22:39.281525 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:22:39.288523 INFO: Using score_cutoff 51.31439003677368 (fac=0.99, q=1)
7:22:39.293523 INFO: Updating optimization_manager: fwhm_rt             : 2.688490152359009 -> 2.6835713386535645
7:22:39.298538 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:22:39.302538 INFO: Updating optimization_manager: score_cutoff        : 50.46316609954834 -> 51.31439003677368
7:22:39.306534 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:22:39.338074 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:22:39.415077 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:22:39.498078 INFO: === checking if optimization conditions were reached ===
7:22:39.505078 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
7:22:39.536082 INFO: Updating optimization_manager: rt_error            : 16.213523585436505 -> 16.48788730117861
7:22:39.542079 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 16.4879.
7:22:39.548081 INFO: ==============================================
7:22:39.554097 INFO: Starting optimization step 6.
7:22:39.559096 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:22:39.564630 INFO: Using classic extraction backend
7:22:39.569624 PROGRESS: Extracting batch of 15870 precursors
7:22:39.573634 INFO: === Search parameters used ===
7:22:39.578632 INFO: rt_error       : 16.48788730117861
7:22:39.583623 INFO: mobility_error : 0.1
7:22:39.586629 INFO: num_candidates : 3
7:22:39.590626 INFO: ms1_error      : 5.0
7:22:39.593625 INFO: ms2_error      : 10.0
7:22:39.597625 INFO: fwhm_rt        : 2.6835713386535645
7:22:39.603619 INFO: quant_window   : 3
7:22:39.609621 INFO: ==============================================
7:22:39.663622 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:22:39.664621 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:22:39.665622 INFO: FWHM in RT is 2.68 seconds, sigma is 0.30
7:22:39.666622 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:22:39.668624 INFO: Starting candidate selection
7:22:40.339418 INFO: Starting candidate scoring
7:22:41.748325 INFO: Finished candidate processing
7:22:41.750331 INFO: Collecting candidate features
7:22:42.078563 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 43232)
7:22:42.080565 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43232)
7:22:42.098563 INFO: Collecting fragment features
7:22:42.246556 INFO: Finished candidate scoring
7:22:42.302559 INFO: performing precursor FDR with 47 features
7:22:42.303566 INFO: Decoy channel: -1
7:22:42.303566 INFO: Competetive: True
7:22:42.411080 INFO: Setting torch num_threads to 2 for FDR classification task
7:22:42.477083 WARNING: dropped 1 target PSMs due to missing features
7:22:42.478082 WARNING: dropped 2 decoy PSMs due to missing features
7:22:42.509084 INFO: Using random state 804472 for train-test-split
7:22:43.708555 INFO: Test AUC: 0.772
7:22:43.709554 INFO: Train AUC: 0.786
7:22:43.710554 INFO: AUC difference: 1.83%
7:22:44.362195 INFO: Resetting torch num_threads to 10
7:22:44.375202 PROGRESS: === Extracted 43232 precursors and 340748 fragments ===
7:22:44.381197 INFO: === FDR correction performed with classifier version 5 ===
7:22:44.397199 PROGRESS: ============================= Precursor FDR =============================
7:22:44.401196 PROGRESS: Total precursors accumulated: 7,583
7:22:44.405198 PROGRESS: Target precursors: 7,526 (99.25%)
7:22:44.409194 PROGRESS: Decoy precursors: 57 (0.75%)
7:22:44.414199 PROGRESS: 
7:22:44.419197 PROGRESS: Precursor Summary:
7:22:44.468195 PROGRESS: Channel   0:	 0.050 FDR: 7,526; 0.010 FDR: 7,526; 0.001 FDR: 6,867
7:22:44.473195 PROGRESS: 
7:22:44.481196 PROGRESS: Protein Summary:
7:22:44.530192 PROGRESS: Channel   0:	 0.050 FDR: 3,633; 0.010 FDR: 3,633; 0.001 FDR: 3,397
7:22:44.540193 PROGRESS: =========================================================================
7:22:44.560200 INFO: Target number of precursors reached.
7:22:44.834067 INFO: fragments_df: keeping 5000 of 340748 [sum(precursor_idx_mask)=176433 sum(mass_error_mask)=340748 stop_rank=5000
7:22:44.946068 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:22:51.995297 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:22:59.124485 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:23:02.699081 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:23:02.705080 INFO: Using score_cutoff 51.21070930480957 (fac=0.99, q=1)
7:23:02.710081 INFO: Updating optimization_manager: fwhm_rt             : 2.6835713386535645 -> 2.689620018005371
7:23:02.714080 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:23:02.717080 INFO: Updating optimization_manager: score_cutoff        : 51.31439003677368 -> 51.21070930480957
7:23:02.721080 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:23:02.738081 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:23:02.798082 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:23:02.871605 INFO: === checking if optimization conditions were reached ===
7:23:02.876605 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
7:23:02.881605 INFO: Updating optimization_manager: rt_error            : 16.48788730117861 -> 16.213523585436505
7:23:02.885604 INFO: Updating optimization_manager: classifier_version  : 5 -> 11
7:23:02.889603 INFO: Updating optimization_manager: score_cutoff        : 51.21070930480957 -> 51.31439003677368
7:23:02.893604 INFO: Updating optimization_manager: fwhm_rt             : 2.689620018005371 -> 2.6835713386535645
7:23:02.897604 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:23:02.901605 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.2135 found after 7 searches.
7:23:02.905605 INFO: ==============================================
7:23:02.909605 PROGRESS: Optimization finished for rt_error.
7:23:03.004605 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:23:03.025608 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:23:03.089607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:23:03.249129 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
7:23:03.257129 PROGRESS: ==============================================
7:23:03.264129 PROGRESS: ms2_error      : 10.0000
7:23:03.271131 PROGRESS: ms1_error      : 5.0000
7:23:03.281130 PROGRESS: rt_error       : 16.2135
7:23:03.289129 PROGRESS: ==============================================
7:23:03.327129 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:23:03.472653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:23:03.677175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:23:04.153223 INFO: Using classic extraction backend
7:23:04.158220 PROGRESS: Extracting batch of 121155 precursors
7:23:04.162220 INFO: === Search parameters used ===
7:23:04.166220 INFO: rt_error       : 16.213523585436505
7:23:04.170220 INFO: mobility_error : 0.1
7:23:04.173221 INFO: num_candidates : 3
7:23:04.177222 INFO: ms1_error      : 5.0
7:23:04.181221 INFO: ms2_error      : 10.0
7:23:04.184221 INFO: fwhm_rt        : 2.6835713386535645
7:23:04.188221 INFO: quant_window   : 3
7:23:04.192220 INFO: ==============================================
7:23:04.290222 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:23:04.291223 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:23:04.292223 INFO: FWHM in RT is 2.68 seconds, sigma is 0.30
7:23:04.293223 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:23:04.294222 INFO: Starting candidate selection
7:23:08.707683 INFO: Removed 120969 precursors with score below cutoff 51.31439003677368
7:23:08.842686 INFO: Starting candidate scoring
7:23:15.017543 INFO: Finished candidate processing
7:23:15.018986 INFO: Collecting candidate features
7:23:15.923180 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 209245)
7:23:15.987180 INFO: Collecting fragment features
7:23:16.403282 INFO: Finished candidate scoring
7:23:16.613284 INFO: === Performing FDR correction with classifier version 11 ===
7:23:16.619296 INFO: performing precursor FDR with 47 features
7:23:16.620300 INFO: Decoy channel: -1
7:23:16.621299 INFO: Competetive: True
7:23:16.939384 INFO: Setting torch num_threads to 2 for FDR classification task
7:23:17.038385 WARNING: dropped 1 decoy PSMs due to missing features
7:23:17.039385 WARNING: FDR calculation for 119110 target and 90134 decoy PSMs
7:23:17.040382 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
7:23:17.253935 INFO: Using random state 818949 for train-test-split
7:23:23.786291 INFO: Test AUC: 0.853
7:23:23.788289 INFO: Train AUC: 0.859
7:23:23.789289 INFO: AUC difference: 0.70%
7:23:24.702390 INFO: Resetting torch num_threads to 10
7:23:24.763391 INFO: Removing fragments below FDR threshold
7:23:25.014915 PROGRESS: ============================= Precursor FDR =============================
7:23:25.018914 PROGRESS: Total precursors accumulated: 57,344
7:23:25.022915 PROGRESS: Target precursors: 56,939 (99.29%)
7:23:25.025914 PROGRESS: Decoy precursors: 405 (0.71%)
7:23:25.029915 PROGRESS: 
7:23:25.033914 PROGRESS: Precursor Summary:
7:23:25.201440 PROGRESS: Channel   0:	 0.050 FDR: 56,939; 0.010 FDR: 56,939; 0.001 FDR: 55,544
7:23:25.206439 PROGRESS: 
7:23:25.209439 PROGRESS: Protein Summary:
7:23:25.430964 PROGRESS: Channel   0:	 0.050 FDR: 6,521; 0.010 FDR: 6,521; 0.001 FDR: 6,508
7:23:25.435964 PROGRESS: =========================================================================
7:23:25.477965 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\psm.parquet
7:23:26.756604 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\frag.parquet
7:23:28.071534 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
7:23:28.365161 PROGRESS: 
7:23:28.366159 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant
7:23:28.368161 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\figures
7:23:28.376163 INFO: Initializing TimingManager
7:23:28.391160 INFO: Initializing RawFileManager
7:28:25.940137 INFO: Determining DIA cycle
7:28:25.962139 INFO: Found cycle with start 0.00 min and length 86.
7:28:26.600184 INFO: RT (min)            : 0.0 - 55.4
7:28:26.602185 INFO: RT duration (sec)   : 3325.7
7:28:26.602185 INFO: RT duration (min)   : 55.4
7:28:26.603184 INFO: Cycle len (scans)   : 86
7:28:26.604184 INFO: Cycle len (sec)     : 1.90
7:28:26.605186 INFO: Number of cycles    : 1747
7:28:26.606183 INFO: MS2 range (m/z)     : 399.5 - 903.5
7:28:26.607184 INFO: Creating DIA data object took: 298.2090127468109
7:28:26.687703 INFO: Initializing CalibrationManager
7:28:26.693705 INFO: Setting up calibration estimators ..
7:28:26.697702 INFO: Found 1 estimator(s) in calibration group 'fragment'
7:28:26.700703 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'}' ..
7:28:26.704702 INFO: Found 3 estimator(s) in calibration group 'precursor'
7:28:26.707700 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
7:28:26.711704 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}}' ..
7:28:26.714702 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
7:28:26.718703 INFO: Done setting up calibration estimators.
7:28:26.721706 INFO: Initializing OptimizationManager
7:28:26.727704 INFO: initial parameter: ms1_error = 30
7:28:26.731704 INFO: initial parameter: ms2_error = 30
7:28:26.734702 INFO: initial parameter: rt_error = 1662.873046875
7:28:26.738705 INFO: initial parameter: mobility_error = 0.1
7:28:26.741703 INFO: initial parameter: num_candidates = 1
7:28:26.744703 INFO: initial parameter: fwhm_rt = 5
7:28:26.748702 INFO: initial parameter: fwhm_mobility = 0.01
7:28:26.751703 INFO: initial parameter: score_cutoff = 0
7:28:26.755700 INFO: initial parameter: classifier_version = -1
7:28:26.761702 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
7:28:26.764701 INFO: FDRManager: loading saved state not requested, will be initialized.
7:28:26.765699 INFO: Initializing FDRManager
7:28:26.766700 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
7:28:26.832700 PROGRESS: Initializing spectral library: 61,104 target precursors potentially observable (0 removed)
7:28:26.938242 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
7:28:26.947242 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 1662.873046875
7:28:26.953241 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
7:28:26.959242 PROGRESS: Starting initial search for precursors.
7:28:26.968241 INFO: Starting optimization step 0.
7:28:26.977241 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:28:26.984241 INFO: Using classic extraction backend
7:28:26.992242 PROGRESS: Extracting batch of 15870 precursors
7:28:26.998243 INFO: === Search parameters used ===
7:28:27.006245 INFO: rt_error       : 1662.873046875
7:28:27.014244 INFO: mobility_error : 0.1
7:28:27.023247 INFO: num_candidates : 1
7:28:27.030250 INFO: ms1_error      : 30
7:28:27.038249 INFO: ms2_error      : 30
7:28:27.049250 INFO: fwhm_rt        : 5
7:28:27.057250 INFO: quant_window   : 3
7:28:27.085246 INFO: ==============================================
7:28:27.135789 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:28:27.136792 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:28:27.137793 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
7:28:27.138788 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
7:28:27.139793 INFO: Starting candidate selection
7:28:41.043175 INFO: Starting candidate scoring
7:28:41.631244 INFO: Finished candidate processing
7:28:41.633160 INFO: Collecting candidate features
7:28:41.744159 INFO: Collecting fragment features
7:28:41.833160 INFO: Finished candidate scoring
7:28:41.860167 INFO: performing precursor FDR with 47 features
7:28:41.861164 INFO: Decoy channel: -1
7:28:41.862169 INFO: Competetive: True
7:28:41.890703 INFO: Setting torch num_threads to 2 for FDR classification task
7:28:41.916703 INFO: Using random state 259133 for train-test-split
7:28:42.251751 INFO: Test AUC: 0.792
7:28:42.252743 INFO: Train AUC: 0.802
7:28:42.253748 INFO: AUC difference: 1.30%
7:28:42.759935 INFO: Resetting torch num_threads to 10
7:28:42.766935 PROGRESS: === Extracted 15870 precursors and 162127 fragments ===
7:28:42.771936 INFO: === FDR correction performed with classifier version -1 ===
7:28:42.783123 PROGRESS: ============================= Precursor FDR =============================
7:28:42.788122 PROGRESS: Total precursors accumulated: 4,071
7:28:42.792891 PROGRESS: Target precursors: 3,889 (95.53%)
7:28:42.796996 PROGRESS: Decoy precursors: 182 (4.47%)
7:28:42.801272 PROGRESS: 
7:28:42.806305 PROGRESS: Precursor Summary:
7:28:42.819303 PROGRESS: Channel   0:	 0.050 FDR: 3,889; 0.010 FDR: 1,403; 0.001 FDR:     0
7:28:42.824323 PROGRESS: 
7:28:42.828320 PROGRESS: Protein Summary:
7:28:42.841263 PROGRESS: Channel   0:	 0.050 FDR: 2,264; 0.010 FDR: 1,038; 0.001 FDR:     0
7:28:42.846260 PROGRESS: =========================================================================
7:28:42.850264 INFO: Target number of precursors reached.
7:28:42.893800 INFO: fragments_df: keeping 5000 of 162127 [sum(precursor_idx_mask)=16197 sum(mass_error_mask)=162127 stop_rank=5000
7:28:42.967513 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:28:43.548350 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:28:44.134442 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:28:47.163513 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
7:28:47.169515 INFO: Using score_cutoff 78.5774642349243 (fac=0.99, q=1)
7:28:47.173514 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.364954948425293
7:28:47.177512 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
7:28:47.180512 INFO: Updating optimization_manager: score_cutoff        : 0 -> 78.5774642349243
7:28:47.184276 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:28:47.198293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:28:47.237295 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:28:47.300291 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
7:28:47.303293 PROGRESS: Required number of precursors found. Starting search parameter optimization.
7:28:47.306293 INFO: Starting optimization step 1.
7:28:47.310293 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:28:47.313294 INFO: Using classic extraction backend
7:28:47.316295 PROGRESS: Extracting batch of 15870 precursors
7:28:47.319295 INFO: === Search parameters used ===
7:28:47.322297 INFO: rt_error       : 1662.873046875
7:28:47.326296 INFO: mobility_error : 0.1
7:28:47.329298 INFO: num_candidates : 3
7:28:47.332297 INFO: ms1_error      : 30
7:28:47.336298 INFO: ms2_error      : 30
7:28:47.340298 INFO: fwhm_rt        : 2.364954948425293
7:28:47.346299 INFO: quant_window   : 3
7:28:47.353299 INFO: ==============================================
7:28:47.397853 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:28:47.398849 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:28:47.399855 INFO: FWHM in RT is 2.36 seconds, sigma is 0.26
7:28:47.401849 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:28:47.402853 INFO: Starting candidate selection
7:29:02.976892 INFO: Starting candidate scoring
7:29:04.448738 INFO: Finished candidate processing
7:29:04.450744 INFO: Collecting candidate features
7:29:04.720297 INFO: Collecting fragment features
7:29:04.847298 INFO: Finished candidate scoring
7:29:04.895159 INFO: performing precursor FDR with 47 features
7:29:04.895159 INFO: Decoy channel: -1
7:29:04.896160 INFO: Competetive: True
7:29:04.960706 INFO: Setting torch num_threads to 2 for FDR classification task
7:29:05.008704 INFO: Using random state 471959 for train-test-split
7:29:05.967195 INFO: Test AUC: 0.680
7:29:05.968834 INFO: Train AUC: 0.689
7:29:05.968834 INFO: AUC difference: 1.27%
7:29:06.505266 INFO: Resetting torch num_threads to 10
7:29:06.514264 PROGRESS: === Extracted 47608 precursors and 458104 fragments ===
7:29:06.519302 INFO: === FDR correction performed with classifier version 0 ===
7:29:06.529302 PROGRESS: ============================= Precursor FDR =============================
7:29:06.534056 PROGRESS: Total precursors accumulated: 6,552
7:29:06.539058 PROGRESS: Target precursors: 6,397 (97.63%)
7:29:06.544026 PROGRESS: Decoy precursors: 155 (2.37%)
7:29:06.548025 PROGRESS: 
7:29:06.552030 PROGRESS: Precursor Summary:
7:29:06.572024 PROGRESS: Channel   0:	 0.050 FDR: 6,397; 0.010 FDR: 5,733; 0.001 FDR: 4,201
7:29:06.576776 PROGRESS: 
7:29:06.580769 PROGRESS: Protein Summary:
7:29:06.601772 PROGRESS: Channel   0:	 0.050 FDR: 3,203; 0.010 FDR: 2,954; 0.001 FDR: 2,368
7:29:06.605769 PROGRESS: =========================================================================
7:29:06.615770 INFO: Target number of precursors reached.
7:29:06.847287 INFO: fragments_df: keeping 5000 of 458104 [sum(precursor_idx_mask)=172387 sum(mass_error_mask)=458104 stop_rank=5000
7:29:06.922211 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:29:10.786484 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:29:14.744482 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:29:17.721827 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:29:17.726828 INFO: Using score_cutoff 75.13945644836426 (fac=0.99, q=1)
7:29:17.730828 INFO: Updating optimization_manager: fwhm_rt             : 2.364954948425293 -> 2.7209815979003906
7:29:17.734828 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:29:17.737826 INFO: Updating optimization_manager: score_cutoff        : 78.5774642349243 -> 75.13945644836426
7:29:17.740829 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:29:17.753827 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:29:17.792827 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:29:17.853826 INFO: === checking if optimization conditions were reached ===
7:29:17.860830 INFO: Updating optimization_manager: ms2_error           : 30 -> 24.325362861095215
7:29:17.864828 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
7:29:17.871829 PROGRESS: ❌ ms2_error      : 24.3254 > 10.0000 or insufficient steps taken.
7:29:17.881829 INFO: Updating optimization_manager: ms1_error           : 30 -> 14.19266924992988
7:29:17.888825 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
7:29:17.894829 PROGRESS: ❌ ms1_error      : 14.1927 > 5.0000 or insufficient steps taken.
7:29:17.898830 INFO: ==============================================
7:29:17.902829 INFO: Starting optimization step 2.
7:29:17.909830 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:29:17.917830 INFO: Using classic extraction backend
7:29:17.924825 PROGRESS: Extracting batch of 15870 precursors
7:29:17.932826 INFO: === Search parameters used ===
7:29:17.938838 INFO: rt_error       : 1662.873046875
7:29:17.945840 INFO: mobility_error : 0.1
7:29:17.950356 INFO: num_candidates : 3
7:29:17.970361 INFO: ms1_error      : 14.19266924992988
7:29:17.977358 INFO: ms2_error      : 24.325362861095215
7:29:17.985361 INFO: fwhm_rt        : 2.7209815979003906
7:29:17.993361 INFO: quant_window   : 3
7:29:18.001362 INFO: ==============================================
7:29:18.048360 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:29:18.049357 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:29:18.050358 INFO: FWHM in RT is 2.72 seconds, sigma is 0.30
7:29:18.051360 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:29:18.052361 INFO: Starting candidate selection
7:29:31.807393 INFO: Starting candidate scoring
7:29:33.135244 INFO: Finished candidate processing
7:29:33.137260 INFO: Collecting candidate features
7:29:33.400863 INFO: Collecting fragment features
7:29:33.529465 INFO: Finished candidate scoring
7:29:33.577465 INFO: performing precursor FDR with 47 features
7:29:33.578467 INFO: Decoy channel: -1
7:29:33.578467 INFO: Competetive: True
7:29:33.644466 INFO: Setting torch num_threads to 2 for FDR classification task
7:29:33.694466 INFO: Using random state 473857 for train-test-split
7:29:34.667278 INFO: Test AUC: 0.695
7:29:34.668279 INFO: Train AUC: 0.706
7:29:34.669280 INFO: AUC difference: 1.50%
7:29:35.237428 INFO: Resetting torch num_threads to 10
7:29:35.246428 PROGRESS: === Extracted 47608 precursors and 448252 fragments ===
7:29:35.251430 INFO: === FDR correction performed with classifier version 1 ===
7:29:35.261430 PROGRESS: ============================= Precursor FDR =============================
7:29:35.265431 PROGRESS: Total precursors accumulated: 6,867
7:29:35.268431 PROGRESS: Target precursors: 6,731 (98.02%)
7:29:35.271430 PROGRESS: Decoy precursors: 136 (1.98%)
7:29:35.275431 PROGRESS: 
7:29:35.278430 PROGRESS: Precursor Summary:
7:29:35.296431 PROGRESS: Channel   0:	 0.050 FDR: 6,731; 0.010 FDR: 6,355; 0.001 FDR: 5,307
7:29:35.299430 PROGRESS: 
7:29:35.303430 PROGRESS: Protein Summary:
7:29:35.322430 PROGRESS: Channel   0:	 0.050 FDR: 3,312; 0.010 FDR: 3,172; 0.001 FDR: 2,786
7:29:35.326431 PROGRESS: =========================================================================
7:29:35.334434 INFO: Target number of precursors reached.
7:29:35.549959 INFO: fragments_df: keeping 5000 of 448252 [sum(precursor_idx_mask)=187292 sum(mass_error_mask)=448252 stop_rank=5000
7:29:35.626962 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:29:40.085540 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:29:45.471316 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:29:48.928508 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:29:48.933506 INFO: Using score_cutoff 70.02615282440185 (fac=0.99, q=1)
7:29:48.937506 INFO: Updating optimization_manager: fwhm_rt             : 2.7209815979003906 -> 2.7042722702026367
7:29:48.940507 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:29:48.944507 INFO: Updating optimization_manager: score_cutoff        : 75.13945644836426 -> 70.02615282440185
7:29:48.947506 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:29:48.961506 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:29:49.002525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:29:49.070119 INFO: === checking if optimization conditions were reached ===
7:29:49.079119 INFO: Updating optimization_manager: ms2_error           : 24.325362861095215 -> 19.79017354050918
7:29:49.083116 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
7:29:49.086119 PROGRESS: ❌ ms2_error      : 19.7902 > 10.0000 or insufficient steps taken.
7:29:49.095120 INFO: Updating optimization_manager: ms1_error           : 14.19266924992988 -> 5.506125433271951
7:29:49.099119 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
7:29:49.102121 PROGRESS: ❌ ms1_error      : 5.5061 > 5.0000 or insufficient steps taken.
7:29:49.106119 INFO: ==============================================
7:29:49.109121 INFO: Starting optimization step 3.
7:29:49.113119 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:29:49.116121 INFO: Using classic extraction backend
7:29:49.120120 PROGRESS: Extracting batch of 15870 precursors
7:29:49.123120 INFO: === Search parameters used ===
7:29:49.126120 INFO: rt_error       : 1662.873046875
7:29:49.130120 INFO: mobility_error : 0.1
7:29:49.134120 INFO: num_candidates : 3
7:29:49.137120 INFO: ms1_error      : 5.506125433271951
7:29:49.142120 INFO: ms2_error      : 19.79017354050918
7:29:49.146119 INFO: fwhm_rt        : 2.7042722702026367
7:29:49.151120 INFO: quant_window   : 3
7:29:49.158120 INFO: ==============================================
7:29:49.199120 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:29:49.200121 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:29:49.201122 INFO: FWHM in RT is 2.70 seconds, sigma is 0.30
7:29:49.202121 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:29:49.203122 INFO: Starting candidate selection
7:30:04.384920 INFO: Starting candidate scoring
7:30:05.850540 INFO: Finished candidate processing
7:30:05.852548 INFO: Collecting candidate features
7:30:06.132070 INFO: Collecting fragment features
7:30:06.264070 INFO: Finished candidate scoring
7:30:06.331592 INFO: performing precursor FDR with 47 features
7:30:06.332591 INFO: Decoy channel: -1
7:30:06.333592 INFO: Competetive: True
7:30:06.400593 INFO: Setting torch num_threads to 2 for FDR classification task
7:30:06.452594 INFO: Using random state 679497 for train-test-split
7:30:07.546998 INFO: Test AUC: 0.700
7:30:07.549000 INFO: Train AUC: 0.712
7:30:07.549000 INFO: AUC difference: 1.66%
7:30:08.183060 INFO: Resetting torch num_threads to 10
7:30:08.192060 PROGRESS: === Extracted 47607 precursors and 437751 fragments ===
7:30:08.198062 INFO: === FDR correction performed with classifier version 2 ===
7:30:08.209060 PROGRESS: ============================= Precursor FDR =============================
7:30:08.215059 PROGRESS: Total precursors accumulated: 7,062
7:30:08.219060 PROGRESS: Target precursors: 6,954 (98.47%)
7:30:08.223060 PROGRESS: Decoy precursors: 108 (1.53%)
7:30:08.227059 PROGRESS: 
7:30:08.230059 PROGRESS: Precursor Summary:
7:30:08.252056 PROGRESS: Channel   0:	 0.050 FDR: 6,954; 0.010 FDR: 6,780; 0.001 FDR: 5,263
7:30:08.256055 PROGRESS: 
7:30:08.259055 PROGRESS: Protein Summary:
7:30:08.281059 PROGRESS: Channel   0:	 0.050 FDR: 3,397; 0.010 FDR: 3,327; 0.001 FDR: 2,791
7:30:08.285061 PROGRESS: =========================================================================
7:30:08.293571 INFO: Target number of precursors reached.
7:30:08.538166 INFO: fragments_df: keeping 5000 of 437751 [sum(precursor_idx_mask)=195981 sum(mass_error_mask)=437751 stop_rank=5000
7:30:08.616185 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:30:14.562994 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:30:20.075062 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:30:23.533787 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:30:23.537786 INFO: Using score_cutoff 64.92142740783692 (fac=0.99, q=1)
7:30:23.542787 INFO: Updating optimization_manager: fwhm_rt             : 2.7042722702026367 -> 2.6907663345336914
7:30:23.545782 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:30:23.549784 INFO: Updating optimization_manager: score_cutoff        : 70.02615282440185 -> 64.92142740783692
7:30:23.552783 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:30:23.567795 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:30:23.610380 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:30:23.677379 INFO: === checking if optimization conditions were reached ===
7:30:23.686378 INFO: Updating optimization_manager: ms2_error           : 19.79017354050918 -> 15.644333815644451
7:30:23.690379 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
7:30:23.693379 PROGRESS: ❌ ms2_error      : 15.6443 > 10.0000 or insufficient steps taken.
7:30:23.702379 INFO: Updating optimization_manager: ms1_error           : 5.506125433271951 -> 5.0
7:30:23.706379 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
7:30:23.710380 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:30:23.713381 INFO: ==============================================
7:30:23.717379 INFO: Starting optimization step 4.
7:30:23.720378 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:30:23.724376 INFO: Using classic extraction backend
7:30:23.728379 PROGRESS: Extracting batch of 15870 precursors
7:30:23.731379 INFO: === Search parameters used ===
7:30:23.735379 INFO: rt_error       : 1662.873046875
7:30:23.738379 INFO: mobility_error : 0.1
7:30:23.743377 INFO: num_candidates : 3
7:30:23.748377 INFO: ms1_error      : 5.0
7:30:23.752376 INFO: ms2_error      : 15.644333815644451
7:30:23.757376 INFO: fwhm_rt        : 2.6907663345336914
7:30:23.763374 INFO: quant_window   : 3
7:30:23.772376 INFO: ==============================================
7:30:23.821391 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:30:23.822393 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:30:23.822393 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:30:23.823906 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:30:23.824922 INFO: Starting candidate selection
7:30:38.935139 INFO: Starting candidate scoring
7:30:40.369324 INFO: Finished candidate processing
7:30:40.370463 INFO: Collecting candidate features
7:30:40.638014 INFO: Collecting fragment features
7:30:40.767012 INFO: Finished candidate scoring
7:30:40.815013 INFO: performing precursor FDR with 47 features
7:30:40.816013 INFO: Decoy channel: -1
7:30:40.817012 INFO: Competetive: True
7:30:40.881146 INFO: Setting torch num_threads to 2 for FDR classification task
7:30:40.930145 INFO: Using random state 374856 for train-test-split
7:30:42.063550 INFO: Test AUC: 0.696
7:30:42.064551 INFO: Train AUC: 0.714
7:30:42.065550 INFO: AUC difference: 2.60%
7:30:42.720183 INFO: Resetting torch num_threads to 10
7:30:42.730185 PROGRESS: === Extracted 47607 precursors and 427026 fragments ===
7:30:42.735185 INFO: === FDR correction performed with classifier version 3 ===
7:30:42.755183 PROGRESS: ============================= Precursor FDR =============================
7:30:42.759184 PROGRESS: Total precursors accumulated: 7,137
7:30:42.762183 PROGRESS: Target precursors: 7,038 (98.61%)
7:30:42.766184 PROGRESS: Decoy precursors: 99 (1.39%)
7:30:42.772184 PROGRESS: 
7:30:42.780184 PROGRESS: Precursor Summary:
7:30:42.806186 PROGRESS: Channel   0:	 0.050 FDR: 7,038; 0.010 FDR: 6,949; 0.001 FDR: 5,436
7:30:42.810184 PROGRESS: 
7:30:42.813185 PROGRESS: Protein Summary:
7:30:42.837197 PROGRESS: Channel   0:	 0.050 FDR: 3,425; 0.010 FDR: 3,395; 0.001 FDR: 2,868
7:30:42.840195 PROGRESS: =========================================================================
7:30:42.849195 INFO: Target number of precursors reached.
7:30:43.107256 INFO: fragments_df: keeping 5000 of 427026 [sum(precursor_idx_mask)=196736 sum(mass_error_mask)=427026 stop_rank=5000
7:30:43.186255 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:30:49.485335 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:30:55.932033 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:30:59.224575 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:30:59.230573 INFO: Using score_cutoff 61.63894355163574 (fac=0.99, q=1)
7:30:59.236573 INFO: Updating optimization_manager: fwhm_rt             : 2.6907663345336914 -> 2.6651992797851562
7:30:59.240576 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:30:59.245573 INFO: Updating optimization_manager: score_cutoff        : 64.92142740783692 -> 61.63894355163574
7:30:59.249573 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:30:59.265573 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:30:59.309577 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:30:59.381597 INFO: === checking if optimization conditions were reached ===
7:30:59.403131 INFO: Updating optimization_manager: ms2_error           : 15.644333815644451 -> 11.881115710510157
7:30:59.413130 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
7:30:59.423127 PROGRESS: ❌ ms2_error      : 11.8811 > 10.0000 or insufficient steps taken.
7:30:59.431131 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:30:59.439129 INFO: ==============================================
7:30:59.448129 INFO: Starting optimization step 5.
7:30:59.478133 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:30:59.487131 INFO: Using classic extraction backend
7:30:59.496129 PROGRESS: Extracting batch of 15870 precursors
7:30:59.502131 INFO: === Search parameters used ===
7:30:59.510129 INFO: rt_error       : 1662.873046875
7:30:59.519131 INFO: mobility_error : 0.1
7:30:59.529130 INFO: num_candidates : 3
7:30:59.540130 INFO: ms1_error      : 5.0
7:30:59.551132 INFO: ms2_error      : 11.881115710510157
7:30:59.558132 INFO: fwhm_rt        : 2.6651992797851562
7:30:59.568131 INFO: quant_window   : 3
7:30:59.578130 INFO: ==============================================
7:30:59.634146 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:30:59.635144 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:30:59.637144 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:30:59.638144 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:30:59.639656 INFO: Starting candidate selection
7:31:13.158914 INFO: Starting candidate scoring
7:31:14.416290 INFO: Finished candidate processing
7:31:14.418292 INFO: Collecting candidate features
7:31:14.683839 INFO: Collecting fragment features
7:31:14.798840 INFO: Finished candidate scoring
7:31:14.846836 INFO: performing precursor FDR with 47 features
7:31:14.847834 INFO: Decoy channel: -1
7:31:14.848835 INFO: Competetive: True
7:31:14.911358 INFO: Setting torch num_threads to 2 for FDR classification task
7:31:14.959371 INFO: Using random state 696625 for train-test-split
7:31:15.971850 INFO: Test AUC: 0.701
7:31:15.973848 INFO: Train AUC: 0.714
7:31:15.974847 INFO: AUC difference: 1.81%
7:31:18.615304 INFO: Resetting torch num_threads to 10
7:31:18.624304 PROGRESS: === Extracted 47603 precursors and 412421 fragments ===
7:31:18.630306 INFO: === FDR correction performed with classifier version 4 ===
7:31:18.641306 PROGRESS: ============================= Precursor FDR =============================
7:31:18.645305 PROGRESS: Total precursors accumulated: 7,167
7:31:18.648304 PROGRESS: Target precursors: 7,078 (98.76%)
7:31:18.651307 PROGRESS: Decoy precursors: 89 (1.24%)
7:31:18.654319 PROGRESS: 
7:31:18.658321 PROGRESS: Precursor Summary:
7:31:18.677850 PROGRESS: Channel   0:	 0.050 FDR: 7,078; 0.010 FDR: 7,030; 0.001 FDR: 6,116
7:31:18.680849 PROGRESS: 
7:31:18.685849 PROGRESS: Protein Summary:
7:31:18.708849 PROGRESS: Channel   0:	 0.050 FDR: 3,448; 0.010 FDR: 3,428; 0.001 FDR: 3,106
7:31:18.714850 PROGRESS: =========================================================================
7:31:18.726849 INFO: Target number of precursors reached.
7:31:18.969966 INFO: fragments_df: keeping 5000 of 412421 [sum(precursor_idx_mask)=193432 sum(mass_error_mask)=412421 stop_rank=5000
7:31:19.068966 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:31:24.333193 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:31:29.793199 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:31:32.749280 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:31:32.754282 INFO: Using score_cutoff 58.91107979278565 (fac=0.99, q=1)
7:31:32.758281 INFO: Updating optimization_manager: fwhm_rt             : 2.6651992797851562 -> 2.6471071243286133
7:31:32.762282 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:31:32.765283 INFO: Updating optimization_manager: score_cutoff        : 61.63894355163574 -> 58.91107979278565
7:31:32.769283 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:31:32.782283 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:31:32.823283 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:31:32.883284 INFO: === checking if optimization conditions were reached ===
7:31:32.892285 INFO: Updating optimization_manager: ms2_error           : 11.881115710510157 -> 10.0
7:31:32.895286 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
7:31:32.899285 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
7:31:32.903285 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:31:32.906285 INFO: ==============================================
7:31:32.921284 PROGRESS: Optimization finished for ms2_error, ms1_error.
7:31:32.994823 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:31:33.011824 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:31:33.057823 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:31:33.123824 INFO: Starting optimization step 0.
7:31:33.131823 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:31:33.141824 INFO: Using classic extraction backend
7:31:33.149825 PROGRESS: Extracting batch of 15870 precursors
7:31:33.159825 INFO: === Search parameters used ===
7:31:33.168824 INFO: rt_error       : 1662.873046875
7:31:33.177824 INFO: mobility_error : 0.1
7:31:33.186825 INFO: num_candidates : 3
7:31:33.194838 INFO: ms1_error      : 5.0
7:31:33.213432 INFO: ms2_error      : 10.0
7:31:33.224433 INFO: fwhm_rt        : 2.6471071243286133
7:31:33.240432 INFO: quant_window   : 3
7:31:33.252433 INFO: ==============================================
7:31:33.306433 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:31:33.307433 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:31:33.309434 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:31:33.310433 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:31:33.312434 INFO: Starting candidate selection
7:31:47.451360 INFO: Starting candidate scoring
7:31:48.742095 INFO: Finished candidate processing
7:31:48.743110 INFO: Collecting candidate features
7:31:49.005710 INFO: Collecting fragment features
7:31:49.118713 INFO: Finished candidate scoring
7:31:49.166713 INFO: performing precursor FDR with 47 features
7:31:49.167714 INFO: Decoy channel: -1
7:31:49.168713 INFO: Competetive: True
7:31:49.227719 INFO: Setting torch num_threads to 2 for FDR classification task
7:31:49.276319 INFO: Using random state 735333 for train-test-split
7:31:50.246109 INFO: Test AUC: 0.715
7:31:50.247109 INFO: Train AUC: 0.716
7:31:50.247109 INFO: AUC difference: 0.21%
7:31:50.779203 INFO: Resetting torch num_threads to 10
7:31:50.787202 PROGRESS: === Extracted 47601 precursors and 407969 fragments ===
7:31:50.792202 INFO: === FDR correction performed with classifier version 5 ===
7:31:50.802204 PROGRESS: ============================= Precursor FDR =============================
7:31:50.805202 PROGRESS: Total precursors accumulated: 7,180
7:31:50.808203 PROGRESS: Target precursors: 7,088 (98.72%)
7:31:50.812204 PROGRESS: Decoy precursors: 92 (1.28%)
7:31:50.815201 PROGRESS: 
7:31:50.818205 PROGRESS: Precursor Summary:
7:31:50.835204 PROGRESS: Channel   0:	 0.050 FDR: 7,088; 0.010 FDR: 7,053; 0.001 FDR: 6,246
7:31:50.840205 PROGRESS: 
7:31:50.845201 PROGRESS: Protein Summary:
7:31:50.867204 PROGRESS: Channel   0:	 0.050 FDR: 3,442; 0.010 FDR: 3,429; 0.001 FDR: 3,138
7:31:50.870204 PROGRESS: =========================================================================
7:31:50.878203 INFO: Target number of precursors reached.
7:31:51.080750 INFO: fragments_df: keeping 5000 of 407969 [sum(precursor_idx_mask)=192273 sum(mass_error_mask)=407969 stop_rank=5000
7:31:51.152752 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:31:56.471000 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:32:01.996714 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:32:04.972150 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:32:04.979147 INFO: Using score_cutoff 57.32222269592285 (fac=0.99, q=1)
7:32:04.983151 INFO: Updating optimization_manager: fwhm_rt             : 2.6471071243286133 -> 2.6485278606414795
7:32:04.987151 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:32:04.991479 INFO: Updating optimization_manager: score_cutoff        : 58.91107979278565 -> 57.32222269592285
7:32:04.996501 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:32:05.017038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:32:05.056038 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:32:05.118043 INFO: === checking if optimization conditions were reached ===
7:32:05.124700 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
7:32:05.154721 INFO: Updating optimization_manager: rt_error            : 1662.873046875 -> 114.98380266795571
7:32:05.162215 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 114.9838.
7:32:05.170216 INFO: ==============================================
7:32:05.180216 INFO: Starting optimization step 1.
7:32:05.192213 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:32:05.201217 INFO: Using classic extraction backend
7:32:05.215218 PROGRESS: Extracting batch of 15870 precursors
7:32:05.224213 INFO: === Search parameters used ===
7:32:05.235216 INFO: rt_error       : 114.98380266795571
7:32:05.244217 INFO: mobility_error : 0.1
7:32:05.254233 INFO: num_candidates : 3
7:32:05.263343 INFO: ms1_error      : 5.0
7:32:05.273340 INFO: ms2_error      : 10.0
7:32:05.283344 INFO: fwhm_rt        : 2.6485278606414795
7:32:05.291341 INFO: quant_window   : 3
7:32:05.303346 INFO: ==============================================
7:32:05.355344 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:32:05.356340 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:32:05.358344 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:32:05.359346 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:32:05.361343 INFO: Starting candidate selection
7:32:06.705858 INFO: Starting candidate scoring
7:32:08.034115 INFO: Finished candidate processing
7:32:08.036126 INFO: Collecting candidate features
7:32:08.284680 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 47599)
7:32:08.301681 INFO: Collecting fragment features
7:32:08.415682 INFO: Finished candidate scoring
7:32:08.461683 INFO: performing precursor FDR with 47 features
7:32:08.462682 INFO: Decoy channel: -1
7:32:08.463683 INFO: Competetive: True
7:32:08.524293 INFO: Setting torch num_threads to 2 for FDR classification task
7:32:08.551295 WARNING: dropped 1 decoy PSMs due to missing features
7:32:08.575293 INFO: Using random state 735333 for train-test-split
7:32:09.556176 INFO: Test AUC: 0.702
7:32:09.557178 INFO: Train AUC: 0.726
7:32:09.557178 INFO: AUC difference: 3.30%
7:32:10.166537 INFO: Resetting torch num_threads to 10
7:32:10.175539 PROGRESS: === Extracted 47599 precursors and 400599 fragments ===
7:32:10.180543 INFO: === FDR correction performed with classifier version 5 ===
7:32:10.191543 PROGRESS: ============================= Precursor FDR =============================
7:32:10.194542 PROGRESS: Total precursors accumulated: 7,498
7:32:10.198544 PROGRESS: Target precursors: 7,430 (99.09%)
7:32:10.203539 PROGRESS: Decoy precursors: 68 (0.91%)
7:32:10.205542 PROGRESS: 
7:32:10.208542 PROGRESS: Precursor Summary:
7:32:10.228543 PROGRESS: Channel   0:	 0.050 FDR: 7,430; 0.010 FDR: 7,430; 0.001 FDR: 6,420
7:32:10.231542 PROGRESS: 
7:32:10.234544 PROGRESS: Protein Summary:
7:32:10.256557 PROGRESS: Channel   0:	 0.050 FDR: 3,582; 0.010 FDR: 3,582; 0.001 FDR: 3,214
7:32:10.259555 PROGRESS: =========================================================================
7:32:10.267559 INFO: Target number of precursors reached.
7:32:10.488089 INFO: fragments_df: keeping 5000 of 400599 [sum(precursor_idx_mask)=200602 sum(mass_error_mask)=400599 stop_rank=5000
7:32:10.563633 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:32:16.519369 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:32:22.703185 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:32:26.133592 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:32:26.138594 INFO: Using score_cutoff 54.22133648872376 (fac=0.99, q=1)
7:32:26.143595 INFO: Updating optimization_manager: fwhm_rt             : 2.6485278606414795 -> 2.672318935394287
7:32:26.147594 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:32:26.150593 INFO: Updating optimization_manager: score_cutoff        : 57.32222269592285 -> 54.22133648872376
7:32:26.154593 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:32:26.171589 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:32:26.228592 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:32:26.314129 INFO: === checking if optimization conditions were reached ===
7:32:26.319129 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
7:32:26.347131 INFO: Updating optimization_manager: rt_error            : 114.98380266795571 -> 39.43299113167215
7:32:26.366132 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 39.4330.
7:32:26.370134 INFO: ==============================================
7:32:26.374131 INFO: Starting optimization step 2.
7:32:26.378132 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:32:26.382132 INFO: Using classic extraction backend
7:32:26.386132 PROGRESS: Extracting batch of 15870 precursors
7:32:26.390133 INFO: === Search parameters used ===
7:32:26.394133 INFO: rt_error       : 39.43299113167215
7:32:26.398133 INFO: mobility_error : 0.1
7:32:26.402134 INFO: num_candidates : 3
7:32:26.406134 INFO: ms1_error      : 5.0
7:32:26.410136 INFO: ms2_error      : 10.0
7:32:26.414135 INFO: fwhm_rt        : 2.672318935394287
7:32:26.418135 INFO: quant_window   : 3
7:32:26.425130 INFO: ==============================================
7:32:26.478132 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:32:26.479133 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:32:26.480134 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:32:26.481130 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:32:26.482132 INFO: Starting candidate selection
7:32:27.282104 INFO: Starting candidate scoring
7:32:28.718683 INFO: Finished candidate processing
7:32:28.720208 INFO: Collecting candidate features
7:32:29.060348 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 47369)
7:32:29.100345 INFO: Collecting fragment features
7:32:29.261347 INFO: Finished candidate scoring
7:32:29.321863 INFO: performing precursor FDR with 47 features
7:32:29.323864 INFO: Decoy channel: -1
7:32:29.323864 INFO: Competetive: True
7:32:29.432864 INFO: Setting torch num_threads to 2 for FDR classification task
7:32:29.476870 WARNING: dropped 3 decoy PSMs due to missing features
7:32:29.510869 INFO: Using random state 735333 for train-test-split
7:32:30.873592 INFO: Test AUC: 0.732
7:32:30.874591 INFO: Train AUC: 0.741
7:32:30.875592 INFO: AUC difference: 1.27%
7:32:31.585230 INFO: Resetting torch num_threads to 10
7:32:31.598231 PROGRESS: === Extracted 47369 precursors and 382682 fragments ===
7:32:31.604229 INFO: === FDR correction performed with classifier version 5 ===
7:32:31.620229 PROGRESS: ============================= Precursor FDR =============================
7:32:31.624230 PROGRESS: Total precursors accumulated: 7,595
7:32:31.628230 PROGRESS: Target precursors: 7,535 (99.21%)
7:32:31.632231 PROGRESS: Decoy precursors: 60 (0.79%)
7:32:31.636234 PROGRESS: 
7:32:31.641231 PROGRESS: Precursor Summary:
7:32:31.675230 PROGRESS: Channel   0:	 0.050 FDR: 7,535; 0.010 FDR: 7,535; 0.001 FDR: 7,194
7:32:31.680230 PROGRESS: 
7:32:31.688231 PROGRESS: Protein Summary:
7:32:31.730230 PROGRESS: Channel   0:	 0.050 FDR: 3,617; 0.010 FDR: 3,617; 0.001 FDR: 3,495
7:32:31.738232 PROGRESS: =========================================================================
7:32:31.762230 INFO: Target number of precursors reached.
7:32:32.043776 INFO: fragments_df: keeping 5000 of 382682 [sum(precursor_idx_mask)=196363 sum(mass_error_mask)=382682 stop_rank=5000
7:32:32.153324 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:32:39.208038 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:32:46.442628 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:32:49.975025 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:32:49.980027 INFO: Using score_cutoff 51.54554135055542 (fac=0.99, q=1)
7:32:49.985025 INFO: Updating optimization_manager: fwhm_rt             : 2.672318935394287 -> 2.6752583980560303
7:32:49.988023 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:32:49.992025 INFO: Updating optimization_manager: score_cutoff        : 54.22133648872376 -> 51.54554135055542
7:32:49.996027 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:32:50.012028 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:32:50.070029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:32:50.154635 INFO: === checking if optimization conditions were reached ===
7:32:50.158635 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
7:32:50.187635 INFO: Updating optimization_manager: rt_error            : 39.43299113167215 -> 16.557902775255624
7:32:50.195636 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 16.5579.
7:32:50.203635 INFO: ==============================================
7:32:50.211635 INFO: Starting optimization step 3.
7:32:50.218635 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:32:50.226636 INFO: Using classic extraction backend
7:32:50.230636 PROGRESS: Extracting batch of 15870 precursors
7:32:50.237636 INFO: === Search parameters used ===
7:32:50.243638 INFO: rt_error       : 16.557902775255624
7:32:50.251633 INFO: mobility_error : 0.1
7:32:50.259635 INFO: num_candidates : 3
7:32:50.266636 INFO: ms1_error      : 5.0
7:32:50.274635 INFO: ms2_error      : 10.0
7:32:50.279633 INFO: fwhm_rt        : 2.6752583980560303
7:32:50.286638 INFO: quant_window   : 3
7:32:50.294636 INFO: ==============================================
7:32:50.357167 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:32:50.358165 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:32:50.359165 INFO: FWHM in RT is 2.68 seconds, sigma is 0.30
7:32:50.360166 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:32:50.361166 INFO: Starting candidate selection
7:32:51.016974 INFO: Starting candidate scoring
7:32:52.352106 INFO: Finished candidate processing
7:32:52.353115 INFO: Collecting candidate features
7:32:52.653156 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43244)
7:32:52.692157 INFO: Collecting fragment features
7:32:52.838158 INFO: Finished candidate scoring
7:32:52.892681 INFO: performing precursor FDR with 47 features
7:32:52.893679 INFO: Decoy channel: -1
7:32:52.894679 INFO: Competetive: True
7:32:52.986682 INFO: Setting torch num_threads to 2 for FDR classification task
7:32:53.052682 WARNING: dropped 1 target PSMs due to missing features
7:32:53.053680 WARNING: dropped 4 decoy PSMs due to missing features
7:32:53.084683 INFO: Using random state 735333 for train-test-split
7:32:54.279121 INFO: Test AUC: 0.776
7:32:54.280125 INFO: Train AUC: 0.782
7:32:54.281125 INFO: AUC difference: 0.78%
7:32:54.938767 INFO: Resetting torch num_threads to 10
7:32:54.950765 PROGRESS: === Extracted 43244 precursors and 340816 fragments ===
7:32:54.955767 INFO: === FDR correction performed with classifier version 5 ===
7:32:54.970771 PROGRESS: ============================= Precursor FDR =============================
7:32:54.974765 PROGRESS: Total precursors accumulated: 7,611
7:32:54.978767 PROGRESS: Target precursors: 7,563 (99.37%)
7:32:54.981762 PROGRESS: Decoy precursors: 48 (0.63%)
7:32:54.985762 PROGRESS: 
7:32:54.988763 PROGRESS: Precursor Summary:
7:32:55.022763 PROGRESS: Channel   0:	 0.050 FDR: 7,563; 0.010 FDR: 7,563; 0.001 FDR: 7,104
7:32:55.026763 PROGRESS: 
7:32:55.029762 PROGRESS: Protein Summary:
7:32:55.085764 PROGRESS: Channel   0:	 0.050 FDR: 3,627; 0.010 FDR: 3,627; 0.001 FDR: 3,464
7:32:55.094766 PROGRESS: =========================================================================
7:32:55.116315 INFO: Target number of precursors reached.
7:32:55.389860 INFO: fragments_df: keeping 5000 of 340816 [sum(precursor_idx_mask)=177375 sum(mass_error_mask)=340816 stop_rank=5000
7:32:55.500869 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:33:02.519038 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:33:09.443908 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:33:12.928097 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:33:12.933095 INFO: Using score_cutoff 51.0263428024292 (fac=0.99, q=1)
7:33:12.937096 INFO: Updating optimization_manager: fwhm_rt             : 2.6752583980560303 -> 2.67258882522583
7:33:12.941096 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:33:12.944093 INFO: Updating optimization_manager: score_cutoff        : 51.54554135055542 -> 51.0263428024292
7:33:12.948097 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:33:12.962097 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:33:13.005095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:33:13.084096 INFO: === checking if optimization conditions were reached ===
7:33:13.088098 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
7:33:13.111099 INFO: Updating optimization_manager: rt_error            : 16.557902775255624 -> 16.731345644112682
7:33:13.115098 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.7313.
7:33:13.119100 INFO: ==============================================
7:33:13.122098 INFO: Starting optimization step 4.
7:33:13.125098 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:33:13.129100 INFO: Using classic extraction backend
7:33:13.133096 PROGRESS: Extracting batch of 15870 precursors
7:33:13.136096 INFO: === Search parameters used ===
7:33:13.139096 INFO: rt_error       : 16.731345644112682
7:33:13.143110 INFO: mobility_error : 0.1
7:33:13.147110 INFO: num_candidates : 3
7:33:13.151109 INFO: ms1_error      : 5.0
7:33:13.154108 INFO: ms2_error      : 10.0
7:33:13.157630 INFO: fwhm_rt        : 2.67258882522583
7:33:13.161628 INFO: quant_window   : 3
7:33:13.165629 INFO: ==============================================
7:33:13.214629 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:33:13.216629 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:33:13.217629 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:33:13.218629 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:33:13.219628 INFO: Starting candidate selection
7:33:13.870219 INFO: Starting candidate scoring
7:33:15.105565 INFO: Finished candidate processing
7:33:15.106570 INFO: Collecting candidate features
7:33:15.361180 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 43191)
7:33:15.378182 INFO: Collecting fragment features
7:33:15.489728 INFO: Finished candidate scoring
7:33:15.534735 INFO: performing precursor FDR with 47 features
7:33:15.535730 INFO: Decoy channel: -1
7:33:15.536728 INFO: Competetive: True
7:33:15.600727 INFO: Setting torch num_threads to 2 for FDR classification task
7:33:15.642731 WARNING: dropped 1 target PSMs due to missing features
7:33:15.643731 WARNING: dropped 5 decoy PSMs due to missing features
7:33:15.667337 INFO: Using random state 735333 for train-test-split
7:33:16.679200 INFO: Test AUC: 0.783
7:33:16.681201 INFO: Train AUC: 0.780
7:33:16.682200 INFO: AUC difference: 0.30%
7:33:17.340278 INFO: Resetting torch num_threads to 10
7:33:17.348278 PROGRESS: === Extracted 43191 precursors and 340266 fragments ===
7:33:17.353279 INFO: === FDR correction performed with classifier version 5 ===
7:33:17.364278 PROGRESS: ============================= Precursor FDR =============================
7:33:17.368280 PROGRESS: Total precursors accumulated: 7,616
7:33:17.371281 PROGRESS: Target precursors: 7,571 (99.41%)
7:33:17.375283 PROGRESS: Decoy precursors: 45 (0.59%)
7:33:17.378283 PROGRESS: 
7:33:17.382282 PROGRESS: Precursor Summary:
7:33:17.404305 PROGRESS: Channel   0:	 0.050 FDR: 7,571; 0.010 FDR: 7,571; 0.001 FDR: 7,254
7:33:17.407306 PROGRESS: 
7:33:17.412306 PROGRESS: Protein Summary:
7:33:17.455838 PROGRESS: Channel   0:	 0.050 FDR: 3,635; 0.010 FDR: 3,635; 0.001 FDR: 3,516
7:33:17.459838 PROGRESS: =========================================================================
7:33:17.467839 INFO: Target number of precursors reached.
7:33:17.670384 INFO: fragments_df: keeping 5000 of 340266 [sum(precursor_idx_mask)=177418 sum(mass_error_mask)=340266 stop_rank=5000
7:33:17.766385 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:33:24.903151 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:33:32.205429 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:33:35.640325 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:33:35.648325 INFO: Using score_cutoff 50.621744579315184 (fac=0.99, q=1)
7:33:35.654324 INFO: Updating optimization_manager: fwhm_rt             : 2.67258882522583 -> 2.6673007011413574
7:33:35.660324 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:33:35.665325 INFO: Updating optimization_manager: score_cutoff        : 51.0263428024292 -> 50.621744579315184
7:33:35.669324 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:33:35.683324 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:33:35.722930 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:33:35.784931 INFO: === checking if optimization conditions were reached ===
7:33:35.788932 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
7:33:35.793931 INFO: Updating optimization_manager: rt_error            : 16.731345644112682 -> 16.557902775255624
7:33:35.797943 INFO: Updating optimization_manager: classifier_version  : 5 -> 9
7:33:35.800933 INFO: Updating optimization_manager: score_cutoff        : 50.621744579315184 -> 51.0263428024292
7:33:35.804932 INFO: Updating optimization_manager: fwhm_rt             : 2.6673007011413574 -> 2.67258882522583
7:33:35.807933 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:33:35.810929 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.5579 found after 5 searches.
7:33:35.814929 INFO: ==============================================
7:33:35.817932 PROGRESS: Optimization finished for rt_error.
7:33:35.881933 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:33:35.894934 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:33:35.932934 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:33:36.068474 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
7:33:36.072476 PROGRESS: ==============================================
7:33:36.077475 PROGRESS: ms2_error      : 10.0000
7:33:36.081474 PROGRESS: ms1_error      : 5.0000
7:33:36.085475 PROGRESS: rt_error       : 16.5579
7:33:36.090474 PROGRESS: ==============================================
7:33:36.116475 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:33:36.211019 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:33:36.375020 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:33:36.813110 INFO: Using classic extraction backend
7:33:36.819110 PROGRESS: Extracting batch of 121155 precursors
7:33:36.825109 INFO: === Search parameters used ===
7:33:36.831109 INFO: rt_error       : 16.557902775255624
7:33:36.836110 INFO: mobility_error : 0.1
7:33:36.844110 INFO: num_candidates : 3
7:33:36.849112 INFO: ms1_error      : 5.0
7:33:36.853111 INFO: ms2_error      : 10.0
7:33:36.858109 INFO: fwhm_rt        : 2.67258882522583
7:33:36.862110 INFO: quant_window   : 3
7:33:36.867111 INFO: ==============================================
7:33:36.960654 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:33:36.962656 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:33:36.964656 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:33:36.966652 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:33:36.968655 INFO: Starting candidate selection
7:33:40.917021 INFO: Removed 117292 precursors with score below cutoff 51.0263428024292
7:33:41.016646 INFO: Starting candidate scoring
7:33:46.961498 INFO: Finished candidate processing
7:33:46.963435 INFO: Collecting candidate features
7:33:47.738501 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 212483)
7:33:47.805507 INFO: Collecting fragment features
7:33:48.197053 INFO: Finished candidate scoring
7:33:48.414600 INFO: === Performing FDR correction with classifier version 9 ===
7:33:48.422600 INFO: performing precursor FDR with 47 features
7:33:48.423601 INFO: Decoy channel: -1
7:33:48.425597 INFO: Competetive: True
7:33:48.659155 INFO: Setting torch num_threads to 2 for FDR classification task
7:33:48.750696 WARNING: dropped 1 target PSMs due to missing features
7:33:48.752699 WARNING: FDR calculation for 120370 target and 92112 decoy PSMs
7:33:48.754697 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
7:33:48.922698 INFO: Using random state 661911 for train-test-split
7:33:54.596697 INFO: Test AUC: 0.854
7:33:54.598698 INFO: Train AUC: 0.861
7:33:54.599698 INFO: AUC difference: 0.87%
7:33:55.426311 INFO: Resetting torch num_threads to 10
7:33:55.482322 INFO: Removing fragments below FDR threshold
7:33:55.685846 PROGRESS: ============================= Precursor FDR =============================
7:33:55.689848 PROGRESS: Total precursors accumulated: 57,516
7:33:55.693848 PROGRESS: Target precursors: 57,122 (99.31%)
7:33:55.697849 PROGRESS: Decoy precursors: 394 (0.69%)
7:33:55.700849 PROGRESS: 
7:33:55.704850 PROGRESS: Precursor Summary:
7:33:55.822393 PROGRESS: Channel   0:	 0.050 FDR: 57,122; 0.010 FDR: 57,122; 0.001 FDR: 55,911
7:33:55.827395 PROGRESS: 
7:33:55.831397 PROGRESS: Protein Summary:
7:33:55.979405 PROGRESS: Channel   0:	 0.050 FDR: 6,524; 0.010 FDR: 6,524; 0.001 FDR: 6,514
7:33:55.986404 PROGRESS: =========================================================================
7:33:56.006574 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\psm.parquet
7:33:57.177148 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\frag.parquet
7:33:58.346768 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
7:33:58.639286 PROGRESS: 
7:33:58.641287 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant
7:33:58.642287 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\figures
7:33:58.650290 INFO: Initializing TimingManager
7:33:58.663287 INFO: Initializing RawFileManager
7:38:40.324750 INFO: Determining DIA cycle
7:38:40.351749 INFO: Found cycle with start 0.00 min and length 86.
7:38:41.022300 INFO: RT (min)            : 0.0 - 55.5
7:38:41.022300 INFO: RT duration (sec)   : 3327.1
7:38:41.023300 INFO: RT duration (min)   : 55.5
7:38:41.024300 INFO: Cycle len (scans)   : 86
7:38:41.025302 INFO: Cycle len (sec)     : 1.90
7:38:41.026300 INFO: Number of cycles    : 1747
7:38:41.027300 INFO: MS2 range (m/z)     : 399.5 - 903.5
7:38:41.027300 INFO: Creating DIA data object took: 282.3570125102997
7:38:41.108304 INFO: Initializing CalibrationManager
7:38:41.115314 INFO: Setting up calibration estimators ..
7:38:41.119314 INFO: Found 1 estimator(s) in calibration group 'fragment'
7:38:41.122313 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'}' ..
7:38:41.126836 INFO: Found 3 estimator(s) in calibration group 'precursor'
7:38:41.129851 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
7:38:41.133851 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}}' ..
7:38:41.137851 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
7:38:41.141850 INFO: Done setting up calibration estimators.
7:38:41.144849 INFO: Initializing OptimizationManager
7:38:41.151850 INFO: initial parameter: ms1_error = 30
7:38:41.154851 INFO: initial parameter: ms2_error = 30
7:38:41.158851 INFO: initial parameter: rt_error = 1663.596435546875
7:38:41.162851 INFO: initial parameter: mobility_error = 0.1
7:38:41.166852 INFO: initial parameter: num_candidates = 1
7:38:41.169850 INFO: initial parameter: fwhm_rt = 5
7:38:41.173851 INFO: initial parameter: fwhm_mobility = 0.01
7:38:41.177852 INFO: initial parameter: score_cutoff = 0
7:38:41.181850 INFO: initial parameter: classifier_version = -1
7:38:41.187851 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
7:38:41.195850 INFO: FDRManager: loading saved state not requested, will be initialized.
7:38:41.196850 INFO: Initializing FDRManager
7:38:41.197852 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
7:38:41.272852 PROGRESS: Initializing spectral library: 61,104 target precursors potentially observable (0 removed)
7:38:41.381395 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
7:38:41.388399 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 1663.596435546875
7:38:41.397400 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
7:38:41.406394 PROGRESS: Starting initial search for precursors.
7:38:41.424399 INFO: Starting optimization step 0.
7:38:41.432398 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:38:41.438396 INFO: Using classic extraction backend
7:38:41.444399 PROGRESS: Extracting batch of 15870 precursors
7:38:41.452399 INFO: === Search parameters used ===
7:38:41.460397 INFO: rt_error       : 1663.596435546875
7:38:41.469399 INFO: mobility_error : 0.1
7:38:41.479396 INFO: num_candidates : 1
7:38:41.488400 INFO: ms1_error      : 30
7:38:41.494399 INFO: ms2_error      : 30
7:38:41.503398 INFO: fwhm_rt        : 5
7:38:41.534399 INFO: quant_window   : 3
7:38:41.566400 INFO: ==============================================
7:38:41.618410 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:38:41.619414 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:38:41.620413 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
7:38:41.621411 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
7:38:41.622411 INFO: Starting candidate selection
7:38:55.856168 INFO: Starting candidate scoring
7:38:56.445101 INFO: Finished candidate processing
7:38:56.446106 INFO: Collecting candidate features
7:38:56.550107 INFO: Collecting fragment features
7:38:56.641110 INFO: Finished candidate scoring
7:38:56.668619 INFO: performing precursor FDR with 47 features
7:38:56.669619 INFO: Decoy channel: -1
7:38:56.669619 INFO: Competetive: True
7:38:56.697619 INFO: Setting torch num_threads to 2 for FDR classification task
7:38:56.723619 INFO: Using random state 533223 for train-test-split
7:38:57.074646 INFO: Test AUC: 0.795
7:38:57.075645 INFO: Train AUC: 0.789
7:38:57.076647 INFO: AUC difference: 0.73%
7:38:57.656188 INFO: Resetting torch num_threads to 10
7:38:57.663189 PROGRESS: === Extracted 15870 precursors and 162184 fragments ===
7:38:57.668189 INFO: === FDR correction performed with classifier version -1 ===
7:38:57.680189 PROGRESS: ============================= Precursor FDR =============================
7:38:57.684189 PROGRESS: Total precursors accumulated: 4,332
7:38:57.687189 PROGRESS: Target precursors: 4,148 (95.75%)
7:38:57.691189 PROGRESS: Decoy precursors: 184 (4.25%)
7:38:57.695189 PROGRESS: 
7:38:57.700189 PROGRESS: Precursor Summary:
7:38:57.726190 PROGRESS: Channel   0:	 0.050 FDR: 4,148; 0.010 FDR: 2,125; 0.001 FDR:   396
7:38:57.731189 PROGRESS: 
7:38:57.735189 PROGRESS: Protein Summary:
7:38:57.750189 PROGRESS: Channel   0:	 0.050 FDR: 2,333; 0.010 FDR: 1,442; 0.001 FDR:   358
7:38:57.754189 PROGRESS: =========================================================================
7:38:57.760190 INFO: Target number of precursors reached.
7:38:57.833190 INFO: fragments_df: keeping 5000 of 162184 [sum(precursor_idx_mask)=23963 sum(mass_error_mask)=162184 stop_rank=5000
7:38:57.919703 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:38:59.054769 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:39:00.088834 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:39:03.615034 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
7:39:03.620034 INFO: Using score_cutoff 77.62335641784668 (fac=0.99, q=1)
7:39:03.624034 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.608821392059326
7:39:03.628034 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
7:39:03.632035 INFO: Updating optimization_manager: score_cutoff        : 0 -> 77.62335641784668
7:39:03.635034 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:39:03.650038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:39:03.692547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:39:03.758547 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
7:39:03.763547 PROGRESS: Required number of precursors found. Starting search parameter optimization.
7:39:03.767547 INFO: Starting optimization step 1.
7:39:03.770547 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:39:03.774547 INFO: Using classic extraction backend
7:39:03.778548 PROGRESS: Extracting batch of 15870 precursors
7:39:03.781548 INFO: === Search parameters used ===
7:39:03.785547 INFO: rt_error       : 1663.596435546875
7:39:03.789547 INFO: mobility_error : 0.1
7:39:03.792547 INFO: num_candidates : 3
7:39:03.796548 INFO: ms1_error      : 30
7:39:03.799547 INFO: ms2_error      : 30
7:39:03.803547 INFO: fwhm_rt        : 2.608821392059326
7:39:03.807548 INFO: quant_window   : 3
7:39:03.811549 INFO: ==============================================
7:39:03.849548 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:39:03.850548 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:39:03.851549 INFO: FWHM in RT is 2.61 seconds, sigma is 0.29
7:39:03.851549 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:39:03.853548 INFO: Starting candidate selection
7:39:19.787676 INFO: Starting candidate scoring
7:39:21.247198 INFO: Finished candidate processing
7:39:21.249207 INFO: Collecting candidate features
7:39:21.515577 INFO: Collecting fragment features
7:39:21.642578 INFO: Finished candidate scoring
7:39:21.689982 INFO: performing precursor FDR with 47 features
7:39:21.691747 INFO: Decoy channel: -1
7:39:21.692765 INFO: Competetive: True
7:39:21.755763 INFO: Setting torch num_threads to 2 for FDR classification task
7:39:21.804783 INFO: Using random state 203026 for train-test-split
7:39:22.807145 INFO: Test AUC: 0.699
7:39:22.808148 INFO: Train AUC: 0.694
7:39:22.809149 INFO: AUC difference: 0.62%
7:39:23.396207 INFO: Resetting torch num_threads to 10
7:39:23.411213 PROGRESS: === Extracted 47608 precursors and 458888 fragments ===
7:39:23.417211 INFO: === FDR correction performed with classifier version 0 ===
7:39:23.431221 PROGRESS: ============================= Precursor FDR =============================
7:39:23.435217 PROGRESS: Total precursors accumulated: 6,529
7:39:23.439219 PROGRESS: Target precursors: 6,360 (97.41%)
7:39:23.442312 PROGRESS: Decoy precursors: 169 (2.59%)
7:39:23.446310 PROGRESS: 
7:39:23.450310 PROGRESS: Precursor Summary:
7:39:23.479309 PROGRESS: Channel   0:	 0.050 FDR: 6,360; 0.010 FDR: 5,625; 0.001 FDR: 3,745
7:39:23.484310 PROGRESS: 
7:39:23.488310 PROGRESS: Protein Summary:
7:39:23.520311 PROGRESS: Channel   0:	 0.050 FDR: 3,165; 0.010 FDR: 2,909; 0.001 FDR: 2,189
7:39:23.525312 PROGRESS: =========================================================================
7:39:23.539315 INFO: Target number of precursors reached.
7:39:23.832837 INFO: fragments_df: keeping 5000 of 458888 [sum(precursor_idx_mask)=169191 sum(mass_error_mask)=458888 stop_rank=5000
7:39:23.928852 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:39:28.127306 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:39:32.496858 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:39:36.129865 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:39:36.138866 INFO: Using score_cutoff 74.83664418640137 (fac=0.99, q=1)
7:39:36.144866 INFO: Updating optimization_manager: fwhm_rt             : 2.608821392059326 -> 2.7094838619232178
7:39:36.148870 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:39:36.152867 INFO: Updating optimization_manager: score_cutoff        : 77.62335641784668 -> 74.83664418640137
7:39:36.155867 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:39:36.171867 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:39:36.228489 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:39:36.306493 INFO: === checking if optimization conditions were reached ===
7:39:36.315490 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.81727023874472
7:39:36.321490 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
7:39:36.328489 PROGRESS: ❌ ms2_error      : 23.8173 > 10.0000 or insufficient steps taken.
7:39:36.341490 INFO: Updating optimization_manager: ms1_error           : 30 -> 14.503311969469543
7:39:36.350490 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
7:39:36.358491 PROGRESS: ❌ ms1_error      : 14.5033 > 5.0000 or insufficient steps taken.
7:39:36.369492 INFO: ==============================================
7:39:36.380489 INFO: Starting optimization step 2.
7:39:36.390490 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:39:36.402492 INFO: Using classic extraction backend
7:39:36.412491 PROGRESS: Extracting batch of 15870 precursors
7:39:36.426492 INFO: === Search parameters used ===
7:39:36.436486 INFO: rt_error       : 1663.596435546875
7:39:36.447484 INFO: mobility_error : 0.1
7:39:36.457495 INFO: num_candidates : 3
7:39:36.469011 INFO: ms1_error      : 14.503311969469543
7:39:36.478013 INFO: ms2_error      : 23.81727023874472
7:39:36.489015 INFO: fwhm_rt        : 2.7094838619232178
7:39:36.502018 INFO: quant_window   : 3
7:39:36.514015 INFO: ==============================================
7:39:36.580014 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:39:36.581014 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:39:36.583016 INFO: FWHM in RT is 2.71 seconds, sigma is 0.30
7:39:36.584017 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:39:36.586015 INFO: Starting candidate selection
7:39:53.437600 INFO: Starting candidate scoring
7:39:55.045769 INFO: Finished candidate processing
7:39:55.047285 INFO: Collecting candidate features
7:39:55.424804 INFO: Collecting fragment features
7:39:55.594355 INFO: Finished candidate scoring
7:39:55.652355 INFO: performing precursor FDR with 47 features
7:39:55.653355 INFO: Decoy channel: -1
7:39:55.654355 INFO: Competetive: True
7:39:55.742369 INFO: Setting torch num_threads to 2 for FDR classification task
7:39:55.812902 INFO: Using random state 842380 for train-test-split
7:39:57.110895 INFO: Test AUC: 0.692
7:39:57.112892 INFO: Train AUC: 0.708
7:39:57.113893 INFO: AUC difference: 2.24%
7:39:57.823566 INFO: Resetting torch num_threads to 10
7:39:57.836566 PROGRESS: === Extracted 47609 precursors and 446256 fragments ===
7:39:57.842569 INFO: === FDR correction performed with classifier version 1 ===
7:39:57.857568 PROGRESS: ============================= Precursor FDR =============================
7:39:57.862568 PROGRESS: Total precursors accumulated: 6,827
7:39:57.867566 PROGRESS: Target precursors: 6,683 (97.89%)
7:39:57.871567 PROGRESS: Decoy precursors: 144 (2.11%)
7:39:57.875563 PROGRESS: 
7:39:57.879566 PROGRESS: Precursor Summary:
7:39:57.911566 PROGRESS: Channel   0:	 0.050 FDR: 6,683; 0.010 FDR: 6,196; 0.001 FDR: 4,367
7:39:57.916566 PROGRESS: 
7:39:57.919566 PROGRESS: Protein Summary:
7:39:57.953568 PROGRESS: Channel   0:	 0.050 FDR: 3,291; 0.010 FDR: 3,116; 0.001 FDR: 2,431
7:39:57.958568 PROGRESS: =========================================================================
7:39:57.970567 INFO: Target number of precursors reached.
7:39:58.230114 INFO: fragments_df: keeping 5000 of 446256 [sum(precursor_idx_mask)=182146 sum(mass_error_mask)=446256 stop_rank=5000
7:39:58.312652 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:40:03.208021 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:40:08.525104 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:40:12.045344 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:40:12.050344 INFO: Using score_cutoff 71.36776136398315 (fac=0.99, q=1)
7:40:12.054346 INFO: Updating optimization_manager: fwhm_rt             : 2.7094838619232178 -> 2.674649238586426
7:40:12.058345 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:40:12.061347 INFO: Updating optimization_manager: score_cutoff        : 74.83664418640137 -> 71.36776136398315
7:40:12.065345 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:40:12.079345 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:40:12.121344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:40:12.187348 INFO: === checking if optimization conditions were reached ===
7:40:12.196348 INFO: Updating optimization_manager: ms2_error           : 23.81727023874472 -> 18.541414030603114
7:40:12.200348 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
7:40:12.206348 PROGRESS: ❌ ms2_error      : 18.5414 > 10.0000 or insufficient steps taken.
7:40:12.218348 INFO: Updating optimization_manager: ms1_error           : 14.503311969469543 -> 5.584015106870197
7:40:12.224348 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
7:40:12.231348 PROGRESS: ❌ ms1_error      : 5.5840 > 5.0000 or insufficient steps taken.
7:40:12.235343 INFO: ==============================================
7:40:12.242347 INFO: Starting optimization step 3.
7:40:12.250347 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:40:12.256346 INFO: Using classic extraction backend
7:40:12.262347 PROGRESS: Extracting batch of 15870 precursors
7:40:12.270358 INFO: === Search parameters used ===
7:40:12.278359 INFO: rt_error       : 1663.596435546875
7:40:12.287895 INFO: mobility_error : 0.1
7:40:12.293894 INFO: num_candidates : 3
7:40:12.302894 INFO: ms1_error      : 5.584015106870197
7:40:12.310895 INFO: ms2_error      : 18.541414030603114
7:40:12.318894 INFO: fwhm_rt        : 2.674649238586426
7:40:12.324895 INFO: quant_window   : 3
7:40:12.339891 INFO: ==============================================
7:40:12.387893 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:40:12.388893 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:40:12.389894 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
7:40:12.390894 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:40:12.391895 INFO: Starting candidate selection
7:40:28.034041 INFO: Starting candidate scoring
7:40:29.648507 INFO: Finished candidate processing
7:40:29.650511 INFO: Collecting candidate features
7:40:29.926024 INFO: Collecting fragment features
7:40:30.059537 INFO: Finished candidate scoring
7:40:30.108537 INFO: performing precursor FDR with 47 features
7:40:30.109538 INFO: Decoy channel: -1
7:40:30.109538 INFO: Competetive: True
7:40:30.172538 INFO: Setting torch num_threads to 2 for FDR classification task
7:40:30.222539 INFO: Using random state 109477 for train-test-split
7:40:31.312623 INFO: Test AUC: 0.702
7:40:31.314623 INFO: Train AUC: 0.713
7:40:31.314623 INFO: AUC difference: 1.48%
7:40:31.949656 INFO: Resetting torch num_threads to 10
7:40:31.958656 PROGRESS: === Extracted 47608 precursors and 435009 fragments ===
7:40:31.963656 INFO: === FDR correction performed with classifier version 2 ===
7:40:31.974657 PROGRESS: ============================= Precursor FDR =============================
7:40:31.977657 PROGRESS: Total precursors accumulated: 7,039
7:40:31.980657 PROGRESS: Target precursors: 6,920 (98.31%)
7:40:31.983658 PROGRESS: Decoy precursors: 119 (1.69%)
7:40:31.986657 PROGRESS: 
7:40:31.990657 PROGRESS: Precursor Summary:
7:40:32.007657 PROGRESS: Channel   0:	 0.050 FDR: 6,920; 0.010 FDR: 6,679; 0.001 FDR: 4,996
7:40:32.011658 PROGRESS: 
7:40:32.014659 PROGRESS: Protein Summary:
7:40:32.034658 PROGRESS: Channel   0:	 0.050 FDR: 3,390; 0.010 FDR: 3,295; 0.001 FDR: 2,690
7:40:32.038657 PROGRESS: =========================================================================
7:40:32.046662 INFO: Target number of precursors reached.
7:40:32.278172 INFO: fragments_df: keeping 5000 of 435009 [sum(precursor_idx_mask)=192214 sum(mass_error_mask)=435009 stop_rank=5000
7:40:32.383687 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:40:37.966242 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:40:43.428541 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:40:46.521470 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:40:46.526471 INFO: Using score_cutoff 67.77996086425782 (fac=0.99, q=1)
7:40:46.531469 INFO: Updating optimization_manager: fwhm_rt             : 2.674649238586426 -> 2.644601583480835
7:40:46.535471 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:40:46.539469 INFO: Updating optimization_manager: score_cutoff        : 71.36776136398315 -> 67.77996086425782
7:40:46.542469 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:40:46.559471 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:40:46.618001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:40:46.692002 INFO: === checking if optimization conditions were reached ===
7:40:46.702003 INFO: Updating optimization_manager: ms2_error           : 18.541414030603114 -> 14.508187124083433
7:40:46.706003 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
7:40:46.710002 PROGRESS: ❌ ms2_error      : 14.5082 > 10.0000 or insufficient steps taken.
7:40:46.720002 INFO: Updating optimization_manager: ms1_error           : 5.584015106870197 -> 5.0
7:40:46.724003 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
7:40:46.728003 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:40:46.732003 INFO: ==============================================
7:40:46.736003 INFO: Starting optimization step 4.
7:40:46.740003 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:40:46.744003 INFO: Using classic extraction backend
7:40:46.748003 PROGRESS: Extracting batch of 15870 precursors
7:40:46.752003 INFO: === Search parameters used ===
7:40:46.756004 INFO: rt_error       : 1663.596435546875
7:40:46.760003 INFO: mobility_error : 0.1
7:40:46.763004 INFO: num_candidates : 3
7:40:46.767004 INFO: ms1_error      : 5.0
7:40:46.771004 INFO: ms2_error      : 14.508187124083433
7:40:46.776003 INFO: fwhm_rt        : 2.644601583480835
7:40:46.782004 INFO: quant_window   : 3
7:40:46.789004 INFO: ==============================================
7:40:46.854539 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:40:46.856539 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:40:46.857539 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:40:46.858539 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:40:46.859540 INFO: Starting candidate selection
7:41:02.725914 INFO: Starting candidate scoring
7:41:04.312645 INFO: Finished candidate processing
7:41:04.313658 INFO: Collecting candidate features
7:41:04.640730 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 47606)
7:41:04.658730 INFO: Collecting fragment features
7:41:04.794728 INFO: Finished candidate scoring
7:41:04.843732 INFO: performing precursor FDR with 47 features
7:41:04.844732 INFO: Decoy channel: -1
7:41:04.845732 INFO: Competetive: True
7:41:04.930346 INFO: Setting torch num_threads to 2 for FDR classification task
7:41:04.973353 WARNING: dropped 3 decoy PSMs due to missing features
7:41:05.008353 INFO: Using random state 872199 for train-test-split
7:41:06.314907 INFO: Test AUC: 0.710
7:41:06.316908 INFO: Train AUC: 0.713
7:41:06.317909 INFO: AUC difference: 0.49%
7:41:07.005560 INFO: Resetting torch num_threads to 10
7:41:07.018561 PROGRESS: === Extracted 47606 precursors and 423237 fragments ===
7:41:07.025561 INFO: === FDR correction performed with classifier version 3 ===
7:41:07.039560 PROGRESS: ============================= Precursor FDR =============================
7:41:07.044560 PROGRESS: Total precursors accumulated: 7,057
7:41:07.048562 PROGRESS: Target precursors: 6,944 (98.40%)
7:41:07.052561 PROGRESS: Decoy precursors: 113 (1.60%)
7:41:07.056561 PROGRESS: 
7:41:07.060561 PROGRESS: Precursor Summary:
7:41:07.088562 PROGRESS: Channel   0:	 0.050 FDR: 6,944; 0.010 FDR: 6,824; 0.001 FDR: 5,266
7:41:07.093563 PROGRESS: 
7:41:07.097563 PROGRESS: Protein Summary:
7:41:07.130130 PROGRESS: Channel   0:	 0.050 FDR: 3,391; 0.010 FDR: 3,345; 0.001 FDR: 2,812
7:41:07.135130 PROGRESS: =========================================================================
7:41:07.148133 INFO: Target number of precursors reached.
7:41:07.431685 INFO: fragments_df: keeping 5000 of 423237 [sum(precursor_idx_mask)=191888 sum(mass_error_mask)=423237 stop_rank=5000
7:41:07.541695 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:41:13.512291 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:41:19.839726 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:41:23.410888 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:41:23.416888 INFO: Using score_cutoff 63.546473741912834 (fac=0.99, q=1)
7:41:23.420889 INFO: Updating optimization_manager: fwhm_rt             : 2.644601583480835 -> 2.6240310668945312
7:41:23.424891 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:41:23.428888 INFO: Updating optimization_manager: score_cutoff        : 67.77996086425782 -> 63.546473741912834
7:41:23.432889 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:41:23.447889 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:41:23.493889 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:41:23.557890 INFO: === checking if optimization conditions were reached ===
7:41:23.565889 INFO: Updating optimization_manager: ms2_error           : 14.508187124083433 -> 11.177554767284558
7:41:23.569890 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
7:41:23.572892 PROGRESS: ❌ ms2_error      : 11.1776 > 10.0000 or insufficient steps taken.
7:41:23.576890 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:41:23.580890 INFO: ==============================================
7:41:23.584890 INFO: Starting optimization step 5.
7:41:23.588890 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:41:23.592891 INFO: Using classic extraction backend
7:41:23.596890 PROGRESS: Extracting batch of 15870 precursors
7:41:23.603892 INFO: === Search parameters used ===
7:41:23.611891 INFO: rt_error       : 1663.596435546875
7:41:23.619891 INFO: mobility_error : 0.1
7:41:23.632891 INFO: num_candidates : 3
7:41:23.641904 INFO: ms1_error      : 5.0
7:41:23.648904 INFO: ms2_error      : 11.177554767284558
7:41:23.654435 INFO: fwhm_rt        : 2.6240310668945312
7:41:23.662435 INFO: quant_window   : 3
7:41:23.671432 INFO: ==============================================
7:41:23.738436 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:41:23.739434 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:41:23.740433 INFO: FWHM in RT is 2.62 seconds, sigma is 0.29
7:41:23.741435 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:41:23.742435 INFO: Starting candidate selection
7:41:39.061373 INFO: Starting candidate scoring
7:41:40.501612 INFO: Finished candidate processing
7:41:40.503123 INFO: Collecting candidate features
7:41:40.751672 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 47601)
7:41:40.769672 INFO: Collecting fragment features
7:41:40.889673 INFO: Finished candidate scoring
7:41:40.938219 INFO: performing precursor FDR with 47 features
7:41:40.939217 INFO: Decoy channel: -1
7:41:40.940217 INFO: Competetive: True
7:41:41.027217 INFO: Setting torch num_threads to 2 for FDR classification task
7:41:41.057219 WARNING: dropped 2 decoy PSMs due to missing features
7:41:41.083220 INFO: Using random state 67546 for train-test-split
7:41:42.249570 INFO: Test AUC: 0.712
7:41:42.250571 INFO: Train AUC: 0.718
7:41:42.251571 INFO: AUC difference: 0.90%
7:41:42.907650 INFO: Resetting torch num_threads to 10
7:41:42.916648 PROGRESS: === Extracted 47601 precursors and 411980 fragments ===
7:41:42.922663 INFO: === FDR correction performed with classifier version 4 ===
7:41:42.933179 PROGRESS: ============================= Precursor FDR =============================
7:41:42.936195 PROGRESS: Total precursors accumulated: 7,053
7:41:42.940193 PROGRESS: Target precursors: 6,938 (98.37%)
7:41:42.944193 PROGRESS: Decoy precursors: 115 (1.63%)
7:41:42.947193 PROGRESS: 
7:41:42.951193 PROGRESS: Precursor Summary:
7:41:42.969198 PROGRESS: Channel   0:	 0.050 FDR: 6,938; 0.010 FDR: 6,830; 0.001 FDR: 5,593
7:41:42.973193 PROGRESS: 
7:41:42.976194 PROGRESS: Protein Summary:
7:41:42.997193 PROGRESS: Channel   0:	 0.050 FDR: 3,380; 0.010 FDR: 3,343; 0.001 FDR: 2,913
7:41:43.002196 PROGRESS: =========================================================================
7:41:43.017195 INFO: Target number of precursors reached.
7:41:43.253740 INFO: fragments_df: keeping 5000 of 411980 [sum(precursor_idx_mask)=188043 sum(mass_error_mask)=411980 stop_rank=5000
7:41:43.333740 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:41:49.501831 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:41:55.458561 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:41:58.632379 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:41:58.638376 INFO: Using score_cutoff 60.30754619979859 (fac=0.99, q=1)
7:41:58.643382 INFO: Updating optimization_manager: fwhm_rt             : 2.6240310668945312 -> 2.5999398231506348
7:41:58.647377 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:41:58.652378 INFO: Updating optimization_manager: score_cutoff        : 63.546473741912834 -> 60.30754619979859
7:41:58.656378 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:41:58.673377 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:41:58.737989 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:41:58.815990 INFO: === checking if optimization conditions were reached ===
7:41:58.824989 INFO: Updating optimization_manager: ms2_error           : 11.177554767284558 -> 10.0
7:41:58.829989 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
7:41:58.833991 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
7:41:58.837991 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:41:58.841990 INFO: ==============================================
7:41:58.845992 PROGRESS: Optimization finished for ms2_error, ms1_error.
7:41:58.949991 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:41:58.970533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:41:59.060537 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:41:59.160541 INFO: Starting optimization step 0.
7:41:59.168547 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:41:59.177545 INFO: Using classic extraction backend
7:41:59.184545 PROGRESS: Extracting batch of 15870 precursors
7:41:59.192542 INFO: === Search parameters used ===
7:41:59.198552 INFO: rt_error       : 1663.596435546875
7:41:59.203545 INFO: mobility_error : 0.1
7:41:59.212560 INFO: num_candidates : 3
7:41:59.220090 INFO: ms1_error      : 5.0
7:41:59.228093 INFO: ms2_error      : 10.0
7:41:59.235098 INFO: fwhm_rt        : 2.5999398231506348
7:41:59.243099 INFO: quant_window   : 3
7:41:59.249093 INFO: ==============================================
7:41:59.313095 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:41:59.314096 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:41:59.315105 INFO: FWHM in RT is 2.60 seconds, sigma is 0.29
7:41:59.316095 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:41:59.318100 INFO: Starting candidate selection
7:42:15.161237 INFO: Starting candidate scoring
7:42:16.738820 INFO: Finished candidate processing
7:42:16.739836 INFO: Collecting candidate features
7:42:17.010042 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 47598)
7:42:17.028043 INFO: Collecting fragment features
7:42:17.150044 INFO: Finished candidate scoring
7:42:17.199044 INFO: performing precursor FDR with 47 features
7:42:17.200044 INFO: Decoy channel: -1
7:42:17.201045 INFO: Competetive: True
7:42:17.265653 INFO: Setting torch num_threads to 2 for FDR classification task
7:42:17.296657 WARNING: dropped 2 decoy PSMs due to missing features
7:42:17.323657 INFO: Using random state 730690 for train-test-split
7:42:18.416682 INFO: Test AUC: 0.700
7:42:18.418683 INFO: Train AUC: 0.721
7:42:18.418683 INFO: AUC difference: 2.94%
7:42:19.156319 INFO: Resetting torch num_threads to 10
7:42:19.166314 PROGRESS: === Extracted 47598 precursors and 407272 fragments ===
7:42:19.171318 INFO: === FDR correction performed with classifier version 5 ===
7:42:19.181315 PROGRESS: ============================= Precursor FDR =============================
7:42:19.185315 PROGRESS: Total precursors accumulated: 7,087
7:42:19.189316 PROGRESS: Target precursors: 6,977 (98.45%)
7:42:19.192316 PROGRESS: Decoy precursors: 110 (1.55%)
7:42:19.196317 PROGRESS: 
7:42:19.199316 PROGRESS: Precursor Summary:
7:42:19.218315 PROGRESS: Channel   0:	 0.050 FDR: 6,977; 0.010 FDR: 6,864; 0.001 FDR: 5,451
7:42:19.222321 PROGRESS: 
7:42:19.225320 PROGRESS: Protein Summary:
7:42:19.247337 PROGRESS: Channel   0:	 0.050 FDR: 3,412; 0.010 FDR: 3,363; 0.001 FDR: 2,862
7:42:19.250871 PROGRESS: =========================================================================
7:42:19.258870 INFO: Target number of precursors reached.
7:42:19.500427 INFO: fragments_df: keeping 5000 of 407272 [sum(precursor_idx_mask)=187164 sum(mass_error_mask)=407272 stop_rank=5000
7:42:19.596430 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:42:25.619151 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:42:31.312725 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:42:34.736812 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:42:34.744813 INFO: Using score_cutoff 57.99602735939026 (fac=0.99, q=1)
7:42:34.751816 INFO: Updating optimization_manager: fwhm_rt             : 2.5999398231506348 -> 2.602531909942627
7:42:34.758817 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:42:34.762816 INFO: Updating optimization_manager: score_cutoff        : 60.30754619979859 -> 57.99602735939026
7:42:34.767830 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:42:34.785367 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:42:34.846371 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:42:34.953360 INFO: === checking if optimization conditions were reached ===
7:42:34.958366 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
7:42:34.990369 INFO: Updating optimization_manager: rt_error            : 1663.596435546875 -> 127.1152175753434
7:42:34.995367 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 127.1152.
7:42:34.999367 INFO: ==============================================
7:42:35.003366 INFO: Starting optimization step 1.
7:42:35.007378 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:42:35.011367 INFO: Using classic extraction backend
7:42:35.016367 PROGRESS: Extracting batch of 15870 precursors
7:42:35.020380 INFO: === Search parameters used ===
7:42:35.024380 INFO: rt_error       : 127.1152175753434
7:42:35.028382 INFO: mobility_error : 0.1
7:42:35.032909 INFO: num_candidates : 3
7:42:35.036910 INFO: ms1_error      : 5.0
7:42:35.040912 INFO: ms2_error      : 10.0
7:42:35.044908 INFO: fwhm_rt        : 2.602531909942627
7:42:35.051908 INFO: quant_window   : 3
7:42:35.060915 INFO: ==============================================
7:42:35.132911 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:42:35.155907 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:42:35.157904 INFO: FWHM in RT is 2.60 seconds, sigma is 0.29
7:42:35.158905 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:42:35.160909 INFO: Starting candidate selection
7:42:36.611126 INFO: Starting candidate scoring
7:42:37.960292 INFO: Finished candidate processing
7:42:37.962302 INFO: Collecting candidate features
7:42:38.203914 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 47588)
7:42:38.219915 INFO: Collecting fragment features
7:42:38.333418 INFO: Finished candidate scoring
7:42:38.380423 INFO: performing precursor FDR with 47 features
7:42:38.381425 INFO: Decoy channel: -1
7:42:38.382423 INFO: Competetive: True
7:42:38.445426 INFO: Setting torch num_threads to 2 for FDR classification task
7:42:38.474454 WARNING: dropped 2 decoy PSMs due to missing features
7:42:38.498454 INFO: Using random state 730690 for train-test-split
7:42:39.502402 INFO: Test AUC: 0.705
7:42:39.503402 INFO: Train AUC: 0.724
7:42:39.504402 INFO: AUC difference: 2.66%
7:42:40.119010 INFO: Resetting torch num_threads to 10
7:42:40.163011 PROGRESS: === Extracted 47588 precursors and 400973 fragments ===
7:42:40.168010 INFO: === FDR correction performed with classifier version 5 ===
7:42:40.178011 PROGRESS: ============================= Precursor FDR =============================
7:42:40.182010 PROGRESS: Total precursors accumulated: 7,378
7:42:40.185010 PROGRESS: Target precursors: 7,295 (98.88%)
7:42:40.188011 PROGRESS: Decoy precursors: 83 (1.12%)
7:42:40.192010 PROGRESS: 
7:42:40.195010 PROGRESS: Precursor Summary:
7:42:40.213010 PROGRESS: Channel   0:	 0.050 FDR: 7,295; 0.010 FDR: 7,263; 0.001 FDR: 5,263
7:42:40.217012 PROGRESS: 
7:42:40.220011 PROGRESS: Protein Summary:
7:42:40.241010 PROGRESS: Channel   0:	 0.050 FDR: 3,511; 0.010 FDR: 3,498; 0.001 FDR: 2,794
7:42:40.244011 PROGRESS: =========================================================================
7:42:40.253013 INFO: Target number of precursors reached.
7:42:40.464558 INFO: fragments_df: keeping 5000 of 400973 [sum(precursor_idx_mask)=196204 sum(mass_error_mask)=400973 stop_rank=5000
7:42:40.540571 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:42:47.119645 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:42:54.030786 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:42:57.496136 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:42:57.502135 INFO: Using score_cutoff 55.58460539474487 (fac=0.99, q=1)
7:42:57.507136 INFO: Updating optimization_manager: fwhm_rt             : 2.602531909942627 -> 2.6224284172058105
7:42:57.511136 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:42:57.515136 INFO: Updating optimization_manager: score_cutoff        : 57.99602735939026 -> 55.58460539474487
7:42:57.518136 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:42:57.534138 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:42:57.590660 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:42:57.664661 INFO: === checking if optimization conditions were reached ===
7:42:57.668661 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
7:42:57.693661 INFO: Updating optimization_manager: rt_error            : 127.1152175753434 -> 47.9785949923669
7:42:57.698662 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 47.9786.
7:42:57.701662 INFO: ==============================================
7:42:57.705662 INFO: Starting optimization step 2.
7:42:57.709661 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:42:57.713661 INFO: Using classic extraction backend
7:42:57.716662 PROGRESS: Extracting batch of 15870 precursors
7:42:57.720661 INFO: === Search parameters used ===
7:42:57.724661 INFO: rt_error       : 47.9785949923669
7:42:57.728663 INFO: mobility_error : 0.1
7:42:57.732662 INFO: num_candidates : 3
7:42:57.740661 INFO: ms1_error      : 5.0
7:42:57.748662 INFO: ms2_error      : 10.0
7:42:57.754662 INFO: fwhm_rt        : 2.6224284172058105
7:42:57.762661 INFO: quant_window   : 3
7:42:57.769663 INFO: ==============================================
7:42:57.827671 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:42:57.828177 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:42:57.829186 INFO: FWHM in RT is 2.62 seconds, sigma is 0.29
7:42:57.830184 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:42:57.831185 INFO: Starting candidate selection
7:42:58.811652 INFO: Starting candidate scoring
7:43:00.218949 INFO: Finished candidate processing
7:43:00.219958 INFO: Collecting candidate features
7:43:00.536480 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 47574)
7:43:00.554481 INFO: Collecting fragment features
7:43:00.709005 INFO: Finished candidate scoring
7:43:00.767005 INFO: performing precursor FDR with 47 features
7:43:00.768005 INFO: Decoy channel: -1
7:43:00.769006 INFO: Competetive: True
7:43:00.856528 INFO: Setting torch num_threads to 2 for FDR classification task
7:43:00.904529 WARNING: dropped 1 target PSMs due to missing features
7:43:00.905529 WARNING: dropped 1 decoy PSMs due to missing features
7:43:00.940529 INFO: Using random state 730690 for train-test-split
7:43:02.221668 INFO: Test AUC: 0.722
7:43:02.222669 INFO: Train AUC: 0.735
7:43:02.223668 INFO: AUC difference: 1.75%
7:43:02.963246 INFO: Resetting torch num_threads to 10
7:43:02.976245 PROGRESS: === Extracted 47574 precursors and 391155 fragments ===
7:43:02.981245 INFO: === FDR correction performed with classifier version 5 ===
7:43:02.995244 PROGRESS: ============================= Precursor FDR =============================
7:43:02.999245 PROGRESS: Total precursors accumulated: 7,475
7:43:03.002245 PROGRESS: Target precursors: 7,404 (99.05%)
7:43:03.006245 PROGRESS: Decoy precursors: 71 (0.95%)
7:43:03.009246 PROGRESS: 
7:43:03.012244 PROGRESS: Precursor Summary:
7:43:03.042245 PROGRESS: Channel   0:	 0.050 FDR: 7,404; 0.010 FDR: 7,404; 0.001 FDR: 6,207
7:43:03.046246 PROGRESS: 
7:43:03.049246 PROGRESS: Protein Summary:
7:43:03.084255 PROGRESS: Channel   0:	 0.050 FDR: 3,562; 0.010 FDR: 3,562; 0.001 FDR: 3,142
7:43:03.088770 PROGRESS: =========================================================================
7:43:03.099770 INFO: Target number of precursors reached.
7:43:03.376294 INFO: fragments_df: keeping 5000 of 391155 [sum(precursor_idx_mask)=196422 sum(mass_error_mask)=391155 stop_rank=5000
7:43:03.485296 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:43:10.464020 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:43:17.221467 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:43:20.661340 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:43:20.667340 INFO: Using score_cutoff 54.09724259605407 (fac=0.99, q=1)
7:43:20.671340 INFO: Updating optimization_manager: fwhm_rt             : 2.6224284172058105 -> 2.627242088317871
7:43:20.675341 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:43:20.679340 INFO: Updating optimization_manager: score_cutoff        : 55.58460539474487 -> 54.09724259605407
7:43:20.683337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:43:20.697338 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:43:20.738338 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:43:20.805338 INFO: === checking if optimization conditions were reached ===
7:43:20.809338 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
7:43:20.833333 INFO: Updating optimization_manager: rt_error            : 47.9785949923669 -> 17.9874693923078
7:43:20.837335 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 17.9875.
7:43:20.841334 INFO: ==============================================
7:43:20.844334 INFO: Starting optimization step 3.
7:43:20.848334 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:43:20.852334 INFO: Using classic extraction backend
7:43:20.856334 PROGRESS: Extracting batch of 15870 precursors
7:43:20.859335 INFO: === Search parameters used ===
7:43:20.863342 INFO: rt_error       : 17.9874693923078
7:43:20.867341 INFO: mobility_error : 0.1
7:43:20.871342 INFO: num_candidates : 3
7:43:20.874853 INFO: ms1_error      : 5.0
7:43:20.877867 INFO: ms2_error      : 10.0
7:43:20.882870 INFO: fwhm_rt        : 2.627242088317871
7:43:20.886867 INFO: quant_window   : 3
7:43:20.894866 INFO: ==============================================
7:43:20.942868 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:43:20.943873 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:43:20.944873 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:43:20.944873 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:43:20.945867 INFO: Starting candidate selection
7:43:21.635803 INFO: Starting candidate scoring
7:43:22.879583 INFO: Finished candidate processing
7:43:22.880587 INFO: Collecting candidate features
7:43:23.109590 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43222)
7:43:23.126593 INFO: Collecting fragment features
7:43:23.236101 INFO: Finished candidate scoring
7:43:23.282102 INFO: performing precursor FDR with 47 features
7:43:23.283102 INFO: Decoy channel: -1
7:43:23.284102 INFO: Competetive: True
7:43:23.351103 INFO: Setting torch num_threads to 2 for FDR classification task
7:43:23.392616 WARNING: dropped 3 target PSMs due to missing features
7:43:23.393616 WARNING: dropped 2 decoy PSMs due to missing features
7:43:23.417616 INFO: Using random state 730690 for train-test-split
7:43:24.406186 INFO: Test AUC: 0.772
7:43:24.407186 INFO: Train AUC: 0.783
7:43:24.408186 INFO: AUC difference: 1.37%
7:43:25.078225 INFO: Resetting torch num_threads to 10
7:43:25.086226 PROGRESS: === Extracted 43222 precursors and 340532 fragments ===
7:43:25.091225 INFO: === FDR correction performed with classifier version 5 ===
7:43:25.102225 PROGRESS: ============================= Precursor FDR =============================
7:43:25.106225 PROGRESS: Total precursors accumulated: 7,531
7:43:25.109225 PROGRESS: Target precursors: 7,464 (99.11%)
7:43:25.113225 PROGRESS: Decoy precursors: 67 (0.89%)
7:43:25.117225 PROGRESS: 
7:43:25.120230 PROGRESS: Precursor Summary:
7:43:25.142737 PROGRESS: Channel   0:	 0.050 FDR: 7,464; 0.010 FDR: 7,464; 0.001 FDR: 6,279
7:43:25.146737 PROGRESS: 
7:43:25.153738 PROGRESS: Protein Summary:
7:43:25.181738 PROGRESS: Channel   0:	 0.050 FDR: 3,592; 0.010 FDR: 3,592; 0.001 FDR: 3,167
7:43:25.187738 PROGRESS: =========================================================================
7:43:25.199738 INFO: Target number of precursors reached.
7:43:25.426252 INFO: fragments_df: keeping 5000 of 340532 [sum(precursor_idx_mask)=175499 sum(mass_error_mask)=340532 stop_rank=5000
7:43:25.505253 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:43:32.444654 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:43:39.426076 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:43:42.593653 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:43:42.600653 INFO: Using score_cutoff 51.938779899215696 (fac=0.99, q=1)
7:43:42.604654 INFO: Updating optimization_manager: fwhm_rt             : 2.627242088317871 -> 2.629716634750366
7:43:42.608652 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:43:42.612654 INFO: Updating optimization_manager: score_cutoff        : 54.09724259605407 -> 51.938779899215696
7:43:42.616655 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:43:42.629654 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:43:42.667667 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:43:42.730198 INFO: === checking if optimization conditions were reached ===
7:43:42.734202 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
7:43:42.754199 INFO: Updating optimization_manager: rt_error            : 17.9874693923078 -> 15.415610931367683
7:43:42.759201 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 15.4156.
7:43:42.763200 INFO: ==============================================
7:43:42.768200 INFO: Starting optimization step 4.
7:43:42.771201 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:43:42.775203 INFO: Using classic extraction backend
7:43:42.778200 PROGRESS: Extracting batch of 15870 precursors
7:43:42.782200 INFO: === Search parameters used ===
7:43:42.785201 INFO: rt_error       : 15.415610931367683
7:43:42.789202 INFO: mobility_error : 0.1
7:43:42.793202 INFO: num_candidates : 3
7:43:42.796200 INFO: ms1_error      : 5.0
7:43:42.800200 INFO: ms2_error      : 10.0
7:43:42.803202 INFO: fwhm_rt        : 2.629716634750366
7:43:42.807203 INFO: quant_window   : 3
7:43:42.810201 INFO: ==============================================
7:43:42.842202 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:43:42.843201 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:43:42.843201 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:43:42.844200 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:43:42.845199 INFO: Starting candidate selection
7:43:43.503622 INFO: Starting candidate scoring
7:43:44.898370 INFO: Finished candidate processing
7:43:44.900376 INFO: Collecting candidate features
7:43:45.244418 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 43372)
7:43:45.263417 INFO: Collecting fragment features
7:43:45.430951 INFO: Finished candidate scoring
7:43:45.487957 INFO: performing precursor FDR with 47 features
7:43:45.488952 INFO: Decoy channel: -1
7:43:45.489951 INFO: Competetive: True
7:43:45.590956 INFO: Setting torch num_threads to 2 for FDR classification task
7:43:45.668960 WARNING: dropped 2 target PSMs due to missing features
7:43:45.670963 WARNING: dropped 2 decoy PSMs due to missing features
7:43:45.708474 INFO: Using random state 730690 for train-test-split
7:43:46.739211 INFO: Test AUC: 0.781
7:43:46.740211 INFO: Train AUC: 0.785
7:43:46.741211 INFO: AUC difference: 0.45%
7:43:47.371240 INFO: Resetting torch num_threads to 10
7:43:47.380240 PROGRESS: === Extracted 43372 precursors and 341775 fragments ===
7:43:47.385240 INFO: === FDR correction performed with classifier version 5 ===
7:43:47.396241 PROGRESS: ============================= Precursor FDR =============================
7:43:47.400240 PROGRESS: Total precursors accumulated: 7,546
7:43:47.404240 PROGRESS: Target precursors: 7,486 (99.20%)
7:43:47.407240 PROGRESS: Decoy precursors: 60 (0.80%)
7:43:47.411241 PROGRESS: 
7:43:47.414245 PROGRESS: Precursor Summary:
7:43:47.436753 PROGRESS: Channel   0:	 0.050 FDR: 7,486; 0.010 FDR: 7,486; 0.001 FDR: 6,593
7:43:47.439754 PROGRESS: 
7:43:47.443753 PROGRESS: Protein Summary:
7:43:47.466753 PROGRESS: Channel   0:	 0.050 FDR: 3,601; 0.010 FDR: 3,601; 0.001 FDR: 3,271
7:43:47.470753 PROGRESS: =========================================================================
7:43:47.478754 INFO: Target number of precursors reached.
7:43:47.681267 INFO: fragments_df: keeping 5000 of 341775 [sum(precursor_idx_mask)=176350 sum(mass_error_mask)=341775 stop_rank=5000
7:43:47.756268 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:43:54.844689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:44:01.903124 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:44:05.444316 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:44:05.450320 INFO: Using score_cutoff 51.58034747314453 (fac=0.99, q=1)
7:44:05.454320 INFO: Updating optimization_manager: fwhm_rt             : 2.629716634750366 -> 2.6334521770477295
7:44:05.458320 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:44:05.461321 INFO: Updating optimization_manager: score_cutoff        : 51.938779899215696 -> 51.58034747314453
7:44:05.465829 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:44:05.480829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:44:05.530829 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:44:05.605830 INFO: === checking if optimization conditions were reached ===
7:44:05.609830 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
7:44:05.636831 INFO: Updating optimization_manager: rt_error            : 15.415610931367683 -> 16.977972373429857
7:44:05.641832 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.9780.
7:44:05.645833 INFO: ==============================================
7:44:05.649834 INFO: Starting optimization step 5.
7:44:05.653834 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:44:05.657832 INFO: Using classic extraction backend
7:44:05.661834 PROGRESS: Extracting batch of 15870 precursors
7:44:05.665832 INFO: === Search parameters used ===
7:44:05.669832 INFO: rt_error       : 16.977972373429857
7:44:05.673832 INFO: mobility_error : 0.1
7:44:05.677833 INFO: num_candidates : 3
7:44:05.681833 INFO: ms1_error      : 5.0
7:44:05.685834 INFO: ms2_error      : 10.0
7:44:05.689834 INFO: fwhm_rt        : 2.6334521770477295
7:44:05.694836 INFO: quant_window   : 3
7:44:05.699833 INFO: ==============================================
7:44:05.747353 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:44:05.748352 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:44:05.749352 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:44:05.750355 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:44:05.752358 INFO: Starting candidate selection
7:44:06.345056 INFO: Starting candidate scoring
7:44:07.581826 INFO: Finished candidate processing
7:44:07.582840 INFO: Collecting candidate features
7:44:07.814385 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 43342)
7:44:07.833384 INFO: Collecting fragment features
7:44:07.932386 INFO: Finished candidate scoring
7:44:07.974928 INFO: performing precursor FDR with 47 features
7:44:07.975927 INFO: Decoy channel: -1
7:44:07.976926 INFO: Competetive: True
7:44:08.053926 INFO: Setting torch num_threads to 2 for FDR classification task
7:44:08.111927 WARNING: dropped 3 target PSMs due to missing features
7:44:08.112929 WARNING: dropped 4 decoy PSMs due to missing features
7:44:08.134929 INFO: Using random state 730690 for train-test-split
7:44:09.032061 INFO: Test AUC: 0.771
7:44:09.033063 INFO: Train AUC: 0.784
7:44:09.034063 INFO: AUC difference: 1.60%
7:44:09.649297 INFO: Resetting torch num_threads to 10
7:44:09.657301 PROGRESS: === Extracted 43342 precursors and 341056 fragments ===
7:44:09.663298 INFO: === FDR correction performed with classifier version 5 ===
7:44:09.674300 PROGRESS: ============================= Precursor FDR =============================
7:44:09.678298 PROGRESS: Total precursors accumulated: 7,543
7:44:09.683299 PROGRESS: Target precursors: 7,487 (99.26%)
7:44:09.686298 PROGRESS: Decoy precursors: 56 (0.74%)
7:44:09.689299 PROGRESS: 
7:44:09.693299 PROGRESS: Precursor Summary:
7:44:09.712315 PROGRESS: Channel   0:	 0.050 FDR: 7,487; 0.010 FDR: 7,487; 0.001 FDR: 6,420
7:44:09.716317 PROGRESS: 
7:44:09.720317 PROGRESS: Protein Summary:
7:44:09.741846 PROGRESS: Channel   0:	 0.050 FDR: 3,589; 0.010 FDR: 3,589; 0.001 FDR: 3,197
7:44:09.745845 PROGRESS: =========================================================================
7:44:09.753846 INFO: Target number of precursors reached.
7:44:09.936846 INFO: fragments_df: keeping 5000 of 341056 [sum(precursor_idx_mask)=176006 sum(mass_error_mask)=341056 stop_rank=5000
7:44:10.005455 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:44:18.686120 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:44:25.613136 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:44:29.104496 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:44:29.110497 INFO: Using score_cutoff 51.67438976898193 (fac=0.99, q=1)
7:44:29.115496 INFO: Updating optimization_manager: fwhm_rt             : 2.6334521770477295 -> 2.639645576477051
7:44:29.119496 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:44:29.123496 INFO: Updating optimization_manager: score_cutoff        : 51.58034747314453 -> 51.67438976898193
7:44:29.127496 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:44:29.143497 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:44:29.201497 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:44:29.276023 INFO: === checking if optimization conditions were reached ===
7:44:29.281022 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
7:44:29.308024 INFO: Updating optimization_manager: rt_error            : 16.977972373429857 -> 17.92136741742517
7:44:29.312023 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.9214.
7:44:29.316023 INFO: ==============================================
7:44:29.320024 INFO: Starting optimization step 6.
7:44:29.324023 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:44:29.328024 INFO: Using classic extraction backend
7:44:29.332024 PROGRESS: Extracting batch of 15870 precursors
7:44:29.336023 INFO: === Search parameters used ===
7:44:29.340024 INFO: rt_error       : 17.92136741742517
7:44:29.344024 INFO: mobility_error : 0.1
7:44:29.350025 INFO: num_candidates : 3
7:44:29.355024 INFO: ms1_error      : 5.0
7:44:29.359024 INFO: ms2_error      : 10.0
7:44:29.363024 INFO: fwhm_rt        : 2.639645576477051
7:44:29.367024 INFO: quant_window   : 3
7:44:29.371024 INFO: ==============================================
7:44:29.420025 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:44:29.421024 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:44:29.422024 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:44:29.423026 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:44:29.424025 INFO: Starting candidate selection
7:44:30.093649 INFO: Starting candidate scoring
7:44:31.487969 INFO: Finished candidate processing
7:44:31.488978 INFO: Collecting candidate features
7:44:31.801026 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 43256)
7:44:31.818026 INFO: Collecting fragment features
7:44:31.958028 INFO: Finished candidate scoring
7:44:32.012035 INFO: performing precursor FDR with 47 features
7:44:32.014035 INFO: Decoy channel: -1
7:44:32.014035 INFO: Competetive: True
7:44:32.101554 INFO: Setting torch num_threads to 2 for FDR classification task
7:44:32.163555 WARNING: dropped 4 target PSMs due to missing features
7:44:32.164555 WARNING: dropped 2 decoy PSMs due to missing features
7:44:32.194556 INFO: Using random state 730690 for train-test-split
7:44:33.360309 INFO: Test AUC: 0.769
7:44:33.361309 INFO: Train AUC: 0.782
7:44:33.362309 INFO: AUC difference: 1.68%
7:44:34.092881 INFO: Resetting torch num_threads to 10
7:44:34.104882 PROGRESS: === Extracted 43256 precursors and 340406 fragments ===
7:44:34.110881 INFO: === FDR correction performed with classifier version 5 ===
7:44:34.125882 PROGRESS: ============================= Precursor FDR =============================
7:44:34.129882 PROGRESS: Total precursors accumulated: 7,543
7:44:34.133881 PROGRESS: Target precursors: 7,475 (99.10%)
7:44:34.137882 PROGRESS: Decoy precursors: 68 (0.90%)
7:44:34.141881 PROGRESS: 
7:44:34.145881 PROGRESS: Precursor Summary:
7:44:34.175882 PROGRESS: Channel   0:	 0.050 FDR: 7,475; 0.010 FDR: 7,475; 0.001 FDR: 6,398
7:44:34.180882 PROGRESS: 
7:44:34.184884 PROGRESS: Protein Summary:
7:44:34.220882 PROGRESS: Channel   0:	 0.050 FDR: 3,584; 0.010 FDR: 3,584; 0.001 FDR: 3,190
7:44:34.224883 PROGRESS: =========================================================================
7:44:34.238883 INFO: Target number of precursors reached.
7:44:34.490407 INFO: fragments_df: keeping 5000 of 340406 [sum(precursor_idx_mask)=175191 sum(mass_error_mask)=340406 stop_rank=5000
7:44:34.568920 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:44:41.554639 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:44:48.551859 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:44:52.123740 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:44:52.129740 INFO: Using score_cutoff 51.34225455780029 (fac=0.99, q=1)
7:44:52.134740 INFO: Updating optimization_manager: fwhm_rt             : 2.639645576477051 -> 2.639719009399414
7:44:52.138742 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:44:52.142740 INFO: Updating optimization_manager: score_cutoff        : 51.67438976898193 -> 51.34225455780029
7:44:52.146740 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:44:52.163741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:44:52.221742 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:44:52.299756 INFO: === checking if optimization conditions were reached ===
7:44:52.304755 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
7:44:52.353274 INFO: Updating optimization_manager: rt_error            : 17.92136741742517 -> 15.753271805325141
7:44:52.359273 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 15.7533.
7:44:52.369273 INFO: ==============================================
7:44:52.380273 INFO: Starting optimization step 7.
7:44:52.399274 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:44:52.408273 INFO: Using classic extraction backend
7:44:52.416274 PROGRESS: Extracting batch of 15870 precursors
7:44:52.420275 INFO: === Search parameters used ===
7:44:52.424276 INFO: rt_error       : 15.753271805325141
7:44:52.430274 INFO: mobility_error : 0.1
7:44:52.438275 INFO: num_candidates : 3
7:44:52.445273 INFO: ms1_error      : 5.0
7:44:52.454274 INFO: ms2_error      : 10.0
7:44:52.461274 INFO: fwhm_rt        : 2.639719009399414
7:44:52.487274 INFO: quant_window   : 3
7:44:52.493274 INFO: ==============================================
7:44:52.557283 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:44:52.558284 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:44:52.559283 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:44:52.560283 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:44:52.562284 INFO: Starting candidate selection
7:44:53.270918 INFO: Starting candidate scoring
7:44:54.631915 INFO: Finished candidate processing
7:44:54.633922 INFO: Collecting candidate features
7:44:54.942451 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 43322)
7:44:54.961454 INFO: Collecting fragment features
7:44:55.085997 INFO: Finished candidate scoring
7:44:55.133997 INFO: performing precursor FDR with 47 features
7:44:55.134997 INFO: Decoy channel: -1
7:44:55.135998 INFO: Competetive: True
7:44:55.201998 INFO: Setting torch num_threads to 2 for FDR classification task
7:44:55.245000 WARNING: dropped 2 target PSMs due to missing features
7:44:55.246000 WARNING: dropped 2 decoy PSMs due to missing features
7:44:55.267998 INFO: Using random state 730690 for train-test-split
7:44:56.198159 INFO: Test AUC: 0.767
7:44:56.199160 INFO: Train AUC: 0.788
7:44:56.200162 INFO: AUC difference: 2.63%
7:44:56.769235 INFO: Resetting torch num_threads to 10
7:44:56.780238 PROGRESS: === Extracted 43322 precursors and 341103 fragments ===
7:44:56.786235 INFO: === FDR correction performed with classifier version 5 ===
7:44:56.800236 PROGRESS: ============================= Precursor FDR =============================
7:44:56.804236 PROGRESS: Total precursors accumulated: 7,520
7:44:56.807240 PROGRESS: Target precursors: 7,463 (99.24%)
7:44:56.811240 PROGRESS: Decoy precursors: 57 (0.76%)
7:44:56.815244 PROGRESS: 
7:44:56.819244 PROGRESS: Precursor Summary:
7:44:56.845757 PROGRESS: Channel   0:	 0.050 FDR: 7,463; 0.010 FDR: 7,463; 0.001 FDR: 6,335
7:44:56.849757 PROGRESS: 
7:44:56.853756 PROGRESS: Protein Summary:
7:44:56.895757 PROGRESS: Channel   0:	 0.050 FDR: 3,589; 0.010 FDR: 3,589; 0.001 FDR: 3,167
7:44:56.900760 PROGRESS: =========================================================================
7:44:56.915757 INFO: Target number of precursors reached.
7:44:57.144276 INFO: fragments_df: keeping 5000 of 341103 [sum(precursor_idx_mask)=175579 sum(mass_error_mask)=341103 stop_rank=5000
7:44:57.233277 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:45:03.924312 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:45:10.899888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:45:14.369088 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:45:14.377088 INFO: Using score_cutoff 52.25631878128051 (fac=0.99, q=1)
7:45:14.383089 INFO: Updating optimization_manager: fwhm_rt             : 2.639719009399414 -> 2.6411499977111816
7:45:14.387088 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:45:14.391088 INFO: Updating optimization_manager: score_cutoff        : 51.34225455780029 -> 52.25631878128051
7:45:14.394088 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:45:14.410090 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:45:14.473091 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:45:14.550091 INFO: === checking if optimization conditions were reached ===
7:45:14.554092 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
7:45:14.583092 INFO: Updating optimization_manager: rt_error            : 15.753271805325141 -> 15.858432310666231
7:45:14.589092 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 15.8584.
7:45:14.596102 INFO: ==============================================
7:45:14.602100 INFO: Starting optimization step 8.
7:45:14.609610 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:45:14.613612 INFO: Using classic extraction backend
7:45:14.621611 PROGRESS: Extracting batch of 15870 precursors
7:45:14.627611 INFO: === Search parameters used ===
7:45:14.634610 INFO: rt_error       : 15.858432310666231
7:45:14.640610 INFO: mobility_error : 0.1
7:45:14.645610 INFO: num_candidates : 3
7:45:14.652611 INFO: ms1_error      : 5.0
7:45:14.659611 INFO: ms2_error      : 10.0
7:45:14.668610 INFO: fwhm_rt        : 2.6411499977111816
7:45:14.676610 INFO: quant_window   : 3
7:45:14.683611 INFO: ==============================================
7:45:14.734611 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:45:14.735610 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:45:14.736609 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:45:14.737610 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:45:14.738610 INFO: Starting candidate selection
7:45:15.381650 INFO: Starting candidate scoring
7:45:16.696628 INFO: Finished candidate processing
7:45:16.697633 INFO: Collecting candidate features
7:45:16.938146 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 43332)
7:45:16.955145 INFO: Collecting fragment features
7:45:17.066147 INFO: Finished candidate scoring
7:45:17.112660 INFO: performing precursor FDR with 47 features
7:45:17.113660 INFO: Decoy channel: -1
7:45:17.114660 INFO: Competetive: True
7:45:17.179662 INFO: Setting torch num_threads to 2 for FDR classification task
7:45:17.238662 WARNING: dropped 2 target PSMs due to missing features
7:45:17.239662 WARNING: dropped 2 decoy PSMs due to missing features
7:45:17.281662 INFO: Using random state 730690 for train-test-split
7:45:18.283231 INFO: Test AUC: 0.774
7:45:18.284231 INFO: Train AUC: 0.784
7:45:18.285230 INFO: AUC difference: 1.31%
7:45:18.951774 INFO: Resetting torch num_threads to 10
7:45:18.960773 PROGRESS: === Extracted 43332 precursors and 341128 fragments ===
7:45:18.965774 INFO: === FDR correction performed with classifier version 5 ===
7:45:18.976774 PROGRESS: ============================= Precursor FDR =============================
7:45:18.979773 PROGRESS: Total precursors accumulated: 7,521
7:45:18.983775 PROGRESS: Target precursors: 7,468 (99.30%)
7:45:18.986774 PROGRESS: Decoy precursors: 53 (0.70%)
7:45:18.990774 PROGRESS: 
7:45:18.993774 PROGRESS: Precursor Summary:
7:45:19.014774 PROGRESS: Channel   0:	 0.050 FDR: 7,468; 0.010 FDR: 7,468; 0.001 FDR: 6,783
7:45:19.018774 PROGRESS: 
7:45:19.022774 PROGRESS: Protein Summary:
7:45:19.045774 PROGRESS: Channel   0:	 0.050 FDR: 3,590; 0.010 FDR: 3,590; 0.001 FDR: 3,340
7:45:19.049774 PROGRESS: =========================================================================
7:45:19.057775 INFO: Target number of precursors reached.
7:45:19.273288 INFO: fragments_df: keeping 5000 of 341128 [sum(precursor_idx_mask)=175698 sum(mass_error_mask)=341128 stop_rank=5000
7:45:19.358293 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:45:25.862268 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:45:32.705763 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:45:36.268967 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:45:36.274967 INFO: Using score_cutoff 51.45747601203919 (fac=0.99, q=1)
7:45:36.278967 INFO: Updating optimization_manager: fwhm_rt             : 2.6411499977111816 -> 2.638733386993408
7:45:36.282967 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:45:36.286968 INFO: Updating optimization_manager: score_cutoff        : 52.25631878128051 -> 51.45747601203919
7:45:36.289968 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:45:36.304967 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:45:36.345968 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:45:36.414479 INFO: === checking if optimization conditions were reached ===
7:45:36.418480 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
7:45:36.424479 INFO: Updating optimization_manager: rt_error            : 15.858432310666231 -> 15.415610931367683
7:45:36.428483 INFO: Updating optimization_manager: classifier_version  : 5 -> 10
7:45:36.432480 INFO: Updating optimization_manager: score_cutoff        : 51.45747601203919 -> 51.58034747314453
7:45:36.436480 INFO: Updating optimization_manager: fwhm_rt             : 2.638733386993408 -> 2.6334521770477295
7:45:36.439480 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:45:36.443480 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 15.4156 found after 9 searches.
7:45:36.446480 INFO: ==============================================
7:45:36.452480 PROGRESS: Optimization finished for rt_error.
7:45:36.525481 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:45:36.556481 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:45:36.606482 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:45:36.747997 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
7:45:36.753996 PROGRESS: ==============================================
7:45:36.760996 PROGRESS: ms2_error      : 10.0000
7:45:36.768996 PROGRESS: ms1_error      : 5.0000
7:45:36.772996 PROGRESS: rt_error       : 15.4156
7:45:36.777996 PROGRESS: ==============================================
7:45:36.809002 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:45:36.909510 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:45:37.123514 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:45:37.594548 INFO: Using classic extraction backend
7:45:37.598548 PROGRESS: Extracting batch of 121155 precursors
7:45:37.602548 INFO: === Search parameters used ===
7:45:37.606548 INFO: rt_error       : 15.415610931367683
7:45:37.609548 INFO: mobility_error : 0.1
7:45:37.613548 INFO: num_candidates : 3
7:45:37.616548 INFO: ms1_error      : 5.0
7:45:37.620549 INFO: ms2_error      : 10.0
7:45:37.623548 INFO: fwhm_rt        : 2.6334521770477295
7:45:37.627548 INFO: quant_window   : 3
7:45:37.630550 INFO: ==============================================
7:45:37.727061 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:45:37.728061 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:45:37.729061 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:45:37.730061 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:45:37.731061 INFO: Starting candidate selection
7:45:41.822785 INFO: Removed 122572 precursors with score below cutoff 51.58034747314453
7:45:41.928296 INFO: Starting candidate scoring
7:45:48.256167 INFO: Finished candidate processing
7:45:48.258171 INFO: Collecting candidate features
7:45:48.958711 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 207895)
7:45:49.017712 INFO: Collecting fragment features
7:45:49.367226 INFO: Finished candidate scoring
7:45:49.552740 INFO: === Performing FDR correction with classifier version 10 ===
7:45:49.561740 INFO: performing precursor FDR with 47 features
7:45:49.562741 INFO: Decoy channel: -1
7:45:49.563740 INFO: Competetive: True
7:45:49.775257 INFO: Setting torch num_threads to 2 for FDR classification task
7:45:49.864258 WARNING: dropped 1 target PSMs due to missing features
7:45:49.865258 WARNING: FDR calculation for 118614 target and 89280 decoy PSMs
7:45:49.867258 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
7:45:50.019772 INFO: Using random state 767542 for train-test-split
7:45:55.871676 INFO: Test AUC: 0.855
7:45:55.873677 INFO: Train AUC: 0.860
7:45:55.874678 INFO: AUC difference: 0.50%
7:45:56.661983 INFO: Resetting torch num_threads to 10
7:45:56.703526 INFO: Removing fragments below FDR threshold
7:45:56.895529 PROGRESS: ============================= Precursor FDR =============================
7:45:56.902688 PROGRESS: Total precursors accumulated: 57,125
7:45:56.909994 PROGRESS: Target precursors: 56,744 (99.33%)
7:45:56.916998 PROGRESS: Decoy precursors: 381 (0.67%)
7:45:56.923002 PROGRESS: 
7:45:56.928003 PROGRESS: Precursor Summary:
7:45:57.039519 PROGRESS: Channel   0:	 0.050 FDR: 56,744; 0.010 FDR: 56,744; 0.001 FDR: 55,092
7:45:57.044518 PROGRESS: 
7:45:57.053520 PROGRESS: Protein Summary:
7:45:57.215043 PROGRESS: Channel   0:	 0.050 FDR: 6,502; 0.010 FDR: 6,502; 0.001 FDR: 6,462
7:45:57.227041 PROGRESS: =========================================================================
7:45:57.270043 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\psm.parquet
7:45:58.327679 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\frag.parquet
7:45:59.431405 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
7:45:59.702467 PROGRESS: 
7:45:59.703467 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant
7:45:59.705464 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\figures
7:45:59.712466 INFO: Initializing TimingManager
7:45:59.725469 INFO: Initializing RawFileManager
7:50:37.236157 INFO: Determining DIA cycle
7:50:37.282151 INFO: Found cycle with start 0.00 min and length 86.
7:50:37.970828 INFO: RT (min)            : 0.0 - 55.4
7:50:37.970828 INFO: RT duration (sec)   : 3326.9
7:50:37.971828 INFO: RT duration (min)   : 55.4
7:50:37.972829 INFO: Cycle len (scans)   : 86
7:50:37.973827 INFO: Cycle len (sec)     : 1.90
7:50:37.974830 INFO: Number of cycles    : 1747
7:50:37.975828 INFO: MS2 range (m/z)     : 399.5 - 903.5
7:50:37.975828 INFO: Creating DIA data object took: 278.2443654537201
7:50:38.061832 INFO: Initializing CalibrationManager
7:50:38.067832 INFO: Setting up calibration estimators ..
7:50:38.071845 INFO: Found 1 estimator(s) in calibration group 'fragment'
7:50:38.075848 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'}' ..
7:50:38.078849 INFO: Found 3 estimator(s) in calibration group 'precursor'
7:50:38.082847 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
7:50:38.086380 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}}' ..
7:50:38.089378 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
7:50:38.093379 INFO: Done setting up calibration estimators.
7:50:38.097380 INFO: Initializing OptimizationManager
7:50:38.103380 INFO: initial parameter: ms1_error = 30
7:50:38.109380 INFO: initial parameter: ms2_error = 30
7:50:38.116380 INFO: initial parameter: rt_error = 1663.4844970703125
7:50:38.123379 INFO: initial parameter: mobility_error = 0.1
7:50:38.132377 INFO: initial parameter: num_candidates = 1
7:50:38.139380 INFO: initial parameter: fwhm_rt = 5
7:50:38.147375 INFO: initial parameter: fwhm_mobility = 0.01
7:50:38.153379 INFO: initial parameter: score_cutoff = 0
7:50:38.161379 INFO: initial parameter: classifier_version = -1
7:50:38.176380 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
7:50:38.186381 INFO: FDRManager: loading saved state not requested, will be initialized.
7:50:38.187383 INFO: Initializing FDRManager
7:50:38.188378 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
7:50:38.311382 PROGRESS: Initializing spectral library: 61,104 target precursors potentially observable (0 removed)
7:50:38.422920 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
7:50:38.428920 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 1663.4844970703125
7:50:38.436920 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
7:50:38.441920 PROGRESS: Starting initial search for precursors.
7:50:38.448920 INFO: Starting optimization step 0.
7:50:38.456920 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:50:38.463921 INFO: Using classic extraction backend
7:50:38.469920 PROGRESS: Extracting batch of 15870 precursors
7:50:38.473921 INFO: === Search parameters used ===
7:50:38.477921 INFO: rt_error       : 1663.4844970703125
7:50:38.484921 INFO: mobility_error : 0.1
7:50:38.491921 INFO: num_candidates : 1
7:50:38.497921 INFO: ms1_error      : 30
7:50:38.506921 INFO: ms2_error      : 30
7:50:38.513921 INFO: fwhm_rt        : 5
7:50:38.519921 INFO: quant_window   : 3
7:50:38.524921 INFO: ==============================================
7:50:38.573939 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:50:38.574936 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:50:38.575938 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
7:50:38.576941 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
7:50:38.577941 INFO: Starting candidate selection
7:50:52.479791 INFO: Starting candidate scoring
7:50:53.079319 INFO: Finished candidate processing
7:50:53.080328 INFO: Collecting candidate features
7:50:53.189560 INFO: Collecting fragment features
7:50:53.275563 INFO: Finished candidate scoring
7:50:53.302560 INFO: performing precursor FDR with 47 features
7:50:53.303560 INFO: Decoy channel: -1
7:50:53.303560 INFO: Competetive: True
7:50:53.332561 INFO: Setting torch num_threads to 2 for FDR classification task
7:50:53.359085 INFO: Using random state 560251 for train-test-split
7:50:53.709302 INFO: Test AUC: 0.779
7:50:53.710304 INFO: Train AUC: 0.781
7:50:53.711304 INFO: AUC difference: 0.26%
7:50:54.318382 INFO: Resetting torch num_threads to 10
7:50:54.325383 PROGRESS: === Extracted 15870 precursors and 162152 fragments ===
7:50:54.330393 INFO: === FDR correction performed with classifier version -1 ===
7:50:54.340382 PROGRESS: ============================= Precursor FDR =============================
7:50:54.343383 PROGRESS: Total precursors accumulated: 3,534
7:50:54.346382 PROGRESS: Target precursors: 3,344 (94.62%)
7:50:54.349387 PROGRESS: Decoy precursors: 190 (5.38%)
7:50:54.352388 PROGRESS: 
7:50:54.355387 PROGRESS: Precursor Summary:
7:50:54.367900 PROGRESS: Channel   0:	 0.050 FDR: 3,141; 0.010 FDR: 1,256; 0.001 FDR:   104
7:50:54.370900 PROGRESS: 
7:50:54.373901 PROGRESS: Protein Summary:
7:50:54.385905 PROGRESS: Channel   0:	 0.050 FDR: 1,899; 0.010 FDR:   932; 0.001 FDR:    97
7:50:54.389902 PROGRESS: =========================================================================
7:50:54.393904 INFO: Target number of precursors reached.
7:50:54.440906 INFO: fragments_df: keeping 5000 of 162152 [sum(precursor_idx_mask)=14209 sum(mass_error_mask)=162152 stop_rank=5000
7:50:54.511907 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:50:55.181129 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:50:55.882949 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:50:59.371361 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
7:50:59.375877 INFO: Using score_cutoff 86.17228943252563 (fac=0.99, q=1)
7:50:59.379877 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.4411847591400146
7:50:59.382880 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
7:50:59.386880 INFO: Updating optimization_manager: score_cutoff        : 0 -> 86.17228943252563
7:50:59.389878 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:50:59.403881 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:50:59.446880 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:50:59.514882 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
7:50:59.518884 PROGRESS: Required number of precursors found. Starting search parameter optimization.
7:50:59.521881 INFO: Starting optimization step 1.
7:50:59.525883 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:50:59.529885 INFO: Using classic extraction backend
7:50:59.533884 PROGRESS: Extracting batch of 15870 precursors
7:50:59.536884 INFO: === Search parameters used ===
7:50:59.540883 INFO: rt_error       : 1663.4844970703125
7:50:59.543883 INFO: mobility_error : 0.1
7:50:59.547880 INFO: num_candidates : 3
7:50:59.550883 INFO: ms1_error      : 30
7:50:59.554886 INFO: ms2_error      : 30
7:50:59.558884 INFO: fwhm_rt        : 2.4411847591400146
7:50:59.561883 INFO: quant_window   : 3
7:50:59.565885 INFO: ==============================================
7:50:59.602884 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:50:59.603885 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:50:59.604883 INFO: FWHM in RT is 2.44 seconds, sigma is 0.27
7:50:59.605883 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:50:59.606884 INFO: Starting candidate selection
7:51:15.637395 INFO: Starting candidate scoring
7:51:17.165778 INFO: Finished candidate processing
7:51:17.166783 INFO: Collecting candidate features
7:51:17.449297 INFO: Collecting fragment features
7:51:17.586299 INFO: Finished candidate scoring
7:51:17.634303 INFO: performing precursor FDR with 47 features
7:51:17.635303 INFO: Decoy channel: -1
7:51:17.636305 INFO: Competetive: True
7:51:17.701814 INFO: Setting torch num_threads to 2 for FDR classification task
7:51:17.752814 INFO: Using random state 126590 for train-test-split
7:51:18.834377 INFO: Test AUC: 0.691
7:51:18.835378 INFO: Train AUC: 0.694
7:51:18.836378 INFO: AUC difference: 0.35%
7:51:19.416919 INFO: Resetting torch num_threads to 10
7:51:19.426919 PROGRESS: === Extracted 47607 precursors and 458062 fragments ===
7:51:19.431921 INFO: === FDR correction performed with classifier version 0 ===
7:51:19.441919 PROGRESS: ============================= Precursor FDR =============================
7:51:19.445921 PROGRESS: Total precursors accumulated: 6,517
7:51:19.448920 PROGRESS: Target precursors: 6,336 (97.22%)
7:51:19.452921 PROGRESS: Decoy precursors: 181 (2.78%)
7:51:19.455920 PROGRESS: 
7:51:19.458921 PROGRESS: Precursor Summary:
7:51:19.476920 PROGRESS: Channel   0:	 0.050 FDR: 6,336; 0.010 FDR: 5,631; 0.001 FDR: 3,199
7:51:19.480921 PROGRESS: 
7:51:19.484922 PROGRESS: Protein Summary:
7:51:19.504922 PROGRESS: Channel   0:	 0.050 FDR: 3,168; 0.010 FDR: 2,910; 0.001 FDR: 1,914
7:51:19.507922 PROGRESS: =========================================================================
7:51:19.516921 INFO: Target number of precursors reached.
7:51:19.752436 INFO: fragments_df: keeping 5000 of 458062 [sum(precursor_idx_mask)=169168 sum(mass_error_mask)=458062 stop_rank=5000
7:51:19.825435 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:51:23.710539 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:51:27.796061 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:51:31.241298 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:51:31.247299 INFO: Using score_cutoff 75.11560949707031 (fac=0.99, q=1)
7:51:31.251298 INFO: Updating optimization_manager: fwhm_rt             : 2.4411847591400146 -> 2.7216832637786865
7:51:31.255299 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:51:31.258299 INFO: Updating optimization_manager: score_cutoff        : 86.17228943252563 -> 75.11560949707031
7:51:31.262298 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:51:31.278299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:51:31.322296 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:51:31.389293 INFO: === checking if optimization conditions were reached ===
7:51:31.397295 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.55141713019883
7:51:31.400296 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
7:51:31.404295 PROGRESS: ❌ ms2_error      : 23.5514 > 10.0000 or insufficient steps taken.
7:51:31.411294 INFO: Updating optimization_manager: ms1_error           : 30 -> 14.34671108627764
7:51:31.415299 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
7:51:31.418298 PROGRESS: ❌ ms1_error      : 14.3467 > 5.0000 or insufficient steps taken.
7:51:31.421299 INFO: ==============================================
7:51:31.424299 INFO: Starting optimization step 2.
7:51:31.428298 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:51:31.430810 INFO: Using classic extraction backend
7:51:31.434810 PROGRESS: Extracting batch of 15870 precursors
7:51:31.437810 INFO: === Search parameters used ===
7:51:31.440811 INFO: rt_error       : 1663.4844970703125
7:51:31.443811 INFO: mobility_error : 0.1
7:51:31.447811 INFO: num_candidates : 3
7:51:31.450810 INFO: ms1_error      : 14.34671108627764
7:51:31.453810 INFO: ms2_error      : 23.55141713019883
7:51:31.456810 INFO: fwhm_rt        : 2.7216832637786865
7:51:31.460812 INFO: quant_window   : 3
7:51:31.464811 INFO: ==============================================
7:51:31.504814 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:51:31.505811 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:51:31.506811 INFO: FWHM in RT is 2.72 seconds, sigma is 0.30
7:51:31.506811 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:51:31.507811 INFO: Starting candidate selection
7:51:46.955359 INFO: Starting candidate scoring
7:51:48.555274 INFO: Finished candidate processing
7:51:48.556793 INFO: Collecting candidate features
7:51:48.904340 INFO: Collecting fragment features
7:51:49.083878 INFO: Finished candidate scoring
7:51:49.142877 INFO: performing precursor FDR with 47 features
7:51:49.143875 INFO: Decoy channel: -1
7:51:49.144875 INFO: Competetive: True
7:51:49.231416 INFO: Setting torch num_threads to 2 for FDR classification task
7:51:49.317415 INFO: Using random state 660621 for train-test-split
7:51:50.655226 INFO: Test AUC: 0.699
7:51:50.656227 INFO: Train AUC: 0.706
7:51:50.657227 INFO: AUC difference: 1.05%
7:51:51.358002 INFO: Resetting torch num_threads to 10
7:51:51.372006 PROGRESS: === Extracted 47608 precursors and 445719 fragments ===
7:51:51.377002 INFO: === FDR correction performed with classifier version 1 ===
7:51:51.391004 PROGRESS: ============================= Precursor FDR =============================
7:51:51.396005 PROGRESS: Total precursors accumulated: 6,851
7:51:51.401007 PROGRESS: Target precursors: 6,705 (97.87%)
7:51:51.406005 PROGRESS: Decoy precursors: 146 (2.13%)
7:51:51.411132 PROGRESS: 
7:51:51.416006 PROGRESS: Precursor Summary:
7:51:51.455024 PROGRESS: Channel   0:	 0.050 FDR: 6,705; 0.010 FDR: 6,404; 0.001 FDR: 5,028
7:51:51.459023 PROGRESS: 
7:51:51.462546 PROGRESS: Protein Summary:
7:51:51.493551 PROGRESS: Channel   0:	 0.050 FDR: 3,324; 0.010 FDR: 3,200; 0.001 FDR: 2,696
7:51:51.497547 PROGRESS: =========================================================================
7:51:51.510550 INFO: Target number of precursors reached.
7:51:51.797174 INFO: fragments_df: keeping 5000 of 445719 [sum(precursor_idx_mask)=187729 sum(mass_error_mask)=445719 stop_rank=5000
7:51:51.903177 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:51:57.298994 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:52:02.882365 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:52:06.453067 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:52:06.462066 INFO: Using score_cutoff 69.40661888809204 (fac=0.99, q=1)
7:52:06.470067 INFO: Updating optimization_manager: fwhm_rt             : 2.7216832637786865 -> 2.689790725708008
7:52:06.476067 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:52:06.482068 INFO: Updating optimization_manager: score_cutoff        : 75.11560949707031 -> 69.40661888809204
7:52:06.488082 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:52:06.505611 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:52:06.563609 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:52:06.637610 INFO: === checking if optimization conditions were reached ===
7:52:06.646611 INFO: Updating optimization_manager: ms2_error           : 23.55141713019883 -> 18.934384435606603
7:52:06.651613 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
7:52:06.654611 PROGRESS: ❌ ms2_error      : 18.9344 > 10.0000 or insufficient steps taken.
7:52:06.664612 INFO: Updating optimization_manager: ms1_error           : 14.34671108627764 -> 5.307579969988714
7:52:06.668612 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
7:52:06.671609 PROGRESS: ❌ ms1_error      : 5.3076 > 5.0000 or insufficient steps taken.
7:52:06.675612 INFO: ==============================================
7:52:06.678608 INFO: Starting optimization step 3.
7:52:06.682607 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:52:06.685610 INFO: Using classic extraction backend
7:52:06.689611 PROGRESS: Extracting batch of 15870 precursors
7:52:06.692611 INFO: === Search parameters used ===
7:52:06.696613 INFO: rt_error       : 1663.4844970703125
7:52:06.699611 INFO: mobility_error : 0.1
7:52:06.703609 INFO: num_candidates : 3
7:52:06.707608 INFO: ms1_error      : 5.307579969988714
7:52:06.714612 INFO: ms2_error      : 18.934384435606603
7:52:06.718612 INFO: fwhm_rt        : 2.689790725708008
7:52:06.723614 INFO: quant_window   : 3
7:52:06.729608 INFO: ==============================================
7:52:06.781161 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:52:06.782161 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:52:06.783167 INFO: FWHM in RT is 2.69 seconds, sigma is 0.30
7:52:06.784160 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:52:06.785167 INFO: Starting candidate selection
7:52:22.579030 INFO: Starting candidate scoring
7:52:23.983005 INFO: Finished candidate processing
7:52:23.984215 INFO: Collecting candidate features
7:52:24.257776 INFO: Collecting fragment features
7:52:24.391307 INFO: Finished candidate scoring
7:52:24.442305 INFO: performing precursor FDR with 47 features
7:52:24.443306 INFO: Decoy channel: -1
7:52:24.444309 INFO: Competetive: True
7:52:24.509321 INFO: Setting torch num_threads to 2 for FDR classification task
7:52:24.560852 INFO: Using random state 390033 for train-test-split
7:52:25.669376 INFO: Test AUC: 0.699
7:52:25.670377 INFO: Train AUC: 0.711
7:52:25.671380 INFO: AUC difference: 1.76%
7:52:26.326151 INFO: Resetting torch num_threads to 10
7:52:26.336151 PROGRESS: === Extracted 47605 precursors and 434968 fragments ===
7:52:26.341147 INFO: === FDR correction performed with classifier version 2 ===
7:52:26.352152 PROGRESS: ============================= Precursor FDR =============================
7:52:26.355149 PROGRESS: Total precursors accumulated: 7,032
7:52:26.358147 PROGRESS: Target precursors: 6,904 (98.18%)
7:52:26.361151 PROGRESS: Decoy precursors: 128 (1.82%)
7:52:26.365150 PROGRESS: 
7:52:26.368153 PROGRESS: Precursor Summary:
7:52:26.386153 PROGRESS: Channel   0:	 0.050 FDR: 6,904; 0.010 FDR: 6,704; 0.001 FDR: 5,110
7:52:26.390151 PROGRESS: 
7:52:26.393151 PROGRESS: Protein Summary:
7:52:26.414150 PROGRESS: Channel   0:	 0.050 FDR: 3,377; 0.010 FDR: 3,312; 0.001 FDR: 2,730
7:52:26.418152 PROGRESS: =========================================================================
7:52:26.426152 INFO: Target number of precursors reached.
7:52:26.671700 INFO: fragments_df: keeping 5000 of 434968 [sum(precursor_idx_mask)=192654 sum(mass_error_mask)=434968 stop_rank=5000
7:52:26.771702 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:52:32.717425 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:52:38.626785 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:52:42.088017 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:52:42.093016 INFO: Using score_cutoff 65.77576307144165 (fac=0.99, q=1)
7:52:42.098016 INFO: Updating optimization_manager: fwhm_rt             : 2.689790725708008 -> 2.659295082092285
7:52:42.101016 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:52:42.105017 INFO: Updating optimization_manager: score_cutoff        : 69.40661888809204 -> 65.77576307144165
7:52:42.108016 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:52:42.121015 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:52:42.162016 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:52:42.228016 INFO: === checking if optimization conditions were reached ===
7:52:42.236017 INFO: Updating optimization_manager: ms2_error           : 18.934384435606603 -> 14.69167290089693
7:52:42.239018 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
7:52:42.242018 PROGRESS: ❌ ms2_error      : 14.6917 > 10.0000 or insufficient steps taken.
7:52:42.251017 INFO: Updating optimization_manager: ms1_error           : 5.307579969988714 -> 5.0
7:52:42.254018 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
7:52:42.257018 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:52:42.260018 INFO: ==============================================
7:52:42.263018 INFO: Starting optimization step 4.
7:52:42.266018 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:52:42.269018 INFO: Using classic extraction backend
7:52:42.273018 PROGRESS: Extracting batch of 15870 precursors
7:52:42.276018 INFO: === Search parameters used ===
7:52:42.279019 INFO: rt_error       : 1663.4844970703125
7:52:42.282018 INFO: mobility_error : 0.1
7:52:42.285019 INFO: num_candidates : 3
7:52:42.288019 INFO: ms1_error      : 5.0
7:52:42.291019 INFO: ms2_error      : 14.69167290089693
7:52:42.294018 INFO: fwhm_rt        : 2.659295082092285
7:52:42.297024 INFO: quant_window   : 3
7:52:42.300023 INFO: ==============================================
7:52:42.336533 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:52:42.337533 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:52:42.338534 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:52:42.338534 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:52:42.339535 INFO: Starting candidate selection
7:52:58.202223 INFO: Starting candidate scoring
7:52:59.641443 INFO: Finished candidate processing
7:52:59.643448 INFO: Collecting candidate features
7:52:59.915962 INFO: Collecting fragment features
7:53:00.060963 INFO: Finished candidate scoring
7:53:00.108475 INFO: performing precursor FDR with 47 features
7:53:00.109491 INFO: Decoy channel: -1
7:53:00.110476 INFO: Competetive: True
7:53:00.173476 INFO: Setting torch num_threads to 2 for FDR classification task
7:53:00.223477 INFO: Using random state 478233 for train-test-split
7:53:01.344551 INFO: Test AUC: 0.701
7:53:01.345551 INFO: Train AUC: 0.715
7:53:01.346553 INFO: AUC difference: 1.97%
7:53:01.956782 INFO: Resetting torch num_threads to 10
7:53:01.965786 PROGRESS: === Extracted 47602 precursors and 423298 fragments ===
7:53:01.971783 INFO: === FDR correction performed with classifier version 3 ===
7:53:01.981782 PROGRESS: ============================= Precursor FDR =============================
7:53:01.984784 PROGRESS: Total precursors accumulated: 7,155
7:53:01.988781 PROGRESS: Target precursors: 7,029 (98.24%)
7:53:01.991782 PROGRESS: Decoy precursors: 126 (1.76%)
7:53:01.995784 PROGRESS: 
7:53:01.998784 PROGRESS: Precursor Summary:
7:53:02.017783 PROGRESS: Channel   0:	 0.050 FDR: 7,029; 0.010 FDR: 6,885; 0.001 FDR: 5,700
7:53:02.021780 PROGRESS: 
7:53:02.024786 PROGRESS: Protein Summary:
7:53:02.045784 PROGRESS: Channel   0:	 0.050 FDR: 3,429; 0.010 FDR: 3,369; 0.001 FDR: 2,946
7:53:02.048785 PROGRESS: =========================================================================
7:53:02.057784 INFO: Target number of precursors reached.
7:53:02.291392 INFO: fragments_df: keeping 5000 of 423298 [sum(precursor_idx_mask)=193413 sum(mass_error_mask)=423298 stop_rank=5000
7:53:02.371002 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:53:08.641517 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:53:14.979374 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:53:18.540779 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:53:18.545781 INFO: Using score_cutoff 62.11379867706299 (fac=0.99, q=1)
7:53:18.549779 INFO: Updating optimization_manager: fwhm_rt             : 2.659295082092285 -> 2.6373021602630615
7:53:18.553777 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:53:18.557779 INFO: Updating optimization_manager: score_cutoff        : 65.77576307144165 -> 62.11379867706299
7:53:18.560779 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:53:18.574776 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:53:18.615794 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:53:18.684396 INFO: === checking if optimization conditions were reached ===
7:53:18.692397 INFO: Updating optimization_manager: ms2_error           : 14.69167290089693 -> 11.284588101385271
7:53:18.696399 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
7:53:18.699398 PROGRESS: ❌ ms2_error      : 11.2846 > 10.0000 or insufficient steps taken.
7:53:18.703395 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:53:18.707395 INFO: ==============================================
7:53:18.710394 INFO: Starting optimization step 5.
7:53:18.714399 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:53:18.717398 INFO: Using classic extraction backend
7:53:18.721400 PROGRESS: Extracting batch of 15870 precursors
7:53:18.724395 INFO: === Search parameters used ===
7:53:18.728400 INFO: rt_error       : 1663.4844970703125
7:53:18.731399 INFO: mobility_error : 0.1
7:53:18.735399 INFO: num_candidates : 3
7:53:18.738398 INFO: ms1_error      : 5.0
7:53:18.742401 INFO: ms2_error      : 11.284588101385271
7:53:18.745396 INFO: fwhm_rt        : 2.6373021602630615
7:53:18.749399 INFO: quant_window   : 3
7:53:18.753400 INFO: ==============================================
7:53:18.790400 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:53:18.791397 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:53:18.793399 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
7:53:18.794397 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:53:18.795398 INFO: Starting candidate selection
7:53:34.406300 INFO: Starting candidate scoring
7:53:35.773016 INFO: Finished candidate processing
7:53:35.773016 INFO: Collecting candidate features
7:53:36.016892 INFO: Collecting fragment features
7:53:36.130902 INFO: Finished candidate scoring
7:53:36.179803 INFO: performing precursor FDR with 47 features
7:53:36.180802 INFO: Decoy channel: -1
7:53:36.181803 INFO: Competetive: True
7:53:36.242805 INFO: Setting torch num_threads to 2 for FDR classification task
7:53:36.291806 INFO: Using random state 197559 for train-test-split
7:53:37.256431 INFO: Test AUC: 0.706
7:53:37.257435 INFO: Train AUC: 0.716
7:53:37.258435 INFO: AUC difference: 1.38%
7:53:37.889016 INFO: Resetting torch num_threads to 10
7:53:37.899023 PROGRESS: === Extracted 47596 precursors and 411750 fragments ===
7:53:37.904025 INFO: === FDR correction performed with classifier version 4 ===
7:53:37.914577 PROGRESS: ============================= Precursor FDR =============================
7:53:37.918227 PROGRESS: Total precursors accumulated: 7,127
7:53:37.922225 PROGRESS: Target precursors: 7,023 (98.54%)
7:53:37.926228 PROGRESS: Decoy precursors: 104 (1.46%)
7:53:37.931228 PROGRESS: 
7:53:37.936342 PROGRESS: Precursor Summary:
7:53:37.956556 PROGRESS: Channel   0:	 0.050 FDR: 7,023; 0.010 FDR: 6,934; 0.001 FDR: 5,508
7:53:37.960486 PROGRESS: 
7:53:37.963487 PROGRESS: Protein Summary:
7:53:37.984487 PROGRESS: Channel   0:	 0.050 FDR: 3,438; 0.010 FDR: 3,397; 0.001 FDR: 2,873
7:53:37.989487 PROGRESS: =========================================================================
7:53:38.007488 INFO: Target number of precursors reached.
7:53:38.217768 INFO: fragments_df: keeping 5000 of 411750 [sum(precursor_idx_mask)=190559 sum(mass_error_mask)=411750 stop_rank=5000
7:53:38.294219 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:53:44.190987 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:53:50.619260 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:53:54.158535 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:53:54.163537 INFO: Using score_cutoff 58.91914827919006 (fac=0.99, q=1)
7:53:54.167536 INFO: Updating optimization_manager: fwhm_rt             : 2.6373021602630615 -> 2.634791851043701
7:53:54.171534 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:53:54.174534 INFO: Updating optimization_manager: score_cutoff        : 62.11379867706299 -> 58.91914827919006
7:53:54.177534 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:53:54.194113 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:53:54.248118 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:53:54.322121 INFO: === checking if optimization conditions were reached ===
7:53:54.333121 INFO: Updating optimization_manager: ms2_error           : 11.284588101385271 -> 10.0
7:53:54.340120 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
7:53:54.348119 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
7:53:54.355120 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
7:53:54.361121 INFO: ==============================================
7:53:54.369118 PROGRESS: Optimization finished for ms2_error, ms1_error.
7:53:54.460665 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:53:54.483664 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:53:54.556664 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:53:54.648664 INFO: Starting optimization step 0.
7:53:54.652668 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:53:54.658666 INFO: Using classic extraction backend
7:53:54.665663 PROGRESS: Extracting batch of 15870 precursors
7:53:54.671666 INFO: === Search parameters used ===
7:53:54.680677 INFO: rt_error       : 1663.4844970703125
7:53:54.686678 INFO: mobility_error : 0.1
7:53:54.692679 INFO: num_candidates : 3
7:53:54.701197 INFO: ms1_error      : 5.0
7:53:54.705200 INFO: ms2_error      : 10.0
7:53:54.714198 INFO: fwhm_rt        : 2.634791851043701
7:53:54.721197 INFO: quant_window   : 3
7:53:54.728198 INFO: ==============================================
7:53:54.800205 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:53:54.801200 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:53:54.802204 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:53:54.802204 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:53:54.804203 INFO: Starting candidate selection
7:54:11.013131 INFO: Starting candidate scoring
7:54:12.534531 INFO: Finished candidate processing
7:54:12.536050 INFO: Collecting candidate features
7:54:12.856591 INFO: Collecting fragment features
7:54:13.029110 INFO: Finished candidate scoring
7:54:13.086109 INFO: performing precursor FDR with 47 features
7:54:13.087111 INFO: Decoy channel: -1
7:54:13.088109 INFO: Competetive: True
7:54:13.174112 INFO: Setting torch num_threads to 2 for FDR classification task
7:54:13.242653 INFO: Using random state 787985 for train-test-split
7:54:14.529579 INFO: Test AUC: 0.714
7:54:14.531581 INFO: Train AUC: 0.720
7:54:14.531581 INFO: AUC difference: 0.93%
7:54:15.297276 INFO: Resetting torch num_threads to 10
7:54:15.309278 PROGRESS: === Extracted 47596 precursors and 407192 fragments ===
7:54:15.315276 INFO: === FDR correction performed with classifier version 5 ===
7:54:15.329277 PROGRESS: ============================= Precursor FDR =============================
7:54:15.332278 PROGRESS: Total precursors accumulated: 7,148
7:54:15.336277 PROGRESS: Target precursors: 7,040 (98.49%)
7:54:15.339280 PROGRESS: Decoy precursors: 108 (1.51%)
7:54:15.342275 PROGRESS: 
7:54:15.345279 PROGRESS: Precursor Summary:
7:54:15.374278 PROGRESS: Channel   0:	 0.050 FDR: 7,040; 0.010 FDR: 6,926; 0.001 FDR: 5,419
7:54:15.378277 PROGRESS: 
7:54:15.381277 PROGRESS: Protein Summary:
7:54:15.415277 PROGRESS: Channel   0:	 0.050 FDR: 3,433; 0.010 FDR: 3,390; 0.001 FDR: 2,844
7:54:15.419275 PROGRESS: =========================================================================
7:54:15.431280 INFO: Target number of precursors reached.
7:54:15.703899 INFO: fragments_df: keeping 5000 of 407192 [sum(precursor_idx_mask)=188453 sum(mass_error_mask)=407192 stop_rank=5000
7:54:15.809440 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:54:21.832175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:54:28.011705 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:54:31.552714 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:54:31.559714 INFO: Using score_cutoff 57.63253480911255 (fac=0.99, q=1)
7:54:31.565713 INFO: Updating optimization_manager: fwhm_rt             : 2.634791851043701 -> 2.628462314605713
7:54:31.571714 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:54:31.576718 INFO: Updating optimization_manager: score_cutoff        : 58.91914827919006 -> 57.63253480911255
7:54:31.580715 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:54:31.595712 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:54:31.636715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:54:31.705713 INFO: === checking if optimization conditions were reached ===
7:54:31.709716 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
7:54:31.730717 INFO: Updating optimization_manager: rt_error            : 1663.4844970703125 -> 115.51597973300039
7:54:31.734716 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 115.5160.
7:54:31.737715 INFO: ==============================================
7:54:31.741718 INFO: Starting optimization step 1.
7:54:31.744717 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:54:31.748729 INFO: Using classic extraction backend
7:54:31.751730 PROGRESS: Extracting batch of 15870 precursors
7:54:31.755729 INFO: === Search parameters used ===
7:54:31.758729 INFO: rt_error       : 115.51597973300039
7:54:31.762241 INFO: mobility_error : 0.1
7:54:31.765252 INFO: num_candidates : 3
7:54:31.768255 INFO: ms1_error      : 5.0
7:54:31.772253 INFO: ms2_error      : 10.0
7:54:31.775260 INFO: fwhm_rt        : 2.628462314605713
7:54:31.779260 INFO: quant_window   : 3
7:54:31.783258 INFO: ==============================================
7:54:31.819256 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:54:31.820257 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:54:31.821257 INFO: FWHM in RT is 2.63 seconds, sigma is 0.29
7:54:31.821257 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:54:31.823256 INFO: Starting candidate selection
7:54:33.291717 INFO: Starting candidate scoring
7:54:34.832751 INFO: Finished candidate processing
7:54:34.834767 INFO: Collecting candidate features
7:54:35.096376 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 47596)
7:54:35.114379 INFO: Collecting fragment features
7:54:35.294897 INFO: Finished candidate scoring
7:54:35.357900 INFO: performing precursor FDR with 47 features
7:54:35.358898 INFO: Decoy channel: -1
7:54:35.359897 INFO: Competetive: True
7:54:35.441905 INFO: Setting torch num_threads to 2 for FDR classification task
7:54:35.472903 WARNING: dropped 1 decoy PSMs due to missing features
7:54:35.499904 INFO: Using random state 787985 for train-test-split
7:54:36.617281 INFO: Test AUC: 0.709
7:54:36.618282 INFO: Train AUC: 0.724
7:54:36.619282 INFO: AUC difference: 2.05%
7:54:37.336910 INFO: Resetting torch num_threads to 10
7:54:37.346907 PROGRESS: === Extracted 47596 precursors and 399398 fragments ===
7:54:37.354908 INFO: === FDR correction performed with classifier version 5 ===
7:54:37.367910 PROGRESS: ============================= Precursor FDR =============================
7:54:37.373910 PROGRESS: Total precursors accumulated: 7,435
7:54:37.377910 PROGRESS: Target precursors: 7,366 (99.07%)
7:54:37.381907 PROGRESS: Decoy precursors: 69 (0.93%)
7:54:37.387911 PROGRESS: 
7:54:37.395908 PROGRESS: Precursor Summary:
7:54:37.434911 PROGRESS: Channel   0:	 0.050 FDR: 7,366; 0.010 FDR: 7,366; 0.001 FDR: 6,377
7:54:37.442909 PROGRESS: 
7:54:37.449909 PROGRESS: Protein Summary:
7:54:37.491909 PROGRESS: Channel   0:	 0.050 FDR: 3,551; 0.010 FDR: 3,551; 0.001 FDR: 3,208
7:54:37.497911 PROGRESS: =========================================================================
7:54:37.508931 INFO: Target number of precursors reached.
7:54:37.742071 INFO: fragments_df: keeping 5000 of 399398 [sum(precursor_idx_mask)=198258 sum(mass_error_mask)=399398 stop_rank=5000
7:54:37.817685 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:54:44.646370 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:54:51.113528 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:54:54.558030 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:54:54.563558 INFO: Using score_cutoff 53.598876783370976 (fac=0.99, q=1)
7:54:54.567558 INFO: Updating optimization_manager: fwhm_rt             : 2.628462314605713 -> 2.646873950958252
7:54:54.571557 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:54:54.575558 INFO: Updating optimization_manager: score_cutoff        : 57.63253480911255 -> 53.598876783370976
7:54:54.578557 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:54:54.592557 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:54:54.638557 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:54:54.706554 INFO: === checking if optimization conditions were reached ===
7:54:54.711555 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
7:54:54.733555 INFO: Updating optimization_manager: rt_error            : 115.51597973300039 -> 50.330025269378766
7:54:54.737559 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 50.3300.
7:54:54.740559 INFO: ==============================================
7:54:54.744559 INFO: Starting optimization step 2.
7:54:54.747559 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:54:54.750562 INFO: Using classic extraction backend
7:54:54.754559 PROGRESS: Extracting batch of 15870 precursors
7:54:54.758557 INFO: === Search parameters used ===
7:54:54.761561 INFO: rt_error       : 50.330025269378766
7:54:54.765562 INFO: mobility_error : 0.1
7:54:54.768560 INFO: num_candidates : 3
7:54:54.772561 INFO: ms1_error      : 5.0
7:54:54.775561 INFO: ms2_error      : 10.0
7:54:54.779559 INFO: fwhm_rt        : 2.646873950958252
7:54:54.784560 INFO: quant_window   : 3
7:54:54.788560 INFO: ==============================================
7:54:54.833102 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:54:54.834103 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:54:54.835100 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:54:54.836101 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:54:54.838101 INFO: Starting candidate selection
7:54:55.758815 INFO: Starting candidate scoring
7:54:57.177290 INFO: Finished candidate processing
7:54:57.179296 INFO: Collecting candidate features
7:54:57.448818 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 47571)
7:54:57.466819 INFO: Collecting fragment features
7:54:57.588363 INFO: Finished candidate scoring
7:54:57.637363 INFO: performing precursor FDR with 47 features
7:54:57.638363 INFO: Decoy channel: -1
7:54:57.639364 INFO: Competetive: True
7:54:57.703362 INFO: Setting torch num_threads to 2 for FDR classification task
7:54:57.733365 WARNING: dropped 2 decoy PSMs due to missing features
7:54:57.760364 INFO: Using random state 787985 for train-test-split
7:54:58.927085 INFO: Test AUC: 0.725
7:54:58.928075 INFO: Train AUC: 0.726
7:54:58.929073 INFO: AUC difference: 0.15%
7:54:59.604666 INFO: Resetting torch num_threads to 10
7:54:59.620666 PROGRESS: === Extracted 47571 precursors and 390288 fragments ===
7:54:59.625669 INFO: === FDR correction performed with classifier version 5 ===
7:54:59.635666 PROGRESS: ============================= Precursor FDR =============================
7:54:59.639668 PROGRESS: Total precursors accumulated: 7,525
7:54:59.642668 PROGRESS: Target precursors: 7,467 (99.23%)
7:54:59.646669 PROGRESS: Decoy precursors: 58 (0.77%)
7:54:59.649668 PROGRESS: 
7:54:59.652670 PROGRESS: Precursor Summary:
7:54:59.672668 PROGRESS: Channel   0:	 0.050 FDR: 7,467; 0.010 FDR: 7,467; 0.001 FDR: 6,478
7:54:59.676668 PROGRESS: 
7:54:59.679671 PROGRESS: Protein Summary:
7:54:59.701667 PROGRESS: Channel   0:	 0.050 FDR: 3,590; 0.010 FDR: 3,590; 0.001 FDR: 3,242
7:54:59.705668 PROGRESS: =========================================================================
7:54:59.713670 INFO: Target number of precursors reached.
7:54:59.954275 INFO: fragments_df: keeping 5000 of 390288 [sum(precursor_idx_mask)=197672 sum(mass_error_mask)=390288 stop_rank=5000
7:55:00.037277 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:55:07.114659 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:55:14.127054 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:55:17.269012 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:55:17.275013 INFO: Using score_cutoff 52.70755030059814 (fac=0.99, q=1)
7:55:17.280013 INFO: Updating optimization_manager: fwhm_rt             : 2.646873950958252 -> 2.651651382446289
7:55:17.283013 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:55:17.287015 INFO: Updating optimization_manager: score_cutoff        : 53.598876783370976 -> 52.70755030059814
7:55:17.291009 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:55:17.305013 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:55:17.352024 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:55:17.422621 INFO: === checking if optimization conditions were reached ===
7:55:17.427621 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
7:55:17.451623 INFO: Updating optimization_manager: rt_error            : 50.330025269378766 -> 23.823813637458567
7:55:17.456621 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 23.8238.
7:55:17.459620 INFO: ==============================================
7:55:17.463628 INFO: Starting optimization step 3.
7:55:17.467618 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:55:17.472616 INFO: Using classic extraction backend
7:55:17.479617 PROGRESS: Extracting batch of 15870 precursors
7:55:17.497616 INFO: === Search parameters used ===
7:55:17.505615 INFO: rt_error       : 23.823813637458567
7:55:17.513616 INFO: mobility_error : 0.1
7:55:17.520616 INFO: num_candidates : 3
7:55:17.529616 INFO: ms1_error      : 5.0
7:55:17.535617 INFO: ms2_error      : 10.0
7:55:17.543618 INFO: fwhm_rt        : 2.651651382446289
7:55:17.552619 INFO: quant_window   : 3
7:55:17.560620 INFO: ==============================================
7:55:17.612148 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:55:17.612148 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:55:17.613147 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:55:17.614148 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:55:17.615147 INFO: Starting candidate selection
7:55:18.331989 INFO: Starting candidate scoring
7:55:19.767741 INFO: Finished candidate processing
7:55:19.768742 INFO: Collecting candidate features
7:55:20.104286 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43199)
7:55:20.146822 INFO: Collecting fragment features
7:55:20.303821 INFO: Finished candidate scoring
7:55:20.358834 INFO: performing precursor FDR with 47 features
7:55:20.359833 INFO: Decoy channel: -1
7:55:20.360834 INFO: Competetive: True
7:55:20.462365 INFO: Setting torch num_threads to 2 for FDR classification task
7:55:20.537366 WARNING: dropped 2 target PSMs due to missing features
7:55:20.538363 WARNING: dropped 3 decoy PSMs due to missing features
7:55:20.574366 INFO: Using random state 787985 for train-test-split
7:55:21.512796 INFO: Test AUC: 0.773
7:55:21.513795 INFO: Train AUC: 0.770
7:55:21.514797 INFO: AUC difference: 0.35%
7:55:22.055728 INFO: Resetting torch num_threads to 10
7:55:22.064728 PROGRESS: === Extracted 43199 precursors and 338909 fragments ===
7:55:22.069729 INFO: === FDR correction performed with classifier version 5 ===
7:55:22.080729 PROGRESS: ============================= Precursor FDR =============================
7:55:22.084728 PROGRESS: Total precursors accumulated: 7,572
7:55:22.089730 PROGRESS: Target precursors: 7,505 (99.12%)
7:55:22.093730 PROGRESS: Decoy precursors: 67 (0.88%)
7:55:22.098730 PROGRESS: 
7:55:22.102729 PROGRESS: Precursor Summary:
7:55:22.122253 PROGRESS: Channel   0:	 0.050 FDR: 7,505; 0.010 FDR: 7,505; 0.001 FDR: 6,739
7:55:22.126253 PROGRESS: 
7:55:22.131577 PROGRESS: Protein Summary:
7:55:22.152578 PROGRESS: Channel   0:	 0.050 FDR: 3,608; 0.010 FDR: 3,608; 0.001 FDR: 3,343
7:55:22.158332 PROGRESS: =========================================================================
7:55:22.166339 INFO: Target number of precursors reached.
7:55:22.361355 INFO: fragments_df: keeping 5000 of 338909 [sum(precursor_idx_mask)=174872 sum(mass_error_mask)=338909 stop_rank=5000
7:55:22.438946 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:55:29.057176 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:55:35.994177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:55:39.544525 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:55:39.553526 INFO: Using score_cutoff 52.37416006622314 (fac=0.99, q=1)
7:55:39.560524 INFO: Updating optimization_manager: fwhm_rt             : 2.651651382446289 -> 2.6536383628845215
7:55:39.566525 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:55:39.571526 INFO: Updating optimization_manager: score_cutoff        : 52.70755030059814 -> 52.37416006622314
7:55:39.575525 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:55:39.592524 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:55:39.643533 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:55:39.710044 INFO: === checking if optimization conditions were reached ===
7:55:39.714045 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
7:55:39.735048 INFO: Updating optimization_manager: rt_error            : 23.823813637458567 -> 14.957654405881406
7:55:39.738048 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 14.9577.
7:55:39.742048 INFO: ==============================================
7:55:39.745051 INFO: Starting optimization step 4.
7:55:39.748051 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:55:39.751050 INFO: Using classic extraction backend
7:55:39.755050 PROGRESS: Extracting batch of 15870 precursors
7:55:39.758050 INFO: === Search parameters used ===
7:55:39.762050 INFO: rt_error       : 14.957654405881406
7:55:39.766050 INFO: mobility_error : 0.1
7:55:39.771050 INFO: num_candidates : 3
7:55:39.778050 INFO: ms1_error      : 5.0
7:55:39.785051 INFO: ms2_error      : 10.0
7:55:39.792053 INFO: fwhm_rt        : 2.6536383628845215
7:55:39.800048 INFO: quant_window   : 3
7:55:39.805049 INFO: ==============================================
7:55:39.858048 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:55:39.859048 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:55:39.860049 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:55:39.861048 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:55:39.863048 INFO: Starting candidate selection
7:55:40.543665 INFO: Starting candidate scoring
7:55:41.922895 INFO: Finished candidate processing
7:55:41.924902 INFO: Collecting candidate features
7:55:42.237430 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 43302)
7:55:42.239430 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 43302)
7:55:42.257431 INFO: Collecting fragment features
7:55:42.398441 INFO: Finished candidate scoring
7:55:42.452956 INFO: performing precursor FDR with 47 features
7:55:42.454957 INFO: Decoy channel: -1
7:55:42.455956 INFO: Competetive: True
7:55:42.548958 INFO: Setting torch num_threads to 2 for FDR classification task
7:55:42.611958 WARNING: dropped 2 target PSMs due to missing features
7:55:42.613959 WARNING: dropped 8 decoy PSMs due to missing features
7:55:42.644959 INFO: Using random state 787985 for train-test-split
7:55:43.794108 INFO: Test AUC: 0.780
7:55:43.796107 INFO: Train AUC: 0.785
7:55:43.797108 INFO: AUC difference: 0.65%
7:55:44.495675 INFO: Resetting torch num_threads to 10
7:55:44.508675 PROGRESS: === Extracted 43302 precursors and 340868 fragments ===
7:55:44.514676 INFO: === FDR correction performed with classifier version 5 ===
7:55:44.530676 PROGRESS: ============================= Precursor FDR =============================
7:55:44.536676 PROGRESS: Total precursors accumulated: 7,594
7:55:44.540676 PROGRESS: Target precursors: 7,529 (99.14%)
7:55:44.545675 PROGRESS: Decoy precursors: 65 (0.86%)
7:55:44.549676 PROGRESS: 
7:55:44.553676 PROGRESS: Precursor Summary:
7:55:44.585677 PROGRESS: Channel   0:	 0.050 FDR: 7,529; 0.010 FDR: 7,529; 0.001 FDR: 7,078
7:55:44.589677 PROGRESS: 
7:55:44.593678 PROGRESS: Protein Summary:
7:55:44.630677 PROGRESS: Channel   0:	 0.050 FDR: 3,617; 0.010 FDR: 3,617; 0.001 FDR: 3,461
7:55:44.634677 PROGRESS: =========================================================================
7:55:44.646677 INFO: Target number of precursors reached.
7:55:44.895199 INFO: fragments_df: keeping 5000 of 340868 [sum(precursor_idx_mask)=176690 sum(mass_error_mask)=340868 stop_rank=5000
7:55:44.998719 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:55:52.118414 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:55:59.058094 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:56:02.731741 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:56:02.737744 INFO: Using score_cutoff 50.44914618530274 (fac=0.99, q=1)
7:56:02.741739 INFO: Updating optimization_manager: fwhm_rt             : 2.6536383628845215 -> 2.6557846069335938
7:56:02.745738 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:56:02.749738 INFO: Updating optimization_manager: score_cutoff        : 52.37416006622314 -> 50.44914618530274
7:56:02.752738 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:56:02.767737 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:56:02.809736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:56:02.876735 INFO: === checking if optimization conditions were reached ===
7:56:02.880737 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
7:56:02.902740 INFO: Updating optimization_manager: rt_error            : 14.957654405881406 -> 19.327718386791854
7:56:02.906741 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 19.3277.
7:56:02.910742 INFO: ==============================================
7:56:02.914754 INFO: Starting optimization step 5.
7:56:02.917743 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:56:02.921742 INFO: Using classic extraction backend
7:56:02.925741 PROGRESS: Extracting batch of 15870 precursors
7:56:02.928742 INFO: === Search parameters used ===
7:56:02.933741 INFO: rt_error       : 19.327718386791854
7:56:02.938753 INFO: mobility_error : 0.1
7:56:02.942756 INFO: num_candidates : 3
7:56:02.945754 INFO: ms1_error      : 5.0
7:56:02.949758 INFO: ms2_error      : 10.0
7:56:02.953753 INFO: fwhm_rt        : 2.6557846069335938
7:56:02.957278 INFO: quant_window   : 3
7:56:02.961281 INFO: ==============================================
7:56:02.996280 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:56:02.997277 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:56:02.998277 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:56:02.999275 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:56:03.000280 INFO: Starting candidate selection
7:56:03.652459 INFO: Starting candidate scoring
7:56:04.900350 INFO: Finished candidate processing
7:56:04.901354 INFO: Collecting candidate features
7:56:05.126867 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 43035)
7:56:05.128868 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43035)
7:56:05.145867 INFO: Collecting fragment features
7:56:05.253385 INFO: Finished candidate scoring
7:56:05.297385 INFO: performing precursor FDR with 47 features
7:56:05.298384 INFO: Decoy channel: -1
7:56:05.299385 INFO: Competetive: True
7:56:05.366385 INFO: Setting torch num_threads to 2 for FDR classification task
7:56:05.423386 WARNING: dropped 2 target PSMs due to missing features
7:56:05.425385 WARNING: dropped 5 decoy PSMs due to missing features
7:56:05.458903 INFO: Using random state 787985 for train-test-split
7:56:06.446956 INFO: Test AUC: 0.763
7:56:06.447956 INFO: Train AUC: 0.783
7:56:06.448956 INFO: AUC difference: 2.46%
7:56:07.051489 INFO: Resetting torch num_threads to 10
7:56:07.060489 PROGRESS: === Extracted 43035 precursors and 338359 fragments ===
7:56:07.065489 INFO: === FDR correction performed with classifier version 5 ===
7:56:07.076490 PROGRESS: ============================= Precursor FDR =============================
7:56:07.080490 PROGRESS: Total precursors accumulated: 7,577
7:56:07.084490 PROGRESS: Target precursors: 7,516 (99.19%)
7:56:07.088490 PROGRESS: Decoy precursors: 61 (0.81%)
7:56:07.091490 PROGRESS: 
7:56:07.095490 PROGRESS: Precursor Summary:
7:56:07.117490 PROGRESS: Channel   0:	 0.050 FDR: 7,516; 0.010 FDR: 7,516; 0.001 FDR: 7,027
7:56:07.121491 PROGRESS: 
7:56:07.125490 PROGRESS: Protein Summary:
7:56:07.149491 PROGRESS: Channel   0:	 0.050 FDR: 3,610; 0.010 FDR: 3,610; 0.001 FDR: 3,455
7:56:07.153490 PROGRESS: =========================================================================
7:56:07.161490 INFO: Target number of precursors reached.
7:56:07.360003 INFO: fragments_df: keeping 5000 of 338359 [sum(precursor_idx_mask)=174716 sum(mass_error_mask)=338359 stop_rank=5000
7:56:07.434005 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:56:14.449897 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:56:21.411217 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:56:24.965423 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:56:24.971423 INFO: Using score_cutoff 50.95806620979309 (fac=0.99, q=1)
7:56:24.975424 INFO: Updating optimization_manager: fwhm_rt             : 2.6557846069335938 -> 2.660797119140625
7:56:24.979423 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:56:24.982424 INFO: Updating optimization_manager: score_cutoff        : 50.44914618530274 -> 50.95806620979309
7:56:24.986427 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:56:24.999934 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:56:25.040935 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:56:25.107935 INFO: === checking if optimization conditions were reached ===
7:56:25.112935 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
7:56:25.133936 INFO: Updating optimization_manager: rt_error            : 19.327718386791854 -> 17.278345131249107
7:56:25.137935 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.2783.
7:56:25.141936 INFO: ==============================================
7:56:25.144936 INFO: Starting optimization step 6.
7:56:25.148936 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:56:25.152936 INFO: Using classic extraction backend
7:56:25.156935 PROGRESS: Extracting batch of 15870 precursors
7:56:25.159935 INFO: === Search parameters used ===
7:56:25.163935 INFO: rt_error       : 17.278345131249107
7:56:25.167936 INFO: mobility_error : 0.1
7:56:25.171936 INFO: num_candidates : 3
7:56:25.174936 INFO: ms1_error      : 5.0
7:56:25.179936 INFO: ms2_error      : 10.0
7:56:25.184936 INFO: fwhm_rt        : 2.660797119140625
7:56:25.191936 INFO: quant_window   : 3
7:56:25.200936 INFO: ==============================================
7:56:25.260450 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:56:25.261450 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:56:25.263450 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:56:25.264450 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:56:25.265450 INFO: Starting candidate selection
7:56:25.916623 INFO: Starting candidate scoring
7:56:27.150338 INFO: Finished candidate processing
7:56:27.151845 INFO: Collecting candidate features
7:56:27.379359 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 43196)
7:56:27.381359 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43196)
7:56:27.398359 INFO: Collecting fragment features
7:56:27.505873 INFO: Finished candidate scoring
7:56:27.568874 INFO: performing precursor FDR with 47 features
7:56:27.569874 INFO: Decoy channel: -1
7:56:27.570874 INFO: Competetive: True
7:56:27.640874 INFO: Setting torch num_threads to 2 for FDR classification task
7:56:27.682875 WARNING: dropped 1 target PSMs due to missing features
7:56:27.683875 WARNING: dropped 2 decoy PSMs due to missing features
7:56:27.707877 INFO: Using random state 787985 for train-test-split
7:56:28.706032 INFO: Test AUC: 0.777
7:56:28.707032 INFO: Train AUC: 0.780
7:56:28.708032 INFO: AUC difference: 0.42%
7:56:29.327574 INFO: Resetting torch num_threads to 10
7:56:29.340576 PROGRESS: === Extracted 43196 precursors and 339803 fragments ===
7:56:29.346573 INFO: === FDR correction performed with classifier version 5 ===
7:56:29.361574 PROGRESS: ============================= Precursor FDR =============================
7:56:29.366575 PROGRESS: Total precursors accumulated: 7,557
7:56:29.370574 PROGRESS: Target precursors: 7,501 (99.26%)
7:56:29.373577 PROGRESS: Decoy precursors: 56 (0.74%)
7:56:29.377575 PROGRESS: 
7:56:29.381574 PROGRESS: Precursor Summary:
7:56:29.415577 PROGRESS: Channel   0:	 0.050 FDR: 7,501; 0.010 FDR: 7,501; 0.001 FDR: 6,732
7:56:29.419576 PROGRESS: 
7:56:29.422575 PROGRESS: Protein Summary:
7:56:29.460576 PROGRESS: Channel   0:	 0.050 FDR: 3,606; 0.010 FDR: 3,606; 0.001 FDR: 3,350
7:56:29.464575 PROGRESS: =========================================================================
7:56:29.486577 INFO: Target number of precursors reached.
7:56:29.726091 INFO: fragments_df: keeping 5000 of 339803 [sum(precursor_idx_mask)=175051 sum(mass_error_mask)=339803 stop_rank=5000
7:56:29.834603 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:56:36.652530 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:56:43.290431 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:56:46.875088 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:56:46.881088 INFO: Using score_cutoff 50.70948932647705 (fac=0.99, q=1)
7:56:46.886089 INFO: Updating optimization_manager: fwhm_rt             : 2.660797119140625 -> 2.653216600418091
7:56:46.890088 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:56:46.895091 INFO: Updating optimization_manager: score_cutoff        : 50.95806620979309 -> 50.70948932647705
7:56:46.898089 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:56:46.915089 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:56:46.971089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:56:47.064636 INFO: === checking if optimization conditions were reached ===
7:56:47.071635 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
7:56:47.113637 INFO: Updating optimization_manager: rt_error            : 17.278345131249107 -> 20.456596706723936
7:56:47.117636 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 20.4566.
7:56:47.121636 INFO: ==============================================
7:56:47.125636 INFO: Starting optimization step 7.
7:56:47.128637 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:56:47.132642 INFO: Using classic extraction backend
7:56:47.136636 PROGRESS: Extracting batch of 15870 precursors
7:56:47.140636 INFO: === Search parameters used ===
7:56:47.143637 INFO: rt_error       : 20.456596706723936
7:56:47.147637 INFO: mobility_error : 0.1
7:56:47.151637 INFO: num_candidates : 3
7:56:47.155636 INFO: ms1_error      : 5.0
7:56:47.158636 INFO: ms2_error      : 10.0
7:56:47.162641 INFO: fwhm_rt        : 2.653216600418091
7:56:47.169637 INFO: quant_window   : 3
7:56:47.176640 INFO: ==============================================
7:56:47.228634 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:56:47.229633 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:56:47.230633 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:56:47.231633 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:56:47.233632 INFO: Starting candidate selection
7:56:47.868149 INFO: Starting candidate scoring
7:56:49.194810 INFO: Finished candidate processing
7:56:49.195817 INFO: Collecting candidate features
7:56:49.482337 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43096)
7:56:49.484337 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43096)
7:56:49.502335 INFO: Collecting fragment features
7:56:49.639821 INFO: Finished candidate scoring
7:56:49.695820 INFO: performing precursor FDR with 47 features
7:56:49.696822 INFO: Decoy channel: -1
7:56:49.697823 INFO: Competetive: True
7:56:49.790838 INFO: Setting torch num_threads to 2 for FDR classification task
7:56:49.849369 WARNING: dropped 1 target PSMs due to missing features
7:56:49.850371 WARNING: dropped 5 decoy PSMs due to missing features
7:56:49.880370 INFO: Using random state 787985 for train-test-split
7:56:51.049108 INFO: Test AUC: 0.762
7:56:51.050108 INFO: Train AUC: 0.777
7:56:51.051637 INFO: AUC difference: 1.92%
7:56:51.836837 INFO: Resetting torch num_threads to 10
7:56:51.849837 PROGRESS: === Extracted 43096 precursors and 338606 fragments ===
7:56:51.854836 INFO: === FDR correction performed with classifier version 5 ===
7:56:51.871837 PROGRESS: ============================= Precursor FDR =============================
7:56:51.875837 PROGRESS: Total precursors accumulated: 7,589
7:56:51.879836 PROGRESS: Target precursors: 7,531 (99.24%)
7:56:51.883838 PROGRESS: Decoy precursors: 58 (0.76%)
7:56:51.887840 PROGRESS: 
7:56:51.891842 PROGRESS: Precursor Summary:
7:56:51.924838 PROGRESS: Channel   0:	 0.050 FDR: 7,531; 0.010 FDR: 7,531; 0.001 FDR: 6,722
7:56:51.928838 PROGRESS: 
7:56:51.932837 PROGRESS: Protein Summary:
7:56:51.970843 PROGRESS: Channel   0:	 0.050 FDR: 3,613; 0.010 FDR: 3,613; 0.001 FDR: 3,345
7:56:51.974838 PROGRESS: =========================================================================
7:56:51.987840 INFO: Target number of precursors reached.
7:56:52.244389 INFO: fragments_df: keeping 5000 of 338606 [sum(precursor_idx_mask)=174934 sum(mass_error_mask)=338606 stop_rank=5000
7:56:52.354936 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:56:59.612058 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:57:06.995461 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:57:10.614669 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:57:10.621666 INFO: Using score_cutoff 50.95610901260376 (fac=0.99, q=1)
7:57:10.626674 INFO: Updating optimization_manager: fwhm_rt             : 2.653216600418091 -> 2.657578706741333
7:57:10.630666 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:57:10.634666 INFO: Updating optimization_manager: score_cutoff        : 50.70948932647705 -> 50.95610901260376
7:57:10.638668 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:57:10.654667 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:57:10.711670 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:57:10.785670 INFO: === checking if optimization conditions were reached ===
7:57:10.790668 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
7:57:10.816669 INFO: Updating optimization_manager: rt_error            : 20.456596706723936 -> 15.571003050752227
7:57:10.820669 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 15.5710.
7:57:10.824669 INFO: ==============================================
7:57:10.829686 INFO: Starting optimization step 8.
7:57:10.833685 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:57:10.837685 INFO: Using classic extraction backend
7:57:10.841685 PROGRESS: Extracting batch of 15870 precursors
7:57:10.845211 INFO: === Search parameters used ===
7:57:10.849212 INFO: rt_error       : 15.571003050752227
7:57:10.853212 INFO: mobility_error : 0.1
7:57:10.857211 INFO: num_candidates : 3
7:57:10.861212 INFO: ms1_error      : 5.0
7:57:10.864211 INFO: ms2_error      : 10.0
7:57:10.869212 INFO: fwhm_rt        : 2.657578706741333
7:57:10.873213 INFO: quant_window   : 3
7:57:10.877212 INFO: ==============================================
7:57:10.926214 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:57:10.927217 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:57:10.928213 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:57:10.929212 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:57:10.930212 INFO: Starting candidate selection
7:57:11.618586 INFO: Starting candidate scoring
7:57:12.848563 INFO: Finished candidate processing
7:57:12.849568 INFO: Collecting candidate features
7:57:13.099105 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 43284)
7:57:13.102118 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43284)
7:57:13.141122 INFO: Collecting fragment features
7:57:13.243121 INFO: Finished candidate scoring
7:57:13.286120 INFO: performing precursor FDR with 47 features
7:57:13.287121 INFO: Decoy channel: -1
7:57:13.288121 INFO: Competetive: True
7:57:13.349649 INFO: Setting torch num_threads to 2 for FDR classification task
7:57:13.390663 WARNING: dropped 2 target PSMs due to missing features
7:57:13.391662 WARNING: dropped 8 decoy PSMs due to missing features
7:57:13.414664 INFO: Using random state 787985 for train-test-split
7:57:14.450433 INFO: Test AUC: 0.771
7:57:14.452431 INFO: Train AUC: 0.784
7:57:14.453432 INFO: AUC difference: 1.68%
7:57:15.137048 INFO: Resetting torch num_threads to 10
7:57:15.148065 PROGRESS: === Extracted 43284 precursors and 340624 fragments ===
7:57:15.153050 INFO: === FDR correction performed with classifier version 5 ===
7:57:15.167052 PROGRESS: ============================= Precursor FDR =============================
7:57:15.171051 PROGRESS: Total precursors accumulated: 7,551
7:57:15.175051 PROGRESS: Target precursors: 7,494 (99.25%)
7:57:15.178050 PROGRESS: Decoy precursors: 57 (0.75%)
7:57:15.182050 PROGRESS: 
7:57:15.186050 PROGRESS: Precursor Summary:
7:57:15.214050 PROGRESS: Channel   0:	 0.050 FDR: 7,494; 0.010 FDR: 7,494; 0.001 FDR: 7,010
7:57:15.218051 PROGRESS: 
7:57:15.222051 PROGRESS: Protein Summary:
7:57:15.271052 PROGRESS: Channel   0:	 0.050 FDR: 3,606; 0.010 FDR: 3,606; 0.001 FDR: 3,440
7:57:15.276051 PROGRESS: =========================================================================
7:57:15.293057 INFO: Target number of precursors reached.
7:57:15.522579 INFO: fragments_df: keeping 5000 of 340624 [sum(precursor_idx_mask)=175648 sum(mass_error_mask)=340624 stop_rank=5000
7:57:15.610126 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:57:22.579453 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:57:29.799796 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:57:33.462764 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:57:33.470763 INFO: Using score_cutoff 50.89532694625855 (fac=0.99, q=1)
7:57:33.477762 INFO: Updating optimization_manager: fwhm_rt             : 2.657578706741333 -> 2.6529293060302734
7:57:33.482762 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:57:33.487762 INFO: Updating optimization_manager: score_cutoff        : 50.95610901260376 -> 50.89532694625855
7:57:33.492764 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:57:33.507766 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:57:33.548764 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:57:33.617764 INFO: === checking if optimization conditions were reached ===
7:57:33.622765 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
7:57:33.644384 INFO: Updating optimization_manager: rt_error            : 15.571003050752227 -> 19.168218414573857
7:57:33.648383 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 19.1682.
7:57:33.651380 INFO: ==============================================
7:57:33.655380 INFO: Starting optimization step 9.
7:57:33.658382 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:57:33.661381 INFO: Using classic extraction backend
7:57:33.665381 PROGRESS: Extracting batch of 15870 precursors
7:57:33.668383 INFO: === Search parameters used ===
7:57:33.671380 INFO: rt_error       : 19.168218414573857
7:57:33.674380 INFO: mobility_error : 0.1
7:57:33.678380 INFO: num_candidates : 3
7:57:33.681385 INFO: ms1_error      : 5.0
7:57:33.684386 INFO: ms2_error      : 10.0
7:57:33.688380 INFO: fwhm_rt        : 2.6529293060302734
7:57:33.693381 INFO: quant_window   : 3
7:57:33.697381 INFO: ==============================================
7:57:33.744381 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:57:33.746382 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:57:33.747381 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:57:33.748381 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:57:33.749382 INFO: Starting candidate selection
7:57:34.403647 INFO: Starting candidate scoring
7:57:35.704976 INFO: Finished candidate processing
7:57:35.706980 INFO: Collecting candidate features
7:57:35.940493 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43105)
7:57:35.943493 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43105)
7:57:35.979494 INFO: Collecting fragment features
7:57:36.086495 INFO: Finished candidate scoring
7:57:36.131500 INFO: performing precursor FDR with 47 features
7:57:36.133500 INFO: Decoy channel: -1
7:57:36.134500 INFO: Competetive: True
7:57:36.201008 INFO: Setting torch num_threads to 2 for FDR classification task
7:57:36.242009 WARNING: dropped 1 target PSMs due to missing features
7:57:36.244008 WARNING: dropped 5 decoy PSMs due to missing features
7:57:36.292009 INFO: Using random state 787985 for train-test-split
7:57:37.252090 INFO: Test AUC: 0.770
7:57:37.254090 INFO: Train AUC: 0.780
7:57:37.255090 INFO: AUC difference: 1.21%
7:57:37.916629 INFO: Resetting torch num_threads to 10
7:57:37.925630 PROGRESS: === Extracted 43105 precursors and 339068 fragments ===
7:57:37.933630 INFO: === FDR correction performed with classifier version 5 ===
7:57:37.946630 PROGRESS: ============================= Precursor FDR =============================
7:57:37.950630 PROGRESS: Total precursors accumulated: 7,584
7:57:37.953630 PROGRESS: Target precursors: 7,522 (99.18%)
7:57:37.957630 PROGRESS: Decoy precursors: 62 (0.82%)
7:57:37.960630 PROGRESS: 
7:57:37.964630 PROGRESS: Precursor Summary:
7:57:37.984630 PROGRESS: Channel   0:	 0.050 FDR: 7,522; 0.010 FDR: 7,522; 0.001 FDR: 6,724
7:57:37.987630 PROGRESS: 
7:57:37.991631 PROGRESS: Protein Summary:
7:57:38.014631 PROGRESS: Channel   0:	 0.050 FDR: 3,616; 0.010 FDR: 3,616; 0.001 FDR: 3,339
7:57:38.018631 PROGRESS: =========================================================================
7:57:38.026631 INFO: Target number of precursors reached.
7:57:38.236144 INFO: fragments_df: keeping 5000 of 339068 [sum(precursor_idx_mask)=175156 sum(mass_error_mask)=339068 stop_rank=5000
7:57:38.334146 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:57:44.990004 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:57:51.936177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:57:58.012719 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:57:58.018716 INFO: Using score_cutoff 50.8750403377533 (fac=0.99, q=1)
7:57:58.022717 INFO: Updating optimization_manager: fwhm_rt             : 2.6529293060302734 -> 2.659968137741089
7:57:58.026716 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:57:58.029717 INFO: Updating optimization_manager: score_cutoff        : 50.89532694625855 -> 50.8750403377533
7:57:58.033717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:57:58.047718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:57:58.089717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:57:58.159719 INFO: === checking if optimization conditions were reached ===
7:57:58.163719 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
7:57:58.186732 INFO: Updating optimization_manager: rt_error            : 19.168218414573857 -> 17.178921437933525
7:57:58.190730 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 17.1789.
7:57:58.193326 INFO: ==============================================
7:57:58.197324 INFO: Starting optimization step 10.
7:57:58.201325 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:57:58.205321 INFO: Using classic extraction backend
7:57:58.209325 PROGRESS: Extracting batch of 15870 precursors
7:57:58.214324 INFO: === Search parameters used ===
7:57:58.220323 INFO: rt_error       : 17.178921437933525
7:57:58.227324 INFO: mobility_error : 0.1
7:57:58.235323 INFO: num_candidates : 3
7:57:58.241324 INFO: ms1_error      : 5.0
7:57:58.247325 INFO: ms2_error      : 10.0
7:57:58.254323 INFO: fwhm_rt        : 2.659968137741089
7:57:58.262323 INFO: quant_window   : 3
7:57:58.267323 INFO: ==============================================
7:57:58.318324 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:57:58.319324 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:57:58.320324 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:57:58.320324 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:57:58.321324 INFO: Starting candidate selection
7:57:58.946770 INFO: Starting candidate scoring
7:58:00.187901 INFO: Finished candidate processing
7:58:00.188910 INFO: Collecting candidate features
7:58:00.430445 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 43201)
7:58:00.431445 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43201)
7:58:00.448978 INFO: Collecting fragment features
7:58:00.584987 INFO: Finished candidate scoring
7:58:00.643982 INFO: performing precursor FDR with 47 features
7:58:00.644981 INFO: Decoy channel: -1
7:58:00.645980 INFO: Competetive: True
7:58:00.713527 INFO: Setting torch num_threads to 2 for FDR classification task
7:58:00.758525 WARNING: dropped 1 target PSMs due to missing features
7:58:00.759524 WARNING: dropped 3 decoy PSMs due to missing features
7:58:00.783525 INFO: Using random state 787985 for train-test-split
7:58:01.789344 INFO: Test AUC: 0.773
7:58:01.790343 INFO: Train AUC: 0.781
7:58:01.791343 INFO: AUC difference: 0.96%
7:58:02.432438 INFO: Resetting torch num_threads to 10
7:58:02.442452 PROGRESS: === Extracted 43201 precursors and 340038 fragments ===
7:58:02.447454 INFO: === FDR correction performed with classifier version 5 ===
7:58:02.458583 PROGRESS: ============================= Precursor FDR =============================
7:58:02.462583 PROGRESS: Total precursors accumulated: 7,597
7:58:02.466585 PROGRESS: Target precursors: 7,533 (99.16%)
7:58:02.469582 PROGRESS: Decoy precursors: 64 (0.84%)
7:58:02.473583 PROGRESS: 
7:58:02.476583 PROGRESS: Precursor Summary:
7:58:02.498583 PROGRESS: Channel   0:	 0.050 FDR: 7,533; 0.010 FDR: 7,533; 0.001 FDR: 6,736
7:58:02.501582 PROGRESS: 
7:58:02.505582 PROGRESS: Protein Summary:
7:58:02.531583 PROGRESS: Channel   0:	 0.050 FDR: 3,621; 0.010 FDR: 3,621; 0.001 FDR: 3,351
7:58:02.537585 PROGRESS: =========================================================================
7:58:02.552585 INFO: Target number of precursors reached.
7:58:02.765189 INFO: fragments_df: keeping 5000 of 340038 [sum(precursor_idx_mask)=175908 sum(mass_error_mask)=340038 stop_rank=5000
7:58:02.843191 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:58:09.899185 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:58:16.791099 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:58:19.976276 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:58:19.982291 INFO: Using score_cutoff 50.76396243896484 (fac=0.99, q=1)
7:58:19.987290 INFO: Updating optimization_manager: fwhm_rt             : 2.659968137741089 -> 2.6601877212524414
7:58:19.991805 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:58:19.995820 INFO: Updating optimization_manager: score_cutoff        : 50.8750403377533 -> 50.76396243896484
7:58:19.999822 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:58:20.017823 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:58:20.085823 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:58:20.161828 INFO: === checking if optimization conditions were reached ===
7:58:20.165826 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 2 ===
7:58:20.194826 INFO: Updating optimization_manager: rt_error            : 17.178921437933525 -> 16.289131719407607
7:58:20.198822 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 16.2891.
7:58:20.202821 INFO: ==============================================
7:58:20.206822 INFO: Starting optimization step 11.
7:58:20.210823 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:58:20.214823 INFO: Using classic extraction backend
7:58:20.218823 PROGRESS: Extracting batch of 15870 precursors
7:58:20.222823 INFO: === Search parameters used ===
7:58:20.226823 INFO: rt_error       : 16.289131719407607
7:58:20.231841 INFO: mobility_error : 0.1
7:58:20.235837 INFO: num_candidates : 3
7:58:20.239837 INFO: ms1_error      : 5.0
7:58:20.244431 INFO: ms2_error      : 10.0
7:58:20.248430 INFO: fwhm_rt        : 2.6601877212524414
7:58:20.252430 INFO: quant_window   : 3
7:58:20.257430 INFO: ==============================================
7:58:20.327431 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:58:20.329434 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:58:20.330433 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:58:20.331431 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:58:20.333432 INFO: Starting candidate selection
7:58:21.005463 INFO: Starting candidate scoring
7:58:22.459855 INFO: Finished candidate processing
7:58:22.461865 INFO: Collecting candidate features
7:58:22.813035 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43302)
7:58:22.815034 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43302)
7:58:22.832034 INFO: Collecting fragment features
7:58:22.982038 INFO: Finished candidate scoring
7:58:23.026649 INFO: performing precursor FDR with 47 features
7:58:23.027649 INFO: Decoy channel: -1
7:58:23.028652 INFO: Competetive: True
7:58:23.092648 INFO: Setting torch num_threads to 2 for FDR classification task
7:58:23.133650 WARNING: dropped 2 target PSMs due to missing features
7:58:23.134650 WARNING: dropped 4 decoy PSMs due to missing features
7:58:23.156650 INFO: Using random state 787985 for train-test-split
7:58:24.070178 INFO: Test AUC: 0.771
7:58:24.071175 INFO: Train AUC: 0.785
7:58:24.072181 INFO: AUC difference: 1.82%
7:58:24.658483 INFO: Resetting torch num_threads to 10
7:58:24.667483 PROGRESS: === Extracted 43302 precursors and 340896 fragments ===
7:58:24.672820 INFO: === FDR correction performed with classifier version 5 ===
7:58:24.683818 PROGRESS: ============================= Precursor FDR =============================
7:58:24.687819 PROGRESS: Total precursors accumulated: 7,587
7:58:24.691867 PROGRESS: Target precursors: 7,526 (99.20%)
7:58:24.696867 PROGRESS: Decoy precursors: 61 (0.80%)
7:58:24.701863 PROGRESS: 
7:58:24.705867 PROGRESS: Precursor Summary:
7:58:24.725864 PROGRESS: Channel   0:	 0.050 FDR: 7,526; 0.010 FDR: 7,526; 0.001 FDR: 6,732
7:58:24.730075 PROGRESS: 
7:58:24.735483 PROGRESS: Protein Summary:
7:58:24.761011 PROGRESS: Channel   0:	 0.050 FDR: 3,615; 0.010 FDR: 3,615; 0.001 FDR: 3,349
7:58:24.765009 PROGRESS: =========================================================================
7:58:24.773008 INFO: Target number of precursors reached.
7:58:24.961014 INFO: fragments_df: keeping 5000 of 340896 [sum(precursor_idx_mask)=176228 sum(mass_error_mask)=340896 stop_rank=5000
7:58:25.037806 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:58:31.374867 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:58:38.551906 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:58:42.199221 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:58:42.205223 INFO: Using score_cutoff 50.25873161315918 (fac=0.99, q=1)
7:58:42.210219 INFO: Updating optimization_manager: fwhm_rt             : 2.6601877212524414 -> 2.6578149795532227
7:58:42.214219 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:58:42.217218 INFO: Updating optimization_manager: score_cutoff        : 50.76396243896484 -> 50.25873161315918
7:58:42.221219 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:58:42.238223 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:58:42.296830 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:58:42.371831 INFO: === checking if optimization conditions were reached ===
7:58:42.374829 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 2 ===
7:58:42.401831 INFO: Updating optimization_manager: rt_error            : 16.289131719407607 -> 19.53670684336411
7:58:42.406830 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 19.5367.
7:58:42.409830 INFO: ==============================================
7:58:42.413830 INFO: Starting optimization step 12.
7:58:42.417830 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:58:42.421833 INFO: Using classic extraction backend
7:58:42.425830 PROGRESS: Extracting batch of 15870 precursors
7:58:42.428830 INFO: === Search parameters used ===
7:58:42.432831 INFO: rt_error       : 19.53670684336411
7:58:42.435830 INFO: mobility_error : 0.1
7:58:42.440830 INFO: num_candidates : 3
7:58:42.447832 INFO: ms1_error      : 5.0
7:58:42.455830 INFO: ms2_error      : 10.0
7:58:42.462830 INFO: fwhm_rt        : 2.6578149795532227
7:58:42.470832 INFO: quant_window   : 3
7:58:42.476830 INFO: ==============================================
7:58:42.537843 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:58:42.538843 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:58:42.539843 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:58:42.540843 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:58:42.542418 INFO: Starting candidate selection
7:58:43.215188 INFO: Starting candidate scoring
7:58:44.545898 INFO: Finished candidate processing
7:58:44.547907 INFO: Collecting candidate features
7:58:44.856432 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 43134)
7:58:44.858432 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43134)
7:58:44.875432 INFO: Collecting fragment features
7:58:45.033441 INFO: Finished candidate scoring
7:58:45.086954 INFO: performing precursor FDR with 47 features
7:58:45.087955 INFO: Decoy channel: -1
7:58:45.088955 INFO: Competetive: True
7:58:45.185956 INFO: Setting torch num_threads to 2 for FDR classification task
7:58:45.249957 WARNING: dropped 1 target PSMs due to missing features
7:58:45.250957 WARNING: dropped 3 decoy PSMs due to missing features
7:58:45.281964 INFO: Using random state 787985 for train-test-split
7:58:46.430102 INFO: Test AUC: 0.766
7:58:46.431102 INFO: Train AUC: 0.778
7:58:46.432101 INFO: AUC difference: 1.56%
7:58:47.183830 INFO: Resetting torch num_threads to 10
7:58:47.199831 PROGRESS: === Extracted 43134 precursors and 339257 fragments ===
7:58:47.204832 INFO: === FDR correction performed with classifier version 5 ===
7:58:47.219835 PROGRESS: ============================= Precursor FDR =============================
7:58:47.223838 PROGRESS: Total precursors accumulated: 7,567
7:58:47.227839 PROGRESS: Target precursors: 7,500 (99.11%)
7:58:47.231838 PROGRESS: Decoy precursors: 67 (0.89%)
7:58:47.234837 PROGRESS: 
7:58:47.238838 PROGRESS: Precursor Summary:
7:58:47.270838 PROGRESS: Channel   0:	 0.050 FDR: 7,500; 0.010 FDR: 7,500; 0.001 FDR: 6,306
7:58:47.274836 PROGRESS: 
7:58:47.278836 PROGRESS: Protein Summary:
7:58:47.315448 PROGRESS: Channel   0:	 0.050 FDR: 3,613; 0.010 FDR: 3,613; 0.001 FDR: 3,185
7:58:47.320448 PROGRESS: =========================================================================
7:58:47.332448 INFO: Target number of precursors reached.
7:58:47.587047 INFO: fragments_df: keeping 5000 of 339257 [sum(precursor_idx_mask)=174814 sum(mass_error_mask)=339257 stop_rank=5000
7:58:47.696047 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:58:54.750853 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:59:02.022317 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:59:05.604958 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:59:05.610956 INFO: Using score_cutoff 50.32683841209411 (fac=0.99, q=1)
7:59:05.615955 INFO: Updating optimization_manager: fwhm_rt             : 2.6578149795532227 -> 2.6550211906433105
7:59:05.619955 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:59:05.623955 INFO: Updating optimization_manager: score_cutoff        : 50.25873161315918 -> 50.32683841209411
7:59:05.626953 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:59:05.643955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:59:05.701955 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:59:05.778955 INFO: === checking if optimization conditions were reached ===
7:59:05.784958 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 2 ===
7:59:05.829969 INFO: Updating optimization_manager: rt_error            : 19.53670684336411 -> 16.657383754342007
7:59:05.836972 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 16.6574.
7:59:05.844482 INFO: ==============================================
7:59:05.849497 INFO: Starting optimization step 13.
7:59:05.858497 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:59:05.865499 INFO: Using classic extraction backend
7:59:05.873499 PROGRESS: Extracting batch of 15870 precursors
7:59:05.880499 INFO: === Search parameters used ===
7:59:05.888499 INFO: rt_error       : 16.657383754342007
7:59:05.894497 INFO: mobility_error : 0.1
7:59:05.902496 INFO: num_candidates : 3
7:59:05.910497 INFO: ms1_error      : 5.0
7:59:05.918497 INFO: ms2_error      : 10.0
7:59:05.927497 INFO: fwhm_rt        : 2.6550211906433105
7:59:05.935498 INFO: quant_window   : 3
7:59:05.944498 INFO: ==============================================
7:59:06.005495 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:59:06.006495 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:59:06.007495 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:59:06.008495 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:59:06.009498 INFO: Starting candidate selection
7:59:06.696975 INFO: Starting candidate scoring
7:59:08.091778 INFO: Finished candidate processing
7:59:08.092792 INFO: Collecting candidate features
7:59:08.332376 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43257)
7:59:08.333381 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43257)
7:59:08.347884 INFO: Collecting fragment features
7:59:08.449894 INFO: Finished candidate scoring
7:59:08.490896 INFO: performing precursor FDR with 47 features
7:59:08.491898 INFO: Decoy channel: -1
7:59:08.492897 INFO: Competetive: True
7:59:08.550896 INFO: Setting torch num_threads to 2 for FDR classification task
7:59:08.588910 WARNING: dropped 3 target PSMs due to missing features
7:59:08.589909 WARNING: dropped 3 decoy PSMs due to missing features
7:59:08.610500 INFO: Using random state 787985 for train-test-split
7:59:09.552701 INFO: Test AUC: 0.772
7:59:09.553702 INFO: Train AUC: 0.784
7:59:09.554701 INFO: AUC difference: 1.53%
7:59:10.219340 INFO: Resetting torch num_threads to 10
7:59:10.230338 PROGRESS: === Extracted 43257 precursors and 340380 fragments ===
7:59:10.235340 INFO: === FDR correction performed with classifier version 5 ===
7:59:10.248339 PROGRESS: ============================= Precursor FDR =============================
7:59:10.252339 PROGRESS: Total precursors accumulated: 7,578
7:59:10.255339 PROGRESS: Target precursors: 7,521 (99.25%)
7:59:10.259339 PROGRESS: Decoy precursors: 57 (0.75%)
7:59:10.263339 PROGRESS: 
7:59:10.266350 PROGRESS: Precursor Summary:
7:59:10.310339 PROGRESS: Channel   0:	 0.050 FDR: 7,521; 0.010 FDR: 7,521; 0.001 FDR: 6,922
7:59:10.314339 PROGRESS: 
7:59:10.318341 PROGRESS: Protein Summary:
7:59:10.355883 PROGRESS: Channel   0:	 0.050 FDR: 3,614; 0.010 FDR: 3,614; 0.001 FDR: 3,417
7:59:10.359880 PROGRESS: =========================================================================
7:59:10.368881 INFO: Target number of precursors reached.
7:59:10.593897 INFO: fragments_df: keeping 5000 of 340380 [sum(precursor_idx_mask)=175763 sum(mass_error_mask)=340380 stop_rank=5000
7:59:10.702430 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:59:17.579558 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:59:24.639462 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:59:28.110140 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:59:28.115139 INFO: Using score_cutoff 50.24867088317871 (fac=0.99, q=1)
7:59:28.120140 INFO: Updating optimization_manager: fwhm_rt             : 2.6550211906433105 -> 2.6545703411102295
7:59:28.123140 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:59:28.127143 INFO: Updating optimization_manager: score_cutoff        : 50.32683841209411 -> 50.24867088317871
7:59:28.130145 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:59:28.144650 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:59:28.184652 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:59:28.252652 INFO: === checking if optimization conditions were reached ===
7:59:28.257652 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 2 ===
7:59:28.280652 INFO: Updating optimization_manager: rt_error            : 16.657383754342007 -> 19.340271046288542
7:59:28.284652 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 19.3403.
7:59:28.287652 INFO: ==============================================
7:59:28.291652 INFO: Starting optimization step 14.
7:59:28.294652 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:59:28.298652 INFO: Using classic extraction backend
7:59:28.301652 PROGRESS: Extracting batch of 15870 precursors
7:59:28.305653 INFO: === Search parameters used ===
7:59:28.308652 INFO: rt_error       : 19.340271046288542
7:59:28.312653 INFO: mobility_error : 0.1
7:59:28.315652 INFO: num_candidates : 3
7:59:28.319652 INFO: ms1_error      : 5.0
7:59:28.322653 INFO: ms2_error      : 10.0
7:59:28.326653 INFO: fwhm_rt        : 2.6545703411102295
7:59:28.330653 INFO: quant_window   : 3
7:59:28.334653 INFO: ==============================================
7:59:28.372653 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:59:28.373653 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:59:28.373653 INFO: FWHM in RT is 2.65 seconds, sigma is 0.30
7:59:28.374658 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:59:28.376657 INFO: Starting candidate selection
7:59:29.091192 INFO: Starting candidate scoring
7:59:30.350408 INFO: Finished candidate processing
7:59:30.351414 INFO: Collecting candidate features
7:59:30.583926 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43171)
7:59:30.585926 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43171)
7:59:30.601926 INFO: Collecting fragment features
7:59:30.707438 INFO: Finished candidate scoring
7:59:30.752439 INFO: performing precursor FDR with 47 features
7:59:30.753438 INFO: Decoy channel: -1
7:59:30.753438 INFO: Competetive: True
7:59:30.822440 INFO: Setting torch num_threads to 2 for FDR classification task
7:59:30.863440 WARNING: dropped 1 target PSMs due to missing features
7:59:30.864440 WARNING: dropped 5 decoy PSMs due to missing features
7:59:30.886446 INFO: Using random state 787985 for train-test-split
7:59:31.873931 INFO: Test AUC: 0.781
7:59:31.874931 INFO: Train AUC: 0.773
7:59:31.875931 INFO: AUC difference: 1.04%
7:59:32.570474 INFO: Resetting torch num_threads to 10
7:59:32.578474 PROGRESS: === Extracted 43171 precursors and 339512 fragments ===
7:59:32.583475 INFO: === FDR correction performed with classifier version 5 ===
7:59:32.593475 PROGRESS: ============================= Precursor FDR =============================
7:59:32.596474 PROGRESS: Total precursors accumulated: 7,561
7:59:32.600475 PROGRESS: Target precursors: 7,492 (99.09%)
7:59:32.603475 PROGRESS: Decoy precursors: 69 (0.91%)
7:59:32.606476 PROGRESS: 
7:59:32.609475 PROGRESS: Precursor Summary:
7:59:32.629477 PROGRESS: Channel   0:	 0.050 FDR: 7,492; 0.010 FDR: 7,492; 0.001 FDR: 6,373
7:59:32.633480 PROGRESS: 
7:59:32.636480 PROGRESS: Protein Summary:
7:59:32.660988 PROGRESS: Channel   0:	 0.050 FDR: 3,604; 0.010 FDR: 3,604; 0.001 FDR: 3,224
7:59:32.666989 PROGRESS: =========================================================================
7:59:32.679989 INFO: Target number of precursors reached.
7:59:32.892994 INFO: fragments_df: keeping 5000 of 339512 [sum(precursor_idx_mask)=174860 sum(mass_error_mask)=339512 stop_rank=5000
7:59:32.966502 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:59:39.428771 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:59:46.416849 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:59:49.964731 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:59:49.972731 INFO: Using score_cutoff 50.91292385787964 (fac=0.99, q=1)
7:59:49.978728 INFO: Updating optimization_manager: fwhm_rt             : 2.6545703411102295 -> 2.655409336090088
7:59:49.983731 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
7:59:49.988729 INFO: Updating optimization_manager: score_cutoff        : 50.24867088317871 -> 50.91292385787964
7:59:49.992729 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:59:50.007728 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:59:50.048730 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:59:50.116730 INFO: === checking if optimization conditions were reached ===
7:59:50.120730 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 2 ===
7:59:50.141731 INFO: Updating optimization_manager: rt_error            : 19.340271046288542 -> 15.839079246818198
7:59:50.145731 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 15.8391.
7:59:50.149733 INFO: ==============================================
7:59:50.152733 INFO: Starting optimization step 15.
7:59:50.155730 PROGRESS: === Extracting elution groups 0 to 8000 ===
7:59:50.158730 INFO: Using classic extraction backend
7:59:50.162731 PROGRESS: Extracting batch of 15870 precursors
7:59:50.165731 INFO: === Search parameters used ===
7:59:50.168733 INFO: rt_error       : 15.839079246818198
7:59:50.172748 INFO: mobility_error : 0.1
7:59:50.175743 INFO: num_candidates : 3
7:59:50.178744 INFO: ms1_error      : 5.0
7:59:50.182744 INFO: ms2_error      : 10.0
7:59:50.185745 INFO: fwhm_rt        : 2.655409336090088
7:59:50.189334 INFO: quant_window   : 3
7:59:50.192335 INFO: ==============================================
7:59:50.227335 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
7:59:50.228334 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
7:59:50.229334 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
7:59:50.229334 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
7:59:50.231334 INFO: Starting candidate selection
7:59:50.952509 INFO: Starting candidate scoring
7:59:52.181021 INFO: Finished candidate processing
7:59:52.182027 INFO: Collecting candidate features
7:59:52.471637 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 43280)
7:59:52.472643 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 43280)
7:59:52.490633 INFO: Collecting fragment features
7:59:52.607633 INFO: Finished candidate scoring
7:59:52.653634 INFO: performing precursor FDR with 47 features
7:59:52.654634 INFO: Decoy channel: -1
7:59:52.655634 INFO: Competetive: True
7:59:52.719177 INFO: Setting torch num_threads to 2 for FDR classification task
7:59:52.761177 WARNING: dropped 1 target PSMs due to missing features
7:59:52.762176 WARNING: dropped 6 decoy PSMs due to missing features
7:59:52.785177 INFO: Using random state 787985 for train-test-split
7:59:53.782696 INFO: Test AUC: 0.773
7:59:53.783695 INFO: Train AUC: 0.783
7:59:53.784696 INFO: AUC difference: 1.30%
7:59:54.454329 INFO: Resetting torch num_threads to 10
7:59:54.463329 PROGRESS: === Extracted 43280 precursors and 340592 fragments ===
7:59:54.467332 INFO: === FDR correction performed with classifier version 5 ===
7:59:54.477330 PROGRESS: ============================= Precursor FDR =============================
7:59:54.481331 PROGRESS: Total precursors accumulated: 7,575
7:59:54.484332 PROGRESS: Target precursors: 7,520 (99.27%)
7:59:54.487332 PROGRESS: Decoy precursors: 55 (0.73%)
7:59:54.490331 PROGRESS: 
7:59:54.493330 PROGRESS: Precursor Summary:
7:59:54.512330 PROGRESS: Channel   0:	 0.050 FDR: 7,520; 0.010 FDR: 7,520; 0.001 FDR: 6,378
7:59:54.515331 PROGRESS: 
7:59:54.519331 PROGRESS: Protein Summary:
7:59:54.543330 PROGRESS: Channel   0:	 0.050 FDR: 3,624; 0.010 FDR: 3,624; 0.001 FDR: 3,226
7:59:54.547331 PROGRESS: =========================================================================
7:59:54.554327 INFO: Target number of precursors reached.
7:59:54.755878 INFO: fragments_df: keeping 5000 of 340592 [sum(precursor_idx_mask)=176041 sum(mass_error_mask)=340592 stop_rank=5000
7:59:54.853880 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:00:02.020864 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:00:08.710057 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:00:12.076305 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:00:12.085303 INFO: Using score_cutoff 50.63913514022827 (fac=0.99, q=1)
8:00:12.092302 INFO: Updating optimization_manager: fwhm_rt             : 2.655409336090088 -> 2.6571364402770996
8:00:12.098300 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:00:12.103302 INFO: Updating optimization_manager: score_cutoff        : 50.91292385787964 -> 50.63913514022827
8:00:12.108664 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:00:12.123673 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:00:12.162674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:00:12.225688 INFO: === checking if optimization conditions were reached ===
8:00:12.230687 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 2 ===
8:00:12.271824 INFO: Updating optimization_manager: rt_error            : 15.839079246818198 -> 19.187312049082934
8:00:12.276825 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 19.1873.
8:00:12.281825 INFO: ==============================================
8:00:12.284823 INFO: Starting optimization step 16.
8:00:12.288825 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:00:12.293825 INFO: Using classic extraction backend
8:00:12.300825 PROGRESS: Extracting batch of 15870 precursors
8:00:12.306823 INFO: === Search parameters used ===
8:00:12.313823 INFO: rt_error       : 19.187312049082934
8:00:12.323824 INFO: mobility_error : 0.1
8:00:12.332823 INFO: num_candidates : 3
8:00:12.341823 INFO: ms1_error      : 5.0
8:00:12.347825 INFO: ms2_error      : 10.0
8:00:12.355833 INFO: fwhm_rt        : 2.6571364402770996
8:00:12.363827 INFO: quant_window   : 3
8:00:12.371825 INFO: ==============================================
8:00:12.426829 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:00:12.427829 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:00:12.428825 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
8:00:12.429827 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:00:12.430826 INFO: Starting candidate selection
8:00:13.126013 INFO: Starting candidate scoring
8:00:14.339202 INFO: Finished candidate processing
8:00:14.341213 INFO: Collecting candidate features
8:00:14.571374 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43144)
8:00:14.587377 INFO: Collecting fragment features
8:00:14.686377 INFO: Finished candidate scoring
8:00:14.728390 INFO: performing precursor FDR with 47 features
8:00:14.729391 INFO: Decoy channel: -1
8:00:14.730389 INFO: Competetive: True
8:00:14.804932 INFO: Setting torch num_threads to 2 for FDR classification task
8:00:14.844934 WARNING: dropped 1 target PSMs due to missing features
8:00:14.845935 WARNING: dropped 4 decoy PSMs due to missing features
8:00:14.866934 INFO: Using random state 787985 for train-test-split
8:00:15.806566 INFO: Test AUC: 0.759
8:00:15.808568 INFO: Train AUC: 0.777
8:00:15.809568 INFO: AUC difference: 2.25%
8:00:16.488741 INFO: Resetting torch num_threads to 10
8:00:16.501331 PROGRESS: === Extracted 43144 precursors and 339483 fragments ===
8:00:16.506332 INFO: === FDR correction performed with classifier version 5 ===
8:00:16.520334 PROGRESS: ============================= Precursor FDR =============================
8:00:16.524335 PROGRESS: Total precursors accumulated: 7,588
8:00:16.528336 PROGRESS: Target precursors: 7,530 (99.24%)
8:00:16.531335 PROGRESS: Decoy precursors: 58 (0.76%)
8:00:16.535335 PROGRESS: 
8:00:16.538338 PROGRESS: Precursor Summary:
8:00:16.570330 PROGRESS: Channel   0:	 0.050 FDR: 7,530; 0.010 FDR: 7,530; 0.001 FDR: 6,508
8:00:16.574328 PROGRESS: 
8:00:16.577328 PROGRESS: Protein Summary:
8:00:16.609328 PROGRESS: Channel   0:	 0.050 FDR: 3,621; 0.010 FDR: 3,621; 0.001 FDR: 3,268
8:00:16.613328 PROGRESS: =========================================================================
8:00:16.627327 INFO: Target number of precursors reached.
8:00:16.891942 INFO: fragments_df: keeping 5000 of 339483 [sum(precursor_idx_mask)=175738 sum(mass_error_mask)=339483 stop_rank=5000
8:00:17.036483 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:00:24.088230 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:00:31.367058 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:00:35.013033 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:00:35.020036 INFO: Using score_cutoff 50.31242377281189 (fac=0.99, q=1)
8:00:35.024050 INFO: Updating optimization_manager: fwhm_rt             : 2.6571364402770996 -> 2.6572113037109375
8:00:35.028046 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:00:35.032049 INFO: Updating optimization_manager: score_cutoff        : 50.63913514022827 -> 50.31242377281189
8:00:35.035563 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:00:35.051577 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:00:35.110577 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:00:35.202580 INFO: === checking if optimization conditions were reached ===
8:00:35.208582 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 2 ===
8:00:35.240581 INFO: Updating optimization_manager: rt_error            : 19.187312049082934 -> 16.923127975111285
8:00:35.244580 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 16.9231.
8:00:35.248584 INFO: ==============================================
8:00:35.252581 INFO: Starting optimization step 17.
8:00:35.255580 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:00:35.259580 INFO: Using classic extraction backend
8:00:35.262582 PROGRESS: Extracting batch of 15870 precursors
8:00:35.266581 INFO: === Search parameters used ===
8:00:35.269579 INFO: rt_error       : 16.923127975111285
8:00:35.272597 INFO: mobility_error : 0.1
8:00:35.276593 INFO: num_candidates : 3
8:00:35.279590 INFO: ms1_error      : 5.0
8:00:35.282594 INFO: ms2_error      : 10.0
8:00:35.286109 INFO: fwhm_rt        : 2.6572113037109375
8:00:35.290125 INFO: quant_window   : 3
8:00:35.297127 INFO: ==============================================
8:00:35.348120 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:00:35.349121 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:00:35.349121 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
8:00:35.350120 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:00:35.352118 INFO: Starting candidate selection
8:00:36.038308 INFO: Starting candidate scoring
8:00:37.436380 INFO: Finished candidate processing
8:00:37.438387 INFO: Collecting candidate features
8:00:37.743013 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 43233)
8:00:37.746016 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43233)
8:00:37.785021 INFO: Collecting fragment features
8:00:37.925536 INFO: Finished candidate scoring
8:00:37.980535 INFO: performing precursor FDR with 47 features
8:00:37.981534 INFO: Decoy channel: -1
8:00:37.982534 INFO: Competetive: True
8:00:38.074125 INFO: Setting torch num_threads to 2 for FDR classification task
8:00:38.138127 WARNING: dropped 1 target PSMs due to missing features
8:00:38.139127 WARNING: dropped 3 decoy PSMs due to missing features
8:00:38.170127 INFO: Using random state 787985 for train-test-split
8:00:39.333381 INFO: Test AUC: 0.774
8:00:39.335380 INFO: Train AUC: 0.779
8:00:39.335380 INFO: AUC difference: 0.76%
8:00:40.073998 INFO: Resetting torch num_threads to 10
8:00:40.085998 PROGRESS: === Extracted 43233 precursors and 340356 fragments ===
8:00:40.091999 INFO: === FDR correction performed with classifier version 5 ===
8:00:40.106999 PROGRESS: ============================= Precursor FDR =============================
8:00:40.110997 PROGRESS: Total precursors accumulated: 7,596
8:00:40.116002 PROGRESS: Target precursors: 7,538 (99.24%)
8:00:40.120000 PROGRESS: Decoy precursors: 58 (0.76%)
8:00:40.124000 PROGRESS: 
8:00:40.127000 PROGRESS: Precursor Summary:
8:00:40.158999 PROGRESS: Channel   0:	 0.050 FDR: 7,538; 0.010 FDR: 7,538; 0.001 FDR: 6,625
8:00:40.164002 PROGRESS: 
8:00:40.168000 PROGRESS: Protein Summary:
8:00:40.205000 PROGRESS: Channel   0:	 0.050 FDR: 3,625; 0.010 FDR: 3,625; 0.001 FDR: 3,316
8:00:40.209000 PROGRESS: =========================================================================
8:00:40.222000 INFO: Target number of precursors reached.
8:00:40.506512 INFO: fragments_df: keeping 5000 of 340356 [sum(precursor_idx_mask)=176237 sum(mass_error_mask)=340356 stop_rank=5000
8:00:40.628050 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:00:47.888971 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:00:55.118457 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:00:58.588743 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:00:58.593740 INFO: Using score_cutoff 49.77201898841858 (fac=0.99, q=1)
8:00:58.597739 INFO: Updating optimization_manager: fwhm_rt             : 2.6572113037109375 -> 2.6613593101501465
8:00:58.600741 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:00:58.603741 INFO: Updating optimization_manager: score_cutoff        : 50.31242377281189 -> 49.77201898841858
8:00:58.606740 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:00:58.619741 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:00:58.655740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:00:58.715746 INFO: === checking if optimization conditions were reached ===
8:00:58.719742 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 2 ===
8:00:58.741744 INFO: Updating optimization_manager: rt_error            : 16.923127975111285 -> 19.13083205530142
8:00:58.744745 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 19.1308.
8:00:58.747743 INFO: ==============================================
8:00:58.751743 INFO: Starting optimization step 18.
8:00:58.754743 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:00:58.757743 INFO: Using classic extraction backend
8:00:58.761745 PROGRESS: Extracting batch of 15870 precursors
8:00:58.764744 INFO: === Search parameters used ===
8:00:58.767743 INFO: rt_error       : 19.13083205530142
8:00:58.770741 INFO: mobility_error : 0.1
8:00:58.773742 INFO: num_candidates : 3
8:00:58.777743 INFO: ms1_error      : 5.0
8:00:58.782743 INFO: ms2_error      : 10.0
8:00:58.787744 INFO: fwhm_rt        : 2.6613593101501465
8:00:58.796743 INFO: quant_window   : 3
8:00:58.802743 INFO: ==============================================
8:00:58.850293 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:00:58.851295 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:00:58.852293 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
8:00:58.853294 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:00:58.855295 INFO: Starting candidate selection
8:00:59.522602 INFO: Starting candidate scoring
8:01:00.816316 INFO: Finished candidate processing
8:01:00.818321 INFO: Collecting candidate features
8:01:01.058838 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 43148)
8:01:01.076841 INFO: Collecting fragment features
8:01:01.182349 INFO: Finished candidate scoring
8:01:01.228353 INFO: performing precursor FDR with 47 features
8:01:01.229351 INFO: Decoy channel: -1
8:01:01.230353 INFO: Competetive: True
8:01:01.300353 INFO: Setting torch num_threads to 2 for FDR classification task
8:01:01.342872 WARNING: dropped 1 target PSMs due to missing features
8:01:01.343873 WARNING: dropped 3 decoy PSMs due to missing features
8:01:01.366874 INFO: Using random state 787985 for train-test-split
8:01:02.336216 INFO: Test AUC: 0.767
8:01:02.337213 INFO: Train AUC: 0.775
8:01:02.338215 INFO: AUC difference: 0.96%
8:01:02.982834 INFO: Resetting torch num_threads to 10
8:01:02.991837 PROGRESS: === Extracted 43148 precursors and 339291 fragments ===
8:01:02.995836 INFO: === FDR correction performed with classifier version 5 ===
8:01:03.006837 PROGRESS: ============================= Precursor FDR =============================
8:01:03.010837 PROGRESS: Total precursors accumulated: 7,563
8:01:03.013836 PROGRESS: Target precursors: 7,499 (99.15%)
8:01:03.017837 PROGRESS: Decoy precursors: 64 (0.85%)
8:01:03.021835 PROGRESS: 
8:01:03.025837 PROGRESS: Precursor Summary:
8:01:03.052835 PROGRESS: Channel   0:	 0.050 FDR: 7,499; 0.010 FDR: 7,499; 0.001 FDR: 6,437
8:01:03.058836 PROGRESS: 
8:01:03.065836 PROGRESS: Protein Summary:
8:01:03.104280 PROGRESS: Channel   0:	 0.050 FDR: 3,616; 0.010 FDR: 3,616; 0.001 FDR: 3,249
8:01:03.111280 PROGRESS: =========================================================================
8:01:03.142279 INFO: Target number of precursors reached.
8:01:03.389371 INFO: fragments_df: keeping 5000 of 339291 [sum(precursor_idx_mask)=175073 sum(mass_error_mask)=339291 stop_rank=5000
8:01:03.469375 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:01:10.585831 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:01:17.675791 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:01:21.113661 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:01:21.119675 INFO: Using score_cutoff 49.79517501983643 (fac=0.99, q=1)
8:01:21.123674 INFO: Updating optimization_manager: fwhm_rt             : 2.6613593101501465 -> 2.6627578735351562
8:01:21.126674 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:01:21.130674 INFO: Updating optimization_manager: score_cutoff        : 49.77201898841858 -> 49.79517501983643
8:01:21.134186 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:01:21.146200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:01:21.184200 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:01:21.245201 INFO: === checking if optimization conditions were reached ===
8:01:21.249198 PROGRESS: === Optimization of rt_error has been performed 19 time(s); minimum number is 2 ===
8:01:21.270198 INFO: Updating optimization_manager: rt_error            : 19.13083205530142 -> 16.783545800661038
8:01:21.274195 PROGRESS: ❌ rt_error       : optimization incomplete after 19 search(es). Will search with parameter 16.7835.
8:01:21.277194 INFO: ==============================================
8:01:21.281195 INFO: Starting optimization step 19.
8:01:21.284195 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:01:21.287195 INFO: Using classic extraction backend
8:01:21.291195 PROGRESS: Extracting batch of 15870 precursors
8:01:21.294195 INFO: === Search parameters used ===
8:01:21.297195 INFO: rt_error       : 16.783545800661038
8:01:21.301195 INFO: mobility_error : 0.1
8:01:21.304198 INFO: num_candidates : 3
8:01:21.308197 INFO: ms1_error      : 5.0
8:01:21.311197 INFO: ms2_error      : 10.0
8:01:21.315197 INFO: fwhm_rt        : 2.6627578735351562
8:01:21.318197 INFO: quant_window   : 3
8:01:21.324195 INFO: ==============================================
8:01:21.372202 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:01:21.373203 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:01:21.374202 INFO: FWHM in RT is 2.66 seconds, sigma is 0.30
8:01:21.375204 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:01:21.376203 INFO: Starting candidate selection
8:01:21.982348 INFO: Starting candidate scoring
8:01:23.191759 INFO: Finished candidate processing
8:01:23.193764 INFO: Collecting candidate features
8:01:23.426280 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 43212)
8:01:23.428280 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 43212)
8:01:23.444279 INFO: Collecting fragment features
8:01:23.546286 INFO: Finished candidate scoring
8:01:23.588287 INFO: performing precursor FDR with 47 features
8:01:23.589288 INFO: Decoy channel: -1
8:01:23.590289 INFO: Competetive: True
8:01:23.647832 INFO: Setting torch num_threads to 2 for FDR classification task
8:01:23.686831 WARNING: dropped 1 target PSMs due to missing features
8:01:23.687832 WARNING: dropped 3 decoy PSMs due to missing features
8:01:23.708834 INFO: Using random state 787985 for train-test-split
8:01:24.891139 INFO: Test AUC: 0.774
8:01:24.892147 INFO: Train AUC: 0.780
8:01:24.893146 INFO: AUC difference: 0.72%
8:01:25.631352 INFO: Resetting torch num_threads to 10
8:01:25.644971 PROGRESS: === Extracted 43212 precursors and 340041 fragments ===
8:01:25.650971 INFO: === FDR correction performed with classifier version 5 ===
8:01:25.667972 PROGRESS: ============================= Precursor FDR =============================
8:01:25.672969 PROGRESS: Total precursors accumulated: 7,605
8:01:25.676971 PROGRESS: Target precursors: 7,548 (99.25%)
8:01:25.680972 PROGRESS: Decoy precursors: 57 (0.75%)
8:01:25.683969 PROGRESS: 
8:01:25.687968 PROGRESS: Precursor Summary:
8:01:25.722973 PROGRESS: Channel   0:	 0.050 FDR: 7,548; 0.010 FDR: 7,548; 0.001 FDR: 6,635
8:01:25.727971 PROGRESS: 
8:01:25.731971 PROGRESS: Protein Summary:
8:01:25.773971 PROGRESS: Channel   0:	 0.050 FDR: 3,636; 0.010 FDR: 3,636; 0.001 FDR: 3,323
8:01:25.777971 PROGRESS: =========================================================================
8:01:25.791973 INFO: Target number of precursors reached.
8:01:26.060611 INFO: fragments_df: keeping 5000 of 340041 [sum(precursor_idx_mask)=176171 sum(mass_error_mask)=340041 stop_rank=5000
8:01:26.182234 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:01:33.341467 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:01:40.636199 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:01:44.260990 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:01:44.265989 INFO: Using score_cutoff 49.63989909553528 (fac=0.99, q=1)
8:01:44.270989 INFO: Updating optimization_manager: fwhm_rt             : 2.6627578735351562 -> 2.666604518890381
8:01:44.273987 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:01:44.277987 INFO: Updating optimization_manager: score_cutoff        : 49.79517501983643 -> 49.63989909553528
8:01:44.280987 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:01:44.294986 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:01:44.335993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:01:44.407992 INFO: === checking if optimization conditions were reached ===
8:01:44.411993 PROGRESS: === Optimization of rt_error has been performed 20 time(s); minimum number is 2 ===
8:01:44.435010 INFO: Updating optimization_manager: rt_error            : 16.783545800661038 -> 16.262466062355614
8:01:44.438538 PROGRESS: ❌ rt_error       : optimization incomplete after 20 search(es). Will search with parameter 16.2625.
8:01:44.442539 INFO: ==============================================
8:01:44.446537 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
8:01:44.449538 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
8:01:44.452538 PROGRESS: ==============================================
8:01:44.456538 PROGRESS: ms2_error      : 10.0000
8:01:44.459538 PROGRESS: ms1_error      : 5.0000
8:01:44.463538 PROGRESS: rt_error       : 16.2625
8:01:44.466540 PROGRESS: ==============================================
8:01:44.487539 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:01:44.583537 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:01:44.747065 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:01:45.214281 INFO: Using classic extraction backend
8:01:45.219281 PROGRESS: Extracting batch of 121155 precursors
8:01:45.222283 INFO: === Search parameters used ===
8:01:45.226282 INFO: rt_error       : 16.262466062355614
8:01:45.230284 INFO: mobility_error : 0.1
8:01:45.233281 INFO: num_candidates : 3
8:01:45.237283 INFO: ms1_error      : 5.0
8:01:45.240281 INFO: ms2_error      : 10.0
8:01:45.244282 INFO: fwhm_rt        : 2.666604518890381
8:01:45.247283 INFO: quant_window   : 3
8:01:45.251283 INFO: ==============================================
8:01:45.326281 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:01:45.327284 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:01:45.328282 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
8:01:45.328282 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:01:45.330281 INFO: Starting candidate selection
8:01:49.289988 INFO: Removed 112728 precursors with score below cutoff 49.63989909553528
8:01:49.387990 INFO: Starting candidate scoring
8:01:55.377836 INFO: Finished candidate processing
8:01:55.378827 INFO: Collecting candidate features
8:01:56.188485 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 217195)
8:01:56.264107 INFO: Collecting fragment features
8:01:56.649626 INFO: Finished candidate scoring
8:01:56.837153 INFO: === Performing FDR correction with classifier version 5 ===
8:01:56.845143 INFO: performing precursor FDR with 47 features
8:01:56.846145 INFO: Decoy channel: -1
8:01:56.847140 INFO: Competetive: True
8:01:57.071667 INFO: Setting torch num_threads to 2 for FDR classification task
8:01:57.161670 WARNING: dropped 1 target PSMs due to missing features
8:01:57.162671 WARNING: FDR calculation for 122138 target and 95056 decoy PSMs
8:01:57.163668 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
8:01:57.328194 INFO: Using random state 787985 for train-test-split
8:02:02.867571 INFO: Test AUC: 0.847
8:02:02.868571 INFO: Train AUC: 0.856
8:02:02.869574 INFO: AUC difference: 1.07%
8:02:03.817700 INFO: Resetting torch num_threads to 10
8:02:03.873704 INFO: Removing fragments below FDR threshold
8:02:04.101258 PROGRESS: ============================= Precursor FDR =============================
8:02:04.106254 PROGRESS: Total precursors accumulated: 57,201
8:02:04.109252 PROGRESS: Target precursors: 56,809 (99.31%)
8:02:04.113253 PROGRESS: Decoy precursors: 392 (0.69%)
8:02:04.116253 PROGRESS: 
8:02:04.119254 PROGRESS: Precursor Summary:
8:02:04.256796 PROGRESS: Channel   0:	 0.050 FDR: 56,809; 0.010 FDR: 56,809; 0.001 FDR: 55,395
8:02:04.260797 PROGRESS: 
8:02:04.264797 PROGRESS: Protein Summary:
8:02:04.462815 PROGRESS: Channel   0:	 0.050 FDR: 6,499; 0.010 FDR: 6,499; 0.001 FDR: 6,470
8:02:04.467813 PROGRESS: =========================================================================
8:02:04.495036 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\psm.parquet
8:02:05.647800 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\frag.parquet
8:02:06.864101 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
8:02:07.159652 PROGRESS: 
8:02:07.161652 INFO: Quantification results path: Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant
8:02:07.162652 INFO: Creating folder Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\figures
8:02:07.170654 INFO: Initializing TimingManager
8:02:07.184651 INFO: Initializing RawFileManager
8:06:44.862794 INFO: Determining DIA cycle
8:06:44.884388 INFO: Found cycle with start 0.00 min and length 86.
8:06:45.485598 INFO: RT (min)            : 0.0 - 55.5
8:06:45.486598 INFO: RT duration (sec)   : 3327.2
8:06:45.487598 INFO: RT duration (min)   : 55.5
8:06:45.488598 INFO: Cycle len (scans)   : 86
8:06:45.489601 INFO: Cycle len (sec)     : 1.90
8:06:45.490599 INFO: Number of cycles    : 1747
8:06:45.491602 INFO: MS2 range (m/z)     : 399.5 - 903.5
8:06:45.492599 INFO: Creating DIA data object took: 278.3019471168518
8:06:45.587598 INFO: Initializing CalibrationManager
8:06:45.602595 INFO: Setting up calibration estimators ..
8:06:45.610595 INFO: Found 1 estimator(s) in calibration group 'fragment'
8:06:45.617602 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'}' ..
8:06:45.626108 INFO: Found 3 estimator(s) in calibration group 'precursor'
8:06:45.633115 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
8:06:45.642115 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}}' ..
8:06:45.648116 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
8:06:45.653115 INFO: Done setting up calibration estimators.
8:06:45.659116 INFO: Initializing OptimizationManager
8:06:45.672116 INFO: initial parameter: ms1_error = 30
8:06:45.678118 INFO: initial parameter: ms2_error = 30
8:06:45.684116 INFO: initial parameter: rt_error = 1663.6044921875
8:06:45.690116 INFO: initial parameter: mobility_error = 0.1
8:06:45.699119 INFO: initial parameter: num_candidates = 1
8:06:45.708117 INFO: initial parameter: fwhm_rt = 5
8:06:45.717115 INFO: initial parameter: fwhm_mobility = 0.01
8:06:45.724117 INFO: initial parameter: score_cutoff = 0
8:06:45.733117 INFO: initial parameter: classifier_version = -1
8:06:45.745119 PROGRESS: Initializing workflow LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
8:06:45.755117 INFO: FDRManager: loading saved state not requested, will be initialized.
8:06:45.756115 INFO: Initializing FDRManager
8:06:45.757116 INFO: Loading classifier store from C:\Program Files (x86)\AlphaDIA1.12.2\_internal\alphadia\constants\classifier
8:06:45.840116 PROGRESS: Initializing spectral library: 61,104 target precursors potentially observable (0 removed)
8:06:45.966640 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
8:06:45.971635 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 1663.6044921875
8:06:45.979640 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
8:06:45.988642 PROGRESS: Starting initial search for precursors.
8:06:46.013636 INFO: Starting optimization step 0.
8:06:46.021640 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:06:46.029639 INFO: Using classic extraction backend
8:06:46.038640 PROGRESS: Extracting batch of 15870 precursors
8:06:46.046639 INFO: === Search parameters used ===
8:06:46.056639 INFO: rt_error       : 1663.6044921875
8:06:46.066641 INFO: mobility_error : 0.1
8:06:46.073639 INFO: num_candidates : 1
8:06:46.081641 INFO: ms1_error      : 30
8:06:46.087646 INFO: ms2_error      : 30
8:06:46.096640 INFO: fwhm_rt        : 5
8:06:46.106641 INFO: quant_window   : 3
8:06:46.113655 INFO: ==============================================
8:06:46.168183 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:06:46.169181 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:06:46.170184 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
8:06:46.171186 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
8:06:46.172181 INFO: Starting candidate selection
8:06:59.882153 INFO: Starting candidate scoring
8:07:00.442855 INFO: Finished candidate processing
8:07:00.443866 INFO: Collecting candidate features
8:07:00.557866 INFO: Collecting fragment features
8:07:00.666414 INFO: Finished candidate scoring
8:07:00.694415 INFO: performing precursor FDR with 47 features
8:07:00.695416 INFO: Decoy channel: -1
8:07:00.695416 INFO: Competetive: True
8:07:00.725417 INFO: Setting torch num_threads to 2 for FDR classification task
8:07:00.754417 INFO: Using random state 827875 for train-test-split
8:07:01.062568 INFO: Test AUC: 0.741
8:07:01.063569 INFO: Train AUC: 0.747
8:07:01.064569 INFO: AUC difference: 0.92%
8:07:01.673087 INFO: Resetting torch num_threads to 10
8:07:01.683088 PROGRESS: === Extracted 15870 precursors and 162002 fragments ===
8:07:01.689089 INFO: === FDR correction performed with classifier version -1 ===
8:07:01.698088 PROGRESS: ============================= Precursor FDR =============================
8:07:01.702090 PROGRESS: Total precursors accumulated: 2,220
8:07:01.705090 PROGRESS: Target precursors: 2,083 (93.83%)
8:07:01.709090 PROGRESS: Decoy precursors: 137 (6.17%)
8:07:01.713092 PROGRESS: 
8:07:01.716092 PROGRESS: Precursor Summary:
8:07:01.724093 PROGRESS: Channel   0:	 0.050 FDR: 1,557; 0.010 FDR:     0; 0.001 FDR:     0
8:07:01.728095 PROGRESS: 
8:07:01.732097 PROGRESS: Protein Summary:
8:07:01.740094 PROGRESS: Channel   0:	 0.050 FDR: 1,172; 0.010 FDR:     0; 0.001 FDR:     0
8:07:01.744095 PROGRESS: =========================================================================
8:07:01.749095 INFO: Target number of precursors not reached yet.
8:07:01.868097 INFO: Starting optimization step 1.
8:07:01.873096 PROGRESS: === Extracting elution groups 8000 to 24000 ===
8:07:01.876096 INFO: Using classic extraction backend
8:07:01.880096 PROGRESS: Extracting batch of 31722 precursors
8:07:01.883094 INFO: === Search parameters used ===
8:07:01.887108 INFO: rt_error       : 1663.6044921875
8:07:01.891109 INFO: mobility_error : 0.1
8:07:01.894109 INFO: num_candidates : 1
8:07:01.898108 INFO: ms1_error      : 30
8:07:01.901173 INFO: ms2_error      : 30
8:07:01.905173 INFO: fwhm_rt        : 5
8:07:01.909174 INFO: quant_window   : 3
8:07:01.912173 INFO: ==============================================
8:07:01.947173 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:07:01.948174 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:07:01.948174 INFO: FWHM in RT is 5.00 seconds, sigma is 0.56
8:07:01.949174 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
8:07:01.950175 INFO: Starting candidate selection
8:07:30.089140 INFO: Starting candidate scoring
8:07:31.153103 INFO: Finished candidate processing
8:07:31.154119 INFO: Collecting candidate features
8:07:31.357735 INFO: Collecting fragment features
8:07:31.458357 INFO: Finished candidate scoring
8:07:31.552357 INFO: performing precursor FDR with 47 features
8:07:31.553357 INFO: Decoy channel: -1
8:07:31.554356 INFO: Competetive: True
8:07:31.641357 INFO: Setting torch num_threads to 2 for FDR classification task
8:07:31.692964 INFO: Using random state 645456 for train-test-split
8:07:32.928291 INFO: Test AUC: 0.856
8:07:32.929305 INFO: Train AUC: 0.847
8:07:32.930304 INFO: AUC difference: 1.12%
8:07:33.606033 INFO: Resetting torch num_threads to 10
8:07:33.669034 PROGRESS: === Extracted 47592 precursors and 486022 fragments ===
8:07:33.675034 INFO: === FDR correction performed with classifier version -1 ===
8:07:33.689049 PROGRESS: ============================= Precursor FDR =============================
8:07:33.693049 PROGRESS: Total precursors accumulated: 16,467
8:07:33.696573 PROGRESS: Target precursors: 15,956 (96.90%)
8:07:33.699573 PROGRESS: Decoy precursors: 511 (3.10%)
8:07:33.703573 PROGRESS: 
8:07:33.707574 PROGRESS: Precursor Summary:
8:07:33.739572 PROGRESS: Channel   0:	 0.050 FDR: 15,956; 0.010 FDR: 14,336; 0.001 FDR: 8,898
8:07:33.743573 PROGRESS: 
8:07:33.747573 PROGRESS: Protein Summary:
8:07:33.784575 PROGRESS: Channel   0:	 0.050 FDR: 4,536; 0.010 FDR: 4,221; 0.001 FDR: 3,257
8:07:33.788575 PROGRESS: =========================================================================
8:07:33.796573 INFO: Target number of precursors reached.
8:07:34.043192 INFO: fragments_df: keeping 5000 of 486022 [sum(precursor_idx_mask)=159795 sum(mass_error_mask)=486022 stop_rank=5000
8:07:34.147195 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:07:56.846824 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:08:19.539551 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:08:23.116258 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
8:08:23.122260 INFO: Using score_cutoff 78.59652501296996 (fac=0.99, q=1)
8:08:23.127259 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 2.732656478881836
8:08:23.131260 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.0
8:08:23.135259 INFO: Updating optimization_manager: score_cutoff        : 0 -> 78.59652501296996
8:08:23.138259 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:08:23.154260 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:08:23.209260 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:08:23.284263 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
8:08:23.288261 PROGRESS: Required number of precursors found. Starting search parameter optimization.
8:08:23.292261 INFO: Starting optimization step 2.
8:08:23.296277 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:08:23.300275 INFO: Using classic extraction backend
8:08:23.304276 PROGRESS: Extracting batch of 15870 precursors
8:08:23.308278 INFO: === Search parameters used ===
8:08:23.312799 INFO: rt_error       : 1663.6044921875
8:08:23.316801 INFO: mobility_error : 0.1
8:08:23.320796 INFO: num_candidates : 3
8:08:23.325799 INFO: ms1_error      : 30
8:08:23.330799 INFO: ms2_error      : 30
8:08:23.338798 INFO: fwhm_rt        : 2.732656478881836
8:08:23.345800 INFO: quant_window   : 3
8:08:23.354801 INFO: ==============================================
8:08:23.408800 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:08:23.409800 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:08:23.410800 INFO: FWHM in RT is 2.73 seconds, sigma is 0.30
8:08:23.411800 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:08:23.412800 INFO: Starting candidate selection
8:08:40.037786 INFO: Starting candidate scoring
8:08:41.619279 INFO: Finished candidate processing
8:08:41.621300 INFO: Collecting candidate features
8:08:41.991842 INFO: Collecting fragment features
8:08:42.172373 INFO: Finished candidate scoring
8:08:42.232382 INFO: performing precursor FDR with 47 features
8:08:42.233380 INFO: Decoy channel: -1
8:08:42.234379 INFO: Competetive: True
8:08:42.322376 INFO: Setting torch num_threads to 2 for FDR classification task
8:08:42.393898 INFO: Using random state 759484 for train-test-split
8:08:43.696068 INFO: Test AUC: 0.701
8:08:43.697067 INFO: Train AUC: 0.684
8:08:43.698068 INFO: AUC difference: 2.50%
8:08:44.341304 INFO: Resetting torch num_threads to 10
8:08:44.353901 PROGRESS: === Extracted 47609 precursors and 459058 fragments ===
8:08:44.359899 INFO: === FDR correction performed with classifier version 1 ===
8:08:44.372897 PROGRESS: ============================= Precursor FDR =============================
8:08:44.376894 PROGRESS: Total precursors accumulated: 6,448
8:08:44.380898 PROGRESS: Target precursors: 6,301 (97.72%)
8:08:44.384897 PROGRESS: Decoy precursors: 147 (2.28%)
8:08:44.387899 PROGRESS: 
8:08:44.391900 PROGRESS: Precursor Summary:
8:08:44.419896 PROGRESS: Channel   0:	 0.050 FDR: 6,301; 0.010 FDR: 5,697; 0.001 FDR: 3,319
8:08:44.423898 PROGRESS: 
8:08:44.427895 PROGRESS: Protein Summary:
8:08:44.458897 PROGRESS: Channel   0:	 0.050 FDR: 3,156; 0.010 FDR: 2,928; 0.001 FDR: 1,997
8:08:44.462899 PROGRESS: =========================================================================
8:08:44.475899 INFO: Target number of precursors reached.
8:08:44.772444 INFO: fragments_df: keeping 5000 of 459058 [sum(precursor_idx_mask)=171282 sum(mass_error_mask)=459058 stop_rank=5000
8:08:44.882991 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:08:49.127023 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:08:53.583879 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:08:57.123810 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:08:57.132339 INFO: Using score_cutoff 73.82055577697754 (fac=0.99, q=1)
8:08:57.138338 INFO: Updating optimization_manager: fwhm_rt             : 2.732656478881836 -> 2.698446035385132
8:08:57.144338 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:08:57.149338 INFO: Updating optimization_manager: score_cutoff        : 78.59652501296996 -> 73.82055577697754
8:08:57.153340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:08:57.167339 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:08:57.208341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:08:57.276338 INFO: === checking if optimization conditions were reached ===
8:08:57.284338 INFO: Updating optimization_manager: ms2_error           : 30 -> 23.56826788156669
8:08:57.288340 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
8:08:57.291340 PROGRESS: ❌ ms2_error      : 23.5683 > 10.0000 or insufficient steps taken.
8:08:57.300339 INFO: Updating optimization_manager: ms1_error           : 30 -> 14.478571821169288
8:08:57.304344 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
8:08:57.307340 PROGRESS: ❌ ms1_error      : 14.4786 > 5.0000 or insufficient steps taken.
8:08:57.310340 INFO: ==============================================
8:08:57.313340 INFO: Starting optimization step 3.
8:08:57.317342 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:08:57.320339 INFO: Using classic extraction backend
8:08:57.323340 PROGRESS: Extracting batch of 15870 precursors
8:08:57.326340 INFO: === Search parameters used ===
8:08:57.330341 INFO: rt_error       : 1663.6044921875
8:08:57.333341 INFO: mobility_error : 0.1
8:08:57.338340 INFO: num_candidates : 3
8:08:57.343341 INFO: ms1_error      : 14.478571821169288
8:08:57.347341 INFO: ms2_error      : 23.56826788156669
8:08:57.356342 INFO: fwhm_rt        : 2.698446035385132
8:08:57.362360 INFO: quant_window   : 3
8:08:57.370357 INFO: ==============================================
8:08:57.409885 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:08:57.410884 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:08:57.411885 INFO: FWHM in RT is 2.70 seconds, sigma is 0.30
8:08:57.412885 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:08:57.413882 INFO: Starting candidate selection
8:09:13.268755 INFO: Starting candidate scoring
8:09:14.747010 INFO: Finished candidate processing
8:09:14.749015 INFO: Collecting candidate features
8:09:15.007531 INFO: Collecting fragment features
8:09:15.134540 INFO: Finished candidate scoring
8:09:15.183054 INFO: performing precursor FDR with 47 features
8:09:15.184055 INFO: Decoy channel: -1
8:09:15.185055 INFO: Competetive: True
8:09:15.267055 INFO: Setting torch num_threads to 2 for FDR classification task
8:09:15.318058 INFO: Using random state 903731 for train-test-split
8:09:16.419904 INFO: Test AUC: 0.696
8:09:16.420906 INFO: Train AUC: 0.696
8:09:16.421905 INFO: AUC difference: 0.03%
8:09:17.093942 INFO: Resetting torch num_threads to 10
8:09:17.102941 PROGRESS: === Extracted 47609 precursors and 445976 fragments ===
8:09:17.107941 INFO: === FDR correction performed with classifier version 2 ===
8:09:17.117944 PROGRESS: ============================= Precursor FDR =============================
8:09:17.121941 PROGRESS: Total precursors accumulated: 6,774
8:09:17.124941 PROGRESS: Target precursors: 6,621 (97.74%)
8:09:17.128942 PROGRESS: Decoy precursors: 153 (2.26%)
8:09:17.131942 PROGRESS: 
8:09:17.134942 PROGRESS: Precursor Summary:
8:09:17.151951 PROGRESS: Channel   0:	 0.050 FDR: 6,621; 0.010 FDR: 6,264; 0.001 FDR: 4,930
8:09:17.155463 PROGRESS: 
8:09:17.159465 PROGRESS: Protein Summary:
8:09:17.178466 PROGRESS: Channel   0:	 0.050 FDR: 3,259; 0.010 FDR: 3,129; 0.001 FDR: 2,672
8:09:17.182464 PROGRESS: =========================================================================
8:09:17.190464 INFO: Target number of precursors reached.
8:09:17.433975 INFO: fragments_df: keeping 5000 of 445976 [sum(precursor_idx_mask)=184017 sum(mass_error_mask)=445976 stop_rank=5000
8:09:17.523979 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:09:22.553439 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:09:27.356266 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:09:30.978112 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:09:30.985110 INFO: Using score_cutoff 70.4806509841919 (fac=0.99, q=1)
8:09:30.992111 INFO: Updating optimization_manager: fwhm_rt             : 2.698446035385132 -> 2.674135208129883
8:09:30.998110 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:09:31.002110 INFO: Updating optimization_manager: score_cutoff        : 73.82055577697754 -> 70.4806509841919
8:09:31.007110 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:09:31.023113 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:09:31.081117 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:09:31.159114 INFO: === checking if optimization conditions were reached ===
8:09:31.168114 INFO: Updating optimization_manager: ms2_error           : 23.56826788156669 -> 18.369793115237584
8:09:31.172127 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
8:09:31.176128 PROGRESS: ❌ ms2_error      : 18.3698 > 10.0000 or insufficient steps taken.
8:09:31.185720 INFO: Updating optimization_manager: ms1_error           : 14.478571821169288 -> 5.51671302910565
8:09:31.189738 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
8:09:31.192738 PROGRESS: ❌ ms1_error      : 5.5167 > 5.0000 or insufficient steps taken.
8:09:31.196737 INFO: ==============================================
8:09:31.199738 INFO: Starting optimization step 4.
8:09:31.203738 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:09:31.206739 INFO: Using classic extraction backend
8:09:31.209734 PROGRESS: Extracting batch of 15870 precursors
8:09:31.213734 INFO: === Search parameters used ===
8:09:31.216737 INFO: rt_error       : 1663.6044921875
8:09:31.220737 INFO: mobility_error : 0.1
8:09:31.223737 INFO: num_candidates : 3
8:09:31.227736 INFO: ms1_error      : 5.51671302910565
8:09:31.233739 INFO: ms2_error      : 18.369793115237584
8:09:31.249741 INFO: fwhm_rt        : 2.674135208129883
8:09:31.254737 INFO: quant_window   : 3
8:09:31.261741 INFO: ==============================================
8:09:31.309739 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:09:31.310737 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:09:31.311734 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
8:09:31.312738 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:09:31.313738 INFO: Starting candidate selection
8:09:46.968091 INFO: Starting candidate scoring
8:09:48.484626 INFO: Finished candidate processing
8:09:48.486631 INFO: Collecting candidate features
8:09:48.763178 INFO: Collecting fragment features
8:09:48.889185 INFO: Finished candidate scoring
8:09:48.937185 INFO: performing precursor FDR with 47 features
8:09:48.938182 INFO: Decoy channel: -1
8:09:48.939185 INFO: Competetive: True
8:09:48.999730 INFO: Setting torch num_threads to 2 for FDR classification task
8:09:49.050731 INFO: Using random state 604554 for train-test-split
8:09:50.157467 INFO: Test AUC: 0.701
8:09:50.159467 INFO: Train AUC: 0.700
8:09:50.159467 INFO: AUC difference: 0.23%
8:09:50.837205 INFO: Resetting torch num_threads to 10
8:09:50.846204 PROGRESS: === Extracted 47609 precursors and 434781 fragments ===
8:09:50.851203 INFO: === FDR correction performed with classifier version 3 ===
8:09:50.861205 PROGRESS: ============================= Precursor FDR =============================
8:09:50.864203 PROGRESS: Total precursors accumulated: 6,991
8:09:50.867206 PROGRESS: Target precursors: 6,873 (98.31%)
8:09:50.870203 PROGRESS: Decoy precursors: 118 (1.69%)
8:09:50.873208 PROGRESS: 
8:09:50.876203 PROGRESS: Precursor Summary:
8:09:50.894206 PROGRESS: Channel   0:	 0.050 FDR: 6,873; 0.010 FDR: 6,728; 0.001 FDR: 4,761
8:09:50.897207 PROGRESS: 
8:09:50.900209 PROGRESS: Protein Summary:
8:09:50.919208 PROGRESS: Channel   0:	 0.050 FDR: 3,369; 0.010 FDR: 3,306; 0.001 FDR: 2,647
8:09:50.922207 PROGRESS: =========================================================================
8:09:50.930206 INFO: Target number of precursors reached.
8:09:51.184817 INFO: fragments_df: keeping 5000 of 434781 [sum(precursor_idx_mask)=193436 sum(mass_error_mask)=434781 stop_rank=5000
8:09:51.281341 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:09:57.174639 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:10:03.112418 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:10:06.257035 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:10:06.264037 INFO: Using score_cutoff 65.98570021820068 (fac=0.99, q=1)
8:10:06.270036 INFO: Updating optimization_manager: fwhm_rt             : 2.674135208129883 -> 2.6664748191833496
8:10:06.275036 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:10:06.279036 INFO: Updating optimization_manager: score_cutoff        : 70.4806509841919 -> 65.98570021820068
8:10:06.283037 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:10:06.298037 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:10:06.337038 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:10:06.406042 INFO: === checking if optimization conditions were reached ===
8:10:06.419043 INFO: Updating optimization_manager: ms2_error           : 18.369793115237584 -> 14.355269462528543
8:10:06.427045 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
8:10:06.438043 PROGRESS: ❌ ms2_error      : 14.3553 > 10.0000 or insufficient steps taken.
8:10:06.463047 INFO: Updating optimization_manager: ms1_error           : 5.51671302910565 -> 5.0
8:10:06.473041 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
8:10:06.483051 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
8:10:06.491052 INFO: ==============================================
8:10:06.498578 INFO: Starting optimization step 5.
8:10:06.507576 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:10:06.515576 INFO: Using classic extraction backend
8:10:06.526576 PROGRESS: Extracting batch of 15870 precursors
8:10:06.538579 INFO: === Search parameters used ===
8:10:06.550577 INFO: rt_error       : 1663.6044921875
8:10:06.562574 INFO: mobility_error : 0.1
8:10:06.571571 INFO: num_candidates : 3
8:10:06.580570 INFO: ms1_error      : 5.0
8:10:06.592571 INFO: ms2_error      : 14.355269462528543
8:10:06.602573 INFO: fwhm_rt        : 2.6664748191833496
8:10:06.613573 INFO: quant_window   : 3
8:10:06.625575 INFO: ==============================================
8:10:06.676577 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:10:06.678579 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:10:06.679578 INFO: FWHM in RT is 2.67 seconds, sigma is 0.30
8:10:06.681578 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:10:06.682579 INFO: Starting candidate selection
8:10:22.169781 INFO: Starting candidate scoring
8:10:23.652046 INFO: Finished candidate processing
8:10:23.653042 INFO: Collecting candidate features
8:10:23.993663 INFO: Collecting fragment features
8:10:24.158189 INFO: Finished candidate scoring
8:10:24.216195 INFO: performing precursor FDR with 47 features
8:10:24.217194 INFO: Decoy channel: -1
8:10:24.218194 INFO: Competetive: True
8:10:24.304812 INFO: Setting torch num_threads to 2 for FDR classification task
8:10:24.373815 INFO: Using random state 799895 for train-test-split
8:10:25.667169 INFO: Test AUC: 0.701
8:10:25.668168 INFO: Train AUC: 0.702
8:10:25.670169 INFO: AUC difference: 0.11%
8:10:26.315787 INFO: Resetting torch num_threads to 10
8:10:26.324789 PROGRESS: === Extracted 47606 precursors and 422969 fragments ===
8:10:26.329789 INFO: === FDR correction performed with classifier version 4 ===
8:10:26.338787 PROGRESS: ============================= Precursor FDR =============================
8:10:26.342790 PROGRESS: Total precursors accumulated: 7,032
8:10:26.344789 PROGRESS: Target precursors: 6,919 (98.39%)
8:10:26.347790 PROGRESS: Decoy precursors: 113 (1.61%)
8:10:26.350789 PROGRESS: 
8:10:26.354789 PROGRESS: Precursor Summary:
8:10:26.389790 PROGRESS: Channel   0:	 0.050 FDR: 6,919; 0.010 FDR: 6,796; 0.001 FDR: 5,556
8:10:26.392791 PROGRESS: 
8:10:26.396793 PROGRESS: Protein Summary:
8:10:26.416797 PROGRESS: Channel   0:	 0.050 FDR: 3,383; 0.010 FDR: 3,336; 0.001 FDR: 2,911
8:10:26.420797 PROGRESS: =========================================================================
8:10:26.427794 INFO: Target number of precursors reached.
8:10:26.686355 INFO: fragments_df: keeping 5000 of 422969 [sum(precursor_idx_mask)=191015 sum(mass_error_mask)=422969 stop_rank=5000
8:10:26.789873 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:10:32.803243 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:10:39.004676 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:10:42.642334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:10:42.649334 INFO: Using score_cutoff 64.1616139640808 (fac=0.99, q=1)
8:10:42.656335 INFO: Updating optimization_manager: fwhm_rt             : 2.6664748191833496 -> 2.6398048400878906
8:10:42.662335 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:10:42.667334 INFO: Updating optimization_manager: score_cutoff        : 65.98570021820068 -> 64.1616139640808
8:10:42.671335 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:10:42.688332 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:10:42.743337 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:10:42.817944 INFO: === checking if optimization conditions were reached ===
8:10:42.826946 INFO: Updating optimization_manager: ms2_error           : 14.355269462528543 -> 11.144786099652531
8:10:42.830945 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
8:10:42.833945 PROGRESS: ❌ ms2_error      : 11.1448 > 10.0000 or insufficient steps taken.
8:10:42.836945 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
8:10:42.839945 INFO: ==============================================
8:10:42.843946 INFO: Starting optimization step 6.
8:10:42.846946 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:10:42.849948 INFO: Using classic extraction backend
8:10:42.852946 PROGRESS: Extracting batch of 15870 precursors
8:10:42.855945 INFO: === Search parameters used ===
8:10:42.859945 INFO: rt_error       : 1663.6044921875
8:10:42.862945 INFO: mobility_error : 0.1
8:10:42.865947 INFO: num_candidates : 3
8:10:42.868945 INFO: ms1_error      : 5.0
8:10:42.871944 INFO: ms2_error      : 11.144786099652531
8:10:42.875946 INFO: fwhm_rt        : 2.6398048400878906
8:10:42.879941 INFO: quant_window   : 3
8:10:42.882945 INFO: ==============================================
8:10:42.929947 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:10:42.930946 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:10:42.931947 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
8:10:42.932946 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:10:42.933945 INFO: Starting candidate selection
8:10:59.187669 INFO: Starting candidate scoring
8:11:00.752861 INFO: Finished candidate processing
8:11:00.753867 INFO: Collecting candidate features
8:11:01.096948 INFO: Collecting fragment features
8:11:01.251954 INFO: Finished candidate scoring
8:11:01.308950 INFO: performing precursor FDR with 47 features
8:11:01.309950 INFO: Decoy channel: -1
8:11:01.310950 INFO: Competetive: True
8:11:01.415479 INFO: Setting torch num_threads to 2 for FDR classification task
8:11:01.485482 INFO: Using random state 904355 for train-test-split
8:11:02.563868 INFO: Test AUC: 0.695
8:11:02.564868 INFO: Train AUC: 0.704
8:11:02.565868 INFO: AUC difference: 1.25%
8:11:03.137643 INFO: Resetting torch num_threads to 10
8:11:03.149641 PROGRESS: === Extracted 47605 precursors and 411742 fragments ===
8:11:03.155643 INFO: === FDR correction performed with classifier version 5 ===
8:11:03.168642 PROGRESS: ============================= Precursor FDR =============================
8:11:03.172643 PROGRESS: Total precursors accumulated: 7,063
8:11:03.176642 PROGRESS: Target precursors: 6,965 (98.61%)
8:11:03.180645 PROGRESS: Decoy precursors: 98 (1.39%)
8:11:03.184643 PROGRESS: 
8:11:03.187644 PROGRESS: Precursor Summary:
8:11:03.214643 PROGRESS: Channel   0:	 0.050 FDR: 6,965; 0.010 FDR: 6,892; 0.001 FDR: 6,105
8:11:03.218643 PROGRESS: 
8:11:03.222644 PROGRESS: Protein Summary:
8:11:03.251644 PROGRESS: Channel   0:	 0.050 FDR: 3,405; 0.010 FDR: 3,373; 0.001 FDR: 3,082
8:11:03.255645 PROGRESS: =========================================================================
8:11:03.265642 INFO: Target number of precursors reached.
8:11:03.525184 INFO: fragments_df: keeping 5000 of 411742 [sum(precursor_idx_mask)=189726 sum(mass_error_mask)=411742 stop_rank=5000
8:11:03.618726 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:11:09.596193 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:11:15.989351 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:11:19.634862 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:11:19.638868 INFO: Using score_cutoff 60.977206590270995 (fac=0.99, q=1)
8:11:19.643868 INFO: Updating optimization_manager: fwhm_rt             : 2.6398048400878906 -> 2.623081684112549
8:11:19.646868 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:11:19.649868 INFO: Updating optimization_manager: score_cutoff        : 64.1616139640808 -> 60.977206590270995
8:11:19.653869 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:11:19.666870 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:11:19.705873 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:11:19.771877 INFO: === checking if optimization conditions were reached ===
8:11:19.779875 INFO: Updating optimization_manager: ms2_error           : 11.144786099652531 -> 10.0
8:11:19.783875 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
8:11:19.787875 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
8:11:19.791875 PROGRESS: ✅ ms1_error      : 5.0000 <= 5.0000
8:11:19.794872 INFO: ==============================================
8:11:19.798874 PROGRESS: Optimization finished for ms2_error, ms1_error.
8:11:19.864877 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:11:19.877889 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:11:19.918480 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:11:19.984480 INFO: Starting optimization step 0.
8:11:19.988481 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:11:19.992479 INFO: Using classic extraction backend
8:11:19.995481 PROGRESS: Extracting batch of 15870 precursors
8:11:19.999483 INFO: === Search parameters used ===
8:11:20.002480 INFO: rt_error       : 1663.6044921875
8:11:20.006481 INFO: mobility_error : 0.1
8:11:20.010482 INFO: num_candidates : 3
8:11:20.014481 INFO: ms1_error      : 5.0
8:11:20.018482 INFO: ms2_error      : 10.0
8:11:20.025481 INFO: fwhm_rt        : 2.623081684112549
8:11:20.030482 INFO: quant_window   : 3
8:11:20.036484 INFO: ==============================================
8:11:20.074484 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:11:20.075483 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:11:20.076482 INFO: FWHM in RT is 2.62 seconds, sigma is 0.29
8:11:20.077479 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:11:20.078483 INFO: Starting candidate selection
8:11:35.461847 INFO: Starting candidate scoring
8:11:36.923388 INFO: Finished candidate processing
8:11:36.925393 INFO: Collecting candidate features
8:11:37.192907 INFO: Collecting fragment features
8:11:37.314911 INFO: Finished candidate scoring
8:11:37.363911 INFO: performing precursor FDR with 47 features
8:11:37.364912 INFO: Decoy channel: -1
8:11:37.365912 INFO: Competetive: True
8:11:37.428432 INFO: Setting torch num_threads to 2 for FDR classification task
8:11:37.478433 INFO: Using random state 806454 for train-test-split
8:11:38.569144 INFO: Test AUC: 0.700
8:11:38.570144 INFO: Train AUC: 0.705
8:11:38.571145 INFO: AUC difference: 0.70%
8:11:39.212774 INFO: Resetting torch num_threads to 10
8:11:39.221773 PROGRESS: === Extracted 47602 precursors and 407041 fragments ===
8:11:39.227774 INFO: === FDR correction performed with classifier version 6 ===
8:11:39.238777 PROGRESS: ============================= Precursor FDR =============================
8:11:39.242776 PROGRESS: Total precursors accumulated: 7,042
8:11:39.245774 PROGRESS: Target precursors: 6,946 (98.64%)
8:11:39.248776 PROGRESS: Decoy precursors: 96 (1.36%)
8:11:39.252775 PROGRESS: 
8:11:39.255778 PROGRESS: Precursor Summary:
8:11:39.275774 PROGRESS: Channel   0:	 0.050 FDR: 6,946; 0.010 FDR: 6,910; 0.001 FDR: 6,018
8:11:39.279775 PROGRESS: 
8:11:39.282775 PROGRESS: Protein Summary:
8:11:39.321769 PROGRESS: Channel   0:	 0.050 FDR: 3,389; 0.010 FDR: 3,377; 0.001 FDR: 3,051
8:11:39.325770 PROGRESS: =========================================================================
8:11:39.335769 INFO: Target number of precursors reached.
8:11:39.564316 INFO: fragments_df: keeping 5000 of 407041 [sum(precursor_idx_mask)=188254 sum(mass_error_mask)=407041 stop_rank=5000
8:11:39.640318 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:11:45.844252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:11:52.287319 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:11:55.507057 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:11:55.512056 INFO: Using score_cutoff 58.553858959579465 (fac=0.99, q=1)
8:11:55.516056 INFO: Updating optimization_manager: fwhm_rt             : 2.623081684112549 -> 2.6164402961730957
8:11:55.520056 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:11:55.524058 INFO: Updating optimization_manager: score_cutoff        : 60.977206590270995 -> 58.553858959579465
8:11:55.528056 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:11:55.540057 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:11:55.578055 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:11:55.640056 INFO: === checking if optimization conditions were reached ===
8:11:55.644057 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
8:11:55.663057 INFO: Updating optimization_manager: rt_error            : 1663.6044921875 -> 96.61714519284743
8:11:55.667057 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 96.6171.
8:11:55.670061 INFO: ==============================================
8:11:55.674057 INFO: Starting optimization step 1.
8:11:55.678059 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:11:55.681058 INFO: Using classic extraction backend
8:11:55.685073 PROGRESS: Extracting batch of 15870 precursors
8:11:55.689071 INFO: === Search parameters used ===
8:11:55.692076 INFO: rt_error       : 96.61714519284743
8:11:55.696073 INFO: mobility_error : 0.1
8:11:55.699325 INFO: num_candidates : 3
8:11:55.703325 INFO: ms1_error      : 5.0
8:11:55.707324 INFO: ms2_error      : 10.0
8:11:55.711324 INFO: fwhm_rt        : 2.6164402961730957
8:11:55.715325 INFO: quant_window   : 3
8:11:55.718325 INFO: ==============================================
8:11:55.752325 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:11:55.753324 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:11:55.754325 INFO: FWHM in RT is 2.62 seconds, sigma is 0.29
8:11:55.754325 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:11:55.755324 INFO: Starting candidate selection
8:11:57.105292 INFO: Starting candidate scoring
8:11:58.698635 INFO: Finished candidate processing
8:11:58.699641 INFO: Collecting candidate features
8:11:59.041715 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 47592)
8:11:59.060714 INFO: Collecting fragment features
8:11:59.230266 INFO: Finished candidate scoring
8:11:59.291261 INFO: performing precursor FDR with 47 features
8:11:59.292261 INFO: Decoy channel: -1
8:11:59.293264 INFO: Competetive: True
8:11:59.392260 INFO: Setting torch num_threads to 2 for FDR classification task
8:11:59.434260 WARNING: dropped 2 decoy PSMs due to missing features
8:11:59.470798 INFO: Using random state 806454 for train-test-split
8:12:00.508417 INFO: Test AUC: 0.714
8:12:00.509415 INFO: Train AUC: 0.706
8:12:00.510418 INFO: AUC difference: 1.12%
8:12:01.072880 INFO: Resetting torch num_threads to 10
8:12:01.081882 PROGRESS: === Extracted 47592 precursors and 398819 fragments ===
8:12:01.088882 INFO: === FDR correction performed with classifier version 6 ===
8:12:01.099880 PROGRESS: ============================= Precursor FDR =============================
8:12:01.103883 PROGRESS: Total precursors accumulated: 7,476
8:12:01.108882 PROGRESS: Target precursors: 7,396 (98.93%)
8:12:01.112883 PROGRESS: Decoy precursors: 80 (1.07%)
8:12:01.119883 PROGRESS: 
8:12:01.126881 PROGRESS: Precursor Summary:
8:12:01.150884 PROGRESS: Channel   0:	 0.050 FDR: 7,396; 0.010 FDR: 7,351; 0.001 FDR: 6,641
8:12:01.159175 PROGRESS: 
8:12:01.167023 PROGRESS: Protein Summary:
8:12:01.206030 PROGRESS: Channel   0:	 0.050 FDR: 3,547; 0.010 FDR: 3,535; 0.001 FDR: 3,288
8:12:01.213156 PROGRESS: =========================================================================
8:12:01.234158 INFO: Target number of precursors reached.
8:12:01.465677 INFO: fragments_df: keeping 5000 of 398819 [sum(precursor_idx_mask)=197752 sum(mass_error_mask)=398819 stop_rank=5000
8:12:01.541076 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:12:07.887444 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:12:14.895391 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:12:18.513062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:12:18.520063 INFO: Using score_cutoff 54.90012325286865 (fac=0.99, q=1)
8:12:18.524063 INFO: Updating optimization_manager: fwhm_rt             : 2.6164402961730957 -> 2.63966703414917
8:12:18.529066 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:12:18.532067 INFO: Updating optimization_manager: score_cutoff        : 58.553858959579465 -> 54.90012325286865
8:12:18.536065 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:12:18.553069 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:12:18.609067 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:12:18.711070 INFO: === checking if optimization conditions were reached ===
8:12:18.717068 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
8:12:18.747617 INFO: Updating optimization_manager: rt_error            : 96.61714519284743 -> 23.49640225628115
8:12:18.751615 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 23.4964.
8:12:18.755613 INFO: ==============================================
8:12:18.759616 INFO: Starting optimization step 2.
8:12:18.762615 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:12:18.766616 INFO: Using classic extraction backend
8:12:18.770616 PROGRESS: Extracting batch of 15870 precursors
8:12:18.774618 INFO: === Search parameters used ===
8:12:18.778620 INFO: rt_error       : 23.49640225628115
8:12:18.782618 INFO: mobility_error : 0.1
8:12:18.785620 INFO: num_candidates : 3
8:12:18.789618 INFO: ms1_error      : 5.0
8:12:18.793619 INFO: ms2_error      : 10.0
8:12:18.797618 INFO: fwhm_rt        : 2.63966703414917
8:12:18.801617 INFO: quant_window   : 3
8:12:18.804614 INFO: ==============================================
8:12:18.862618 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:12:18.863616 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:12:18.864617 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
8:12:18.865620 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:12:18.867615 INFO: Starting candidate selection
8:12:19.573476 INFO: Starting candidate scoring
8:12:20.912122 INFO: Finished candidate processing
8:12:20.913128 INFO: Collecting candidate features
8:12:21.191683 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 43118)
8:12:21.229683 INFO: Collecting fragment features
8:12:21.356215 INFO: Finished candidate scoring
8:12:21.408221 INFO: performing precursor FDR with 47 features
8:12:21.409221 INFO: Decoy channel: -1
8:12:21.410221 INFO: Competetive: True
8:12:21.508849 INFO: Setting torch num_threads to 2 for FDR classification task
8:12:21.573845 WARNING: dropped 2 target PSMs due to missing features
8:12:21.574847 WARNING: dropped 3 decoy PSMs due to missing features
8:12:21.604847 INFO: Using random state 806454 for train-test-split
8:12:22.779284 INFO: Test AUC: 0.748
8:12:22.781284 INFO: Train AUC: 0.752
8:12:22.782284 INFO: AUC difference: 0.49%
8:12:23.447992 INFO: Resetting torch num_threads to 10
8:12:23.458995 PROGRESS: === Extracted 43118 precursors and 338621 fragments ===
8:12:23.464991 INFO: === FDR correction performed with classifier version 6 ===
8:12:23.478993 PROGRESS: ============================= Precursor FDR =============================
8:12:23.482990 PROGRESS: Total precursors accumulated: 7,553
8:12:23.486992 PROGRESS: Target precursors: 7,506 (99.38%)
8:12:23.491004 PROGRESS: Decoy precursors: 47 (0.62%)
8:12:23.495005 PROGRESS: 
8:12:23.498002 PROGRESS: Precursor Summary:
8:12:23.529214 PROGRESS: Channel   0:	 0.050 FDR: 7,506; 0.010 FDR: 7,506; 0.001 FDR: 6,792
8:12:23.533217 PROGRESS: 
8:12:23.537215 PROGRESS: Protein Summary:
8:12:23.574216 PROGRESS: Channel   0:	 0.050 FDR: 3,598; 0.010 FDR: 3,598; 0.001 FDR: 3,346
8:12:23.578217 PROGRESS: =========================================================================
8:12:23.590217 INFO: Target number of precursors reached.
8:12:23.834762 INFO: fragments_df: keeping 5000 of 338621 [sum(precursor_idx_mask)=174845 sum(mass_error_mask)=338621 stop_rank=5000
8:12:23.938761 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:12:31.044368 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:12:38.134964 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:12:41.654040 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:12:41.661041 INFO: Using score_cutoff 52.35699749565124 (fac=0.99, q=1)
8:12:41.667039 INFO: Updating optimization_manager: fwhm_rt             : 2.63966703414917 -> 2.640660285949707
8:12:41.671040 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:12:41.676045 INFO: Updating optimization_manager: score_cutoff        : 54.90012325286865 -> 52.35699749565124
8:12:41.680040 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:12:41.696040 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:12:41.740041 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:12:41.809585 INFO: === checking if optimization conditions were reached ===
8:12:41.813586 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
8:12:41.835588 INFO: Updating optimization_manager: rt_error            : 23.49640225628115 -> 11.385441934625426
8:12:41.839587 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 11.3854.
8:12:41.843588 INFO: ==============================================
8:12:41.846587 INFO: Starting optimization step 3.
8:12:41.849590 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:12:41.853590 INFO: Using classic extraction backend
8:12:41.856591 PROGRESS: Extracting batch of 15870 precursors
8:12:41.859587 INFO: === Search parameters used ===
8:12:41.863588 INFO: rt_error       : 11.385441934625426
8:12:41.866587 INFO: mobility_error : 0.1
8:12:41.869584 INFO: num_candidates : 3
8:12:41.872588 INFO: ms1_error      : 5.0
8:12:41.876589 INFO: ms2_error      : 10.0
8:12:41.880588 INFO: fwhm_rt        : 2.640660285949707
8:12:41.884589 INFO: quant_window   : 3
8:12:41.890591 INFO: ==============================================
8:12:41.935586 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:12:41.936584 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:12:41.937585 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
8:12:41.938588 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:12:41.939590 INFO: Starting candidate selection
8:12:42.520669 INFO: Starting candidate scoring
8:12:43.757962 INFO: Finished candidate processing
8:12:43.758968 INFO: Collecting candidate features
8:12:44.014516 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 43543)
8:12:44.033529 INFO: Collecting fragment features
8:12:44.154059 INFO: Finished candidate scoring
8:12:44.204061 INFO: performing precursor FDR with 47 features
8:12:44.205064 INFO: Decoy channel: -1
8:12:44.205064 INFO: Competetive: True
8:12:44.283075 INFO: Setting torch num_threads to 2 for FDR classification task
8:12:44.332611 WARNING: dropped 3 target PSMs due to missing features
8:12:44.333610 WARNING: dropped 6 decoy PSMs due to missing features
8:12:44.361611 INFO: Using random state 806454 for train-test-split
8:12:45.377831 INFO: Test AUC: 0.768
8:12:45.378831 INFO: Train AUC: 0.778
8:12:45.379832 INFO: AUC difference: 1.19%
8:12:45.941916 INFO: Resetting torch num_threads to 10
8:12:45.950915 PROGRESS: === Extracted 43543 precursors and 343264 fragments ===
8:12:45.955917 INFO: === FDR correction performed with classifier version 6 ===
8:12:45.965917 PROGRESS: ============================= Precursor FDR =============================
8:12:45.968914 PROGRESS: Total precursors accumulated: 7,536
8:12:45.971915 PROGRESS: Target precursors: 7,487 (99.35%)
8:12:45.975915 PROGRESS: Decoy precursors: 49 (0.65%)
8:12:45.978914 PROGRESS: 
8:12:45.981917 PROGRESS: Precursor Summary:
8:12:46.000916 PROGRESS: Channel   0:	 0.050 FDR: 7,487; 0.010 FDR: 7,487; 0.001 FDR: 7,207
8:12:46.003917 PROGRESS: 
8:12:46.006916 PROGRESS: Protein Summary:
8:12:46.027914 PROGRESS: Channel   0:	 0.050 FDR: 3,591; 0.010 FDR: 3,591; 0.001 FDR: 3,489
8:12:46.031918 PROGRESS: =========================================================================
8:12:46.038931 INFO: Target number of precursors reached.
8:12:46.247462 INFO: fragments_df: keeping 5000 of 343264 [sum(precursor_idx_mask)=178483 sum(mass_error_mask)=343264 stop_rank=5000
8:12:46.328007 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:12:53.397895 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:13:00.578500 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:13:04.174147 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:13:04.180146 INFO: Using score_cutoff 52.48929182739258 (fac=0.99, q=1)
8:13:04.185146 INFO: Updating optimization_manager: fwhm_rt             : 2.640660285949707 -> 2.6391382217407227
8:13:04.188145 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:13:04.191144 INFO: Updating optimization_manager: score_cutoff        : 52.35699749565124 -> 52.48929182739258
8:13:04.195143 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:13:04.208145 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:13:04.251145 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:13:04.324145 INFO: === checking if optimization conditions were reached ===
8:13:04.332159 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
8:13:04.357688 INFO: Updating optimization_manager: rt_error            : 11.385441934625426 -> 17.642603995999096
8:13:04.361687 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 17.6426.
8:13:04.365687 INFO: ==============================================
8:13:04.368687 INFO: Starting optimization step 4.
8:13:04.372692 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:13:04.375689 INFO: Using classic extraction backend
8:13:04.379687 PROGRESS: Extracting batch of 15870 precursors
8:13:04.382687 INFO: === Search parameters used ===
8:13:04.386688 INFO: rt_error       : 17.642603995999096
8:13:04.389687 INFO: mobility_error : 0.1
8:13:04.393689 INFO: num_candidates : 3
8:13:04.396687 INFO: ms1_error      : 5.0
8:13:04.400687 INFO: ms2_error      : 10.0
8:13:04.403690 INFO: fwhm_rt        : 2.6391382217407227
8:13:04.411689 INFO: quant_window   : 3
8:13:04.417689 INFO: ==============================================
8:13:04.477690 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:13:04.478689 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:13:04.479690 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
8:13:04.480689 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:13:04.482690 INFO: Starting candidate selection
8:13:05.138680 INFO: Starting candidate scoring
8:13:06.367387 INFO: Finished candidate processing
8:13:06.369394 INFO: Collecting candidate features
8:13:06.608942 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 43140)
8:13:06.626944 INFO: Collecting fragment features
8:13:06.732945 INFO: Finished candidate scoring
8:13:06.777945 INFO: performing precursor FDR with 47 features
8:13:06.778946 INFO: Decoy channel: -1
8:13:06.779943 INFO: Competetive: True
8:13:06.849481 INFO: Setting torch num_threads to 2 for FDR classification task
8:13:06.890479 WARNING: dropped 3 target PSMs due to missing features
8:13:06.891480 WARNING: dropped 5 decoy PSMs due to missing features
8:13:06.913479 INFO: Using random state 806454 for train-test-split
8:13:07.881223 INFO: Test AUC: 0.771
8:13:07.882224 INFO: Train AUC: 0.769
8:13:07.883224 INFO: AUC difference: 0.34%
8:13:08.547343 INFO: Resetting torch num_threads to 10
8:13:08.556339 PROGRESS: === Extracted 43140 precursors and 339156 fragments ===
8:13:08.560340 INFO: === FDR correction performed with classifier version 6 ===
8:13:08.571339 PROGRESS: ============================= Precursor FDR =============================
8:13:08.574338 PROGRESS: Total precursors accumulated: 7,567
8:13:08.577338 PROGRESS: Target precursors: 7,511 (99.26%)
8:13:08.581340 PROGRESS: Decoy precursors: 56 (0.74%)
8:13:08.584340 PROGRESS: 
8:13:08.587352 PROGRESS: Precursor Summary:
8:13:08.606944 PROGRESS: Channel   0:	 0.050 FDR: 7,511; 0.010 FDR: 7,511; 0.001 FDR: 7,026
8:13:08.610942 PROGRESS: 
8:13:08.613944 PROGRESS: Protein Summary:
8:13:08.636943 PROGRESS: Channel   0:	 0.050 FDR: 3,595; 0.010 FDR: 3,595; 0.001 FDR: 3,428
8:13:08.640948 PROGRESS: =========================================================================
8:13:08.648946 INFO: Target number of precursors reached.
8:13:08.857555 INFO: fragments_df: keeping 5000 of 339156 [sum(precursor_idx_mask)=175495 sum(mass_error_mask)=339156 stop_rank=5000
8:13:08.948551 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:13:15.582476 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:13:22.511105 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:13:26.135324 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:13:26.140324 INFO: Using score_cutoff 52.446873916625975 (fac=0.99, q=1)
8:13:26.145854 INFO: Updating optimization_manager: fwhm_rt             : 2.6391382217407227 -> 2.645129442214966
8:13:26.150852 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:13:26.153851 INFO: Updating optimization_manager: score_cutoff        : 52.48929182739258 -> 52.446873916625975
8:13:26.157848 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:13:26.172851 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:13:26.215851 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:13:26.283852 INFO: === checking if optimization conditions were reached ===
8:13:26.288852 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
8:13:26.310853 INFO: Updating optimization_manager: rt_error            : 17.642603995999096 -> 16.513851242410713
8:13:26.314850 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.5139.
8:13:26.318853 INFO: ==============================================
8:13:26.322855 INFO: Starting optimization step 5.
8:13:26.326854 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:13:26.330853 INFO: Using classic extraction backend
8:13:26.333853 PROGRESS: Extracting batch of 15870 precursors
8:13:26.337853 INFO: === Search parameters used ===
8:13:26.341853 INFO: rt_error       : 16.513851242410713
8:13:26.345853 INFO: mobility_error : 0.1
8:13:26.348849 INFO: num_candidates : 3
8:13:26.352851 INFO: ms1_error      : 5.0
8:13:26.356851 INFO: ms2_error      : 10.0
8:13:26.359850 INFO: fwhm_rt        : 2.645129442214966
8:13:26.363850 INFO: quant_window   : 3
8:13:26.367848 INFO: ==============================================
8:13:26.417365 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:13:26.418365 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:13:26.419365 INFO: FWHM in RT is 2.65 seconds, sigma is 0.29
8:13:26.421365 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:13:26.422365 INFO: Starting candidate selection
8:13:27.074340 INFO: Starting candidate scoring
8:13:28.333489 INFO: Finished candidate processing
8:13:28.334493 INFO: Collecting candidate features
8:13:28.561010 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 43222)
8:13:28.580010 INFO: Collecting fragment features
8:13:28.706531 INFO: Finished candidate scoring
8:13:28.751530 INFO: performing precursor FDR with 47 features
8:13:28.752531 INFO: Decoy channel: -1
8:13:28.753531 INFO: Competetive: True
8:13:28.813531 INFO: Setting torch num_threads to 2 for FDR classification task
8:13:28.853531 WARNING: dropped 3 target PSMs due to missing features
8:13:28.854532 WARNING: dropped 6 decoy PSMs due to missing features
8:13:28.878532 INFO: Using random state 806454 for train-test-split
8:13:29.869155 INFO: Test AUC: 0.768
8:13:29.870155 INFO: Train AUC: 0.773
8:13:29.871156 INFO: AUC difference: 0.53%
8:13:30.583761 INFO: Resetting torch num_threads to 10
8:13:30.592762 PROGRESS: === Extracted 43222 precursors and 339983 fragments ===
8:13:30.597765 INFO: === FDR correction performed with classifier version 6 ===
8:13:30.608763 PROGRESS: ============================= Precursor FDR =============================
8:13:30.611765 PROGRESS: Total precursors accumulated: 7,536
8:13:30.615769 PROGRESS: Target precursors: 7,481 (99.27%)
8:13:30.618766 PROGRESS: Decoy precursors: 55 (0.73%)
8:13:30.622767 PROGRESS: 
8:13:30.625768 PROGRESS: Precursor Summary:
8:13:30.645780 PROGRESS: Channel   0:	 0.050 FDR: 7,481; 0.010 FDR: 7,481; 0.001 FDR: 7,143
8:13:30.649784 PROGRESS: 
8:13:30.652916 PROGRESS: Protein Summary:
8:13:30.676914 PROGRESS: Channel   0:	 0.050 FDR: 3,587; 0.010 FDR: 3,587; 0.001 FDR: 3,467
8:13:30.680917 PROGRESS: =========================================================================
8:13:30.688916 INFO: Target number of precursors reached.
8:13:30.896934 INFO: fragments_df: keeping 5000 of 339983 [sum(precursor_idx_mask)=174952 sum(mass_error_mask)=339983 stop_rank=5000
8:13:30.994308 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:13:38.123583 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:13:45.069727 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:13:51.343148 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:13:51.350146 INFO: Using score_cutoff 52.35001371002197 (fac=0.99, q=1)
8:13:51.355147 INFO: Updating optimization_manager: fwhm_rt             : 2.645129442214966 -> 2.6402244567871094
8:13:51.359146 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:13:51.362147 INFO: Updating optimization_manager: score_cutoff        : 52.446873916625975 -> 52.35001371002197
8:13:51.366147 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:13:51.384153 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:13:51.463669 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:13:51.564670 INFO: === checking if optimization conditions were reached ===
8:13:51.574668 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
8:13:51.609670 INFO: Updating optimization_manager: rt_error            : 16.513851242410713 -> 17.182518105278707
8:13:51.618669 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.1825.
8:13:51.629669 INFO: ==============================================
8:13:51.640670 INFO: Starting optimization step 6.
8:13:51.662670 PROGRESS: === Extracting elution groups 0 to 8000 ===
8:13:51.673671 INFO: Using classic extraction backend
8:13:51.683688 PROGRESS: Extracting batch of 15870 precursors
8:13:51.695219 INFO: === Search parameters used ===
8:13:51.706221 INFO: rt_error       : 17.182518105278707
8:13:51.717219 INFO: mobility_error : 0.1
8:13:51.725219 INFO: num_candidates : 3
8:13:51.734219 INFO: ms1_error      : 5.0
8:13:51.743221 INFO: ms2_error      : 10.0
8:13:51.751220 INFO: fwhm_rt        : 2.6402244567871094
8:13:51.762219 INFO: quant_window   : 3
8:13:51.771219 INFO: ==============================================
8:13:51.841219 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:13:51.842217 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:13:51.843220 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
8:13:51.844220 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:13:51.845220 INFO: Starting candidate selection
8:13:52.511142 INFO: Starting candidate scoring
8:13:53.765011 INFO: Finished candidate processing
8:13:53.766015 INFO: Collecting candidate features
8:13:53.998414 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 43186)
8:13:54.014414 INFO: Collecting fragment features
8:13:54.112413 INFO: Finished candidate scoring
8:13:54.155413 INFO: performing precursor FDR with 47 features
8:13:54.156411 INFO: Decoy channel: -1
8:13:54.157413 INFO: Competetive: True
8:13:54.227528 INFO: Setting torch num_threads to 2 for FDR classification task
8:13:54.269528 WARNING: dropped 2 target PSMs due to missing features
8:13:54.270528 WARNING: dropped 5 decoy PSMs due to missing features
8:13:54.292528 INFO: Using random state 806454 for train-test-split
8:13:55.171381 INFO: Test AUC: 0.765
8:13:55.173382 INFO: Train AUC: 0.770
8:13:55.174381 INFO: AUC difference: 0.60%
8:13:55.729326 INFO: Resetting torch num_threads to 10
8:13:55.739325 PROGRESS: === Extracted 43186 precursors and 339614 fragments ===
8:13:55.747910 INFO: === FDR correction performed with classifier version 6 ===
8:13:55.758901 PROGRESS: ============================= Precursor FDR =============================
8:13:55.764330 PROGRESS: Total precursors accumulated: 7,553
8:13:55.769186 PROGRESS: Target precursors: 7,503 (99.34%)
8:13:55.774184 PROGRESS: Decoy precursors: 50 (0.66%)
8:13:55.779186 PROGRESS: 
8:13:55.783185 PROGRESS: Precursor Summary:
8:13:55.803186 PROGRESS: Channel   0:	 0.050 FDR: 7,503; 0.010 FDR: 7,503; 0.001 FDR: 7,211
8:13:55.807092 PROGRESS: 
8:13:55.812094 PROGRESS: Protein Summary:
8:13:55.836093 PROGRESS: Channel   0:	 0.050 FDR: 3,597; 0.010 FDR: 3,597; 0.001 FDR: 3,486
8:13:55.843096 PROGRESS: =========================================================================
8:13:55.858095 INFO: Target number of precursors reached.
8:13:56.061014 INFO: fragments_df: keeping 5000 of 339614 [sum(precursor_idx_mask)=175343 sum(mass_error_mask)=339614 stop_rank=5000
8:13:56.153754 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
8:14:02.669274 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
8:14:09.703103 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
8:14:13.305861 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
8:14:13.311862 INFO: Using score_cutoff 52.49899287872314 (fac=0.99, q=1)
8:14:13.315862 INFO: Updating optimization_manager: fwhm_rt             : 2.6402244567871094 -> 2.63966703414917
8:14:13.319865 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:14:13.323864 INFO: Updating optimization_manager: score_cutoff        : 52.35001371002197 -> 52.49899287872314
8:14:13.327864 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:14:13.343862 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:14:13.400865 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:14:13.474895 INFO: === checking if optimization conditions were reached ===
8:14:13.478900 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
8:14:13.484898 INFO: Updating optimization_manager: rt_error            : 17.182518105278707 -> 11.385441934625426
8:14:13.487896 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
8:14:13.492436 INFO: Updating optimization_manager: score_cutoff        : 52.49899287872314 -> 52.48929182739258
8:14:13.496427 INFO: Updating optimization_manager: fwhm_rt             : 2.63966703414917 -> 2.6391382217407227
8:14:13.499426 INFO: Updating optimization_manager: fwhm_mobility       : 0.0 -> 0.0
8:14:13.503425 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 11.3854 found after 7 searches.
8:14:13.507425 INFO: ==============================================
8:14:13.510425 PROGRESS: Optimization finished for rt_error.
8:14:13.599431 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:14:13.616434 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:14:13.671432 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:14:13.826986 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
8:14:13.835989 PROGRESS: ==============================================
8:14:13.843990 PROGRESS: ms2_error      : 10.0000
8:14:13.852988 PROGRESS: ms1_error      : 5.0000
8:14:13.857997 PROGRESS: rt_error       : 11.3854
8:14:13.866989 PROGRESS: ==============================================
8:14:13.899993 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
8:14:14.052560 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
8:14:14.278169 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
8:14:14.751430 INFO: Using classic extraction backend
8:14:14.756431 PROGRESS: Extracting batch of 121155 precursors
8:14:14.760431 INFO: === Search parameters used ===
8:14:14.763430 INFO: rt_error       : 11.385441934625426
8:14:14.767429 INFO: mobility_error : 0.1
8:14:14.771431 INFO: num_candidates : 3
8:14:14.774430 INFO: ms1_error      : 5.0
8:14:14.778434 INFO: ms2_error      : 10.0
8:14:14.782429 INFO: fwhm_rt        : 2.6391382217407227
8:14:14.785430 INFO: quant_window   : 3
8:14:14.789432 INFO: ==============================================
8:14:14.883435 INFO: Duty cycle consists of 86 frames, 1.90 seconds cycle time
8:14:14.884432 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
8:14:14.885431 INFO: FWHM in RT is 2.64 seconds, sigma is 0.29
8:14:14.886432 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
8:14:14.887433 INFO: Starting candidate selection
8:14:18.981868 INFO: Removed 128710 precursors with score below cutoff 52.48929182739258
8:14:19.130392 INFO: Starting candidate scoring
8:14:25.069339 INFO: Finished candidate processing
8:14:25.071355 INFO: Collecting candidate features
8:14:25.948964 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 204150)
8:14:26.010499 INFO: Collecting fragment features
8:14:26.416067 INFO: Finished candidate scoring
8:14:26.611700 INFO: === Performing FDR correction with classifier version 10 ===
8:14:26.618701 INFO: performing precursor FDR with 47 features
8:14:26.619699 INFO: Decoy channel: -1
8:14:26.620702 INFO: Competetive: True
8:14:26.925312 INFO: Setting torch num_threads to 2 for FDR classification task
8:14:27.021924 WARNING: dropped 1 decoy PSMs due to missing features
8:14:27.022924 WARNING: FDR calculation for 117435 target and 86714 decoy PSMs
8:14:27.023924 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
8:14:27.241943 INFO: Using random state 95389 for train-test-split
8:14:33.467772 INFO: Test AUC: 0.846
8:14:33.468772 INFO: Train AUC: 0.848
8:14:33.469772 INFO: AUC difference: 0.26%
8:14:34.436915 INFO: Resetting torch num_threads to 10
8:14:34.496918 INFO: Removing fragments below FDR threshold
8:14:34.750453 PROGRESS: ============================= Precursor FDR =============================
8:14:34.755452 PROGRESS: Total precursors accumulated: 57,037
8:14:34.759466 PROGRESS: Target precursors: 56,648 (99.32%)
8:14:34.763466 PROGRESS: Decoy precursors: 389 (0.68%)
8:14:34.767465 PROGRESS: 
8:14:34.771466 PROGRESS: Precursor Summary:
8:14:34.936990 PROGRESS: Channel   0:	 0.050 FDR: 56,648; 0.010 FDR: 56,648; 0.001 FDR: 55,495
8:14:34.940994 PROGRESS: 
8:14:34.944994 PROGRESS: Protein Summary:
8:14:35.150528 PROGRESS: Channel   0:	 0.050 FDR: 6,484; 0.010 FDR: 6,484; 0.001 FDR: 6,463
8:14:35.154529 PROGRESS: =========================================================================
8:14:35.180527 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\psm.parquet
8:14:36.334217 INFO: Saving results to Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\frag.parquet
8:14:37.553956 INFO: Finished workflow for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
8:14:39.951234 PROGRESS: Processing search outputs
8:14:39.952235 PROGRESS: Performing protein grouping and FDR
8:14:39.953236 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
8:14:40.297294 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
8:14:40.660823 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
8:14:41.024437 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
8:14:41.399501 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
8:14:41.756076 INFO: Building output for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
8:14:42.115219 INFO: Building combined output
8:14:42.193217 INFO: Performing protein inference
8:14:43.026951 INFO: Inference strategy: library. Using library grouping for protein inference
8:14:43.032952 INFO: Performing protein FDR
8:14:50.681458 INFO: Normalizing q-values using 6,542 targets and 1,494 decoys
8:14:50.687458 INFO: Test AUC: 1.000
8:14:50.688458 INFO: Train AUC: 0.999
8:14:50.689458 INFO: AUC difference: 0.05%
8:14:52.328118 PROGRESS: ================ Protein FDR =================
8:14:52.329119 PROGRESS: Unique protein groups in output
8:14:52.330119 PROGRESS:   1% protein FDR: 6,540
8:14:52.330119 PROGRESS: 
8:14:52.331119 PROGRESS: Unique precursor in output
8:14:52.332118 PROGRESS:   1% protein FDR: 61,004
8:14:52.333119 PROGRESS: ================================================
8:14:52.503120 PROGRESS: Building search statistics
8:14:52.809649 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\optimization_manager.pkl
8:14:52.817164 INFO: Initializing OptimizationManager
8:14:52.846164 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\calibration_manager.pkl
8:14:52.850164 INFO: Initializing CalibrationManager
8:14:52.880164 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\raw_file_manager.pkl
8:14:52.886164 INFO: Initializing RawFileManager
8:14:53.023166 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\optimization_manager.pkl
8:14:53.030166 INFO: Initializing OptimizationManager
8:14:53.059172 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\calibration_manager.pkl
8:14:53.065688 INFO: Initializing CalibrationManager
8:14:53.113688 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\raw_file_manager.pkl
8:14:53.121688 INFO: Initializing RawFileManager
8:14:53.268691 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\optimization_manager.pkl
8:14:53.275690 INFO: Initializing OptimizationManager
8:14:53.321211 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\calibration_manager.pkl
8:14:53.327211 INFO: Initializing CalibrationManager
8:14:53.380211 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\raw_file_manager.pkl
8:14:53.389211 INFO: Initializing RawFileManager
8:14:53.532212 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\optimization_manager.pkl
8:14:53.538213 INFO: Initializing OptimizationManager
8:14:53.566740 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\calibration_manager.pkl
8:14:53.572740 INFO: Initializing CalibrationManager
8:14:53.603740 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\raw_file_manager.pkl
8:14:53.609742 INFO: Initializing RawFileManager
8:14:53.752741 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\optimization_manager.pkl
8:14:53.759743 INFO: Initializing OptimizationManager
8:14:53.790743 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\calibration_manager.pkl
8:14:53.796742 INFO: Initializing CalibrationManager
8:14:53.842263 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\raw_file_manager.pkl
8:14:53.852264 INFO: Initializing RawFileManager
8:14:53.999267 INFO: Loaded OptimizationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\optimization_manager.pkl
8:14:54.005265 INFO: Initializing OptimizationManager
8:14:54.035266 INFO: Loaded CalibrationManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\calibration_manager.pkl
8:14:54.041266 INFO: Initializing CalibrationManager
8:14:54.087787 INFO: Loaded RawFileManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\raw_file_manager.pkl
8:14:54.092787 INFO: Initializing RawFileManager
8:14:54.118786 INFO: Writing stat output to disk
8:14:54.119806 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\stat.tsv to disk
8:14:54.164788 PROGRESS: Building internal statistics
8:14:54.200788 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3\timing_manager.pkl
8:14:54.201802 INFO: Initializing TimingManager
8:14:54.224788 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2\timing_manager.pkl
8:14:54.225789 INFO: Initializing TimingManager
8:14:54.265789 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1\timing_manager.pkl
8:14:54.266789 INFO: Initializing TimingManager
8:14:54.288789 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3\timing_manager.pkl
8:14:54.289789 INFO: Initializing TimingManager
8:14:54.311797 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2\timing_manager.pkl
8:14:54.312797 INFO: Initializing TimingManager
8:14:54.333311 INFO: Loaded TimingManager from Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\quant\LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1\timing_manager.pkl
8:14:54.334311 INFO: Initializing TimingManager
8:14:54.336311 INFO: Writing internal output to disk
8:14:54.336311 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\internal.tsv to disk
8:14:54.343312 PROGRESS: Performing label free quantification
8:14:54.551312 INFO: Accumulating fragment data
8:14:54.554319 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP3
8:14:55.073879 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP2
8:14:57.040574 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_B_REP1
8:14:58.732221 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP3
8:15:00.460877 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP2
8:15:02.284553 INFO: reading frag file for LFQ_ZenoTOF8600_ZenoSWATH_85VW_15min_Nano_50ng_Condition_A_REP1
8:15:04.420253 PROGRESS: Performing label free quantification on the precursor level
8:15:04.421252 INFO: Filtering fragments by quality
8:15:04.846296 INFO: Performing label-free quantification using directLFQ
8:15:05.518342 INFO: 61004 lfq-groups total
8:15:30.303657 INFO: using 10 processes
8:17:05.528560 INFO: Writing precursor output to disk
8:17:05.529559 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\precursor.matrix.tsv to disk
8:17:07.163523 PROGRESS: Performing label free quantification on the peptide level
8:17:07.164526 INFO: Filtering fragments by quality
8:17:07.753651 INFO: Performing label-free quantification using directLFQ
8:17:08.356784 INFO: 53237 lfq-groups total
8:17:27.434051 INFO: using 10 processes
8:18:48.154579 INFO: Writing peptide output to disk
8:18:48.155580 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\peptide.matrix.tsv to disk
8:18:49.359190 PROGRESS: Performing label free quantification on the pg level
8:18:49.360190 INFO: Filtering fragments by quality
8:18:49.770711 INFO: Performing label-free quantification using directLFQ
8:18:50.221752 INFO: 6540 lfq-groups total
8:18:52.794013 INFO: using 10 processes
8:19:17.996421 INFO: Writing pg output to disk
8:19:17.997421 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\pg.matrix.tsv to disk
8:19:18.476466 INFO: Writing psm output to disk
8:19:18.477472 INFO: Saving Q:\ACTIVE\2024\LFQbenchmark_2ndgeneration\DATA_ANALYSIS\AlphaDIA\precursors.tsv to disk
8:20:33.481075 PROGRESS: Building MBR spectral library
8:20:33.668599 INFO: Running MbrLibraryBuilder
8:20:34.193661 INFO: MBR spectral library contains 61,004 precursors, 6,540 proteins
8:20:34.195658 INFO: Writing MBR spectral library to disk
8:20:53.134005 PROGRESS: =================== Search Finished ===================
