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0:00:00.000283 PROGRESS: 
0:00:00.000318 PROGRESS: version: 1.7.0
0:00:00.000355 PROGRESS: hostname: fwooper
0:00:00.000411 PROGRESS: date: 2024-09-03 10:26:35
0:00:00.000448 PROGRESS: =================== Environment ===================
0:00:00.000484 PROGRESS: alphatims       : 1.0.8
0:00:00.000516 PROGRESS: alpharaw        : 0.4.5
0:00:00.000548 PROGRESS: alphabase       : 1.2.5
0:00:00.000580 PROGRESS: alphapeptdeep   : 1.2.1
0:00:00.000612 PROGRESS: directlfq       : 0.2.19
0:00:00.000643 PROGRESS: ===================================================
0:00:00.000688 INFO: loading default config from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/default.yaml
0:00:00.017889 INFO: ├──version: 1 
0:00:00.017973 INFO: ├──general
0:00:00.018021 INFO: │   ├──thread_count: 10 
0:00:00.018060 INFO: │   ├──[32;20mthread_count: 80 (user defined)[0m
0:00:00.018101 INFO: │   ├──reuse_calibration: False 
0:00:00.018141 INFO: │   ├──reuse_quant: False 
0:00:00.018179 INFO: │   ├──astral_ms1: False 
0:00:00.018218 INFO: │   ├──log_level: INFO 
0:00:00.018257 INFO: │   ├──wsl: False 
0:00:00.018295 INFO: │   ├──mmap_detector_events: False 
0:00:00.018333 INFO: │   └──use_gpu: True 
0:00:00.018368 INFO: ├──library_loading
0:00:00.018409 INFO: │   └──rt_heuristic: 180 
0:00:00.018445 INFO: ├──library_prediction
0:00:00.018485 INFO: │   ├──predict: False 
0:00:00.018521 INFO: │   ├──[32;20mpredict: True (user defined)[0m
0:00:00.018559 INFO: │   ├──enzyme: trypsin 
0:00:00.018597 INFO: │   ├──fixed_modifications: Carbamidomethyl@C 
0:00:00.018635 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein N-term 
0:00:00.018673 INFO: │   ├──max_var_mod_num: 2 
0:00:00.018708 INFO: │   ├──[32;20mmax_var_mod_num: 1 (user defined)[0m
0:00:00.018746 INFO: │   ├──missed_cleavages: 1 
0:00:00.018783 INFO: │   ├──precursor_len
0:00:00.018822 INFO: │   │   ├──7 
0:00:00.018858 INFO: │   │   ├──[32;20m6 (user defined)[0m
0:00:00.018896 INFO: │   │   └──35 
0:00:00.018931 INFO: │   │   └──[32;20m40 (user defined)[0m
0:00:00.018968 INFO: │   ├──precursor_charge
0:00:00.019007 INFO: │   │   ├──2 
0:00:00.019042 INFO: │   │   ├──[32;20m1 (user defined)[0m
0:00:00.019079 INFO: │   │   └──4 
0:00:00.019115 INFO: │   ├──precursor_mz
0:00:00.019154 INFO: │   │   ├──400 
0:00:00.019193 INFO: │   │   └──1200 
0:00:00.019230 INFO: │   │   └──[32;20m1000 (user defined)[0m
0:00:00.019266 INFO: │   ├──fragment_mz
0:00:00.019305 INFO: │   │   ├──200 
0:00:00.019341 INFO: │   │   ├──[32;20m50 (user defined)[0m
0:00:00.019378 INFO: │   │   └──2000 
0:00:00.019419 INFO: │   ├──nce: 25.0 
0:00:00.019457 INFO: │   ├──fragment_types: b;y 
0:00:00.019501 INFO: │   ├──max_fragment_charge: 2 
0:00:00.019539 INFO: │   ├──instrument: Lumos 
0:00:00.019573 INFO: │   ├──[32;20minstrument: QEHFX (user defined)[0m
0:00:00.019610 INFO: │   └──checkpoint_folder_path: None 
0:00:00.019647 INFO: ├──search
0:00:00.019686 INFO: │   ├──channel_filter: 0 
0:00:00.019721 INFO: │   ├──[32;20mchannel_filter:  (user defined)[0m
0:00:00.019759 INFO: │   ├──exclude_shared_ions: True 
0:00:00.019798 INFO: │   ├──compete_for_fragments: True 
0:00:00.019835 INFO: │   ├──target_num_candidates: 2 
0:00:00.019872 INFO: │   ├──target_ms1_tolerance: 15 
0:00:00.019907 INFO: │   ├──[32;20mtarget_ms1_tolerance: 5 (user defined)[0m
0:00:00.019953 INFO: │   ├──target_ms2_tolerance: 15 
0:00:00.019990 INFO: │   ├──[32;20mtarget_ms2_tolerance: 10 (user defined)[0m
0:00:00.020030 INFO: │   ├──target_mobility_tolerance: 0.04 
0:00:00.020069 INFO: │   ├──target_rt_tolerance: 60 
0:00:00.020104 INFO: │   ├──[32;20mtarget_rt_tolerance: 300 (user defined)[0m
0:00:00.020142 INFO: │   ├──quant_window: 3 
0:00:00.020180 INFO: │   └──quant_all: True 
0:00:00.020217 INFO: ├──search_advanced
0:00:00.020256 INFO: │   └──top_k_fragments: 12 
0:00:00.020292 INFO: ├──calibration
0:00:00.020331 INFO: │   ├──min_epochs: 3 
0:00:00.020369 INFO: │   ├──batch_size: 8000 
0:00:00.020407 INFO: │   ├──recalibration_target: 200 
0:00:00.020444 INFO: │   ├──max_epochs: 20 
0:00:00.020482 INFO: │   ├──final_full_calibration: False 
0:00:00.020518 INFO: │   └──norm_rt_mode: linear 
0:00:00.020554 INFO: ├──search_initial
0:00:00.020592 INFO: │   ├──initial_num_candidates: 1 
0:00:00.020628 INFO: │   ├──[32;20minitial_num_candidates: 2 (user defined)[0m
0:00:00.020666 INFO: │   ├──initial_ms1_tolerance: 30 
0:00:00.020701 INFO: │   ├──[32;20minitial_ms1_tolerance: 20 (user defined)[0m
0:00:00.020738 INFO: │   ├──initial_ms2_tolerance: 30 
0:00:00.020772 INFO: │   ├──[32;20minitial_ms2_tolerance: 20 (user defined)[0m
0:00:00.020811 INFO: │   ├──initial_mobility_tolerance: 0.08 
0:00:00.020850 INFO: │   └──initial_rt_tolerance: 240 
0:00:00.020886 INFO: │   └──[32;20minitial_rt_tolerance: 500 (user defined)[0m
0:00:00.020922 INFO: ├──selection_config
0:00:00.020962 INFO: │   ├──peak_len_rt: 10.0 
0:00:00.021002 INFO: │   ├──sigma_scale_rt: 0.5 
0:00:00.021039 INFO: │   ├──peak_len_mobility: 0.01 
0:00:00.021077 INFO: │   ├──sigma_scale_mobility: 1.0 
0:00:00.021114 INFO: │   ├──top_k_precursors: 3 
0:00:00.021152 INFO: │   ├──kernel_size: 30 
0:00:00.021189 INFO: │   ├──f_mobility: 1.0 
0:00:00.021227 INFO: │   ├──f_rt: 0.99 
0:00:00.021264 INFO: │   ├──center_fraction: 0.5 
0:00:00.021300 INFO: │   ├──min_size_mobility: 8 
0:00:00.021336 INFO: │   ├──min_size_rt: 3 
0:00:00.021372 INFO: │   ├──max_size_mobility: 20 
0:00:00.021409 INFO: │   ├──max_size_rt: 15 
0:00:00.021445 INFO: │   ├──group_channels: False 
0:00:00.021482 INFO: │   ├──use_weighted_score: True 
0:00:00.021519 INFO: │   ├──join_close_candidates: False 
0:00:00.021556 INFO: │   ├──join_close_candidates_scan_threshold: 0.6 
0:00:00.021594 INFO: │   └──join_close_candidates_cycle_threshold: 0.6 
0:00:00.021631 INFO: ├──scoring_config
0:00:00.021669 INFO: │   ├──score_grouped: False 
0:00:00.021707 INFO: │   ├──top_k_isotopes: 3 
0:00:00.021744 INFO: │   ├──reference_channel: -1 
0:00:00.021780 INFO: │   ├──precursor_mz_tolerance: 10 
0:00:00.021818 INFO: │   └──fragment_mz_tolerance: 15 
0:00:00.021853 INFO: ├──multiplexing
0:00:00.021892 INFO: │   ├──enabled: False 
0:00:00.021929 INFO: │   ├──target_channels: 4,8 
0:00:00.021967 INFO: │   ├──decoy_channel: 12 
0:00:00.022005 INFO: │   ├──reference_channel: 0 
0:00:00.022043 INFO: │   └──competetive_scoring: True 
0:00:00.022079 INFO: ├──fdr
0:00:00.022118 INFO: │   ├──fdr: 0.01 
0:00:00.022156 INFO: │   ├──group_level: proteins 
0:00:00.022195 INFO: │   ├──competetive_scoring: True 
0:00:00.022232 INFO: │   ├──keep_decoys: False 
0:00:00.022269 INFO: │   ├──channel_wise_fdr: False 
0:00:00.022307 INFO: │   └──inference_strategy: heuristic 
0:00:00.022343 INFO: ├──search_output
0:00:00.022382 INFO: │   ├──peptide_level_lfq: False 
0:00:00.022420 INFO: │   ├──precursor_level_lfq: False 
0:00:00.022462 INFO: │   ├──min_k_fragments: 12 
0:00:00.022501 INFO: │   ├──min_correlation: 0.9 
0:00:00.022540 INFO: │   ├──num_samples_quadratic: 50 
0:00:00.022578 INFO: │   ├──min_nonnan: 3 
0:00:00.022615 INFO: │   ├──normalize_lfq: True 
0:00:00.022653 INFO: │   └──file_format: tsv 
0:00:00.022688 INFO: ├──optimization_manager
0:00:00.022727 INFO: │   ├──fwhm_rt: 5 
0:00:00.022765 INFO: │   ├──fwhm_mobility: 0.01 
0:00:00.022801 INFO: │   └──score_cutoff: 0 
0:00:00.022837 INFO: ├──transfer_library
0:00:00.022876 INFO: │   ├──enabled: False 
0:00:00.022915 INFO: │   ├──fragment_types: b;y 
0:00:00.022952 INFO: │   ├──max_charge: 2 
0:00:00.022990 INFO: │   ├──top_k_samples: 3 
0:00:00.023027 INFO: │   ├──norm_delta_max: True 
0:00:00.023065 INFO: │   ├──precursor_correlation_cutoff: 0.5 
0:00:00.023104 INFO: │   └──fragment_correlation_ratio: 0.75 
0:00:00.023140 INFO: ├──transfer_learning
0:00:00.023178 INFO: │   ├──enabled: False 
0:00:00.023216 INFO: │   ├──batch_size: 2000 
0:00:00.023255 INFO: │   ├──max_lr: 0.0001 
0:00:00.023293 INFO: │   ├──train_ratio: 0.8 
0:00:00.023332 INFO: │   ├──test_interval: 1 
0:00:00.023370 INFO: │   ├──lr_patience: 3 
0:00:00.023408 INFO: │   ├──epochs: 51 
0:00:00.023447 INFO: │   ├──warmup_epochs: 5 
0:00:00.023491 INFO: │   ├──nce: 25 
0:00:00.023530 INFO: │   └──instrument: Lumos 
0:00:00.023564 INFO: │   └──[32;20minstrument: QEHFX (user defined)[0m
0:00:00.023600 INFO: └──calibration_manager
0:00:00.023636 INFO:     ├──0
0:00:00.023675 INFO:     │   ├──name: fragment 
0:00:00.023712 INFO:     │   └──estimators
0:00:00.023749 INFO:     │       └──0
0:00:00.023788 INFO:     │           ├──name: mz 
0:00:00.023827 INFO:     │           ├──model: LOESSRegression 
0:00:00.023863 INFO:     │           ├──model_args
0:00:00.023902 INFO:     │           │   └──n_kernels: 2 
0:00:00.023939 INFO:     │           ├──input_columns
0:00:00.023978 INFO:     │           │   └──mz_library 
0:00:00.024016 INFO:     │           ├──target_columns
0:00:00.024053 INFO:     │           │   └──mz_observed 
0:00:00.024089 INFO:     │           ├──output_columns
0:00:00.024127 INFO:     │           │   └──mz_calibrated 
0:00:00.024164 INFO:     │           └──transform_deviation: 1e6 
0:00:00.024201 INFO:     └──1
0:00:00.024239 INFO:         ├──name: precursor 
0:00:00.024276 INFO:         └──estimators
0:00:00.024311 INFO:             ├──0
0:00:00.024349 INFO:             │   ├──name: mz 
0:00:00.024388 INFO:             │   ├──model: LOESSRegression 
0:00:00.024423 INFO:             │   ├──model_args
0:00:00.024461 INFO:             │   │   └──n_kernels: 2 
0:00:00.024497 INFO:             │   ├──input_columns
0:00:00.024535 INFO:             │   │   └──mz_library 
0:00:00.024572 INFO:             │   ├──target_columns
0:00:00.024610 INFO:             │   │   └──mz_observed 
0:00:00.024646 INFO:             │   ├──output_columns
0:00:00.024684 INFO:             │   │   └──mz_calibrated 
0:00:00.024721 INFO:             │   └──transform_deviation: 1e6 
0:00:00.024758 INFO:             ├──1
0:00:00.024796 INFO:             │   ├──name: rt 
0:00:00.024835 INFO:             │   ├──model: LOESSRegression 
0:00:00.024871 INFO:             │   ├──model_args
0:00:00.024909 INFO:             │   │   └──n_kernels: 6 
0:00:00.024945 INFO:             │   ├──input_columns
0:00:00.024983 INFO:             │   │   └──rt_library 
0:00:00.025018 INFO:             │   ├──target_columns
0:00:00.025055 INFO:             │   │   └──rt_observed 
0:00:00.025092 INFO:             │   └──output_columns
0:00:00.025132 INFO:             │       └──rt_calibrated 
0:00:00.025168 INFO:             └──2
0:00:00.025206 INFO:                 ├──name: mobility 
0:00:00.025244 INFO:                 ├──model: LOESSRegression 
0:00:00.025280 INFO:                 ├──model_args
0:00:00.025319 INFO:                 │   └──n_kernels: 2 
0:00:00.025356 INFO:                 ├──input_columns
0:00:00.025394 INFO:                 │   └──mobility_library 
0:00:00.025432 INFO:                 ├──target_columns
0:00:00.025469 INFO:                 │   └──mobility_observed 
0:00:00.025505 INFO:                 └──output_columns
0:00:00.025543 INFO:                     └──mobility_calibrated 
0:00:00.026165 PROGRESS: No library provided. Building library from fasta files.
0:00:00.026214 INFO: Running FastaDigest
0:00:01.481874 INFO: Digesting fasta file
0:00:09.850321 INFO: Adding modifications
0:02:53.862049 INFO: Removing non-canonical amino acids
0:03:01.220795 INFO: Fasta library contains 5,414,253 precursors
0:03:01.220992 PROGRESS: Predicting library properties.
0:03:01.221069 INFO: Running PeptDeepPrediction
0:03:01.221224 INFO: Device set to gpu
0:03:02.480838 INFO: Loading PeptDeep models from None
0:03:02.480974 INFO: Using external ms2 model: 'None/ms2.pth'
0:03:02.481035 INFO:  -- This model file does not exist
0:03:02.481080 INFO: Using external rt model: 'None/rt.pth'
0:03:02.481118 INFO:  -- This model file does not exist
0:03:02.481156 INFO: Using external ccs model: 'None/ccs.pth'
0:03:02.481194 INFO:  -- This model file does not exist
0:03:02.481233 INFO: Predicting RT, MS2 and mobility
0:03:02.495351 INFO: Predicting RT ...
0:03:56.667110 INFO: Predicting mobility ...
0:05:32.277177 INFO: Predicting MS2 ...
0:07:47.015988 INFO: Adding fragment mz information
0:07:47.542019 INFO: Adding fragment intensity information
0:07:48.067741 INFO: Adding precursor information
0:07:48.072914 INFO: Running PrecursorInitializer
0:07:48.114375 INFO: Running AnnotateFasta
0:07:48.421266 INFO: Dropping decoys from input library before annotation
0:08:16.329021 INFO: Running IsotopeGenerator
0:08:48.127260 INFO: Running RTNormalization
0:08:48.128044 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:08:48.128150 INFO: Saving library to /home/robbe/alphadia/Proteobench/speclib.hdf
0:09:18.009338 INFO: Running DecoyGenerator
0:11:35.277138 INFO: Running FlattenLibrary
0:12:12.699368 INFO: Running InitFlatColumns
0:12:13.204395 INFO: Running LogFlatLibraryStats
0:12:13.204551 INFO: ============ Library Stats ============
0:12:13.204603 INFO: Number of precursors: 10,798,740
0:12:15.579963 INFO: 	thereof targets:5,414,253
0:12:15.580236 INFO: 	thereof decoys: 5,384,487
0:12:15.679089 INFO: Number of elution groups: 5,414,253
0:12:15.679231 INFO: 	average size: 1.99
0:12:16.022897 INFO: Number of proteins: 118,137
0:12:16.057284 INFO: Number of channels: 1 ([0])
0:12:16.057524 INFO: Isotopes Distribution for 4 isotopes
0:12:16.057571 INFO: =======================================
0:12:16.073464 PROGRESS: Starting Search Workflows
0:12:16.073884 PROGRESS: Loading raw file 1/6: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
0:12:16.074088 INFO: Creating parent folder for workflows at /home/robbe/alphadia/Proteobench/.progress
0:12:16.074347 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01 at /home/robbe/alphadia/Proteobench/.progress/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
0:12:45.503031 INFO: Determining DIA cycle
0:12:45.789063 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
0:12:45.795265 INFO: Determining DIA cycle
0:12:46.024891 INFO: Found cycle with start 0.00 min and length 151.
0:12:46.172361 INFO: ============ Raw file stats ============
0:12:46.172724 INFO: RT (min)            : 0.0 - 150.0
0:12:46.172807 INFO: RT duration (sec)   : 8999.7
0:12:46.172846 INFO: RT duration (min)   : 150.0
0:12:46.172972 INFO: Cycle len (scans)   : 151
0:12:46.173026 INFO: Cycle len (sec)     : 5.83
0:12:46.173062 INFO: Number of cycles    : 1542
0:12:46.173126 INFO: MS2 range (m/z)     : 396.4 - 1004.7
0:12:46.173164 INFO: ========================================
0:12:48.708914 INFO: Initializing CalibrationManager
0:12:48.709215 INFO: Loading calibration config
0:12:48.709346 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6'}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6'}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated']}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated']}]}]
0:12:48.709439 INFO: Calibration group :fragment, found 1 estimator(s)
0:12:48.709561 INFO: Calibration group :precursor, found 3 estimator(s)
0:12:48.709661 INFO: Disabling ion mobility calibration
0:12:48.709708 INFO: removed mobility estimator from group precursor
0:12:48.709809 INFO: Initializing OptimizationManager
0:12:48.709919 INFO: initial parameter: fwhm_rt = 5
0:12:48.709992 INFO: initial parameter: fwhm_mobility = 0.01
0:12:48.710062 INFO: initial parameter: score_cutoff = 0
0:12:48.710181 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
0:12:48.710292 INFO: Initializing OptimizationManager
0:12:48.710336 INFO: initial parameter: current_epoch = 0
0:12:48.710371 INFO: initial parameter: current_step = 0
0:12:48.710405 INFO: initial parameter: ms1_error = 20
0:12:48.710436 INFO: initial parameter: ms2_error = 20
0:12:48.710468 INFO: initial parameter: rt_error = 500
0:12:48.710501 INFO: initial parameter: mobility_error = 0.08
0:12:48.710532 INFO: initial parameter: column_type = library
0:12:48.710563 INFO: initial parameter: num_candidates = 2
0:12:48.710595 INFO: initial parameter: recalibration_target = 200
0:12:48.710626 INFO: initial parameter: accumulated_precursors = 0
0:12:48.710657 INFO: initial parameter: accumulated_precursors_01FDR = 0
0:12:48.710688 INFO: initial parameter: accumulated_precursors_001FDR = 0
0:12:48.710740 INFO: Initializing FDRManager
0:12:48.710791 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/classifier
0:12:50.625984 PROGRESS: 5,414,253 target precursors potentially observable (0 removed)
0:12:53.944425 INFO: === checking if epoch conditions were reached ===
0:12:53.944695 INFO: ❌ ms2_error      : 20.0000 > 10
0:12:53.944800 INFO: ❌ rt_error       : 500.0000 > 300
0:12:53.944885 INFO: ❌ current_epoch  : 0 < 3
0:12:53.944958 INFO: ==============================================
0:12:54.160556 INFO: calibration group: precursor, predicting mz
0:12:54.160806 WARNING: mz prediction was skipped as it has not been fitted yet
0:12:54.160854 INFO: calibration group: precursor, predicting rt
0:12:54.160926 WARNING: rt prediction was skipped as it has not been fitted yet
0:12:54.160976 INFO: calibration group: fragment, predicting mz
0:12:54.161047 WARNING: mz prediction was skipped as it has not been fitted yet
0:12:54.161101 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
0:12:54.255804 PROGRESS: Extracting batch of 15809 precursors
0:12:56.790887 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:12:56.791032 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:12:56.791091 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:12:56.791130 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:12:58.752315 INFO: Starting candidate selection
0:13:57.907195 INFO: Starting candidate scoring
0:17:50.066871 INFO: Finished candidate processing
0:17:50.067126 INFO: Collecting candidate features
0:17:53.201634 INFO: Collecting fragment features
0:17:55.227920 INFO: Finished candidate scoring
0:17:55.641453 PROGRESS: === Epoch 0, step 0, extracted 26686 precursors and 166291 fragments ===
0:17:55.641881 INFO: performing precursor FDR with 47 features
0:17:55.641948 INFO: Decoy channel: -1
0:17:55.641986 INFO: Competetive: True
0:18:00.123688 INFO: Test AUC: 0.506
0:18:00.124012 INFO: Train AUC: 0.533
0:18:00.124106 INFO: AUC difference: 5.07%
0:18:00.124186 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:00.298814 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:18:00.299953 PROGRESS: ============================= Precursor FDR =============================
0:18:00.300104 PROGRESS: Total precursors accumulated: 1
0:18:00.300192 PROGRESS: Target precursors: 1 (100.00%)
0:18:00.300267 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:00.300338 PROGRESS: 
0:18:00.300410 PROGRESS: Precursor Summary:
0:18:00.302263 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:18:00.302407 PROGRESS: 
0:18:00.302493 PROGRESS: Protein Summary:
0:18:00.304522 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
0:18:00.304657 PROGRESS: =========================================================================
0:18:00.305683 PROGRESS: === Epoch 0, step 1, extracting elution groups 8000 to 24000 ===
0:18:01.018529 PROGRESS: Extracting batch of 31616 precursors
0:18:01.031096 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:18:01.031232 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:18:01.031295 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:18:01.031348 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:18:01.031801 INFO: Starting candidate selection
0:18:05.367139 INFO: Starting candidate scoring
0:18:07.204628 INFO: Finished candidate processing
0:18:07.205160 INFO: Collecting candidate features
0:18:09.529921 INFO: Collecting fragment features
0:18:10.145904 INFO: Finished candidate scoring
0:18:10.472479 PROGRESS: === Epoch 0, step 1, extracted 53042 precursors and 330571 fragments ===
0:18:10.472929 INFO: performing precursor FDR with 47 features
0:18:10.472995 INFO: Decoy channel: -1
0:18:10.473033 INFO: Competetive: True
0:18:16.777244 INFO: Test AUC: 0.542
0:18:16.777457 INFO: Train AUC: 0.558
0:18:16.777506 INFO: AUC difference: 2.85%
0:18:17.521911 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:18:17.528686 PROGRESS: ============================= Precursor FDR =============================
0:18:17.528899 PROGRESS: Total precursors accumulated: 20,621
0:18:17.528989 PROGRESS: Target precursors: 11,929 (57.85%)
0:18:17.529067 PROGRESS: Decoy precursors: 8,692 (42.15%)
0:18:17.529138 PROGRESS: 
0:18:17.529208 PROGRESS: Precursor Summary:
0:18:17.531087 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:18:17.531248 PROGRESS: 
0:18:17.531335 PROGRESS: Protein Summary:
0:18:17.533309 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:18:17.533447 PROGRESS: =========================================================================
0:18:17.534428 PROGRESS: === Epoch 0, step 2, extracting elution groups 24000 to 56000 ===
0:18:17.733784 PROGRESS: Extracting batch of 63238 precursors
0:18:17.761695 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:18:17.761831 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:18:17.761886 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:18:17.761925 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:18:17.762262 INFO: Starting candidate selection
0:18:22.692213 INFO: Starting candidate scoring
0:18:25.271926 INFO: Finished candidate processing
0:18:25.272131 INFO: Collecting candidate features
0:18:27.686973 INFO: Collecting fragment features
0:18:28.310000 INFO: Finished candidate scoring
0:18:28.653610 PROGRESS: === Epoch 0, step 2, extracted 105910 precursors and 656052 fragments ===
0:18:28.654319 INFO: performing precursor FDR with 47 features
0:18:28.654404 INFO: Decoy channel: -1
0:18:28.654442 INFO: Competetive: True
0:18:41.420813 INFO: Test AUC: 0.552
0:18:41.421049 INFO: Train AUC: 0.570
0:18:41.421100 INFO: AUC difference: 3.06%
0:18:41.594759 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:18:41.596738 PROGRESS: ============================= Precursor FDR =============================
0:18:41.596910 PROGRESS: Total precursors accumulated: 388
0:18:41.596999 PROGRESS: Target precursors: 356 (91.75%)
0:18:41.597075 PROGRESS: Decoy precursors: 32 (8.25%)
0:18:41.597149 PROGRESS: 
0:18:41.597224 PROGRESS: Precursor Summary:
0:18:41.599121 PROGRESS: Channel   0:	 0.05 FDR:   306; 0.01 FDR:   176; 0.001 FDR:   175
0:18:41.599270 PROGRESS: 
0:18:41.599357 PROGRESS: Protein Summary:
0:18:41.601486 PROGRESS: Channel   0:	 0.05 FDR:   296; 0.01 FDR:   170; 0.001 FDR:   169
0:18:41.601630 PROGRESS: =========================================================================
0:18:41.602673 PROGRESS: === Epoch 0, step 3, extracting elution groups 56000 to 120000 ===
0:18:41.812933 PROGRESS: Extracting batch of 126431 precursors
0:18:41.846673 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:18:41.846808 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:18:41.846866 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:18:41.846905 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:18:41.847257 INFO: Starting candidate selection
0:18:48.182459 INFO: Starting candidate scoring
0:18:52.237202 INFO: Finished candidate processing
0:18:52.238165 INFO: Collecting candidate features
0:18:55.157805 INFO: Collecting fragment features
0:18:55.921719 INFO: Finished candidate scoring
0:18:56.434200 PROGRESS: === Epoch 0, step 3, extracted 212351 precursors and 1318792 fragments ===
0:18:56.434676 INFO: performing precursor FDR with 47 features
0:18:56.434747 INFO: Decoy channel: -1
0:18:56.434785 INFO: Competetive: True
0:19:23.802352 INFO: Test AUC: 0.549
0:19:23.802602 INFO: Train AUC: 0.572
0:19:23.802679 INFO: AUC difference: 3.99%
0:19:24.003552 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:19:24.005116 PROGRESS: ============================= Precursor FDR =============================
0:19:24.005300 PROGRESS: Total precursors accumulated: 994
0:19:24.005441 PROGRESS: Target precursors: 908 (91.35%)
0:19:24.005556 PROGRESS: Decoy precursors: 86 (8.65%)
0:19:24.005662 PROGRESS: 
0:19:24.005769 PROGRESS: Precursor Summary:
0:19:24.008107 PROGRESS: Channel   0:	 0.05 FDR:   771; 0.01 FDR:   542; 0.001 FDR:   460
0:19:24.008281 PROGRESS: 
0:19:24.008404 PROGRESS: Protein Summary:
0:19:24.011056 PROGRESS: Channel   0:	 0.05 FDR:   698; 0.01 FDR:   501; 0.001 FDR:   426
0:19:24.011223 PROGRESS: =========================================================================
0:19:24.013474 INFO: calibration group: precursor, fitting rt estimator 
0:19:24.152772 INFO: calibration group: fragment, fitting mz estimator 
0:19:24.773825 INFO: === checking if epoch conditions were reached ===
0:19:24.774046 INFO: ✅ ms2_error      : 10.0000 <= 10
0:19:24.774153 INFO: ❌ rt_error       : 342.4091 > 300
0:19:24.774240 INFO: ❌ current_epoch  : 0 < 3
0:19:24.774316 INFO: ==============================================
0:19:25.037279 INFO: calibration group: precursor, predicting mz
0:19:25.037576 WARNING: mz prediction was skipped as it has not been fitted yet
0:19:25.037627 INFO: calibration group: precursor, predicting rt
0:19:33.645417 INFO: calibration group: fragment, predicting mz
0:19:54.100137 PROGRESS: === Epoch 1, step 0, extracting elution groups 0 to 8000 ===
0:19:54.293873 PROGRESS: Extracting batch of 15782 precursors
0:19:54.302178 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:19:54.302298 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:19:54.302369 INFO: FWHM in RT is 19.17 seconds, sigma is 0.70
0:19:54.302409 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:19:54.302804 INFO: Starting candidate selection
0:19:58.712225 INFO: Starting candidate scoring
0:20:00.379988 INFO: Finished candidate processing
0:20:00.380128 INFO: Collecting candidate features
0:20:02.526273 INFO: Collecting fragment features
0:20:03.052760 INFO: Finished candidate scoring
0:20:03.328052 PROGRESS: === Epoch 1, step 0, extracted 26651 precursors and 148558 fragments ===
0:20:03.328462 INFO: performing precursor FDR with 47 features
0:20:03.328525 INFO: Decoy channel: -1
0:20:03.328565 INFO: Competetive: True
0:20:04.998467 INFO: Test AUC: 0.557
0:20:04.998632 INFO: Train AUC: 0.587
0:20:04.998681 INFO: AUC difference: 5.09%
0:20:04.998723 WARNING: AUC difference > 5%. This may indicate overfitting.
0:20:05.163938 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:20:05.165006 PROGRESS: ============================= Precursor FDR =============================
0:20:05.165155 PROGRESS: Total precursors accumulated: 80
0:20:05.165244 PROGRESS: Target precursors: 74 (92.50%)
0:20:05.165322 PROGRESS: Decoy precursors: 6 (7.50%)
0:20:05.165394 PROGRESS: 
0:20:05.165466 PROGRESS: Precursor Summary:
0:20:05.167198 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    52; 0.001 FDR:    52
0:20:05.167330 PROGRESS: 
0:20:05.167410 PROGRESS: Protein Summary:
0:20:05.169315 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    52; 0.001 FDR:    52
0:20:05.169451 PROGRESS: =========================================================================
0:20:05.170421 PROGRESS: === Epoch 1, step 1, extracting elution groups 8000 to 24000 ===
0:20:05.278964 PROGRESS: Extracting batch of 31579 precursors
0:20:05.288813 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:20:05.288960 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:20:05.289012 INFO: FWHM in RT is 19.17 seconds, sigma is 0.70
0:20:05.289051 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:20:05.289329 INFO: Starting candidate selection
0:20:09.763310 INFO: Starting candidate scoring
0:20:11.846995 INFO: Finished candidate processing
0:20:11.847154 INFO: Collecting candidate features
0:20:14.394887 INFO: Collecting fragment features
0:20:14.934099 INFO: Finished candidate scoring
0:20:15.261721 PROGRESS: === Epoch 1, step 1, extracted 53364 precursors and 297123 fragments ===
0:20:15.262167 INFO: performing precursor FDR with 47 features
0:20:15.262231 INFO: Decoy channel: -1
0:20:15.262271 INFO: Competetive: True
0:20:19.682622 INFO: Test AUC: 0.553
0:20:19.682778 INFO: Train AUC: 0.589
0:20:19.682825 INFO: AUC difference: 6.12%
0:20:19.682868 WARNING: AUC difference > 5%. This may indicate overfitting.
0:20:19.850461 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:20:19.851580 PROGRESS: ============================= Precursor FDR =============================
0:20:19.851728 PROGRESS: Total precursors accumulated: 234
0:20:19.851831 PROGRESS: Target precursors: 213 (91.03%)
0:20:19.851911 PROGRESS: Decoy precursors: 21 (8.97%)
0:20:19.851983 PROGRESS: 
0:20:19.852054 PROGRESS: Precursor Summary:
0:20:19.853888 PROGRESS: Channel   0:	 0.05 FDR:   189; 0.01 FDR:   159; 0.001 FDR:    89
0:20:19.854027 PROGRESS: 
0:20:19.854112 PROGRESS: Protein Summary:
0:20:19.856139 PROGRESS: Channel   0:	 0.05 FDR:   183; 0.01 FDR:   153; 0.001 FDR:    86
0:20:19.856278 PROGRESS: =========================================================================
0:20:19.857305 PROGRESS: === Epoch 1, step 2, extracting elution groups 24000 to 56000 ===
0:20:19.981915 PROGRESS: Extracting batch of 63188 precursors
0:20:20.002532 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:20:20.002674 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:20:20.002739 INFO: FWHM in RT is 19.17 seconds, sigma is 0.70
0:20:20.002781 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:20:20.003140 INFO: Starting candidate selection
0:20:24.908345 INFO: Starting candidate scoring
0:20:27.491498 INFO: Finished candidate processing
0:20:27.491624 INFO: Collecting candidate features
0:20:30.191121 INFO: Collecting fragment features
0:20:30.767032 INFO: Finished candidate scoring
0:20:31.115967 PROGRESS: === Epoch 1, step 2, extracted 106790 precursors and 594498 fragments ===
0:20:31.116440 INFO: performing precursor FDR with 47 features
0:20:31.116503 INFO: Decoy channel: -1
0:20:31.116542 INFO: Competetive: True
0:20:43.077385 INFO: Test AUC: 0.561
0:20:43.077552 INFO: Train AUC: 0.586
0:20:43.077602 INFO: AUC difference: 4.30%
0:20:43.267065 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:20:43.268440 PROGRESS: ============================= Precursor FDR =============================
0:20:43.268612 PROGRESS: Total precursors accumulated: 609
0:20:43.268709 PROGRESS: Target precursors: 554 (90.97%)
0:20:43.268785 PROGRESS: Decoy precursors: 55 (9.03%)
0:20:43.268862 PROGRESS: 
0:20:43.268956 PROGRESS: Precursor Summary:
0:20:43.271685 PROGRESS: Channel   0:	 0.05 FDR:   456; 0.01 FDR:   367; 0.001 FDR:   331
0:20:43.271827 PROGRESS: 
0:20:43.271921 PROGRESS: Protein Summary:
0:20:43.274211 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   346; 0.001 FDR:   313
0:20:43.274349 PROGRESS: =========================================================================
0:20:43.275503 PROGRESS: === Epoch 1, step 3, extracting elution groups 56000 to 120000 ===
0:20:43.430071 PROGRESS: Extracting batch of 126462 precursors
0:20:43.468167 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:20:43.468335 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:20:43.468395 INFO: FWHM in RT is 19.17 seconds, sigma is 0.70
0:20:43.468435 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:20:43.468833 INFO: Starting candidate selection
0:20:50.335722 INFO: Starting candidate scoring
0:20:54.317841 INFO: Finished candidate processing
0:20:54.317996 INFO: Collecting candidate features
0:20:57.254781 INFO: Collecting fragment features
0:20:58.014177 INFO: Finished candidate scoring
0:20:58.516430 PROGRESS: === Epoch 1, step 3, extracted 213366 precursors and 1188233 fragments ===
0:20:58.516867 INFO: performing precursor FDR with 47 features
0:20:58.516931 INFO: Decoy channel: -1
0:20:58.516970 INFO: Competetive: True
0:21:25.817258 INFO: Test AUC: 0.561
0:21:25.817507 INFO: Train AUC: 0.581
0:21:25.817577 INFO: AUC difference: 3.34%
0:21:26.015521 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:21:26.016971 PROGRESS: ============================= Precursor FDR =============================
0:21:26.017140 PROGRESS: Total precursors accumulated: 1,363
0:21:26.017249 PROGRESS: Target precursors: 1,238 (90.83%)
0:21:26.017343 PROGRESS: Decoy precursors: 125 (9.17%)
0:21:26.017437 PROGRESS: 
0:21:26.017526 PROGRESS: Precursor Summary:
0:21:26.019889 PROGRESS: Channel   0:	 0.05 FDR: 1,017; 0.01 FDR:   825; 0.001 FDR:   509
0:21:26.020050 PROGRESS: 
0:21:26.020158 PROGRESS: Protein Summary:
0:21:26.022986 PROGRESS: Channel   0:	 0.05 FDR:   890; 0.01 FDR:   724; 0.001 FDR:   471
0:21:26.023146 PROGRESS: =========================================================================
0:21:26.025521 INFO: calibration group: precursor, fitting rt estimator 
0:21:26.164509 INFO: calibration group: fragment, fitting mz estimator 
0:21:26.781393 INFO: === checking if epoch conditions were reached ===
0:21:26.781605 INFO: ✅ ms2_error      : 10.0000 <= 10
0:21:26.781706 INFO: ✅ rt_error       : 300.0000 <= 300
0:21:26.781791 INFO: ❌ current_epoch  : 1 < 3
0:21:26.781869 INFO: ==============================================
0:21:26.992235 INFO: calibration group: precursor, predicting mz
0:21:26.992559 WARNING: mz prediction was skipped as it has not been fitted yet
0:21:26.992614 INFO: calibration group: precursor, predicting rt
0:21:35.264711 INFO: calibration group: fragment, predicting mz
0:21:56.142446 PROGRESS: === Epoch 2, step 0, extracting elution groups 0 to 8000 ===
0:21:56.316369 PROGRESS: Extracting batch of 15809 precursors
0:21:56.324383 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:21:56.324503 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:21:56.324562 INFO: FWHM in RT is 18.13 seconds, sigma is 0.66
0:21:56.324602 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:21:56.324996 INFO: Starting candidate selection
0:22:00.452415 INFO: Starting candidate scoring
0:22:02.017316 INFO: Finished candidate processing
0:22:02.017445 INFO: Collecting candidate features
0:22:04.088684 INFO: Collecting fragment features
0:22:04.592264 INFO: Finished candidate scoring
0:22:04.847652 PROGRESS: === Epoch 2, step 0, extracted 27651 precursors and 151065 fragments ===
0:22:04.848027 INFO: performing precursor FDR with 47 features
0:22:04.848089 INFO: Decoy channel: -1
0:22:04.848128 INFO: Competetive: True
0:22:06.141133 INFO: Test AUC: 0.543
0:22:06.141277 INFO: Train AUC: 0.587
0:22:06.141325 INFO: AUC difference: 7.58%
0:22:06.141367 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:06.802498 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:22:06.803551 PROGRESS: ============================= Precursor FDR =============================
0:22:06.803701 PROGRESS: Total precursors accumulated: 98
0:22:06.803790 PROGRESS: Target precursors: 89 (90.82%)
0:22:06.803867 PROGRESS: Decoy precursors: 9 (9.18%)
0:22:06.803940 PROGRESS: 
0:22:06.804011 PROGRESS: Precursor Summary:
0:22:06.805724 PROGRESS: Channel   0:	 0.05 FDR:    73; 0.01 FDR:    22; 0.001 FDR:    22
0:22:06.805868 PROGRESS: 
0:22:06.805952 PROGRESS: Protein Summary:
0:22:06.807842 PROGRESS: Channel   0:	 0.05 FDR:    70; 0.01 FDR:    22; 0.001 FDR:    22
0:22:06.807982 PROGRESS: =========================================================================
0:22:06.808916 PROGRESS: === Epoch 2, step 1, extracting elution groups 8000 to 24000 ===
0:22:06.913074 PROGRESS: Extracting batch of 31597 precursors
0:22:06.922913 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:22:06.923039 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:06.923090 INFO: FWHM in RT is 18.13 seconds, sigma is 0.66
0:22:06.923128 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:06.923398 INFO: Starting candidate selection
0:22:11.145160 INFO: Starting candidate scoring
0:22:13.249247 INFO: Finished candidate processing
0:22:13.249421 INFO: Collecting candidate features
0:22:15.418929 INFO: Collecting fragment features
0:22:15.951115 INFO: Finished candidate scoring
0:22:16.225473 PROGRESS: === Epoch 2, step 1, extracted 55267 precursors and 300938 fragments ===
0:22:16.226322 INFO: performing precursor FDR with 47 features
0:22:16.226409 INFO: Decoy channel: -1
0:22:16.226446 INFO: Competetive: True
0:22:21.137910 INFO: Test AUC: 0.555
0:22:21.138062 INFO: Train AUC: 0.593
0:22:21.138109 INFO: AUC difference: 6.42%
0:22:21.138147 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:21.306476 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:22:21.307588 PROGRESS: ============================= Precursor FDR =============================
0:22:21.307786 PROGRESS: Total precursors accumulated: 285
0:22:21.307909 PROGRESS: Target precursors: 259 (90.88%)
0:22:21.307990 PROGRESS: Decoy precursors: 26 (9.12%)
0:22:21.308064 PROGRESS: 
0:22:21.308137 PROGRESS: Precursor Summary:
0:22:21.309933 PROGRESS: Channel   0:	 0.05 FDR:   207; 0.01 FDR:   134; 0.001 FDR:    75
0:22:21.310075 PROGRESS: 
0:22:21.310158 PROGRESS: Protein Summary:
0:22:21.312239 PROGRESS: Channel   0:	 0.05 FDR:   199; 0.01 FDR:   130; 0.001 FDR:    73
0:22:21.312406 PROGRESS: =========================================================================
0:22:21.313805 PROGRESS: === Epoch 2, step 2, extracting elution groups 24000 to 56000 ===
0:22:21.433245 PROGRESS: Extracting batch of 63233 precursors
0:22:21.450968 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:22:21.451123 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:21.451176 INFO: FWHM in RT is 18.13 seconds, sigma is 0.66
0:22:21.451215 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:21.451501 INFO: Starting candidate selection
0:22:26.310317 INFO: Starting candidate scoring
0:22:28.975337 INFO: Finished candidate processing
0:22:28.975599 INFO: Collecting candidate features
0:22:31.293297 INFO: Collecting fragment features
0:22:31.865847 INFO: Finished candidate scoring
0:22:32.199012 PROGRESS: === Epoch 2, step 2, extracted 111180 precursors and 606348 fragments ===
0:22:32.199447 INFO: performing precursor FDR with 47 features
0:22:32.199524 INFO: Decoy channel: -1
0:22:32.199563 INFO: Competetive: True
0:22:44.364282 INFO: Test AUC: 0.555
0:22:44.364435 INFO: Train AUC: 0.589
0:22:44.364487 INFO: AUC difference: 5.74%
0:22:44.364530 WARNING: AUC difference > 5%. This may indicate overfitting.
0:22:44.554269 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:22:44.555870 PROGRESS: ============================= Precursor FDR =============================
0:22:44.556042 PROGRESS: Total precursors accumulated: 733
0:22:44.556134 PROGRESS: Target precursors: 666 (90.86%)
0:22:44.556211 PROGRESS: Decoy precursors: 67 (9.14%)
0:22:44.556285 PROGRESS: 
0:22:44.556358 PROGRESS: Precursor Summary:
0:22:44.558454 PROGRESS: Channel   0:	 0.05 FDR:   527; 0.01 FDR:   428; 0.001 FDR:   248
0:22:44.558602 PROGRESS: 
0:22:44.558682 PROGRESS: Protein Summary:
0:22:44.561214 PROGRESS: Channel   0:	 0.05 FDR:   487; 0.01 FDR:   399; 0.001 FDR:   235
0:22:44.561363 PROGRESS: =========================================================================
0:22:44.562942 PROGRESS: === Epoch 2, step 3, extracting elution groups 56000 to 120000 ===
0:22:44.711080 PROGRESS: Extracting batch of 126409 precursors
0:22:44.746088 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:22:44.746226 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:22:44.746290 INFO: FWHM in RT is 18.13 seconds, sigma is 0.66
0:22:44.746332 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:22:44.746665 INFO: Starting candidate selection
0:22:51.218764 INFO: Starting candidate scoring
0:22:55.430726 INFO: Finished candidate processing
0:22:55.431629 INFO: Collecting candidate features
0:22:58.194751 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 221492)
0:22:58.216597 INFO: Collecting fragment features
0:22:58.941688 INFO: Finished candidate scoring
0:22:59.431127 PROGRESS: === Epoch 2, step 3, extracted 221492 precursors and 1213391 fragments ===
0:22:59.431589 INFO: performing precursor FDR with 47 features
0:22:59.431652 INFO: Decoy channel: -1
0:22:59.431690 INFO: Competetive: True
0:22:59.780413 WARNING: dropped 1 target PSMs due to missing features
0:23:27.341971 INFO: Test AUC: 0.559
0:23:27.342130 INFO: Train AUC: 0.581
0:23:27.342180 INFO: AUC difference: 3.79%
0:23:27.536891 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:23:27.538237 PROGRESS: ============================= Precursor FDR =============================
0:23:27.538391 PROGRESS: Total precursors accumulated: 1,306
0:23:27.538483 PROGRESS: Target precursors: 1,189 (91.04%)
0:23:27.538560 PROGRESS: Decoy precursors: 117 (8.96%)
0:23:27.538920 PROGRESS: 
0:23:27.539031 PROGRESS: Precursor Summary:
0:23:27.541288 PROGRESS: Channel   0:	 0.05 FDR:   993; 0.01 FDR:   681; 0.001 FDR:   482
0:23:27.541429 PROGRESS: 
0:23:27.541513 PROGRESS: Protein Summary:
0:23:27.544136 PROGRESS: Channel   0:	 0.05 FDR:   880; 0.01 FDR:   612; 0.001 FDR:   444
0:23:27.544274 PROGRESS: =========================================================================
0:23:27.546477 INFO: calibration group: precursor, fitting rt estimator 
0:23:27.682260 INFO: calibration group: fragment, fitting mz estimator 
0:23:28.300582 INFO: === checking if epoch conditions were reached ===
0:23:28.300799 INFO: ✅ ms2_error      : 10.0000 <= 10
0:23:28.300906 INFO: ✅ rt_error       : 300.0000 <= 300
0:23:28.300990 INFO: ✅ current_epoch  : 2 >= 3
0:23:28.301064 INFO: ==============================================
0:23:28.330636 INFO: calibration group: precursor, predicting mz
0:23:28.330987 WARNING: mz prediction was skipped as it has not been fitted yet
0:23:28.331039 INFO: calibration group: precursor, predicting rt
0:23:36.556275 INFO: calibration group: fragment, predicting mz
0:23:57.587269 PROGRESS: Extracting batch of 10696137 precursors
0:24:00.320538 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
0:24:00.320690 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:24:00.320751 INFO: FWHM in RT is 17.78 seconds, sigma is 0.65
0:24:00.320792 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:24:00.321229 INFO: Starting candidate selection
0:28:34.753122 INFO: Applying score cutoff of 66.23512481689453
0:28:35.068793 INFO: Removed 15251797 precursors with score below cutoff
0:28:37.715772 INFO: Starting candidate scoring
0:29:58.968779 INFO: Finished candidate processing
0:29:58.969087 INFO: Collecting candidate features
0:30:14.562683 INFO: Collecting fragment features
0:30:20.856885 INFO: Finished candidate scoring
0:30:25.998407 INFO: performing precursor FDR with 47 features
0:30:25.998562 INFO: Decoy channel: -1
0:30:25.998605 INFO: Competetive: True
0:37:26.580232 INFO: Test AUC: 0.578
0:37:26.580561 INFO: Train AUC: 0.582
0:37:26.580618 INFO: AUC difference: 0.54%
0:37:27.281815 INFO: Removing fragments below FDR threshold
0:37:28.059541 PROGRESS: ============================= Precursor FDR =============================
0:37:28.059914 PROGRESS: Total precursors accumulated: 42,789
0:37:28.060035 PROGRESS: Target precursors: 42,366 (99.01%)
0:37:28.060118 PROGRESS: Decoy precursors: 423 (0.99%)
0:37:28.060194 PROGRESS: 
0:37:28.060268 PROGRESS: Precursor Summary:
0:37:28.088824 PROGRESS: Channel   0:	 0.05 FDR: 42,366; 0.01 FDR: 42,366; 0.001 FDR: 31,113
0:37:28.089101 PROGRESS: 
0:37:28.089187 PROGRESS: Protein Summary:
0:37:28.126861 PROGRESS: Channel   0:	 0.05 FDR: 8,285; 0.01 FDR: 8,285; 0.001 FDR: 6,527
0:37:28.127140 PROGRESS: =========================================================================
0:37:28.773419 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
0:37:29.474784 PROGRESS: Loading raw file 2/6: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
0:37:29.475043 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03 at /home/robbe/alphadia/Proteobench/.progress/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
0:37:58.522913 INFO: Determining DIA cycle
0:37:58.546126 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
0:37:58.553771 INFO: Determining DIA cycle
0:37:58.578157 INFO: Found cycle with start 0.00 min and length 151.
0:37:58.625933 INFO: ============ Raw file stats ============
0:37:58.626313 INFO: RT (min)            : 0.0 - 150.0
0:37:58.626424 INFO: RT duration (sec)   : 8999.7
0:37:58.626464 INFO: RT duration (min)   : 150.0
0:37:58.626581 INFO: Cycle len (scans)   : 151
0:37:58.626627 INFO: Cycle len (sec)     : 5.84
0:37:58.626663 INFO: Number of cycles    : 1542
0:37:58.626732 INFO: MS2 range (m/z)     : 396.4 - 1004.7
0:37:58.626770 INFO: ========================================
0:38:01.424148 INFO: Initializing CalibrationManager
0:38:01.424701 INFO: Loading calibration config
0:38:01.427482 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'function': LOESSRegression()}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'function': LOESSRegression(n_kernels=2)}]}]
0:38:01.427672 INFO: Calibration group :fragment, found 1 estimator(s)
0:38:01.427998 INFO: Calibration group :precursor, found 3 estimator(s)
0:38:01.428135 INFO: Disabling ion mobility calibration
0:38:01.428190 INFO: removed mobility estimator from group precursor
0:38:01.428314 INFO: Initializing OptimizationManager
0:38:01.428430 INFO: initial parameter: fwhm_rt = 5
0:38:01.428506 INFO: initial parameter: fwhm_mobility = 0.01
0:38:01.428576 INFO: initial parameter: score_cutoff = 0
0:38:01.428705 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
0:38:01.428841 INFO: Initializing OptimizationManager
0:38:01.428885 INFO: initial parameter: current_epoch = 0
0:38:01.428921 INFO: initial parameter: current_step = 0
0:38:01.428955 INFO: initial parameter: ms1_error = 20
0:38:01.428988 INFO: initial parameter: ms2_error = 20
0:38:01.429020 INFO: initial parameter: rt_error = 500
0:38:01.429053 INFO: initial parameter: mobility_error = 0.08
0:38:01.429085 INFO: initial parameter: column_type = library
0:38:01.429117 INFO: initial parameter: num_candidates = 2
0:38:01.429148 INFO: initial parameter: recalibration_target = 200
0:38:01.429179 INFO: initial parameter: accumulated_precursors = 0
0:38:01.429211 INFO: initial parameter: accumulated_precursors_01FDR = 0
0:38:01.429242 INFO: initial parameter: accumulated_precursors_001FDR = 0
0:38:01.429304 INFO: Initializing FDRManager
0:38:01.429371 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/classifier
0:38:02.960491 PROGRESS: 5,414,253 target precursors potentially observable (0 removed)
0:38:05.804999 INFO: === checking if epoch conditions were reached ===
0:38:05.805282 INFO: ❌ ms2_error      : 20.0000 > 10
0:38:05.805391 INFO: ❌ rt_error       : 500.0000 > 300
0:38:05.805473 INFO: ❌ current_epoch  : 0 < 3
0:38:05.805547 INFO: ==============================================
0:38:06.046972 INFO: calibration group: precursor, predicting mz
0:38:06.047245 WARNING: mz prediction was skipped as it has not been fitted yet
0:38:06.047294 INFO: calibration group: precursor, predicting rt
0:38:06.047369 WARNING: rt prediction was skipped as it has not been fitted yet
0:38:06.047426 INFO: calibration group: fragment, predicting mz
0:38:06.047508 WARNING: mz prediction was skipped as it has not been fitted yet
0:38:06.047561 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
0:38:06.142598 PROGRESS: Extracting batch of 15794 precursors
0:38:06.151317 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:38:06.151449 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:38:06.151523 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:38:06.151563 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:38:06.152549 INFO: Starting candidate selection
0:38:09.005286 INFO: Starting candidate scoring
0:38:10.160469 INFO: Finished candidate processing
0:38:10.160596 INFO: Collecting candidate features
0:38:11.864110 INFO: Collecting fragment features
0:38:12.328192 INFO: Finished candidate scoring
0:38:12.555707 PROGRESS: === Epoch 0, step 0, extracted 26868 precursors and 164292 fragments ===
0:38:12.556046 INFO: performing precursor FDR with 47 features
0:38:12.556110 INFO: Decoy channel: -1
0:38:12.556149 INFO: Competetive: True
0:38:13.973036 INFO: Test AUC: 0.499
0:38:13.973196 INFO: Train AUC: 0.513
0:38:13.973244 INFO: AUC difference: 2.77%
0:38:14.133268 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:38:14.136543 PROGRESS: ============================= Precursor FDR =============================
0:38:14.136750 PROGRESS: Total precursors accumulated: 6,947
0:38:14.136840 PROGRESS: Target precursors: 3,621 (52.12%)
0:38:14.136918 PROGRESS: Decoy precursors: 3,326 (47.88%)
0:38:14.136992 PROGRESS: 
0:38:14.137066 PROGRESS: Precursor Summary:
0:38:14.138844 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:38:14.138994 PROGRESS: 
0:38:14.139080 PROGRESS: Protein Summary:
0:38:14.141019 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:38:14.141150 PROGRESS: =========================================================================
0:38:14.142102 PROGRESS: === Epoch 0, step 1, extracting elution groups 8000 to 24000 ===
0:38:14.256392 PROGRESS: Extracting batch of 31594 precursors
0:38:14.267269 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:38:14.267409 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:38:14.267461 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:38:14.267505 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:38:14.267804 INFO: Starting candidate selection
0:38:17.956223 INFO: Starting candidate scoring
0:38:19.459579 INFO: Finished candidate processing
0:38:19.459743 INFO: Collecting candidate features
0:38:21.302086 INFO: Collecting fragment features
0:38:21.796363 INFO: Finished candidate scoring
0:38:22.049677 PROGRESS: === Epoch 0, step 1, extracted 53315 precursors and 327060 fragments ===
0:38:22.050060 INFO: performing precursor FDR with 47 features
0:38:22.050136 INFO: Decoy channel: -1
0:38:22.050194 INFO: Competetive: True
0:38:26.688597 INFO: Test AUC: 0.537
0:38:26.688754 INFO: Train AUC: 0.550
0:38:26.688804 INFO: AUC difference: 2.32%
0:38:26.852864 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:38:26.853932 PROGRESS: ============================= Precursor FDR =============================
0:38:26.854087 PROGRESS: Total precursors accumulated: 3
0:38:26.854177 PROGRESS: Target precursors: 3 (100.00%)
0:38:26.854253 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:26.854323 PROGRESS: 
0:38:26.854395 PROGRESS: Precursor Summary:
0:38:26.856240 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:38:26.856372 PROGRESS: 
0:38:26.856452 PROGRESS: Protein Summary:
0:38:26.858478 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
0:38:26.858609 PROGRESS: =========================================================================
0:38:26.859669 PROGRESS: === Epoch 0, step 2, extracting elution groups 24000 to 56000 ===
0:38:26.984333 PROGRESS: Extracting batch of 63221 precursors
0:38:27.000532 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:38:27.000675 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:38:27.000726 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:38:27.000764 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:38:27.001029 INFO: Starting candidate selection
0:38:32.343803 INFO: Starting candidate scoring
0:38:34.650947 INFO: Finished candidate processing
0:38:34.651081 INFO: Collecting candidate features
0:38:36.540439 INFO: Collecting fragment features
0:38:37.045225 INFO: Finished candidate scoring
0:38:37.350076 PROGRESS: === Epoch 0, step 2, extracted 107183 precursors and 656243 fragments ===
0:38:37.350422 INFO: performing precursor FDR with 47 features
0:38:37.350481 INFO: Decoy channel: -1
0:38:37.350522 INFO: Competetive: True
0:38:49.861012 INFO: Test AUC: 0.548
0:38:49.861172 INFO: Train AUC: 0.565
0:38:49.861228 INFO: AUC difference: 3.12%
0:38:50.028473 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:38:50.029541 PROGRESS: ============================= Precursor FDR =============================
0:38:50.029692 PROGRESS: Total precursors accumulated: 415
0:38:50.029788 PROGRESS: Target precursors: 378 (91.08%)
0:38:50.029872 PROGRESS: Decoy precursors: 37 (8.92%)
0:38:50.029950 PROGRESS: 
0:38:50.030028 PROGRESS: Precursor Summary:
0:38:50.031845 PROGRESS: Channel   0:	 0.05 FDR:   301; 0.01 FDR:   236; 0.001 FDR:   136
0:38:50.031999 PROGRESS: 
0:38:50.032092 PROGRESS: Protein Summary:
0:38:50.034164 PROGRESS: Channel   0:	 0.05 FDR:   290; 0.01 FDR:   226; 0.001 FDR:   130
0:38:50.034305 PROGRESS: =========================================================================
0:38:50.036064 INFO: calibration group: precursor, fitting rt estimator 
0:38:50.133562 INFO: calibration group: fragment, fitting mz estimator 
0:38:50.665150 INFO: === checking if epoch conditions were reached ===
0:38:50.665350 INFO: ❌ ms2_error      : 14.4131 > 10
0:38:50.665447 INFO: ❌ rt_error       : 302.1066 > 300
0:38:50.666006 INFO: ❌ current_epoch  : 0 < 3
0:38:50.666130 INFO: ==============================================
0:38:50.875437 INFO: calibration group: precursor, predicting mz
0:38:50.875705 WARNING: mz prediction was skipped as it has not been fitted yet
0:38:50.875753 INFO: calibration group: precursor, predicting rt
0:38:58.942737 INFO: calibration group: fragment, predicting mz
0:39:18.853053 PROGRESS: === Epoch 1, step 0, extracting elution groups 0 to 8000 ===
0:39:19.041201 PROGRESS: Extracting batch of 15804 precursors
0:39:19.047855 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:39:19.047989 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:39:19.048064 INFO: FWHM in RT is 18.86 seconds, sigma is 0.69
0:39:19.048110 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:39:19.048595 INFO: Starting candidate selection
0:39:22.614214 INFO: Starting candidate scoring
0:39:23.963577 INFO: Finished candidate processing
0:39:23.963721 INFO: Collecting candidate features
0:39:25.757889 INFO: Collecting fragment features
0:39:26.190300 INFO: Finished candidate scoring
0:39:26.423664 PROGRESS: === Epoch 1, step 0, extracted 26915 precursors and 155984 fragments ===
0:39:26.424011 INFO: performing precursor FDR with 47 features
0:39:26.424071 INFO: Decoy channel: -1
0:39:26.424111 INFO: Competetive: True
0:39:27.776119 INFO: Test AUC: 0.555
0:39:27.776283 INFO: Train AUC: 0.570
0:39:27.776333 INFO: AUC difference: 2.63%
0:39:28.621536 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:39:28.622522 PROGRESS: ============================= Precursor FDR =============================
0:39:28.622665 PROGRESS: Total precursors accumulated: 72
0:39:28.622752 PROGRESS: Target precursors: 66 (91.67%)
0:39:28.622828 PROGRESS: Decoy precursors: 6 (8.33%)
0:39:28.622900 PROGRESS: 
0:39:28.622973 PROGRESS: Precursor Summary:
0:39:28.624672 PROGRESS: Channel   0:	 0.05 FDR:    61; 0.01 FDR:    42; 0.001 FDR:    42
0:39:28.624812 PROGRESS: 
0:39:28.624895 PROGRESS: Protein Summary:
0:39:28.626785 PROGRESS: Channel   0:	 0.05 FDR:    60; 0.01 FDR:    41; 0.001 FDR:    41
0:39:28.626927 PROGRESS: =========================================================================
0:39:28.627892 PROGRESS: === Epoch 1, step 1, extracting elution groups 8000 to 24000 ===
0:39:28.755006 PROGRESS: Extracting batch of 31595 precursors
0:39:28.764654 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:39:28.764779 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:39:28.764828 INFO: FWHM in RT is 18.86 seconds, sigma is 0.69
0:39:28.764868 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:39:28.765126 INFO: Starting candidate selection
0:39:32.932131 INFO: Starting candidate scoring
0:39:34.769410 INFO: Finished candidate processing
0:39:34.769529 INFO: Collecting candidate features
0:39:36.694222 INFO: Collecting fragment features
0:39:37.174998 INFO: Finished candidate scoring
0:39:37.436258 PROGRESS: === Epoch 1, step 1, extracted 53940 precursors and 314437 fragments ===
0:39:37.436582 INFO: performing precursor FDR with 47 features
0:39:37.436638 INFO: Decoy channel: -1
0:39:37.436676 INFO: Competetive: True
0:39:42.649166 INFO: Test AUC: 0.560
0:39:42.649306 INFO: Train AUC: 0.569
0:39:42.649355 INFO: AUC difference: 1.47%
0:39:42.809104 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:39:42.810135 PROGRESS: ============================= Precursor FDR =============================
0:39:42.810278 PROGRESS: Total precursors accumulated: 188
0:39:42.810365 PROGRESS: Target precursors: 171 (90.96%)
0:39:42.810442 PROGRESS: Decoy precursors: 17 (9.04%)
0:39:42.810514 PROGRESS: 
0:39:42.810585 PROGRESS: Precursor Summary:
0:39:42.812330 PROGRESS: Channel   0:	 0.05 FDR:   113; 0.01 FDR:    53; 0.001 FDR:    53
0:39:42.812462 PROGRESS: 
0:39:42.812541 PROGRESS: Protein Summary:
0:39:42.814472 PROGRESS: Channel   0:	 0.05 FDR:   108; 0.01 FDR:    51; 0.001 FDR:    51
0:39:42.814600 PROGRESS: =========================================================================
0:39:42.815595 PROGRESS: === Epoch 1, step 2, extracting elution groups 24000 to 56000 ===
0:39:42.943227 PROGRESS: Extracting batch of 63219 precursors
0:39:42.959622 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:39:42.959755 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:39:42.959807 INFO: FWHM in RT is 18.86 seconds, sigma is 0.69
0:39:42.959848 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:39:42.960156 INFO: Starting candidate selection
0:39:47.562363 INFO: Starting candidate scoring
0:39:50.095550 INFO: Finished candidate processing
0:39:50.095866 INFO: Collecting candidate features
0:39:52.176365 INFO: Collecting fragment features
0:39:52.681218 INFO: Finished candidate scoring
0:39:53.055795 PROGRESS: === Epoch 1, step 2, extracted 107703 precursors and 625857 fragments ===
0:39:53.056135 INFO: performing precursor FDR with 47 features
0:39:53.056191 INFO: Decoy channel: -1
0:39:53.056229 INFO: Competetive: True
0:40:04.883131 INFO: Test AUC: 0.555
0:40:04.883337 INFO: Train AUC: 0.572
0:40:04.883387 INFO: AUC difference: 3.03%
0:40:05.098618 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:40:05.099760 PROGRESS: ============================= Precursor FDR =============================
0:40:05.099900 PROGRESS: Total precursors accumulated: 588
0:40:05.099996 PROGRESS: Target precursors: 538 (91.50%)
0:40:05.100073 PROGRESS: Decoy precursors: 50 (8.50%)
0:40:05.100143 PROGRESS: 
0:40:05.100215 PROGRESS: Precursor Summary:
0:40:05.102157 PROGRESS: Channel   0:	 0.05 FDR:   472; 0.01 FDR:   254; 0.001 FDR:   222
0:40:05.102303 PROGRESS: 
0:40:05.102392 PROGRESS: Protein Summary:
0:40:05.104566 PROGRESS: Channel   0:	 0.05 FDR:   445; 0.01 FDR:   239; 0.001 FDR:   209
0:40:05.104701 PROGRESS: =========================================================================
0:40:05.105799 PROGRESS: === Epoch 1, step 3, extracting elution groups 56000 to 120000 ===
0:40:05.275946 PROGRESS: Extracting batch of 126383 precursors
0:40:05.305245 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:40:05.305373 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:40:05.305429 INFO: FWHM in RT is 18.86 seconds, sigma is 0.69
0:40:05.305467 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:40:05.305779 INFO: Starting candidate selection
0:40:11.873249 INFO: Starting candidate scoring
0:40:15.997851 INFO: Finished candidate processing
0:40:15.997969 INFO: Collecting candidate features
0:40:18.276457 INFO: Collecting fragment features
0:40:18.864718 INFO: Finished candidate scoring
0:40:19.296062 PROGRESS: === Epoch 1, step 3, extracted 215136 precursors and 1252944 fragments ===
0:40:19.296409 INFO: performing precursor FDR with 47 features
0:40:19.296463 INFO: Decoy channel: -1
0:40:19.296499 INFO: Competetive: True
0:40:44.391752 INFO: Test AUC: 0.555
0:40:44.391928 INFO: Train AUC: 0.570
0:40:44.391979 INFO: AUC difference: 2.77%
0:40:44.615685 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
0:40:44.617016 PROGRESS: ============================= Precursor FDR =============================
0:40:44.617162 PROGRESS: Total precursors accumulated: 1,392
0:40:44.617250 PROGRESS: Target precursors: 1,269 (91.16%)
0:40:44.617326 PROGRESS: Decoy precursors: 123 (8.84%)
0:40:44.617396 PROGRESS: 
0:40:44.617481 PROGRESS: Precursor Summary:
0:40:44.619738 PROGRESS: Channel   0:	 0.05 FDR: 1,063; 0.01 FDR:   850; 0.001 FDR:   547
0:40:44.619895 PROGRESS: 
0:40:44.619983 PROGRESS: Protein Summary:
0:40:44.622638 PROGRESS: Channel   0:	 0.05 FDR:   932; 0.01 FDR:   747; 0.001 FDR:   493
0:40:44.622774 PROGRESS: =========================================================================
0:40:44.625105 INFO: calibration group: precursor, fitting rt estimator 
0:40:44.720710 INFO: calibration group: fragment, fitting mz estimator 
0:40:45.271270 INFO: === checking if epoch conditions were reached ===
0:40:45.271491 INFO: ✅ ms2_error      : 10.0000 <= 10
0:40:45.271598 INFO: ✅ rt_error       : 300.0000 <= 300
0:40:45.271680 INFO: ❌ current_epoch  : 1 < 3
0:40:45.271755 INFO: ==============================================
0:40:45.481973 INFO: calibration group: precursor, predicting mz
0:40:45.482253 WARNING: mz prediction was skipped as it has not been fitted yet
0:40:45.482310 INFO: calibration group: precursor, predicting rt
0:40:53.333166 INFO: calibration group: fragment, predicting mz
0:41:13.286144 PROGRESS: === Epoch 2, step 0, extracting elution groups 0 to 8000 ===
0:41:13.443437 PROGRESS: Extracting batch of 15809 precursors
0:41:13.450377 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:41:13.450487 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:41:13.450541 INFO: FWHM in RT is 18.14 seconds, sigma is 0.66
0:41:13.450581 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:41:13.450925 INFO: Starting candidate selection
0:41:17.294024 INFO: Starting candidate scoring
0:41:18.684448 INFO: Finished candidate processing
0:41:18.684576 INFO: Collecting candidate features
0:41:20.608064 INFO: Collecting fragment features
0:41:21.060916 INFO: Finished candidate scoring
0:41:21.329329 PROGRESS: === Epoch 2, step 0, extracted 28323 precursors and 153337 fragments ===
0:41:21.329658 INFO: performing precursor FDR with 47 features
0:41:21.329717 INFO: Decoy channel: -1
0:41:21.329753 INFO: Competetive: True
0:41:22.573119 INFO: Test AUC: 0.564
0:41:22.573260 INFO: Train AUC: 0.578
0:41:22.573308 INFO: AUC difference: 2.47%
0:41:22.731742 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:41:22.732696 PROGRESS: ============================= Precursor FDR =============================
0:41:22.732834 PROGRESS: Total precursors accumulated: 86
0:41:22.732929 PROGRESS: Target precursors: 78 (90.70%)
0:41:22.733006 PROGRESS: Decoy precursors: 8 (9.30%)
0:41:22.733077 PROGRESS: 
0:41:22.733147 PROGRESS: Precursor Summary:
0:41:22.734837 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    58; 0.001 FDR:    58
0:41:22.734973 PROGRESS: 
0:41:22.735056 PROGRESS: Protein Summary:
0:41:22.736949 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    58; 0.001 FDR:    58
0:41:22.737077 PROGRESS: =========================================================================
0:41:22.738062 PROGRESS: === Epoch 2, step 1, extracting elution groups 8000 to 24000 ===
0:41:22.844946 PROGRESS: Extracting batch of 31631 precursors
0:41:22.853363 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:41:22.853479 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:41:22.853528 INFO: FWHM in RT is 18.14 seconds, sigma is 0.66
0:41:22.853566 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:41:22.853799 INFO: Starting candidate selection
0:41:27.171918 INFO: Starting candidate scoring
0:41:29.076738 INFO: Finished candidate processing
0:41:29.076880 INFO: Collecting candidate features
0:41:31.034098 INFO: Collecting fragment features
0:41:31.486564 INFO: Finished candidate scoring
0:41:31.745153 PROGRESS: === Epoch 2, step 1, extracted 56260 precursors and 303172 fragments ===
0:41:31.745465 INFO: performing precursor FDR with 47 features
0:41:31.745520 INFO: Decoy channel: -1
0:41:31.745557 INFO: Competetive: True
0:41:36.446517 INFO: Test AUC: 0.558
0:41:36.446663 INFO: Train AUC: 0.583
0:41:36.446710 INFO: AUC difference: 4.37%
0:41:36.605312 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:41:36.606349 PROGRESS: ============================= Precursor FDR =============================
0:41:36.606495 PROGRESS: Total precursors accumulated: 298
0:41:36.606584 PROGRESS: Target precursors: 272 (91.28%)
0:41:36.606659 PROGRESS: Decoy precursors: 26 (8.72%)
0:41:36.606730 PROGRESS: 
0:41:36.606800 PROGRESS: Precursor Summary:
0:41:36.608620 PROGRESS: Channel   0:	 0.05 FDR:   234; 0.01 FDR:   192; 0.001 FDR:    19
0:41:36.608756 PROGRESS: 
0:41:36.608848 PROGRESS: Protein Summary:
0:41:36.610866 PROGRESS: Channel   0:	 0.05 FDR:   225; 0.01 FDR:   186; 0.001 FDR:    18
0:41:36.611003 PROGRESS: =========================================================================
0:41:36.612048 PROGRESS: === Epoch 2, step 2, extracting elution groups 24000 to 56000 ===
0:41:36.733717 PROGRESS: Extracting batch of 63204 precursors
0:41:36.749227 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:41:36.749357 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:41:36.749406 INFO: FWHM in RT is 18.14 seconds, sigma is 0.66
0:41:36.749444 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:41:36.749693 INFO: Starting candidate selection
0:41:41.478529 INFO: Starting candidate scoring
0:41:43.998379 INFO: Finished candidate processing
0:41:43.998518 INFO: Collecting candidate features
0:41:45.993273 INFO: Collecting fragment features
0:41:46.513013 INFO: Finished candidate scoring
0:41:46.838015 PROGRESS: === Epoch 2, step 2, extracted 112238 precursors and 605792 fragments ===
0:41:46.838404 INFO: performing precursor FDR with 47 features
0:41:46.838461 INFO: Decoy channel: -1
0:41:46.838499 INFO: Competetive: True
0:41:59.069842 INFO: Test AUC: 0.559
0:41:59.069997 INFO: Train AUC: 0.578
0:41:59.070047 INFO: AUC difference: 3.27%
0:41:59.238527 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:41:59.239691 PROGRESS: ============================= Precursor FDR =============================
0:41:59.239841 PROGRESS: Total precursors accumulated: 698
0:41:59.239926 PROGRESS: Target precursors: 637 (91.26%)
0:41:59.240000 PROGRESS: Decoy precursors: 61 (8.74%)
0:41:59.240070 PROGRESS: 
0:41:59.240142 PROGRESS: Precursor Summary:
0:41:59.242066 PROGRESS: Channel   0:	 0.05 FDR:   473; 0.01 FDR:   344; 0.001 FDR:    40
0:41:59.242204 PROGRESS: 
0:41:59.242287 PROGRESS: Protein Summary:
0:41:59.244477 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   328; 0.001 FDR:    40
0:41:59.244615 PROGRESS: =========================================================================
0:41:59.245752 PROGRESS: === Epoch 2, step 3, extracting elution groups 56000 to 120000 ===
0:41:59.394964 PROGRESS: Extracting batch of 126484 precursors
0:41:59.427420 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:41:59.427562 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:41:59.427623 INFO: FWHM in RT is 18.14 seconds, sigma is 0.66
0:41:59.427662 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:41:59.427960 INFO: Starting candidate selection
0:42:06.074117 INFO: Starting candidate scoring
0:42:10.277646 INFO: Finished candidate processing
0:42:10.277768 INFO: Collecting candidate features
0:42:12.599198 INFO: Collecting fragment features
0:42:13.196680 INFO: Finished candidate scoring
0:42:13.612028 PROGRESS: === Epoch 2, step 3, extracted 224441 precursors and 1208753 fragments ===
0:42:13.612367 INFO: performing precursor FDR with 47 features
0:42:13.612422 INFO: Decoy channel: -1
0:42:13.612458 INFO: Competetive: True
0:42:42.619693 INFO: Test AUC: 0.559
0:42:42.619922 INFO: Train AUC: 0.575
0:42:42.619973 INFO: AUC difference: 2.81%
0:42:42.875916 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
0:42:42.877354 PROGRESS: ============================= Precursor FDR =============================
0:42:42.877502 PROGRESS: Total precursors accumulated: 1,490
0:42:42.877589 PROGRESS: Target precursors: 1,360 (91.28%)
0:42:42.878295 PROGRESS: Decoy precursors: 130 (8.72%)
0:42:42.878386 PROGRESS: 
0:42:42.878458 PROGRESS: Precursor Summary:
0:42:42.880659 PROGRESS: Channel   0:	 0.05 FDR: 1,160; 0.01 FDR:   918; 0.001 FDR:     0
0:42:42.880792 PROGRESS: 
0:42:42.880874 PROGRESS: Protein Summary:
0:42:42.883426 PROGRESS: Channel   0:	 0.05 FDR: 1,009; 0.01 FDR:   802; 0.001 FDR:     0
0:42:42.883568 PROGRESS: =========================================================================
0:42:42.885921 INFO: calibration group: precursor, fitting rt estimator 
0:42:43.040763 INFO: calibration group: fragment, fitting mz estimator 
0:42:43.587030 INFO: === checking if epoch conditions were reached ===
0:42:43.587232 INFO: ✅ ms2_error      : 10.0000 <= 10
0:42:43.587327 INFO: ✅ rt_error       : 300.0000 <= 300
0:42:43.587412 INFO: ✅ current_epoch  : 2 >= 3
0:42:43.587497 INFO: ==============================================
0:42:43.642214 INFO: calibration group: precursor, predicting mz
0:42:43.642545 WARNING: mz prediction was skipped as it has not been fitted yet
0:42:43.642601 INFO: calibration group: precursor, predicting rt
0:42:51.508220 INFO: calibration group: fragment, predicting mz
0:43:11.798805 PROGRESS: Extracting batch of 10696137 precursors
0:43:13.873768 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:43:13.873899 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:43:13.873955 INFO: FWHM in RT is 17.09 seconds, sigma is 0.62
0:43:13.873993 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:43:13.874309 INFO: Starting candidate selection
0:47:48.027787 INFO: Applying score cutoff of 60.79728982925415
0:47:48.263782 INFO: Removed 14221128 precursors with score below cutoff
0:47:50.971468 INFO: Starting candidate scoring
0:49:26.654895 INFO: Finished candidate processing
0:49:26.655310 INFO: Collecting candidate features
0:49:44.759763 INFO: Collecting fragment features
0:49:52.034538 INFO: Finished candidate scoring
0:49:57.253172 INFO: performing precursor FDR with 47 features
0:49:57.253327 INFO: Decoy channel: -1
0:49:57.253368 INFO: Competetive: True
0:57:25.392036 INFO: Test AUC: 0.577
0:57:25.392282 INFO: Train AUC: 0.579
0:57:25.392335 INFO: AUC difference: 0.34%
0:57:26.136518 INFO: Removing fragments below FDR threshold
0:57:26.632382 PROGRESS: ============================= Precursor FDR =============================
0:57:26.632697 PROGRESS: Total precursors accumulated: 46,094
0:57:26.632802 PROGRESS: Target precursors: 45,638 (99.01%)
0:57:26.632881 PROGRESS: Decoy precursors: 456 (0.99%)
0:57:26.632958 PROGRESS: 
0:57:26.633030 PROGRESS: Precursor Summary:
0:57:26.658888 PROGRESS: Channel   0:	 0.05 FDR: 45,638; 0.01 FDR: 45,638; 0.001 FDR: 29,468
0:57:26.659144 PROGRESS: 
0:57:26.659228 PROGRESS: Protein Summary:
0:57:26.693940 PROGRESS: Channel   0:	 0.05 FDR: 8,483; 0.01 FDR: 8,483; 0.001 FDR: 6,124
0:57:26.694195 PROGRESS: =========================================================================
0:57:27.720794 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
0:57:28.562860 PROGRESS: Loading raw file 3/6: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
0:57:28.563082 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02 at /home/robbe/alphadia/Proteobench/.progress/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
0:58:00.873577 INFO: Determining DIA cycle
0:58:00.896832 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
0:58:00.903898 INFO: Determining DIA cycle
0:58:00.922884 INFO: Found cycle with start 0.00 min and length 151.
0:58:00.983346 INFO: ============ Raw file stats ============
0:58:00.983714 INFO: RT (min)            : 0.0 - 150.0
0:58:00.983792 INFO: RT duration (sec)   : 8999.7
0:58:00.983829 INFO: RT duration (min)   : 150.0
0:58:00.983949 INFO: Cycle len (scans)   : 151
0:58:00.983995 INFO: Cycle len (sec)     : 5.84
0:58:00.984030 INFO: Number of cycles    : 1542
0:58:00.984093 INFO: MS2 range (m/z)     : 396.4 - 1004.7
0:58:00.984133 INFO: ========================================
0:58:03.138289 INFO: Initializing CalibrationManager
0:58:03.138588 INFO: Loading calibration config
0:58:03.139477 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'function': LOESSRegression()}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'function': LOESSRegression(n_kernels=2)}]}]
0:58:03.139622 INFO: Calibration group :fragment, found 1 estimator(s)
0:58:03.139766 INFO: Calibration group :precursor, found 3 estimator(s)
0:58:03.139879 INFO: Disabling ion mobility calibration
0:58:03.139930 INFO: removed mobility estimator from group precursor
0:58:03.140042 INFO: Initializing OptimizationManager
0:58:03.140155 INFO: initial parameter: fwhm_rt = 5
0:58:03.140228 INFO: initial parameter: fwhm_mobility = 0.01
0:58:03.140297 INFO: initial parameter: score_cutoff = 0
0:58:03.140416 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
0:58:03.140530 INFO: Initializing OptimizationManager
0:58:03.140572 INFO: initial parameter: current_epoch = 0
0:58:03.140605 INFO: initial parameter: current_step = 0
0:58:03.140637 INFO: initial parameter: ms1_error = 20
0:58:03.140667 INFO: initial parameter: ms2_error = 20
0:58:03.140697 INFO: initial parameter: rt_error = 500
0:58:03.140728 INFO: initial parameter: mobility_error = 0.08
0:58:03.140758 INFO: initial parameter: column_type = library
0:58:03.140787 INFO: initial parameter: num_candidates = 2
0:58:03.140817 INFO: initial parameter: recalibration_target = 200
0:58:03.140847 INFO: initial parameter: accumulated_precursors = 0
0:58:03.140876 INFO: initial parameter: accumulated_precursors_01FDR = 0
0:58:03.140904 INFO: initial parameter: accumulated_precursors_001FDR = 0
0:58:03.140961 INFO: Initializing FDRManager
0:58:03.141024 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/classifier
0:58:04.700126 PROGRESS: 5,414,253 target precursors potentially observable (0 removed)
0:58:08.130159 INFO: === checking if epoch conditions were reached ===
0:58:08.130432 INFO: ❌ ms2_error      : 20.0000 > 10
0:58:08.130529 INFO: ❌ rt_error       : 500.0000 > 300
0:58:08.130609 INFO: ❌ current_epoch  : 0 < 3
0:58:08.130683 INFO: ==============================================
0:58:08.342375 INFO: calibration group: precursor, predicting mz
0:58:08.342627 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:08.342672 INFO: calibration group: precursor, predicting rt
0:58:08.342743 WARNING: rt prediction was skipped as it has not been fitted yet
0:58:08.342789 INFO: calibration group: fragment, predicting mz
0:58:08.342858 WARNING: mz prediction was skipped as it has not been fitted yet
0:58:08.342906 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
0:58:08.437765 PROGRESS: Extracting batch of 15793 precursors
0:58:08.443404 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:58:08.443522 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:08.443577 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:58:08.443615 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:58:08.443900 INFO: Starting candidate selection
0:58:11.187405 INFO: Starting candidate scoring
0:58:12.261017 INFO: Finished candidate processing
0:58:12.261155 INFO: Collecting candidate features
0:58:13.930448 INFO: Collecting fragment features
0:58:14.356790 INFO: Finished candidate scoring
0:58:14.576223 PROGRESS: === Epoch 0, step 0, extracted 26242 precursors and 178277 fragments ===
0:58:14.576538 INFO: performing precursor FDR with 47 features
0:58:14.576595 INFO: Decoy channel: -1
0:58:14.576631 INFO: Competetive: True
0:58:15.892545 INFO: Test AUC: 0.520
0:58:15.892717 INFO: Train AUC: 0.520
0:58:15.892792 INFO: AUC difference: 0.04%
0:58:16.057082 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:58:16.059973 PROGRESS: ============================= Precursor FDR =============================
0:58:16.060173 PROGRESS: Total precursors accumulated: 6,792
0:58:16.060300 PROGRESS: Target precursors: 3,582 (52.74%)
0:58:16.060415 PROGRESS: Decoy precursors: 3,210 (47.26%)
0:58:16.060525 PROGRESS: 
0:58:16.060634 PROGRESS: Precursor Summary:
0:58:16.062474 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:58:16.062641 PROGRESS: 
0:58:16.062766 PROGRESS: Protein Summary:
0:58:16.064708 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
0:58:16.064864 PROGRESS: =========================================================================
0:58:16.065882 PROGRESS: === Epoch 0, step 1, extracting elution groups 8000 to 24000 ===
0:58:16.166625 PROGRESS: Extracting batch of 31553 precursors
0:58:16.175543 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:58:16.175663 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:16.175738 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:58:16.175795 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:58:16.176074 INFO: Starting candidate selection
0:58:19.420064 INFO: Starting candidate scoring
0:58:20.888166 INFO: Finished candidate processing
0:58:20.888350 INFO: Collecting candidate features
0:58:22.858372 INFO: Collecting fragment features
0:58:23.321881 INFO: Finished candidate scoring
0:58:23.582327 PROGRESS: === Epoch 0, step 1, extracted 52565 precursors and 356991 fragments ===
0:58:23.582757 INFO: performing precursor FDR with 47 features
0:58:23.582819 INFO: Decoy channel: -1
0:58:23.582861 INFO: Competetive: True
0:58:28.108057 INFO: Test AUC: 0.536
0:58:28.108207 INFO: Train AUC: 0.555
0:58:28.108255 INFO: AUC difference: 3.41%
0:58:28.274100 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:58:28.275072 PROGRESS: ============================= Precursor FDR =============================
0:58:28.275215 PROGRESS: Total precursors accumulated: 89
0:58:28.275302 PROGRESS: Target precursors: 81 (91.01%)
0:58:28.275376 PROGRESS: Decoy precursors: 8 (8.99%)
0:58:28.275447 PROGRESS: 
0:58:28.275525 PROGRESS: Precursor Summary:
0:58:28.277248 PROGRESS: Channel   0:	 0.05 FDR:    66; 0.01 FDR:    53; 0.001 FDR:    53
0:58:28.277380 PROGRESS: 
0:58:28.277460 PROGRESS: Protein Summary:
0:58:28.279350 PROGRESS: Channel   0:	 0.05 FDR:    66; 0.01 FDR:    53; 0.001 FDR:    53
0:58:28.279483 PROGRESS: =========================================================================
0:58:28.280502 PROGRESS: === Epoch 0, step 2, extracting elution groups 24000 to 56000 ===
0:58:28.392660 PROGRESS: Extracting batch of 63205 precursors
0:58:28.408574 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:58:28.408702 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:28.408757 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:58:28.408795 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:58:28.409101 INFO: Starting candidate selection
0:58:32.528995 INFO: Starting candidate scoring
0:58:34.772616 INFO: Finished candidate processing
0:58:34.772740 INFO: Collecting candidate features
0:58:36.740662 INFO: Collecting fragment features
0:58:37.262773 INFO: Finished candidate scoring
0:58:37.598732 PROGRESS: === Epoch 0, step 2, extracted 105131 precursors and 712920 fragments ===
0:58:37.599083 INFO: performing precursor FDR with 47 features
0:58:37.599142 INFO: Decoy channel: -1
0:58:37.599177 INFO: Competetive: True
0:58:49.250318 INFO: Test AUC: 0.549
0:58:49.250460 INFO: Train AUC: 0.566
0:58:49.250509 INFO: AUC difference: 3.04%
0:58:49.418034 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:58:49.419112 PROGRESS: ============================= Precursor FDR =============================
0:58:49.419252 PROGRESS: Total precursors accumulated: 384
0:58:49.419338 PROGRESS: Target precursors: 350 (91.15%)
0:58:49.419412 PROGRESS: Decoy precursors: 34 (8.85%)
0:58:49.419489 PROGRESS: 
0:58:49.419560 PROGRESS: Precursor Summary:
0:58:49.421387 PROGRESS: Channel   0:	 0.05 FDR:   295; 0.01 FDR:   197; 0.001 FDR:   168
0:58:49.421524 PROGRESS: 
0:58:49.421608 PROGRESS: Protein Summary:
0:58:49.423686 PROGRESS: Channel   0:	 0.05 FDR:   285; 0.01 FDR:   190; 0.001 FDR:   163
0:58:49.423824 PROGRESS: =========================================================================
0:58:49.424859 PROGRESS: === Epoch 0, step 3, extracting elution groups 56000 to 120000 ===
0:58:49.582339 PROGRESS: Extracting batch of 126427 precursors
0:58:49.612126 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:58:49.612260 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:58:49.612309 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
0:58:49.612347 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
0:58:49.612617 INFO: Starting candidate selection
0:58:55.791160 INFO: Starting candidate scoring
0:58:59.481270 INFO: Finished candidate processing
0:58:59.481396 INFO: Collecting candidate features
0:59:01.668584 INFO: Collecting fragment features
0:59:02.243752 INFO: Finished candidate scoring
0:59:02.691794 PROGRESS: === Epoch 0, step 3, extracted 209897 precursors and 1419726 fragments ===
0:59:02.692140 INFO: performing precursor FDR with 47 features
0:59:02.692198 INFO: Decoy channel: -1
0:59:02.692235 INFO: Competetive: True
0:59:28.967571 INFO: Test AUC: 0.557
0:59:28.967834 INFO: Train AUC: 0.569
0:59:28.967886 INFO: AUC difference: 2.15%
0:59:29.172564 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
0:59:29.173915 PROGRESS: ============================= Precursor FDR =============================
0:59:29.174644 PROGRESS: Total precursors accumulated: 951
0:59:29.174776 PROGRESS: Target precursors: 869 (91.38%)
0:59:29.174857 PROGRESS: Decoy precursors: 82 (8.62%)
0:59:29.174933 PROGRESS: 
0:59:29.175004 PROGRESS: Precursor Summary:
0:59:29.177141 PROGRESS: Channel   0:	 0.05 FDR:   711; 0.01 FDR:   546; 0.001 FDR:    81
0:59:29.177286 PROGRESS: 
0:59:29.177369 PROGRESS: Protein Summary:
0:59:29.179817 PROGRESS: Channel   0:	 0.05 FDR:   645; 0.01 FDR:   494; 0.001 FDR:    80
0:59:29.179960 PROGRESS: =========================================================================
0:59:29.182099 INFO: calibration group: precursor, fitting rt estimator 
0:59:29.264771 INFO: calibration group: fragment, fitting mz estimator 
0:59:29.812932 INFO: === checking if epoch conditions were reached ===
0:59:29.813184 INFO: ✅ ms2_error      : 10.0000 <= 10
0:59:29.813290 INFO: ❌ rt_error       : 324.7697 > 300
0:59:29.813380 INFO: ❌ current_epoch  : 0 < 3
0:59:29.813462 INFO: ==============================================
0:59:30.041433 INFO: calibration group: precursor, predicting mz
0:59:30.041765 WARNING: mz prediction was skipped as it has not been fitted yet
0:59:30.041819 INFO: calibration group: precursor, predicting rt
0:59:38.460809 INFO: calibration group: fragment, predicting mz
0:59:58.392949 PROGRESS: === Epoch 1, step 0, extracting elution groups 0 to 8000 ===
0:59:58.542311 PROGRESS: Extracting batch of 15821 precursors
0:59:58.549550 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
0:59:58.549666 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
0:59:58.549720 INFO: FWHM in RT is 20.59 seconds, sigma is 0.75
0:59:58.549759 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
0:59:58.550097 INFO: Starting candidate selection
1:00:02.671662 INFO: Starting candidate scoring
1:00:04.036583 INFO: Finished candidate processing
1:00:04.036705 INFO: Collecting candidate features
1:00:05.928275 INFO: Collecting fragment features
1:00:06.391958 INFO: Finished candidate scoring
1:00:06.657566 PROGRESS: === Epoch 1, step 0, extracted 25048 precursors and 152821 fragments ===
1:00:06.657900 INFO: performing precursor FDR with 47 features
1:00:06.657955 INFO: Decoy channel: -1
1:00:06.657992 INFO: Competetive: True
1:00:07.989403 INFO: Test AUC: 0.540
1:00:07.989560 INFO: Train AUC: 0.582
1:00:07.989608 INFO: AUC difference: 7.25%
1:00:07.989648 WARNING: AUC difference > 5%. This may indicate overfitting.
1:00:08.142667 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:00:08.143675 PROGRESS: ============================= Precursor FDR =============================
1:00:08.143822 PROGRESS: Total precursors accumulated: 78
1:00:08.143910 PROGRESS: Target precursors: 72 (92.31%)
1:00:08.143985 PROGRESS: Decoy precursors: 6 (7.69%)
1:00:08.144056 PROGRESS: 
1:00:08.144127 PROGRESS: Precursor Summary:
1:00:08.145818 PROGRESS: Channel   0:	 0.05 FDR:    53; 0.01 FDR:    32; 0.001 FDR:    32
1:00:08.145952 PROGRESS: 
1:00:08.146034 PROGRESS: Protein Summary:
1:00:08.147900 PROGRESS: Channel   0:	 0.05 FDR:    53; 0.01 FDR:    32; 0.001 FDR:    32
1:00:08.148030 PROGRESS: =========================================================================
1:00:08.149014 PROGRESS: === Epoch 1, step 1, extracting elution groups 8000 to 24000 ===
1:00:08.272463 PROGRESS: Extracting batch of 31606 precursors
1:00:08.281812 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:00:08.281938 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:00:08.281987 INFO: FWHM in RT is 20.59 seconds, sigma is 0.75
1:00:08.282025 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:00:08.282273 INFO: Starting candidate selection
1:00:12.042939 INFO: Starting candidate scoring
1:00:13.647528 INFO: Finished candidate processing
1:00:13.647746 INFO: Collecting candidate features
1:00:15.492503 INFO: Collecting fragment features
1:00:15.955607 INFO: Finished candidate scoring
1:00:16.226801 PROGRESS: === Epoch 1, step 1, extracted 49909 precursors and 302584 fragments ===
1:00:16.227119 INFO: performing precursor FDR with 47 features
1:00:16.227174 INFO: Decoy channel: -1
1:00:16.227211 INFO: Competetive: True
1:00:20.535007 INFO: Test AUC: 0.559
1:00:20.535154 INFO: Train AUC: 0.583
1:00:20.535201 INFO: AUC difference: 4.21%
1:00:20.695114 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:00:20.696169 PROGRESS: ============================= Precursor FDR =============================
1:00:20.696318 PROGRESS: Total precursors accumulated: 227
1:00:20.696416 PROGRESS: Target precursors: 208 (91.63%)
1:00:20.696492 PROGRESS: Decoy precursors: 19 (8.37%)
1:00:20.696563 PROGRESS: 
1:00:20.696633 PROGRESS: Precursor Summary:
1:00:20.698406 PROGRESS: Channel   0:	 0.05 FDR:   173; 0.01 FDR:   134; 0.001 FDR:    88
1:00:20.698547 PROGRESS: 
1:00:20.698630 PROGRESS: Protein Summary:
1:00:20.700591 PROGRESS: Channel   0:	 0.05 FDR:   169; 0.01 FDR:   130; 0.001 FDR:    86
1:00:20.700721 PROGRESS: =========================================================================
1:00:20.701751 PROGRESS: === Epoch 1, step 2, extracting elution groups 24000 to 56000 ===
1:00:20.820692 PROGRESS: Extracting batch of 63211 precursors
1:00:20.837595 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:00:20.837723 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:00:20.837776 INFO: FWHM in RT is 20.59 seconds, sigma is 0.75
1:00:20.837814 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:00:20.838073 INFO: Starting candidate selection
1:00:25.326249 INFO: Starting candidate scoring
1:00:27.631330 INFO: Finished candidate processing
1:00:27.631543 INFO: Collecting candidate features
1:00:29.782211 INFO: Collecting fragment features
1:00:30.279975 INFO: Finished candidate scoring
1:00:30.613400 PROGRESS: === Epoch 1, step 2, extracted 100087 precursors and 610228 fragments ===
1:00:30.613826 INFO: performing precursor FDR with 47 features
1:00:30.613885 INFO: Decoy channel: -1
1:00:30.613922 INFO: Competetive: True
1:00:42.734609 INFO: Test AUC: 0.556
1:00:42.734761 INFO: Train AUC: 0.582
1:00:42.734809 INFO: AUC difference: 4.59%
1:00:42.900410 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:00:42.901546 PROGRESS: ============================= Precursor FDR =============================
1:00:42.901689 PROGRESS: Total precursors accumulated: 551
1:00:42.901775 PROGRESS: Target precursors: 503 (91.29%)
1:00:42.901852 PROGRESS: Decoy precursors: 48 (8.71%)
1:00:42.901924 PROGRESS: 
1:00:42.901996 PROGRESS: Precursor Summary:
1:00:42.903903 PROGRESS: Channel   0:	 0.05 FDR:   406; 0.01 FDR:   249; 0.001 FDR:   201
1:00:42.904054 PROGRESS: 
1:00:42.904142 PROGRESS: Protein Summary:
1:00:42.906288 PROGRESS: Channel   0:	 0.05 FDR:   388; 0.01 FDR:   239; 0.001 FDR:   193
1:00:42.906415 PROGRESS: =========================================================================
1:00:42.907485 PROGRESS: === Epoch 1, step 3, extracting elution groups 56000 to 120000 ===
1:00:43.046078 PROGRESS: Extracting batch of 126404 precursors
1:00:43.078514 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:00:43.078645 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:00:43.078699 INFO: FWHM in RT is 20.59 seconds, sigma is 0.75
1:00:43.078737 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:00:43.079041 INFO: Starting candidate selection
1:00:49.630589 INFO: Starting candidate scoring
1:00:53.409723 INFO: Finished candidate processing
1:00:53.409842 INFO: Collecting candidate features
1:00:55.643338 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 200243)
1:00:55.644115 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 200243)
1:00:55.663887 INFO: Collecting fragment features
1:00:56.233649 INFO: Finished candidate scoring
1:00:56.662620 PROGRESS: === Epoch 1, step 3, extracted 200243 precursors and 1220040 fragments ===
1:00:56.662954 INFO: performing precursor FDR with 47 features
1:00:56.663011 INFO: Decoy channel: -1
1:00:56.663048 INFO: Competetive: True
1:00:56.962312 WARNING: dropped 1 decoy PSMs due to missing features
1:01:22.577462 INFO: Test AUC: 0.563
1:01:22.577615 INFO: Train AUC: 0.577
1:01:22.577666 INFO: AUC difference: 2.45%
1:01:22.762079 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:01:22.763374 PROGRESS: ============================= Precursor FDR =============================
1:01:22.763525 PROGRESS: Total precursors accumulated: 1,035
1:01:22.763613 PROGRESS: Target precursors: 943 (91.11%)
1:01:22.763688 PROGRESS: Decoy precursors: 92 (8.89%)
1:01:22.763759 PROGRESS: 
1:01:22.763832 PROGRESS: Precursor Summary:
1:01:22.765992 PROGRESS: Channel   0:	 0.05 FDR:   794; 0.01 FDR:   561; 0.001 FDR:   408
1:01:22.766135 PROGRESS: 
1:01:22.766220 PROGRESS: Protein Summary:
1:01:22.768701 PROGRESS: Channel   0:	 0.05 FDR:   724; 0.01 FDR:   515; 0.001 FDR:   387
1:01:22.768841 PROGRESS: =========================================================================
1:01:22.770948 INFO: calibration group: precursor, fitting rt estimator 
1:01:22.858202 INFO: calibration group: fragment, fitting mz estimator 
1:01:23.398249 INFO: === checking if epoch conditions were reached ===
1:01:23.398463 INFO: ✅ ms2_error      : 10.0000 <= 10
1:01:23.398557 INFO: ✅ rt_error       : 300.0000 <= 300
1:01:23.398637 INFO: ❌ current_epoch  : 1 < 3
1:01:23.398711 INFO: ==============================================
1:01:23.623751 INFO: calibration group: precursor, predicting mz
1:01:23.624036 WARNING: mz prediction was skipped as it has not been fitted yet
1:01:23.624093 INFO: calibration group: precursor, predicting rt
1:01:32.093773 INFO: calibration group: fragment, predicting mz
1:01:51.885196 PROGRESS: === Epoch 2, step 0, extracting elution groups 0 to 8000 ===
1:01:52.137243 PROGRESS: Extracting batch of 15837 precursors
1:01:52.144827 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:01:52.144940 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:01:52.144996 INFO: FWHM in RT is 19.01 seconds, sigma is 0.69
1:01:52.145034 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:01:52.145937 INFO: Starting candidate selection
1:01:55.803529 INFO: Starting candidate scoring
1:01:57.121259 INFO: Finished candidate processing
1:01:57.121424 INFO: Collecting candidate features
1:01:58.888688 INFO: Collecting fragment features
1:01:59.316523 INFO: Finished candidate scoring
1:01:59.553889 PROGRESS: === Epoch 2, step 0, extracted 27065 precursors and 162845 fragments ===
1:01:59.554219 INFO: performing precursor FDR with 47 features
1:01:59.554277 INFO: Decoy channel: -1
1:01:59.554315 INFO: Competetive: True
1:02:00.945342 INFO: Test AUC: 0.555
1:02:00.945477 INFO: Train AUC: 0.584
1:02:00.945525 INFO: AUC difference: 5.03%
1:02:00.945566 WARNING: AUC difference > 5%. This may indicate overfitting.
1:02:01.095299 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:02:01.096233 PROGRESS: ============================= Precursor FDR =============================
1:02:01.096374 PROGRESS: Total precursors accumulated: 106
1:02:01.096461 PROGRESS: Target precursors: 96 (90.57%)
1:02:01.096538 PROGRESS: Decoy precursors: 10 (9.43%)
1:02:01.096611 PROGRESS: 
1:02:01.096683 PROGRESS: Precursor Summary:
1:02:01.098367 PROGRESS: Channel   0:	 0.05 FDR:    82; 0.01 FDR:    68; 0.001 FDR:    68
1:02:01.098504 PROGRESS: 
1:02:01.098598 PROGRESS: Protein Summary:
1:02:01.100505 PROGRESS: Channel   0:	 0.05 FDR:    81; 0.01 FDR:    67; 0.001 FDR:    67
1:02:01.100642 PROGRESS: =========================================================================
1:02:01.101602 PROGRESS: === Epoch 2, step 1, extracting elution groups 8000 to 24000 ===
1:02:01.218522 PROGRESS: Extracting batch of 31593 precursors
1:02:01.226932 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:02:01.227048 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:02:01.227098 INFO: FWHM in RT is 19.01 seconds, sigma is 0.69
1:02:01.227138 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:02:01.227377 INFO: Starting candidate selection
1:02:05.595285 INFO: Starting candidate scoring
1:02:07.266936 INFO: Finished candidate processing
1:02:07.267077 INFO: Collecting candidate features
1:02:09.003342 INFO: Collecting fragment features
1:02:09.449888 INFO: Finished candidate scoring
1:02:09.702996 PROGRESS: === Epoch 2, step 1, extracted 53678 precursors and 322529 fragments ===
1:02:09.703323 INFO: performing precursor FDR with 47 features
1:02:09.703378 INFO: Decoy channel: -1
1:02:09.703414 INFO: Competetive: True
1:02:14.342498 INFO: Test AUC: 0.561
1:02:14.342645 INFO: Train AUC: 0.591
1:02:14.342694 INFO: AUC difference: 5.08%
1:02:14.342730 WARNING: AUC difference > 5%. This may indicate overfitting.
1:02:14.495893 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:02:14.496938 PROGRESS: ============================= Precursor FDR =============================
1:02:14.497078 PROGRESS: Total precursors accumulated: 301
1:02:14.497164 PROGRESS: Target precursors: 276 (91.69%)
1:02:14.497238 PROGRESS: Decoy precursors: 25 (8.31%)
1:02:14.497309 PROGRESS: 
1:02:14.497380 PROGRESS: Precursor Summary:
1:02:14.499192 PROGRESS: Channel   0:	 0.05 FDR:   223; 0.01 FDR:   160; 0.001 FDR:   146
1:02:14.499335 PROGRESS: 
1:02:14.499422 PROGRESS: Protein Summary:
1:02:14.501454 PROGRESS: Channel   0:	 0.05 FDR:   218; 0.01 FDR:   156; 0.001 FDR:   143
1:02:14.501590 PROGRESS: =========================================================================
1:02:14.502612 PROGRESS: === Epoch 2, step 2, extracting elution groups 24000 to 56000 ===
1:02:14.624108 PROGRESS: Extracting batch of 63186 precursors
1:02:14.639821 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:02:14.639966 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:02:14.640017 INFO: FWHM in RT is 19.01 seconds, sigma is 0.69
1:02:14.640054 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:02:14.640309 INFO: Starting candidate selection
1:02:19.599961 INFO: Starting candidate scoring
1:02:22.164747 INFO: Finished candidate processing
1:02:22.164866 INFO: Collecting candidate features
1:02:24.161420 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 107865)
1:02:24.175499 INFO: Collecting fragment features
1:02:24.674506 INFO: Finished candidate scoring
1:02:24.979556 PROGRESS: === Epoch 2, step 2, extracted 107865 precursors and 648029 fragments ===
1:02:24.979882 INFO: performing precursor FDR with 47 features
1:02:24.979935 INFO: Decoy channel: -1
1:02:24.979973 INFO: Competetive: True
1:02:25.117524 WARNING: dropped 1 target PSMs due to missing features
1:02:37.304793 INFO: Test AUC: 0.559
1:02:37.304941 INFO: Train AUC: 0.585
1:02:37.304990 INFO: AUC difference: 4.57%
1:02:37.474139 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:02:37.475344 PROGRESS: ============================= Precursor FDR =============================
1:02:37.475502 PROGRESS: Total precursors accumulated: 794
1:02:37.475592 PROGRESS: Target precursors: 722 (90.93%)
1:02:37.475666 PROGRESS: Decoy precursors: 72 (9.07%)
1:02:37.475735 PROGRESS: 
1:02:37.475806 PROGRESS: Precursor Summary:
1:02:37.477764 PROGRESS: Channel   0:	 0.05 FDR:   521; 0.01 FDR:   319; 0.001 FDR:   221
1:02:37.477925 PROGRESS: 
1:02:37.478040 PROGRESS: Protein Summary:
1:02:37.480467 PROGRESS: Channel   0:	 0.05 FDR:   479; 0.01 FDR:   295; 0.001 FDR:   207
1:02:37.480611 PROGRESS: =========================================================================
1:02:37.481748 PROGRESS: === Epoch 2, step 3, extracting elution groups 56000 to 120000 ===
1:02:37.646491 PROGRESS: Extracting batch of 126383 precursors
1:02:37.677323 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:02:37.677463 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:02:37.677514 INFO: FWHM in RT is 19.01 seconds, sigma is 0.69
1:02:37.677552 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:02:37.677809 INFO: Starting candidate selection
1:02:43.870317 INFO: Starting candidate scoring
1:02:47.813692 INFO: Finished candidate processing
1:02:47.813921 INFO: Collecting candidate features
1:02:50.187648 INFO: Collecting fragment features
1:02:50.788943 INFO: Finished candidate scoring
1:02:51.209048 PROGRESS: === Epoch 2, step 3, extracted 215343 precursors and 1294680 fragments ===
1:02:51.209454 INFO: performing precursor FDR with 47 features
1:02:51.209510 INFO: Decoy channel: -1
1:02:51.209547 INFO: Competetive: True
1:02:51.506290 WARNING: dropped 1 target PSMs due to missing features
1:03:17.780155 INFO: Test AUC: 0.563
1:03:17.780305 INFO: Train AUC: 0.580
1:03:17.780353 INFO: AUC difference: 3.07%
1:03:17.970650 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:03:17.972041 PROGRESS: ============================= Precursor FDR =============================
1:03:17.972191 PROGRESS: Total precursors accumulated: 1,526
1:03:17.972278 PROGRESS: Target precursors: 1,389 (91.02%)
1:03:17.972363 PROGRESS: Decoy precursors: 137 (8.98%)
1:03:17.972436 PROGRESS: 
1:03:17.972505 PROGRESS: Precursor Summary:
1:03:17.974869 PROGRESS: Channel   0:	 0.05 FDR: 1,115; 0.01 FDR:   875; 0.001 FDR:   546
1:03:17.975001 PROGRESS: 
1:03:17.975081 PROGRESS: Protein Summary:
1:03:17.977808 PROGRESS: Channel   0:	 0.05 FDR:   967; 0.01 FDR:   764; 0.001 FDR:   481
1:03:17.977945 PROGRESS: =========================================================================
1:03:17.980324 INFO: calibration group: precursor, fitting rt estimator 
1:03:18.081090 INFO: calibration group: fragment, fitting mz estimator 
1:03:18.656795 INFO: === checking if epoch conditions were reached ===
1:03:18.657014 INFO: ✅ ms2_error      : 10.0000 <= 10
1:03:18.657118 INFO: ✅ rt_error       : 300.0000 <= 300
1:03:18.657197 INFO: ✅ current_epoch  : 2 >= 3
1:03:18.657270 INFO: ==============================================
1:03:18.683763 INFO: calibration group: precursor, predicting mz
1:03:18.684107 WARNING: mz prediction was skipped as it has not been fitted yet
1:03:18.684156 INFO: calibration group: precursor, predicting rt
1:03:26.714086 INFO: calibration group: fragment, predicting mz
1:03:47.032863 PROGRESS: Extracting batch of 10696137 precursors
1:03:49.429588 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:03:49.429723 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:03:49.429781 INFO: FWHM in RT is 18.39 seconds, sigma is 0.67
1:03:49.429836 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:03:49.430187 INFO: Starting candidate selection
1:08:25.749553 INFO: Applying score cutoff of 58.25690005493164
1:08:26.106456 INFO: Removed 10472943 precursors with score below cutoff
1:08:28.762335 INFO: Starting candidate scoring
1:10:52.682157 INFO: Finished candidate processing
1:10:52.682917 INFO: Collecting candidate features
1:11:17.994691 INFO: Collecting fragment features
1:11:28.507922 INFO: Finished candidate scoring
1:11:38.360660 INFO: performing precursor FDR with 47 features
1:11:38.360812 INFO: Decoy channel: -1
1:11:38.360853 INFO: Competetive: True
1:23:43.174046 INFO: Test AUC: 0.576
1:23:43.174294 INFO: Train AUC: 0.578
1:23:43.174349 INFO: AUC difference: 0.27%
1:23:44.183995 INFO: Removing fragments below FDR threshold
1:23:44.924268 PROGRESS: ============================= Precursor FDR =============================
1:23:44.924578 PROGRESS: Total precursors accumulated: 48,130
1:23:44.924684 PROGRESS: Target precursors: 47,654 (99.01%)
1:23:44.924761 PROGRESS: Decoy precursors: 476 (0.99%)
1:23:44.924836 PROGRESS: 
1:23:44.924908 PROGRESS: Precursor Summary:
1:23:44.951121 PROGRESS: Channel   0:	 0.05 FDR: 47,654; 0.01 FDR: 47,654; 0.001 FDR: 31,406
1:23:44.951385 PROGRESS: 
1:23:44.951481 PROGRESS: Protein Summary:
1:23:44.988343 PROGRESS: Channel   0:	 0.05 FDR: 8,635; 0.01 FDR: 8,635; 0.001 FDR: 6,390
1:23:44.988613 PROGRESS: =========================================================================
1:23:45.658992 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
1:23:46.210043 PROGRESS: Loading raw file 4/6: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:23:46.210263 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 at /home/robbe/alphadia/Proteobench/.progress/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:24:17.017835 INFO: Determining DIA cycle
1:24:17.035783 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
1:24:17.041862 INFO: Determining DIA cycle
1:24:17.066297 INFO: Found cycle with start 0.00 min and length 151.
1:24:17.226942 INFO: ============ Raw file stats ============
1:24:17.227379 INFO: RT (min)            : 0.0 - 150.0
1:24:17.227486 INFO: RT duration (sec)   : 8999.7
1:24:17.227527 INFO: RT duration (min)   : 150.0
1:24:17.227648 INFO: Cycle len (scans)   : 151
1:24:17.227694 INFO: Cycle len (sec)     : 5.83
1:24:17.227730 INFO: Number of cycles    : 1542
1:24:17.227817 INFO: MS2 range (m/z)     : 396.4 - 1004.7
1:24:17.227857 INFO: ========================================
1:24:21.196775 INFO: Initializing CalibrationManager
1:24:21.197194 INFO: Loading calibration config
1:24:21.198088 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'function': LOESSRegression()}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'function': LOESSRegression(n_kernels=2)}]}]
1:24:21.198253 INFO: Calibration group :fragment, found 1 estimator(s)
1:24:21.198430 INFO: Calibration group :precursor, found 3 estimator(s)
1:24:21.198567 INFO: Disabling ion mobility calibration
1:24:21.198620 INFO: removed mobility estimator from group precursor
1:24:21.198750 INFO: Initializing OptimizationManager
1:24:21.198870 INFO: initial parameter: fwhm_rt = 5
1:24:21.198945 INFO: initial parameter: fwhm_mobility = 0.01
1:24:21.199014 INFO: initial parameter: score_cutoff = 0
1:24:21.199135 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:24:21.199255 INFO: Initializing OptimizationManager
1:24:21.199300 INFO: initial parameter: current_epoch = 0
1:24:21.199332 INFO: initial parameter: current_step = 0
1:24:21.199365 INFO: initial parameter: ms1_error = 20
1:24:21.199399 INFO: initial parameter: ms2_error = 20
1:24:21.199431 INFO: initial parameter: rt_error = 500
1:24:21.199471 INFO: initial parameter: mobility_error = 0.08
1:24:21.199503 INFO: initial parameter: column_type = library
1:24:21.199534 INFO: initial parameter: num_candidates = 2
1:24:21.199564 INFO: initial parameter: recalibration_target = 200
1:24:21.199595 INFO: initial parameter: accumulated_precursors = 0
1:24:21.199626 INFO: initial parameter: accumulated_precursors_01FDR = 0
1:24:21.199656 INFO: initial parameter: accumulated_precursors_001FDR = 0
1:24:21.199722 INFO: Initializing FDRManager
1:24:21.199777 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/classifier
1:24:23.215744 PROGRESS: 5,414,253 target precursors potentially observable (0 removed)
1:24:28.083440 INFO: === checking if epoch conditions were reached ===
1:24:28.084461 INFO: ❌ ms2_error      : 20.0000 > 10
1:24:28.084593 INFO: ❌ rt_error       : 500.0000 > 300
1:24:28.084678 INFO: ❌ current_epoch  : 0 < 3
1:24:28.084753 INFO: ==============================================
1:24:28.316748 INFO: calibration group: precursor, predicting mz
1:24:28.317674 WARNING: mz prediction was skipped as it has not been fitted yet
1:24:28.317774 INFO: calibration group: precursor, predicting rt
1:24:28.317870 WARNING: rt prediction was skipped as it has not been fitted yet
1:24:28.317941 INFO: calibration group: fragment, predicting mz
1:24:28.318020 WARNING: mz prediction was skipped as it has not been fitted yet
1:24:28.318079 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
1:24:28.417340 PROGRESS: Extracting batch of 15810 precursors
1:24:28.427394 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:24:28.427536 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:24:28.427607 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:24:28.427646 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:24:28.428226 INFO: Starting candidate selection
1:24:31.504909 INFO: Starting candidate scoring
1:24:32.633170 INFO: Finished candidate processing
1:24:32.633310 INFO: Collecting candidate features
1:24:34.586272 INFO: Collecting fragment features
1:24:35.049784 INFO: Finished candidate scoring
1:24:35.291620 PROGRESS: === Epoch 0, step 0, extracted 26990 precursors and 170627 fragments ===
1:24:35.291978 INFO: performing precursor FDR with 47 features
1:24:35.292037 INFO: Decoy channel: -1
1:24:35.292074 INFO: Competetive: True
1:24:36.564353 INFO: Test AUC: 0.545
1:24:36.564557 INFO: Train AUC: 0.545
1:24:36.564653 INFO: AUC difference: 0.00%
1:24:36.728918 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:24:36.732291 PROGRESS: ============================= Precursor FDR =============================
1:24:36.732492 PROGRESS: Total precursors accumulated: 6,997
1:24:36.732580 PROGRESS: Target precursors: 4,001 (57.18%)
1:24:36.732655 PROGRESS: Decoy precursors: 2,996 (42.82%)
1:24:36.732727 PROGRESS: 
1:24:36.732800 PROGRESS: Precursor Summary:
1:24:36.734736 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:24:36.734886 PROGRESS: 
1:24:36.734969 PROGRESS: Protein Summary:
1:24:36.736855 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:24:36.736994 PROGRESS: =========================================================================
1:24:36.737923 PROGRESS: === Epoch 0, step 1, extracting elution groups 8000 to 24000 ===
1:24:36.858321 PROGRESS: Extracting batch of 31593 precursors
1:24:36.868630 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:24:36.868763 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:24:36.868816 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:24:36.868853 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:24:36.869123 INFO: Starting candidate selection
1:24:40.525235 INFO: Starting candidate scoring
1:24:42.198702 INFO: Finished candidate processing
1:24:42.198842 INFO: Collecting candidate features
1:24:44.134106 INFO: Collecting fragment features
1:24:44.663540 INFO: Finished candidate scoring
1:24:44.980161 PROGRESS: === Epoch 0, step 1, extracted 53490 precursors and 338889 fragments ===
1:24:44.980520 INFO: performing precursor FDR with 47 features
1:24:44.980581 INFO: Decoy channel: -1
1:24:44.980618 INFO: Competetive: True
1:24:49.183642 INFO: Test AUC: 0.551
1:24:49.183799 INFO: Train AUC: 0.563
1:24:49.183847 INFO: AUC difference: 2.20%
1:24:49.345348 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:24:49.346397 PROGRESS: ============================= Precursor FDR =============================
1:24:49.346544 PROGRESS: Total precursors accumulated: 120
1:24:49.346630 PROGRESS: Target precursors: 109 (90.83%)
1:24:49.346704 PROGRESS: Decoy precursors: 11 (9.17%)
1:24:49.346774 PROGRESS: 
1:24:49.346846 PROGRESS: Precursor Summary:
1:24:49.348541 PROGRESS: Channel   0:	 0.05 FDR:    52; 0.01 FDR:    39; 0.001 FDR:    39
1:24:49.348679 PROGRESS: 
1:24:49.348760 PROGRESS: Protein Summary:
1:24:49.350614 PROGRESS: Channel   0:	 0.05 FDR:    52; 0.01 FDR:    39; 0.001 FDR:    39
1:24:49.350748 PROGRESS: =========================================================================
1:24:49.351717 PROGRESS: === Epoch 0, step 2, extracting elution groups 24000 to 56000 ===
1:24:49.475694 PROGRESS: Extracting batch of 63235 precursors
1:24:49.492847 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:24:49.492999 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:24:49.493051 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:24:49.493089 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:24:49.493366 INFO: Starting candidate selection
1:24:54.074836 INFO: Starting candidate scoring
1:24:56.288697 INFO: Finished candidate processing
1:24:56.288944 INFO: Collecting candidate features
1:24:58.341610 INFO: Collecting fragment features
1:24:58.891669 INFO: Finished candidate scoring
1:24:59.222688 PROGRESS: === Epoch 0, step 2, extracted 107015 precursors and 677196 fragments ===
1:24:59.223056 INFO: performing precursor FDR with 47 features
1:24:59.223115 INFO: Decoy channel: -1
1:24:59.223153 INFO: Competetive: True
1:25:09.736981 INFO: Test AUC: 0.551
1:25:09.737150 INFO: Train AUC: 0.569
1:25:09.737199 INFO: AUC difference: 3.11%
1:25:09.908921 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:25:09.910070 PROGRESS: ============================= Precursor FDR =============================
1:25:09.910217 PROGRESS: Total precursors accumulated: 407
1:25:09.910303 PROGRESS: Target precursors: 371 (91.15%)
1:25:09.910377 PROGRESS: Decoy precursors: 36 (8.85%)
1:25:09.910448 PROGRESS: 
1:25:09.910518 PROGRESS: Precursor Summary:
1:25:09.912381 PROGRESS: Channel   0:	 0.05 FDR:   309; 0.01 FDR:   180; 0.001 FDR:   140
1:25:09.912527 PROGRESS: 
1:25:09.912608 PROGRESS: Protein Summary:
1:25:09.914712 PROGRESS: Channel   0:	 0.05 FDR:   289; 0.01 FDR:   172; 0.001 FDR:   136
1:25:09.914840 PROGRESS: =========================================================================
1:25:09.915917 PROGRESS: === Epoch 0, step 3, extracting elution groups 56000 to 120000 ===
1:25:10.441951 PROGRESS: Extracting batch of 126406 precursors
1:25:10.474149 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:25:10.474306 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:25:10.474356 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:25:10.474394 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:25:10.474679 INFO: Starting candidate selection
1:25:16.591527 INFO: Starting candidate scoring
1:25:20.239535 INFO: Finished candidate processing
1:25:20.239671 INFO: Collecting candidate features
1:25:22.589823 INFO: Collecting fragment features
1:25:23.207211 INFO: Finished candidate scoring
1:25:23.632588 PROGRESS: === Epoch 0, step 3, extracted 214528 precursors and 1358307 fragments ===
1:25:23.632943 INFO: performing precursor FDR with 47 features
1:25:23.633000 INFO: Decoy channel: -1
1:25:23.633036 INFO: Competetive: True
1:25:49.445180 INFO: Test AUC: 0.556
1:25:49.446004 INFO: Train AUC: 0.571
1:25:49.446097 INFO: AUC difference: 2.58%
1:25:49.642174 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:25:49.643541 PROGRESS: ============================= Precursor FDR =============================
1:25:49.643700 PROGRESS: Total precursors accumulated: 1,104
1:25:49.643792 PROGRESS: Target precursors: 1,009 (91.39%)
1:25:49.643868 PROGRESS: Decoy precursors: 95 (8.61%)
1:25:49.643939 PROGRESS: 
1:25:49.644010 PROGRESS: Precursor Summary:
1:25:49.646111 PROGRESS: Channel   0:	 0.05 FDR:   838; 0.01 FDR:   609; 0.001 FDR:   400
1:25:49.646259 PROGRESS: 
1:25:49.646344 PROGRESS: Protein Summary:
1:25:49.648858 PROGRESS: Channel   0:	 0.05 FDR:   736; 0.01 FDR:   537; 0.001 FDR:   367
1:25:49.648998 PROGRESS: =========================================================================
1:25:49.651110 INFO: calibration group: precursor, fitting rt estimator 
1:25:49.776159 INFO: calibration group: fragment, fitting mz estimator 
1:25:50.395104 INFO: === checking if epoch conditions were reached ===
1:25:50.395343 INFO: ✅ ms2_error      : 10.0000 <= 10
1:25:50.395447 INFO: ❌ rt_error       : 327.7977 > 300
1:25:50.395543 INFO: ❌ current_epoch  : 0 < 3
1:25:50.395618 INFO: ==============================================
1:25:50.599074 INFO: calibration group: precursor, predicting mz
1:25:50.599368 WARNING: mz prediction was skipped as it has not been fitted yet
1:25:50.599418 INFO: calibration group: precursor, predicting rt
1:25:58.811095 INFO: calibration group: fragment, predicting mz
1:26:16.510352 PROGRESS: === Epoch 1, step 0, extracting elution groups 0 to 8000 ===
1:26:16.706038 PROGRESS: Extracting batch of 15796 precursors
1:26:16.713448 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:26:16.713572 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:26:16.713628 INFO: FWHM in RT is 19.51 seconds, sigma is 0.71
1:26:16.713665 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:26:16.714046 INFO: Starting candidate selection
1:26:21.251292 INFO: Starting candidate scoring
1:26:22.603526 INFO: Finished candidate processing
1:26:22.603664 INFO: Collecting candidate features
1:26:24.429342 INFO: Collecting fragment features
1:26:24.882624 INFO: Finished candidate scoring
1:26:25.165288 PROGRESS: === Epoch 1, step 0, extracted 26160 precursors and 147684 fragments ===
1:26:25.165646 INFO: performing precursor FDR with 47 features
1:26:25.165707 INFO: Decoy channel: -1
1:26:25.165744 INFO: Competetive: True
1:26:26.419915 INFO: Test AUC: 0.538
1:26:26.420061 INFO: Train AUC: 0.584
1:26:26.420109 INFO: AUC difference: 7.86%
1:26:26.420150 WARNING: AUC difference > 5%. This may indicate overfitting.
1:26:26.571598 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:26:26.572594 PROGRESS: ============================= Precursor FDR =============================
1:26:26.572737 PROGRESS: Total precursors accumulated: 69
1:26:26.572822 PROGRESS: Target precursors: 63 (91.30%)
1:26:26.572897 PROGRESS: Decoy precursors: 6 (8.70%)
1:26:26.572968 PROGRESS: 
1:26:26.573038 PROGRESS: Precursor Summary:
1:26:26.574731 PROGRESS: Channel   0:	 0.05 FDR:    54; 0.01 FDR:    38; 0.001 FDR:    38
1:26:26.574871 PROGRESS: 
1:26:26.574955 PROGRESS: Protein Summary:
1:26:26.576805 PROGRESS: Channel   0:	 0.05 FDR:    54; 0.01 FDR:    38; 0.001 FDR:    38
1:26:26.576938 PROGRESS: =========================================================================
1:26:26.577888 PROGRESS: === Epoch 1, step 1, extracting elution groups 8000 to 24000 ===
1:26:26.690265 PROGRESS: Extracting batch of 31587 precursors
1:26:26.699983 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:26:26.700115 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:26:26.700165 INFO: FWHM in RT is 19.51 seconds, sigma is 0.71
1:26:26.700203 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:26:26.700464 INFO: Starting candidate selection
1:26:30.803663 INFO: Starting candidate scoring
1:26:32.429271 INFO: Finished candidate processing
1:26:32.429403 INFO: Collecting candidate features
1:26:34.322731 INFO: Collecting fragment features
1:26:34.801169 INFO: Finished candidate scoring
1:26:35.075715 PROGRESS: === Epoch 1, step 1, extracted 52610 precursors and 299605 fragments ===
1:26:35.076067 INFO: performing precursor FDR with 47 features
1:26:35.076126 INFO: Decoy channel: -1
1:26:35.076163 INFO: Competetive: True
1:26:39.611100 INFO: Test AUC: 0.561
1:26:39.611257 INFO: Train AUC: 0.586
1:26:39.611306 INFO: AUC difference: 4.26%
1:26:39.772356 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:26:39.773419 PROGRESS: ============================= Precursor FDR =============================
1:26:39.773565 PROGRESS: Total precursors accumulated: 252
1:26:39.773663 PROGRESS: Target precursors: 230 (91.27%)
1:26:39.773741 PROGRESS: Decoy precursors: 22 (8.73%)
1:26:39.773812 PROGRESS: 
1:26:39.773883 PROGRESS: Precursor Summary:
1:26:39.775654 PROGRESS: Channel   0:	 0.05 FDR:   193; 0.01 FDR:   111; 0.001 FDR:    94
1:26:39.775794 PROGRESS: 
1:26:39.775878 PROGRESS: Protein Summary:
1:26:39.777879 PROGRESS: Channel   0:	 0.05 FDR:   190; 0.01 FDR:   108; 0.001 FDR:    91
1:26:39.778014 PROGRESS: =========================================================================
1:26:39.778996 PROGRESS: === Epoch 1, step 2, extracting elution groups 24000 to 56000 ===
1:26:39.959450 PROGRESS: Extracting batch of 63222 precursors
1:26:39.976108 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:26:39.976252 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:26:39.976303 INFO: FWHM in RT is 19.51 seconds, sigma is 0.71
1:26:39.976341 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:26:39.976604 INFO: Starting candidate selection
1:26:46.438582 INFO: Starting candidate scoring
1:26:48.930353 INFO: Finished candidate processing
1:26:48.930483 INFO: Collecting candidate features
1:26:52.143921 INFO: Collecting fragment features
1:26:52.724060 INFO: Finished candidate scoring
1:26:53.063125 PROGRESS: === Epoch 1, step 2, extracted 105552 precursors and 603032 fragments ===
1:26:53.063493 INFO: performing precursor FDR with 47 features
1:26:53.063554 INFO: Decoy channel: -1
1:26:53.063591 INFO: Competetive: True
1:27:03.657869 INFO: Test AUC: 0.560
1:27:03.658028 INFO: Train AUC: 0.582
1:27:03.658076 INFO: AUC difference: 3.89%
1:27:03.824291 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:27:03.825525 PROGRESS: ============================= Precursor FDR =============================
1:27:03.825674 PROGRESS: Total precursors accumulated: 657
1:27:03.825759 PROGRESS: Target precursors: 598 (91.02%)
1:27:03.825846 PROGRESS: Decoy precursors: 59 (8.98%)
1:27:03.825918 PROGRESS: 
1:27:03.825989 PROGRESS: Precursor Summary:
1:27:03.827951 PROGRESS: Channel   0:	 0.05 FDR:   469; 0.01 FDR:   344; 0.001 FDR:   251
1:27:03.828101 PROGRESS: 
1:27:03.828186 PROGRESS: Protein Summary:
1:27:03.830431 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   325; 0.001 FDR:   239
1:27:03.830569 PROGRESS: =========================================================================
1:27:03.831707 PROGRESS: === Epoch 1, step 3, extracting elution groups 56000 to 120000 ===
1:27:03.974200 PROGRESS: Extracting batch of 126390 precursors
1:27:04.006583 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:27:04.006729 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:27:04.006778 INFO: FWHM in RT is 19.51 seconds, sigma is 0.71
1:27:04.006815 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:27:04.007086 INFO: Starting candidate selection
1:27:10.209528 INFO: Starting candidate scoring
1:27:14.002882 INFO: Finished candidate processing
1:27:14.003338 INFO: Collecting candidate features
1:27:16.592192 INFO: Collecting fragment features
1:27:17.165212 INFO: Finished candidate scoring
1:27:17.588116 PROGRESS: === Epoch 1, step 3, extracted 211277 precursors and 1205146 fragments ===
1:27:17.588626 INFO: performing precursor FDR with 47 features
1:27:17.588693 INFO: Decoy channel: -1
1:27:17.588732 INFO: Competetive: True
1:27:43.517997 INFO: Test AUC: 0.558
1:27:43.518185 INFO: Train AUC: 0.579
1:27:43.518236 INFO: AUC difference: 3.67%
1:27:43.727724 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:27:43.729993 PROGRESS: ============================= Precursor FDR =============================
1:27:43.730199 PROGRESS: Total precursors accumulated: 1,413
1:27:43.730293 PROGRESS: Target precursors: 1,285 (90.94%)
1:27:43.730369 PROGRESS: Decoy precursors: 128 (9.06%)
1:27:43.730441 PROGRESS: 
1:27:43.730512 PROGRESS: Precursor Summary:
1:27:43.733244 PROGRESS: Channel   0:	 0.05 FDR: 1,014; 0.01 FDR:   747; 0.001 FDR:   651
1:27:43.733432 PROGRESS: 
1:27:43.733521 PROGRESS: Protein Summary:
1:27:43.736254 PROGRESS: Channel   0:	 0.05 FDR:   884; 0.01 FDR:   654; 0.001 FDR:   573
1:27:43.736396 PROGRESS: =========================================================================
1:27:43.739270 INFO: calibration group: precursor, fitting rt estimator 
1:27:43.881526 INFO: calibration group: fragment, fitting mz estimator 
1:27:44.506910 INFO: === checking if epoch conditions were reached ===
1:27:44.507177 INFO: ✅ ms2_error      : 10.0000 <= 10
1:27:44.507276 INFO: ✅ rt_error       : 300.0000 <= 300
1:27:44.507361 INFO: ❌ current_epoch  : 1 < 3
1:27:44.507438 INFO: ==============================================
1:27:44.743635 INFO: calibration group: precursor, predicting mz
1:27:44.743969 WARNING: mz prediction was skipped as it has not been fitted yet
1:27:44.744020 INFO: calibration group: precursor, predicting rt
1:27:53.443239 INFO: calibration group: fragment, predicting mz
1:28:13.699208 PROGRESS: === Epoch 2, step 0, extracting elution groups 0 to 8000 ===
1:28:13.867361 PROGRESS: Extracting batch of 15813 precursors
1:28:13.873755 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:28:13.873874 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:13.873935 INFO: FWHM in RT is 18.41 seconds, sigma is 0.67
1:28:13.873975 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:28:13.874279 INFO: Starting candidate selection
1:28:18.465948 INFO: Starting candidate scoring
1:28:19.784988 INFO: Finished candidate processing
1:28:19.785139 INFO: Collecting candidate features
1:28:21.645065 INFO: Collecting fragment features
1:28:22.085246 INFO: Finished candidate scoring
1:28:22.338409 PROGRESS: === Epoch 2, step 0, extracted 27915 precursors and 156036 fragments ===
1:28:22.338743 INFO: performing precursor FDR with 47 features
1:28:22.338809 INFO: Decoy channel: -1
1:28:22.338850 INFO: Competetive: True
1:28:23.684943 INFO: Test AUC: 0.543
1:28:23.685087 INFO: Train AUC: 0.594
1:28:23.685135 INFO: AUC difference: 8.62%
1:28:23.685175 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:23.843328 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:28:23.844339 PROGRESS: ============================= Precursor FDR =============================
1:28:23.844484 PROGRESS: Total precursors accumulated: 125
1:28:23.844571 PROGRESS: Target precursors: 114 (91.20%)
1:28:23.844645 PROGRESS: Decoy precursors: 11 (8.80%)
1:28:23.844715 PROGRESS: 
1:28:23.844784 PROGRESS: Precursor Summary:
1:28:23.846504 PROGRESS: Channel   0:	 0.05 FDR:    79; 0.01 FDR:    79; 0.001 FDR:    79
1:28:23.846633 PROGRESS: 
1:28:23.846723 PROGRESS: Protein Summary:
1:28:23.848655 PROGRESS: Channel   0:	 0.05 FDR:    78; 0.01 FDR:    78; 0.001 FDR:    78
1:28:23.848783 PROGRESS: =========================================================================
1:28:23.849793 PROGRESS: === Epoch 2, step 1, extracting elution groups 8000 to 24000 ===
1:28:23.957900 PROGRESS: Extracting batch of 31604 precursors
1:28:23.967351 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:28:23.967482 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:23.967534 INFO: FWHM in RT is 18.41 seconds, sigma is 0.67
1:28:23.967573 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:28:23.967833 INFO: Starting candidate selection
1:28:27.708870 INFO: Starting candidate scoring
1:28:29.466994 INFO: Finished candidate processing
1:28:29.467128 INFO: Collecting candidate features
1:28:31.495346 INFO: Collecting fragment features
1:28:32.036313 INFO: Finished candidate scoring
1:28:32.408402 PROGRESS: === Epoch 2, step 1, extracted 55619 precursors and 311179 fragments ===
1:28:32.408864 INFO: performing precursor FDR with 47 features
1:28:32.408935 INFO: Decoy channel: -1
1:28:32.408973 INFO: Competetive: True
1:28:37.175994 INFO: Test AUC: 0.562
1:28:37.176151 INFO: Train AUC: 0.598
1:28:37.176200 INFO: AUC difference: 5.99%
1:28:37.176238 WARNING: AUC difference > 5%. This may indicate overfitting.
1:28:37.344699 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:28:37.345770 PROGRESS: ============================= Precursor FDR =============================
1:28:37.345917 PROGRESS: Total precursors accumulated: 333
1:28:37.346004 PROGRESS: Target precursors: 304 (91.29%)
1:28:37.346078 PROGRESS: Decoy precursors: 29 (8.71%)
1:28:37.346148 PROGRESS: 
1:28:37.346218 PROGRESS: Precursor Summary:
1:28:37.348071 PROGRESS: Channel   0:	 0.05 FDR:   212; 0.01 FDR:   155; 0.001 FDR:   151
1:28:37.348207 PROGRESS: 
1:28:37.348286 PROGRESS: Protein Summary:
1:28:37.350371 PROGRESS: Channel   0:	 0.05 FDR:   209; 0.01 FDR:   153; 0.001 FDR:   149
1:28:37.350499 PROGRESS: =========================================================================
1:28:37.351571 PROGRESS: === Epoch 2, step 2, extracting elution groups 24000 to 56000 ===
1:28:37.551839 PROGRESS: Extracting batch of 63232 precursors
1:28:37.583967 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:28:37.584099 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:28:37.584152 INFO: FWHM in RT is 18.41 seconds, sigma is 0.67
1:28:37.584191 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:28:37.584492 INFO: Starting candidate selection
1:28:42.420186 INFO: Starting candidate scoring
1:28:44.865118 INFO: Finished candidate processing
1:28:44.865241 INFO: Collecting candidate features
1:28:46.847353 INFO: Collecting fragment features
1:28:47.393694 INFO: Finished candidate scoring
1:28:47.731391 PROGRESS: === Epoch 2, step 2, extracted 111656 precursors and 627824 fragments ===
1:28:47.731792 INFO: performing precursor FDR with 47 features
1:28:47.731854 INFO: Decoy channel: -1
1:28:47.731891 INFO: Competetive: True
1:29:00.063722 INFO: Test AUC: 0.559
1:29:00.063901 INFO: Train AUC: 0.593
1:29:00.063970 INFO: AUC difference: 5.79%
1:29:00.064023 WARNING: AUC difference > 5%. This may indicate overfitting.
1:29:00.251259 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:29:00.252551 PROGRESS: ============================= Precursor FDR =============================
1:29:00.252759 PROGRESS: Total precursors accumulated: 823
1:29:00.252888 PROGRESS: Target precursors: 749 (91.01%)
1:29:00.252969 PROGRESS: Decoy precursors: 74 (8.99%)
1:29:00.253044 PROGRESS: 
1:29:00.253114 PROGRESS: Precursor Summary:
1:29:00.255182 PROGRESS: Channel   0:	 0.05 FDR:   631; 0.01 FDR:   416; 0.001 FDR:   298
1:29:00.255312 PROGRESS: 
1:29:00.255393 PROGRESS: Protein Summary:
1:29:00.257772 PROGRESS: Channel   0:	 0.05 FDR:   582; 0.01 FDR:   385; 0.001 FDR:   278
1:29:00.257913 PROGRESS: =========================================================================
1:29:00.259448 PROGRESS: === Epoch 2, step 3, extracting elution groups 56000 to 120000 ===
1:29:00.429246 PROGRESS: Extracting batch of 126477 precursors
1:29:00.461320 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:29:00.461474 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:29:00.461535 INFO: FWHM in RT is 18.41 seconds, sigma is 0.67
1:29:00.461575 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:29:00.461974 INFO: Starting candidate selection
1:29:07.813310 INFO: Starting candidate scoring
1:29:11.997446 INFO: Finished candidate processing
1:29:11.998074 INFO: Collecting candidate features
1:29:14.333064 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 223043)
1:29:14.355693 INFO: Collecting fragment features
1:29:14.955483 INFO: Finished candidate scoring
1:29:15.389773 PROGRESS: === Epoch 2, step 3, extracted 223043 precursors and 1249769 fragments ===
1:29:15.390109 INFO: performing precursor FDR with 47 features
1:29:15.390163 INFO: Decoy channel: -1
1:29:15.390199 INFO: Competetive: True
1:29:15.711726 WARNING: dropped 1 target PSMs due to missing features
1:29:40.891347 INFO: Test AUC: 0.559
1:29:40.891644 INFO: Train AUC: 0.583
1:29:40.891718 INFO: AUC difference: 4.04%
1:29:41.100022 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:29:41.101801 PROGRESS: ============================= Precursor FDR =============================
1:29:41.101997 PROGRESS: Total precursors accumulated: 1,530
1:29:41.102114 PROGRESS: Target precursors: 1,399 (91.44%)
1:29:41.102223 PROGRESS: Decoy precursors: 131 (8.56%)
1:29:41.102317 PROGRESS: 
1:29:41.102408 PROGRESS: Precursor Summary:
1:29:41.104891 PROGRESS: Channel   0:	 0.05 FDR: 1,196; 0.01 FDR:   961; 0.001 FDR:   605
1:29:41.105071 PROGRESS: 
1:29:41.105194 PROGRESS: Protein Summary:
1:29:41.108247 PROGRESS: Channel   0:	 0.05 FDR: 1,054; 0.01 FDR:   850; 0.001 FDR:   550
1:29:41.108411 PROGRESS: =========================================================================
1:29:41.111097 INFO: calibration group: precursor, fitting rt estimator 
1:29:41.221180 INFO: calibration group: fragment, fitting mz estimator 
1:29:41.777762 INFO: === checking if epoch conditions were reached ===
1:29:41.777984 INFO: ✅ ms2_error      : 10.0000 <= 10
1:29:41.778149 INFO: ✅ rt_error       : 300.0000 <= 300
1:29:41.778295 INFO: ✅ current_epoch  : 2 >= 3
1:29:41.778415 INFO: ==============================================
1:29:41.843587 INFO: calibration group: precursor, predicting mz
1:29:41.843959 WARNING: mz prediction was skipped as it has not been fitted yet
1:29:41.844020 INFO: calibration group: precursor, predicting rt
1:29:49.978323 INFO: calibration group: fragment, predicting mz
1:30:10.171417 PROGRESS: Extracting batch of 10696137 precursors
1:30:12.890969 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:30:12.891106 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:30:12.891164 INFO: FWHM in RT is 17.81 seconds, sigma is 0.65
1:30:12.891204 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:30:12.891581 INFO: Starting candidate selection
1:34:48.905095 INFO: Applying score cutoff of 64.73463668823243
1:34:49.176826 INFO: Removed 14240967 precursors with score below cutoff
1:34:52.260931 INFO: Starting candidate scoring
1:36:25.442057 INFO: Finished candidate processing
1:36:25.442307 INFO: Collecting candidate features
1:36:43.534059 INFO: Collecting fragment features
1:36:50.919867 INFO: Finished candidate scoring
1:36:55.844004 INFO: performing precursor FDR with 47 features
1:36:55.844151 INFO: Decoy channel: -1
1:36:55.844192 INFO: Competetive: True
1:43:19.644006 INFO: Test AUC: 0.580
1:43:19.644251 INFO: Train AUC: 0.582
1:43:19.644303 INFO: AUC difference: 0.34%
1:43:20.389598 INFO: Removing fragments below FDR threshold
1:43:20.901903 PROGRESS: ============================= Precursor FDR =============================
1:43:20.902305 PROGRESS: Total precursors accumulated: 47,696
1:43:20.902431 PROGRESS: Target precursors: 47,224 (99.01%)
1:43:20.902514 PROGRESS: Decoy precursors: 472 (0.99%)
1:43:20.902592 PROGRESS: 
1:43:20.902664 PROGRESS: Precursor Summary:
1:43:20.929276 PROGRESS: Channel   0:	 0.05 FDR: 47,224; 0.01 FDR: 47,224; 0.001 FDR: 31,056
1:43:20.929519 PROGRESS: 
1:43:20.929605 PROGRESS: Protein Summary:
1:43:20.965940 PROGRESS: Channel   0:	 0.05 FDR: 8,618; 0.01 FDR: 8,618; 0.001 FDR: 6,354
1:43:20.966188 PROGRESS: =========================================================================
1:43:21.554520 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:43:22.385942 PROGRESS: Loading raw file 5/6: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
1:43:22.386157 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03 at /home/robbe/alphadia/Proteobench/.progress/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
1:43:49.638999 INFO: Determining DIA cycle
1:43:49.662210 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
1:43:49.668679 INFO: Determining DIA cycle
1:43:49.687692 INFO: Found cycle with start 0.00 min and length 151.
1:43:49.736197 INFO: ============ Raw file stats ============
1:43:49.736538 INFO: RT (min)            : 0.0 - 150.0
1:43:49.736623 INFO: RT duration (sec)   : 8999.7
1:43:49.736660 INFO: RT duration (min)   : 150.0
1:43:49.736778 INFO: Cycle len (scans)   : 151
1:43:49.736822 INFO: Cycle len (sec)     : 5.84
1:43:49.736856 INFO: Number of cycles    : 1542
1:43:49.736918 INFO: MS2 range (m/z)     : 396.4 - 1004.7
1:43:49.736955 INFO: ========================================
1:43:51.880446 INFO: Initializing CalibrationManager
1:43:51.880766 INFO: Loading calibration config
1:43:51.881658 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'function': LOESSRegression()}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'function': LOESSRegression(n_kernels=2)}]}]
1:43:51.881806 INFO: Calibration group :fragment, found 1 estimator(s)
1:43:51.881962 INFO: Calibration group :precursor, found 3 estimator(s)
1:43:51.882084 INFO: Disabling ion mobility calibration
1:43:51.882133 INFO: removed mobility estimator from group precursor
1:43:51.882245 INFO: Initializing OptimizationManager
1:43:51.882364 INFO: initial parameter: fwhm_rt = 5
1:43:51.882441 INFO: initial parameter: fwhm_mobility = 0.01
1:43:51.882511 INFO: initial parameter: score_cutoff = 0
1:43:51.882635 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
1:43:51.882753 INFO: Initializing OptimizationManager
1:43:51.882798 INFO: initial parameter: current_epoch = 0
1:43:51.882833 INFO: initial parameter: current_step = 0
1:43:51.882865 INFO: initial parameter: ms1_error = 20
1:43:51.882896 INFO: initial parameter: ms2_error = 20
1:43:51.882926 INFO: initial parameter: rt_error = 500
1:43:51.882959 INFO: initial parameter: mobility_error = 0.08
1:43:51.882990 INFO: initial parameter: column_type = library
1:43:51.883021 INFO: initial parameter: num_candidates = 2
1:43:51.883051 INFO: initial parameter: recalibration_target = 200
1:43:51.883083 INFO: initial parameter: accumulated_precursors = 0
1:43:51.883113 INFO: initial parameter: accumulated_precursors_01FDR = 0
1:43:51.883143 INFO: initial parameter: accumulated_precursors_001FDR = 0
1:43:51.883199 INFO: Initializing FDRManager
1:43:51.883262 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/classifier
1:43:53.683143 PROGRESS: 5,414,253 target precursors potentially observable (0 removed)
1:43:56.424916 INFO: === checking if epoch conditions were reached ===
1:43:56.425221 INFO: ❌ ms2_error      : 20.0000 > 10
1:43:56.425340 INFO: ❌ rt_error       : 500.0000 > 300
1:43:56.425426 INFO: ❌ current_epoch  : 0 < 3
1:43:56.425504 INFO: ==============================================
1:43:56.639399 INFO: calibration group: precursor, predicting mz
1:43:56.639709 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:56.639763 INFO: calibration group: precursor, predicting rt
1:43:56.639841 WARNING: rt prediction was skipped as it has not been fitted yet
1:43:56.639890 INFO: calibration group: fragment, predicting mz
1:43:56.639965 WARNING: mz prediction was skipped as it has not been fitted yet
1:43:56.640016 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
1:43:56.736404 PROGRESS: Extracting batch of 15784 precursors
1:43:56.742200 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:43:56.742315 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:43:56.742371 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:43:56.742409 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:43:56.742769 INFO: Starting candidate selection
1:43:59.650450 INFO: Starting candidate scoring
1:44:00.719087 INFO: Finished candidate processing
1:44:00.719212 INFO: Collecting candidate features
1:44:02.513772 INFO: Collecting fragment features
1:44:02.952921 INFO: Finished candidate scoring
1:44:03.195792 PROGRESS: === Epoch 0, step 0, extracted 26854 precursors and 160064 fragments ===
1:44:03.196115 INFO: performing precursor FDR with 47 features
1:44:03.196171 INFO: Decoy channel: -1
1:44:03.196207 INFO: Competetive: True
1:44:04.453094 INFO: Test AUC: 0.550
1:44:04.453238 INFO: Train AUC: 0.532
1:44:04.453285 INFO: AUC difference: 3.35%
1:44:04.625823 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:44:04.628746 PROGRESS: ============================= Precursor FDR =============================
1:44:04.628927 PROGRESS: Total precursors accumulated: 6,987
1:44:04.629013 PROGRESS: Target precursors: 3,808 (54.50%)
1:44:04.629088 PROGRESS: Decoy precursors: 3,179 (45.50%)
1:44:04.629159 PROGRESS: 
1:44:04.629230 PROGRESS: Precursor Summary:
1:44:04.630951 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:44:04.631100 PROGRESS: 
1:44:04.631183 PROGRESS: Protein Summary:
1:44:04.633024 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
1:44:04.633159 PROGRESS: =========================================================================
1:44:04.634085 PROGRESS: === Epoch 0, step 1, extracting elution groups 8000 to 24000 ===
1:44:04.736759 PROGRESS: Extracting batch of 31606 precursors
1:44:04.745613 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:44:04.745731 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:44:04.745781 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:44:04.745831 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:44:04.746074 INFO: Starting candidate selection
1:44:08.220151 INFO: Starting candidate scoring
1:44:09.745387 INFO: Finished candidate processing
1:44:09.745514 INFO: Collecting candidate features
1:44:11.662050 INFO: Collecting fragment features
1:44:12.134605 INFO: Finished candidate scoring
1:44:12.417243 PROGRESS: === Epoch 0, step 1, extracted 53398 precursors and 318571 fragments ===
1:44:12.417928 INFO: performing precursor FDR with 47 features
1:44:12.418015 INFO: Decoy channel: -1
1:44:12.418053 INFO: Competetive: True
1:44:16.654342 INFO: Test AUC: 0.544
1:44:16.654486 INFO: Train AUC: 0.558
1:44:16.654535 INFO: AUC difference: 2.53%
1:44:16.813246 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:44:16.814312 PROGRESS: ============================= Precursor FDR =============================
1:44:16.814461 PROGRESS: Total precursors accumulated: 155
1:44:16.814546 PROGRESS: Target precursors: 141 (90.97%)
1:44:16.814620 PROGRESS: Decoy precursors: 14 (9.03%)
1:44:16.814690 PROGRESS: 
1:44:16.814763 PROGRESS: Precursor Summary:
1:44:16.816459 PROGRESS: Channel   0:	 0.05 FDR:   109; 0.01 FDR:     0; 0.001 FDR:     0
1:44:16.816606 PROGRESS: 
1:44:16.816692 PROGRESS: Protein Summary:
1:44:16.818572 PROGRESS: Channel   0:	 0.05 FDR:   108; 0.01 FDR:     0; 0.001 FDR:     0
1:44:16.818703 PROGRESS: =========================================================================
1:44:16.819639 PROGRESS: === Epoch 0, step 2, extracting elution groups 24000 to 56000 ===
1:44:16.957858 PROGRESS: Extracting batch of 63220 precursors
1:44:16.975077 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:44:16.975204 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:44:16.975252 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:44:16.975288 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:44:16.975561 INFO: Starting candidate selection
1:44:21.382302 INFO: Starting candidate scoring
1:44:23.623594 INFO: Finished candidate processing
1:44:23.623720 INFO: Collecting candidate features
1:44:25.630706 INFO: Collecting fragment features
1:44:26.151897 INFO: Finished candidate scoring
1:44:26.487005 PROGRESS: === Epoch 0, step 2, extracted 107087 precursors and 637007 fragments ===
1:44:26.487349 INFO: performing precursor FDR with 47 features
1:44:26.487405 INFO: Decoy channel: -1
1:44:26.487442 INFO: Competetive: True
1:44:37.378268 INFO: Test AUC: 0.552
1:44:37.378418 INFO: Train AUC: 0.569
1:44:37.378468 INFO: AUC difference: 3.06%
1:44:37.548522 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:44:37.549606 PROGRESS: ============================= Precursor FDR =============================
1:44:37.549750 PROGRESS: Total precursors accumulated: 438
1:44:37.549836 PROGRESS: Target precursors: 398 (90.87%)
1:44:37.549912 PROGRESS: Decoy precursors: 40 (9.13%)
1:44:37.549984 PROGRESS: 
1:44:37.550057 PROGRESS: Precursor Summary:
1:44:37.551925 PROGRESS: Channel   0:	 0.05 FDR:   343; 0.01 FDR:   206; 0.001 FDR:   111
1:44:37.552070 PROGRESS: 
1:44:37.552153 PROGRESS: Protein Summary:
1:44:37.554239 PROGRESS: Channel   0:	 0.05 FDR:   327; 0.01 FDR:   196; 0.001 FDR:   108
1:44:37.554378 PROGRESS: =========================================================================
1:44:37.556128 INFO: calibration group: precursor, fitting rt estimator 
1:44:37.647552 INFO: calibration group: fragment, fitting mz estimator 
1:44:38.086183 INFO: === checking if epoch conditions were reached ===
1:44:38.086358 INFO: ❌ ms2_error      : 14.1198 > 10
1:44:38.086454 INFO: ❌ rt_error       : 308.0716 > 300
1:44:38.086541 INFO: ❌ current_epoch  : 0 < 3
1:44:38.086617 INFO: ==============================================
1:44:38.320408 INFO: calibration group: precursor, predicting mz
1:44:38.320673 WARNING: mz prediction was skipped as it has not been fitted yet
1:44:38.320721 INFO: calibration group: precursor, predicting rt
1:44:46.750162 INFO: calibration group: fragment, predicting mz
1:45:06.900900 PROGRESS: === Epoch 1, step 0, extracting elution groups 0 to 8000 ===
1:45:07.119012 PROGRESS: Extracting batch of 15813 precursors
1:45:07.124070 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:45:07.124171 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:45:07.124220 INFO: FWHM in RT is 18.75 seconds, sigma is 0.68
1:45:07.124258 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:45:07.124498 INFO: Starting candidate selection
1:45:10.975133 INFO: Starting candidate scoring
1:45:12.285645 INFO: Finished candidate processing
1:45:12.285764 INFO: Collecting candidate features
1:45:14.171878 INFO: Collecting fragment features
1:45:14.601326 INFO: Finished candidate scoring
1:45:14.854172 PROGRESS: === Epoch 1, step 0, extracted 27655 precursors and 155466 fragments ===
1:45:14.854496 INFO: performing precursor FDR with 47 features
1:45:14.854553 INFO: Decoy channel: -1
1:45:14.854592 INFO: Competetive: True
1:45:16.064388 INFO: Test AUC: 0.545
1:45:16.064519 INFO: Train AUC: 0.578
1:45:16.064567 INFO: AUC difference: 5.80%
1:45:16.064603 WARNING: AUC difference > 5%. This may indicate overfitting.
1:45:16.214641 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:45:16.215575 PROGRESS: ============================= Precursor FDR =============================
1:45:16.215718 PROGRESS: Total precursors accumulated: 91
1:45:16.215803 PROGRESS: Target precursors: 83 (91.21%)
1:45:16.215879 PROGRESS: Decoy precursors: 8 (8.79%)
1:45:16.215949 PROGRESS: 
1:45:16.216020 PROGRESS: Precursor Summary:
1:45:16.217682 PROGRESS: Channel   0:	 0.05 FDR:    67; 0.01 FDR:    32; 0.001 FDR:    32
1:45:16.217816 PROGRESS: 
1:45:16.217898 PROGRESS: Protein Summary:
1:45:16.219752 PROGRESS: Channel   0:	 0.05 FDR:    67; 0.01 FDR:    32; 0.001 FDR:    32
1:45:16.219887 PROGRESS: =========================================================================
1:45:16.220837 PROGRESS: === Epoch 1, step 1, extracting elution groups 8000 to 24000 ===
1:45:16.329161 PROGRESS: Extracting batch of 31599 precursors
1:45:16.338507 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:45:16.338621 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:45:16.338670 INFO: FWHM in RT is 18.75 seconds, sigma is 0.68
1:45:16.338708 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:45:16.338949 INFO: Starting candidate selection
1:45:20.885611 INFO: Starting candidate scoring
1:45:22.542811 INFO: Finished candidate processing
1:45:22.542933 INFO: Collecting candidate features
1:45:24.451404 INFO: Collecting fragment features
1:45:24.903476 INFO: Finished candidate scoring
1:45:25.179595 PROGRESS: === Epoch 1, step 1, extracted 55272 precursors and 310664 fragments ===
1:45:25.179929 INFO: performing precursor FDR with 47 features
1:45:25.179987 INFO: Decoy channel: -1
1:45:25.180026 INFO: Competetive: True
1:45:29.821605 INFO: Test AUC: 0.553
1:45:29.821750 INFO: Train AUC: 0.583
1:45:29.821802 INFO: AUC difference: 5.09%
1:45:29.821839 WARNING: AUC difference > 5%. This may indicate overfitting.
1:45:29.979773 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:45:29.980791 PROGRESS: ============================= Precursor FDR =============================
1:45:29.980936 PROGRESS: Total precursors accumulated: 277
1:45:29.981022 PROGRESS: Target precursors: 254 (91.70%)
1:45:29.981098 PROGRESS: Decoy precursors: 23 (8.30%)
1:45:29.981171 PROGRESS: 
1:45:29.981242 PROGRESS: Precursor Summary:
1:45:29.982989 PROGRESS: Channel   0:	 0.05 FDR:   203; 0.01 FDR:   134; 0.001 FDR:    85
1:45:29.983129 PROGRESS: 
1:45:29.983211 PROGRESS: Protein Summary:
1:45:29.985217 PROGRESS: Channel   0:	 0.05 FDR:   196; 0.01 FDR:   131; 0.001 FDR:    83
1:45:29.985355 PROGRESS: =========================================================================
1:45:29.986351 PROGRESS: === Epoch 1, step 2, extracting elution groups 24000 to 56000 ===
1:45:30.105578 PROGRESS: Extracting batch of 63243 precursors
1:45:30.122437 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:45:30.122564 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:45:30.122612 INFO: FWHM in RT is 18.75 seconds, sigma is 0.68
1:45:30.122651 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:45:30.122904 INFO: Starting candidate selection
1:45:34.551412 INFO: Starting candidate scoring
1:45:36.913001 INFO: Finished candidate processing
1:45:36.913123 INFO: Collecting candidate features
1:45:38.905176 INFO: Collecting fragment features
1:45:39.399901 INFO: Finished candidate scoring
1:45:39.722968 PROGRESS: === Epoch 1, step 2, extracted 110146 precursors and 616725 fragments ===
1:45:39.723656 INFO: performing precursor FDR with 47 features
1:45:39.723739 INFO: Decoy channel: -1
1:45:39.723777 INFO: Competetive: True
1:45:50.757102 INFO: Test AUC: 0.550
1:45:50.757254 INFO: Train AUC: 0.582
1:45:50.757303 INFO: AUC difference: 5.41%
1:45:50.757341 WARNING: AUC difference > 5%. This may indicate overfitting.
1:45:50.925939 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:45:50.927093 PROGRESS: ============================= Precursor FDR =============================
1:45:50.927244 PROGRESS: Total precursors accumulated: 608
1:45:50.927344 PROGRESS: Target precursors: 554 (91.12%)
1:45:50.927422 PROGRESS: Decoy precursors: 54 (8.88%)
1:45:50.927503 PROGRESS: 
1:45:50.927574 PROGRESS: Precursor Summary:
1:45:50.929539 PROGRESS: Channel   0:	 0.05 FDR:   453; 0.01 FDR:   328; 0.001 FDR:   268
1:45:50.929688 PROGRESS: 
1:45:50.929773 PROGRESS: Protein Summary:
1:45:50.932023 PROGRESS: Channel   0:	 0.05 FDR:   423; 0.01 FDR:   306; 0.001 FDR:   252
1:45:50.932163 PROGRESS: =========================================================================
1:45:50.933297 PROGRESS: === Epoch 1, step 3, extracting elution groups 56000 to 120000 ===
1:45:51.075360 PROGRESS: Extracting batch of 126497 precursors
1:45:51.107731 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:45:51.107864 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:45:51.107914 INFO: FWHM in RT is 18.75 seconds, sigma is 0.68
1:45:51.107952 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:45:51.108212 INFO: Starting candidate selection
1:45:57.599352 INFO: Starting candidate scoring
1:46:01.496910 INFO: Finished candidate processing
1:46:01.497043 INFO: Collecting candidate features
1:46:03.856338 INFO: Collecting fragment features
1:46:04.510258 INFO: Finished candidate scoring
1:46:04.975900 PROGRESS: === Epoch 1, step 3, extracted 221244 precursors and 1242844 fragments ===
1:46:04.976313 INFO: performing precursor FDR with 47 features
1:46:04.976371 INFO: Decoy channel: -1
1:46:04.976407 INFO: Competetive: True
1:46:30.869833 INFO: Test AUC: 0.561
1:46:30.869990 INFO: Train AUC: 0.576
1:46:30.870061 INFO: AUC difference: 2.72%
1:46:31.061718 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
1:46:31.063147 PROGRESS: ============================= Precursor FDR =============================
1:46:31.063317 PROGRESS: Total precursors accumulated: 1,342
1:46:31.063427 PROGRESS: Target precursors: 1,225 (91.28%)
1:46:31.063533 PROGRESS: Decoy precursors: 117 (8.72%)
1:46:31.063626 PROGRESS: 
1:46:31.063715 PROGRESS: Precursor Summary:
1:46:31.066021 PROGRESS: Channel   0:	 0.05 FDR: 1,003; 0.01 FDR:   776; 0.001 FDR:   569
1:46:31.066186 PROGRESS: 
1:46:31.066289 PROGRESS: Protein Summary:
1:46:31.069124 PROGRESS: Channel   0:	 0.05 FDR:   879; 0.01 FDR:   691; 0.001 FDR:   507
1:46:31.069279 PROGRESS: =========================================================================
1:46:31.071620 INFO: calibration group: precursor, fitting rt estimator 
1:46:31.214498 INFO: calibration group: fragment, fitting mz estimator 
1:46:31.829053 INFO: === checking if epoch conditions were reached ===
1:46:31.829305 INFO: ✅ ms2_error      : 10.0000 <= 10
1:46:31.829436 INFO: ✅ rt_error       : 300.0000 <= 300
1:46:31.829545 INFO: ❌ current_epoch  : 1 < 3
1:46:31.829650 INFO: ==============================================
1:46:32.032850 INFO: calibration group: precursor, predicting mz
1:46:32.033160 WARNING: mz prediction was skipped as it has not been fitted yet
1:46:32.033224 INFO: calibration group: precursor, predicting rt
1:46:40.049582 INFO: calibration group: fragment, predicting mz
1:47:00.677921 PROGRESS: === Epoch 2, step 0, extracting elution groups 0 to 8000 ===
1:47:00.861305 PROGRESS: Extracting batch of 15810 precursors
1:47:00.866896 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:47:00.867006 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:47:00.867063 INFO: FWHM in RT is 18.22 seconds, sigma is 0.66
1:47:00.867101 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:47:00.867385 INFO: Starting candidate selection
1:47:04.741039 INFO: Starting candidate scoring
1:47:06.123549 INFO: Finished candidate processing
1:47:06.123704 INFO: Collecting candidate features
1:47:07.905941 INFO: Collecting fragment features
1:47:08.331751 INFO: Finished candidate scoring
1:47:08.570950 PROGRESS: === Epoch 2, step 0, extracted 28723 precursors and 150328 fragments ===
1:47:08.571278 INFO: performing precursor FDR with 47 features
1:47:08.571334 INFO: Decoy channel: -1
1:47:08.571372 INFO: Competetive: True
1:47:09.840650 INFO: Test AUC: 0.538
1:47:09.840814 INFO: Train AUC: 0.593
1:47:09.840881 INFO: AUC difference: 9.17%
1:47:09.840960 WARNING: AUC difference > 5%. This may indicate overfitting.
1:47:09.997560 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:47:09.998580 PROGRESS: ============================= Precursor FDR =============================
1:47:09.998739 PROGRESS: Total precursors accumulated: 94
1:47:09.998838 PROGRESS: Target precursors: 86 (91.49%)
1:47:09.998915 PROGRESS: Decoy precursors: 8 (8.51%)
1:47:09.998986 PROGRESS: 
1:47:09.999055 PROGRESS: Precursor Summary:
1:47:10.000770 PROGRESS: Channel   0:	 0.05 FDR:    80; 0.01 FDR:    71; 0.001 FDR:    71
1:47:10.000916 PROGRESS: 
1:47:10.001001 PROGRESS: Protein Summary:
1:47:10.002908 PROGRESS: Channel   0:	 0.05 FDR:    78; 0.01 FDR:    69; 0.001 FDR:    69
1:47:10.003034 PROGRESS: =========================================================================
1:47:10.004015 PROGRESS: === Epoch 2, step 1, extracting elution groups 8000 to 24000 ===
1:47:10.162162 PROGRESS: Extracting batch of 31609 precursors
1:47:10.172787 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:47:10.172930 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:47:10.172982 INFO: FWHM in RT is 18.22 seconds, sigma is 0.66
1:47:10.173019 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:47:10.173299 INFO: Starting candidate selection
1:47:13.929110 INFO: Starting candidate scoring
1:47:15.549760 INFO: Finished candidate processing
1:47:15.549883 INFO: Collecting candidate features
1:47:17.346534 INFO: Collecting fragment features
1:47:17.812325 INFO: Finished candidate scoring
1:47:18.064154 PROGRESS: === Epoch 2, step 1, extracted 57085 precursors and 301770 fragments ===
1:47:18.064487 INFO: performing precursor FDR with 47 features
1:47:18.064546 INFO: Decoy channel: -1
1:47:18.064583 INFO: Competetive: True
1:47:22.804578 INFO: Test AUC: 0.550
1:47:22.804735 INFO: Train AUC: 0.593
1:47:22.804787 INFO: AUC difference: 7.29%
1:47:22.804830 WARNING: AUC difference > 5%. This may indicate overfitting.
1:47:22.966757 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:47:22.967833 PROGRESS: ============================= Precursor FDR =============================
1:47:22.967989 PROGRESS: Total precursors accumulated: 295
1:47:22.968087 PROGRESS: Target precursors: 271 (91.86%)
1:47:22.968169 PROGRESS: Decoy precursors: 24 (8.14%)
1:47:22.968247 PROGRESS: 
1:47:22.968322 PROGRESS: Precursor Summary:
1:47:22.970170 PROGRESS: Channel   0:	 0.05 FDR:   239; 0.01 FDR:   152; 0.001 FDR:   143
1:47:22.970309 PROGRESS: 
1:47:22.970404 PROGRESS: Protein Summary:
1:47:22.972521 PROGRESS: Channel   0:	 0.05 FDR:   229; 0.01 FDR:   144; 0.001 FDR:   137
1:47:22.972656 PROGRESS: =========================================================================
1:47:22.973716 PROGRESS: === Epoch 2, step 2, extracting elution groups 24000 to 56000 ===
1:47:23.099505 PROGRESS: Extracting batch of 63229 precursors
1:47:23.115428 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:47:23.115567 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:47:23.115619 INFO: FWHM in RT is 18.22 seconds, sigma is 0.66
1:47:23.115658 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:47:23.115925 INFO: Starting candidate selection
1:47:27.557383 INFO: Starting candidate scoring
1:47:29.969335 INFO: Finished candidate processing
1:47:29.969485 INFO: Collecting candidate features
1:47:32.122465 INFO: Collecting fragment features
1:47:32.645074 INFO: Finished candidate scoring
1:47:33.020231 PROGRESS: === Epoch 2, step 2, extracted 114670 precursors and 601755 fragments ===
1:47:33.020574 INFO: performing precursor FDR with 47 features
1:47:33.020634 INFO: Decoy channel: -1
1:47:33.020670 INFO: Competetive: True
1:47:44.821158 INFO: Test AUC: 0.555
1:47:44.821419 INFO: Train AUC: 0.587
1:47:44.821472 INFO: AUC difference: 5.44%
1:47:44.821515 WARNING: AUC difference > 5%. This may indicate overfitting.
1:47:45.001661 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:47:45.002908 PROGRESS: ============================= Precursor FDR =============================
1:47:45.003056 PROGRESS: Total precursors accumulated: 729
1:47:45.003144 PROGRESS: Target precursors: 668 (91.63%)
1:47:45.003221 PROGRESS: Decoy precursors: 61 (8.37%)
1:47:45.003292 PROGRESS: 
1:47:45.003364 PROGRESS: Precursor Summary:
1:47:45.005398 PROGRESS: Channel   0:	 0.05 FDR:   554; 0.01 FDR:   412; 0.001 FDR:   337
1:47:45.005541 PROGRESS: 
1:47:45.005625 PROGRESS: Protein Summary:
1:47:45.007936 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   379; 0.001 FDR:   312
1:47:45.008072 PROGRESS: =========================================================================
1:47:45.009288 PROGRESS: === Epoch 2, step 3, extracting elution groups 56000 to 120000 ===
1:47:45.217281 PROGRESS: Extracting batch of 126425 precursors
1:47:45.256017 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:47:45.256165 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:47:45.256233 INFO: FWHM in RT is 18.22 seconds, sigma is 0.66
1:47:45.256273 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:47:45.256677 INFO: Starting candidate selection
1:47:51.487471 INFO: Starting candidate scoring
1:47:55.487912 INFO: Finished candidate processing
1:47:55.488038 INFO: Collecting candidate features
1:47:57.797965 INFO: Collecting fragment features
1:47:58.383311 INFO: Finished candidate scoring
1:47:58.819408 PROGRESS: === Epoch 2, step 3, extracted 228761 precursors and 1203138 fragments ===
1:47:58.819818 INFO: performing precursor FDR with 47 features
1:47:58.819878 INFO: Decoy channel: -1
1:47:58.819915 INFO: Competetive: True
1:48:27.301145 INFO: Test AUC: 0.561
1:48:27.301300 INFO: Train AUC: 0.581
1:48:27.301350 INFO: AUC difference: 3.38%
1:48:27.550764 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
1:48:27.552733 PROGRESS: ============================= Precursor FDR =============================
1:48:27.552928 PROGRESS: Total precursors accumulated: 1,554
1:48:27.553046 PROGRESS: Target precursors: 1,417 (91.18%)
1:48:27.553152 PROGRESS: Decoy precursors: 137 (8.82%)
1:48:27.553254 PROGRESS: 
1:48:27.553355 PROGRESS: Precursor Summary:
1:48:27.555768 PROGRESS: Channel   0:	 0.05 FDR: 1,082; 0.01 FDR:   809; 0.001 FDR:   602
1:48:27.555917 PROGRESS: 
1:48:27.556000 PROGRESS: Protein Summary:
1:48:27.558682 PROGRESS: Channel   0:	 0.05 FDR:   947; 0.01 FDR:   705; 0.001 FDR:   535
1:48:27.558819 PROGRESS: =========================================================================
1:48:27.561128 INFO: calibration group: precursor, fitting rt estimator 
1:48:27.723094 INFO: calibration group: fragment, fitting mz estimator 
1:48:28.309766 INFO: === checking if epoch conditions were reached ===
1:48:28.310037 INFO: ✅ ms2_error      : 10.0000 <= 10
1:48:28.310169 INFO: ✅ rt_error       : 300.0000 <= 300
1:48:28.310285 INFO: ✅ current_epoch  : 2 >= 3
1:48:28.310390 INFO: ==============================================
1:48:28.345231 INFO: calibration group: precursor, predicting mz
1:48:28.345621 WARNING: mz prediction was skipped as it has not been fitted yet
1:48:28.345690 INFO: calibration group: precursor, predicting rt
1:48:36.447414 INFO: calibration group: fragment, predicting mz
1:48:56.943554 PROGRESS: Extracting batch of 10696137 precursors
1:48:58.967408 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:48:58.967559 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:48:58.967613 INFO: FWHM in RT is 17.27 seconds, sigma is 0.63
1:48:58.967651 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:48:58.967953 INFO: Starting candidate selection
1:53:32.311171 INFO: Applying score cutoff of 68.45713366699219
1:53:32.481484 INFO: Removed 17016442 precursors with score below cutoff
1:53:35.222579 INFO: Starting candidate scoring
1:54:30.741618 INFO: Finished candidate processing
1:54:30.742013 INFO: Collecting candidate features
1:54:42.167426 INFO: Collecting fragment features
1:54:46.346662 INFO: Finished candidate scoring
1:54:50.518123 INFO: performing precursor FDR with 47 features
1:54:50.518267 INFO: Decoy channel: -1
1:54:50.518307 INFO: Competetive: True
1:58:55.804685 INFO: Test AUC: 0.579
1:58:55.804846 INFO: Train AUC: 0.583
1:58:55.804895 INFO: AUC difference: 0.67%
1:58:56.377084 INFO: Removing fragments below FDR threshold
1:58:56.654735 PROGRESS: ============================= Precursor FDR =============================
1:58:56.655030 PROGRESS: Total precursors accumulated: 40,581
1:58:56.655132 PROGRESS: Target precursors: 40,180 (99.01%)
1:58:56.655210 PROGRESS: Decoy precursors: 401 (0.99%)
1:58:56.655282 PROGRESS: 
1:58:56.655359 PROGRESS: Precursor Summary:
1:58:56.676918 PROGRESS: Channel   0:	 0.05 FDR: 40,180; 0.01 FDR: 40,180; 0.001 FDR: 26,879
1:58:56.677171 PROGRESS: 
1:58:56.677256 PROGRESS: Protein Summary:
1:58:56.706927 PROGRESS: Channel   0:	 0.05 FDR: 7,929; 0.01 FDR: 7,929; 0.001 FDR: 5,874
1:58:56.707176 PROGRESS: =========================================================================
1:58:57.428677 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
1:58:58.091130 PROGRESS: Loading raw file 6/6: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
1:58:58.091340 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02 at /home/robbe/alphadia/Proteobench/.progress/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
1:59:31.433700 INFO: Determining DIA cycle
1:59:31.451697 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
1:59:31.458504 INFO: Determining DIA cycle
1:59:31.482799 INFO: Found cycle with start 0.00 min and length 151.
1:59:31.537607 INFO: ============ Raw file stats ============
1:59:31.537983 INFO: RT (min)            : 0.0 - 150.0
1:59:31.538065 INFO: RT duration (sec)   : 8999.7
1:59:31.538102 INFO: RT duration (min)   : 150.0
1:59:31.538224 INFO: Cycle len (scans)   : 151
1:59:31.538269 INFO: Cycle len (sec)     : 5.84
1:59:31.538303 INFO: Number of cycles    : 1541
1:59:31.538364 INFO: MS2 range (m/z)     : 396.4 - 1004.7
1:59:31.538403 INFO: ========================================
1:59:34.996367 INFO: Initializing CalibrationManager
1:59:34.996688 INFO: Loading calibration config
1:59:34.997552 INFO: Calibration config: [{'name': 'fragment', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}]}, {'name': 'precursor', 'estimators': [{'name': 'mz', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'transform_deviation': '1e6', 'function': LOESSRegression(n_kernels=2)}, {'name': 'rt', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}, 'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'function': LOESSRegression()}, {'name': 'mobility', 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'function': LOESSRegression(n_kernels=2)}]}]
1:59:34.997710 INFO: Calibration group :fragment, found 1 estimator(s)
1:59:34.997846 INFO: Calibration group :precursor, found 3 estimator(s)
1:59:34.997961 INFO: Disabling ion mobility calibration
1:59:34.998010 INFO: removed mobility estimator from group precursor
1:59:34.998122 INFO: Initializing OptimizationManager
1:59:34.998234 INFO: initial parameter: fwhm_rt = 5
1:59:34.998307 INFO: initial parameter: fwhm_mobility = 0.01
1:59:34.998376 INFO: initial parameter: score_cutoff = 0
1:59:34.998497 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
1:59:34.998615 INFO: Initializing OptimizationManager
1:59:34.998659 INFO: initial parameter: current_epoch = 0
1:59:34.998693 INFO: initial parameter: current_step = 0
1:59:34.998726 INFO: initial parameter: ms1_error = 20
1:59:34.998757 INFO: initial parameter: ms2_error = 20
1:59:34.998788 INFO: initial parameter: rt_error = 500
1:59:34.998820 INFO: initial parameter: mobility_error = 0.08
1:59:34.998851 INFO: initial parameter: column_type = library
1:59:34.998882 INFO: initial parameter: num_candidates = 2
1:59:34.998913 INFO: initial parameter: recalibration_target = 200
1:59:34.998944 INFO: initial parameter: accumulated_precursors = 0
1:59:34.998974 INFO: initial parameter: accumulated_precursors_01FDR = 0
1:59:34.999005 INFO: initial parameter: accumulated_precursors_001FDR = 0
1:59:34.999062 INFO: Initializing FDRManager
1:59:34.999116 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.10.13/envs/alphadia/lib/python3.10/site-packages/alphadia/constants/classifier
1:59:36.518473 PROGRESS: 5,414,253 target precursors potentially observable (0 removed)
1:59:39.085259 INFO: === checking if epoch conditions were reached ===
1:59:39.085547 INFO: ❌ ms2_error      : 20.0000 > 10
1:59:39.085662 INFO: ❌ rt_error       : 500.0000 > 300
1:59:39.085746 INFO: ❌ current_epoch  : 0 < 3
1:59:39.085825 INFO: ==============================================
1:59:39.299279 INFO: calibration group: precursor, predicting mz
1:59:39.299562 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:39.299610 INFO: calibration group: precursor, predicting rt
1:59:39.299682 WARNING: rt prediction was skipped as it has not been fitted yet
1:59:39.299730 INFO: calibration group: fragment, predicting mz
1:59:39.299800 WARNING: mz prediction was skipped as it has not been fitted yet
1:59:39.299859 PROGRESS: === Epoch 0, step 0, extracting elution groups 0 to 8000 ===
1:59:39.394376 PROGRESS: Extracting batch of 15797 precursors
1:59:39.400173 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:59:39.400280 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:39.400336 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:59:39.400373 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:39.400716 INFO: Starting candidate selection
1:59:42.395410 INFO: Starting candidate scoring
1:59:43.528573 INFO: Finished candidate processing
1:59:43.528698 INFO: Collecting candidate features
1:59:45.189157 INFO: Collecting fragment features
1:59:45.624437 INFO: Finished candidate scoring
1:59:45.845694 PROGRESS: === Epoch 0, step 0, extracted 26174 precursors and 174589 fragments ===
1:59:45.846034 INFO: performing precursor FDR with 47 features
1:59:45.846095 INFO: Decoy channel: -1
1:59:45.846133 INFO: Competetive: True
1:59:46.945569 INFO: Test AUC: 0.522
1:59:46.945712 INFO: Train AUC: 0.522
1:59:46.945760 INFO: AUC difference: 0.16%
1:59:47.096618 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:59:47.097603 PROGRESS: ============================= Precursor FDR =============================
1:59:47.097744 PROGRESS: Total precursors accumulated: 2
1:59:47.097831 PROGRESS: Target precursors: 2 (100.00%)
1:59:47.097908 PROGRESS: Decoy precursors: 0 (0.00%)
1:59:47.097979 PROGRESS: 
1:59:47.098050 PROGRESS: Precursor Summary:
1:59:47.099846 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:59:47.099978 PROGRESS: 
1:59:47.100060 PROGRESS: Protein Summary:
1:59:47.102013 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
1:59:47.102141 PROGRESS: =========================================================================
1:59:47.103151 PROGRESS: === Epoch 0, step 1, extracting elution groups 8000 to 24000 ===
1:59:47.203998 PROGRESS: Extracting batch of 31593 precursors
1:59:47.212482 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:59:47.212600 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:47.212648 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:59:47.212685 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:47.212925 INFO: Starting candidate selection
1:59:51.196234 INFO: Starting candidate scoring
1:59:52.705766 INFO: Finished candidate processing
1:59:52.705901 INFO: Collecting candidate features
1:59:54.589280 INFO: Collecting fragment features
1:59:55.056177 INFO: Finished candidate scoring
1:59:55.343115 PROGRESS: === Epoch 0, step 1, extracted 52168 precursors and 349263 fragments ===
1:59:55.343538 INFO: performing precursor FDR with 47 features
1:59:55.343603 INFO: Decoy channel: -1
1:59:55.343641 INFO: Competetive: True
1:59:59.029899 INFO: Test AUC: 0.533
1:59:59.030057 INFO: Train AUC: 0.554
1:59:59.030105 INFO: AUC difference: 3.68%
1:59:59.190751 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
1:59:59.191746 PROGRESS: ============================= Precursor FDR =============================
1:59:59.191891 PROGRESS: Total precursors accumulated: 30
1:59:59.191975 PROGRESS: Target precursors: 28 (93.33%)
1:59:59.192048 PROGRESS: Decoy precursors: 2 (6.67%)
1:59:59.192118 PROGRESS: 
1:59:59.192187 PROGRESS: Precursor Summary:
1:59:59.193841 PROGRESS: Channel   0:	 0.05 FDR:    24; 0.01 FDR:    18; 0.001 FDR:    18
1:59:59.193980 PROGRESS: 
1:59:59.194062 PROGRESS: Protein Summary:
1:59:59.195892 PROGRESS: Channel   0:	 0.05 FDR:    24; 0.01 FDR:    18; 0.001 FDR:    18
1:59:59.196025 PROGRESS: =========================================================================
1:59:59.197017 PROGRESS: === Epoch 0, step 2, extracting elution groups 24000 to 56000 ===
1:59:59.313830 PROGRESS: Extracting batch of 63220 precursors
1:59:59.331990 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
1:59:59.332135 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:59:59.332204 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:59:59.332243 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:59:59.332616 INFO: Starting candidate selection
2:00:03.871915 INFO: Starting candidate scoring
2:00:06.123658 INFO: Finished candidate processing
2:00:06.123793 INFO: Collecting candidate features
2:00:08.189299 INFO: Collecting fragment features
2:00:08.761754 INFO: Finished candidate scoring
2:00:09.110229 PROGRESS: === Epoch 0, step 2, extracted 104538 precursors and 701864 fragments ===
2:00:09.110635 INFO: performing precursor FDR with 47 features
2:00:09.110699 INFO: Decoy channel: -1
2:00:09.110736 INFO: Competetive: True
2:00:20.176860 INFO: Test AUC: 0.547
2:00:20.177020 INFO: Train AUC: 0.566
2:00:20.177072 INFO: AUC difference: 3.25%
2:00:20.349128 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
2:00:20.350856 PROGRESS: ============================= Precursor FDR =============================
2:00:20.351008 PROGRESS: Total precursors accumulated: 257
2:00:20.351107 PROGRESS: Target precursors: 235 (91.44%)
2:00:20.351189 PROGRESS: Decoy precursors: 22 (8.56%)
2:00:20.351262 PROGRESS: 
2:00:20.351336 PROGRESS: Precursor Summary:
2:00:20.353243 PROGRESS: Channel   0:	 0.05 FDR:   198; 0.01 FDR:   160; 0.001 FDR:   140
2:00:20.353391 PROGRESS: 
2:00:20.353478 PROGRESS: Protein Summary:
2:00:20.355515 PROGRESS: Channel   0:	 0.05 FDR:   188; 0.01 FDR:   151; 0.001 FDR:   131
2:00:20.355658 PROGRESS: =========================================================================
2:00:20.356702 PROGRESS: === Epoch 0, step 3, extracting elution groups 56000 to 120000 ===
2:00:20.506471 PROGRESS: Extracting batch of 126443 precursors
2:00:20.542125 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:00:20.542275 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:00:20.542328 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:00:20.542367 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:00:20.542694 INFO: Starting candidate selection
2:00:27.492920 INFO: Starting candidate scoring
2:00:31.230859 INFO: Finished candidate processing
2:00:31.230992 INFO: Collecting candidate features
2:00:33.812678 INFO: Collecting fragment features
2:00:34.475521 INFO: Finished candidate scoring
2:00:34.974876 PROGRESS: === Epoch 0, step 3, extracted 209246 precursors and 1405449 fragments ===
2:00:34.975267 INFO: performing precursor FDR with 47 features
2:00:34.975328 INFO: Decoy channel: -1
2:00:34.975365 INFO: Competetive: True
2:00:56.867087 INFO: Test AUC: 0.551
2:00:56.867255 INFO: Train AUC: 0.570
2:00:56.867305 INFO: AUC difference: 3.18%
2:00:57.060034 PROGRESS: === checking if recalibration conditions were reached, target 200 precursors ===
2:00:57.061295 PROGRESS: ============================= Precursor FDR =============================
2:00:57.061465 PROGRESS: Total precursors accumulated: 720
2:00:57.061554 PROGRESS: Target precursors: 653 (90.69%)
2:00:57.061630 PROGRESS: Decoy precursors: 67 (9.31%)
2:00:57.061703 PROGRESS: 
2:00:57.061774 PROGRESS: Precursor Summary:
2:00:57.063870 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   431; 0.001 FDR:   341
2:00:57.064018 PROGRESS: 
2:00:57.064100 PROGRESS: Protein Summary:
2:00:57.066433 PROGRESS: Channel   0:	 0.05 FDR:   510; 0.01 FDR:   405; 0.001 FDR:   321
2:00:57.066565 PROGRESS: =========================================================================
2:00:57.068594 INFO: calibration group: precursor, fitting rt estimator 
2:00:58.099317 INFO: calibration group: fragment, fitting mz estimator 
2:00:58.721229 INFO: === checking if epoch conditions were reached ===
2:00:58.721446 INFO: ❌ ms2_error      : 10.4357 > 10
2:00:58.721540 INFO: ❌ rt_error       : 346.3266 > 300
2:00:58.721620 INFO: ❌ current_epoch  : 0 < 3
2:00:58.721693 INFO: ==============================================
2:00:58.941821 INFO: calibration group: precursor, predicting mz
2:00:58.942129 WARNING: mz prediction was skipped as it has not been fitted yet
2:00:58.942177 INFO: calibration group: precursor, predicting rt
2:01:07.312512 INFO: calibration group: fragment, predicting mz
2:01:27.415744 PROGRESS: === Epoch 1, step 0, extracting elution groups 0 to 8000 ===
2:01:27.554380 PROGRESS: Extracting batch of 15823 precursors
2:01:27.560333 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:01:27.560446 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:27.560494 INFO: FWHM in RT is 20.27 seconds, sigma is 0.74
2:01:27.560533 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:27.560774 INFO: Starting candidate selection
2:01:31.359735 INFO: Starting candidate scoring
2:01:32.713275 INFO: Finished candidate processing
2:01:32.713408 INFO: Collecting candidate features
2:01:34.595711 INFO: Collecting fragment features
2:01:35.053667 INFO: Finished candidate scoring
2:01:35.329798 PROGRESS: === Epoch 1, step 0, extracted 24279 precursors and 147414 fragments ===
2:01:35.330140 INFO: performing precursor FDR with 47 features
2:01:35.330199 INFO: Decoy channel: -1
2:01:35.330248 INFO: Competetive: True
2:01:36.115977 INFO: Test AUC: 0.548
2:01:36.116125 INFO: Train AUC: 0.575
2:01:36.116173 INFO: AUC difference: 4.73%
2:01:36.267972 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
2:01:36.269509 PROGRESS: ============================= Precursor FDR =============================
2:01:36.269662 PROGRESS: Total precursors accumulated: 84
2:01:36.269748 PROGRESS: Target precursors: 77 (91.67%)
2:01:36.269826 PROGRESS: Decoy precursors: 7 (8.33%)
2:01:36.269897 PROGRESS: 
2:01:36.269967 PROGRESS: Precursor Summary:
2:01:36.271663 PROGRESS: Channel   0:	 0.05 FDR:    53; 0.01 FDR:    44; 0.001 FDR:    44
2:01:36.271803 PROGRESS: 
2:01:36.271887 PROGRESS: Protein Summary:
2:01:36.273746 PROGRESS: Channel   0:	 0.05 FDR:    52; 0.01 FDR:    43; 0.001 FDR:    43
2:01:36.273881 PROGRESS: =========================================================================
2:01:36.274826 PROGRESS: === Epoch 1, step 1, extracting elution groups 8000 to 24000 ===
2:01:36.383790 PROGRESS: Extracting batch of 31628 precursors
2:01:36.394111 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:01:36.394243 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:36.394294 INFO: FWHM in RT is 20.27 seconds, sigma is 0.74
2:01:36.394331 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:36.394585 INFO: Starting candidate selection
2:01:40.083417 INFO: Starting candidate scoring
2:01:41.758131 INFO: Finished candidate processing
2:01:41.758259 INFO: Collecting candidate features
2:01:43.724713 INFO: Collecting fragment features
2:01:44.208616 INFO: Finished candidate scoring
2:01:44.497273 PROGRESS: === Epoch 1, step 1, extracted 48464 precursors and 296498 fragments ===
2:01:44.497622 INFO: performing precursor FDR with 47 features
2:01:44.497680 INFO: Decoy channel: -1
2:01:44.497717 INFO: Competetive: True
2:01:48.075171 INFO: Test AUC: 0.548
2:01:48.075324 INFO: Train AUC: 0.586
2:01:48.075374 INFO: AUC difference: 6.35%
2:01:48.075409 WARNING: AUC difference > 5%. This may indicate overfitting.
2:01:48.232630 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
2:01:48.233627 PROGRESS: ============================= Precursor FDR =============================
2:01:48.233773 PROGRESS: Total precursors accumulated: 169
2:01:48.233869 PROGRESS: Target precursors: 153 (90.53%)
2:01:48.233945 PROGRESS: Decoy precursors: 16 (9.47%)
2:01:48.234015 PROGRESS: 
2:01:48.234085 PROGRESS: Precursor Summary:
2:01:48.235811 PROGRESS: Channel   0:	 0.05 FDR:   118; 0.01 FDR:    58; 0.001 FDR:    58
2:01:48.235944 PROGRESS: 
2:01:48.236025 PROGRESS: Protein Summary:
2:01:48.237927 PROGRESS: Channel   0:	 0.05 FDR:   114; 0.01 FDR:    58; 0.001 FDR:    58
2:01:48.238061 PROGRESS: =========================================================================
2:01:48.239008 PROGRESS: === Epoch 1, step 2, extracting elution groups 24000 to 56000 ===
2:01:48.358637 PROGRESS: Extracting batch of 63224 precursors
2:01:48.376369 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:01:48.376510 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:01:48.376561 INFO: FWHM in RT is 20.27 seconds, sigma is 0.74
2:01:48.376599 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:01:48.376861 INFO: Starting candidate selection
2:01:52.871128 INFO: Starting candidate scoring
2:01:55.199004 INFO: Finished candidate processing
2:01:55.199137 INFO: Collecting candidate features
2:01:57.201677 INFO: Collecting fragment features
2:01:57.723321 INFO: Finished candidate scoring
2:01:58.059346 PROGRESS: === Epoch 1, step 2, extracted 97021 precursors and 588906 fragments ===
2:01:58.059711 INFO: performing precursor FDR with 47 features
2:01:58.059768 INFO: Decoy channel: -1
2:01:58.059805 INFO: Competetive: True
2:02:07.739396 INFO: Test AUC: 0.561
2:02:07.739562 INFO: Train AUC: 0.582
2:02:07.739612 INFO: AUC difference: 3.55%
2:02:07.910067 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
2:02:07.911192 PROGRESS: ============================= Precursor FDR =============================
2:02:07.911344 PROGRESS: Total precursors accumulated: 497
2:02:07.911430 PROGRESS: Target precursors: 453 (91.15%)
2:02:07.911513 PROGRESS: Decoy precursors: 44 (8.85%)
2:02:07.911585 PROGRESS: 
2:02:07.911657 PROGRESS: Precursor Summary:
2:02:07.913562 PROGRESS: Channel   0:	 0.05 FDR:   348; 0.01 FDR:   245; 0.001 FDR:   119
2:02:07.914437 PROGRESS: 
2:02:07.914550 PROGRESS: Protein Summary:
2:02:07.916696 PROGRESS: Channel   0:	 0.05 FDR:   332; 0.01 FDR:   237; 0.001 FDR:   116
2:02:07.916832 PROGRESS: =========================================================================
2:02:07.917889 PROGRESS: === Epoch 1, step 3, extracting elution groups 56000 to 120000 ===
2:02:08.058529 PROGRESS: Extracting batch of 126392 precursors
2:02:08.093090 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:02:08.093230 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:02:08.093280 INFO: FWHM in RT is 20.27 seconds, sigma is 0.74
2:02:08.093319 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:02:08.093582 INFO: Starting candidate selection
2:02:14.016325 INFO: Starting candidate scoring
2:02:17.667442 INFO: Finished candidate processing
2:02:17.667686 INFO: Collecting candidate features
2:02:20.022272 INFO: Collecting fragment features
2:02:20.628642 INFO: Finished candidate scoring
2:02:21.081677 PROGRESS: === Epoch 1, step 3, extracted 193479 precursors and 1175062 fragments ===
2:02:21.082108 INFO: performing precursor FDR with 47 features
2:02:21.082168 INFO: Decoy channel: -1
2:02:21.082205 INFO: Competetive: True
2:02:40.756910 INFO: Test AUC: 0.561
2:02:40.757072 INFO: Train AUC: 0.580
2:02:40.757122 INFO: AUC difference: 3.33%
2:02:41.010324 PROGRESS: === checking if recalibration conditions were reached, target 400 precursors ===
2:02:41.011657 PROGRESS: ============================= Precursor FDR =============================
2:02:41.011806 PROGRESS: Total precursors accumulated: 1,054
2:02:41.011892 PROGRESS: Target precursors: 958 (90.89%)
2:02:41.011966 PROGRESS: Decoy precursors: 96 (9.11%)
2:02:41.012038 PROGRESS: 
2:02:41.012108 PROGRESS: Precursor Summary:
2:02:41.014254 PROGRESS: Channel   0:	 0.05 FDR:   784; 0.01 FDR:   570; 0.001 FDR:   409
2:02:41.014396 PROGRESS: 
2:02:41.014479 PROGRESS: Protein Summary:
2:02:41.016951 PROGRESS: Channel   0:	 0.05 FDR:   701; 0.01 FDR:   518; 0.001 FDR:   382
2:02:41.017087 PROGRESS: =========================================================================
2:02:41.019189 INFO: calibration group: precursor, fitting rt estimator 
2:02:41.155519 INFO: calibration group: fragment, fitting mz estimator 
2:02:41.776124 INFO: === checking if epoch conditions were reached ===
2:02:41.776348 INFO: ✅ ms2_error      : 10.0000 <= 10
2:02:41.776446 INFO: ❌ rt_error       : 307.9956 > 300
2:02:41.776526 INFO: ❌ current_epoch  : 1 < 3
2:02:41.776600 INFO: ==============================================
2:02:41.986761 INFO: calibration group: precursor, predicting mz
2:02:41.987062 WARNING: mz prediction was skipped as it has not been fitted yet
2:02:41.987113 INFO: calibration group: precursor, predicting rt
2:02:50.229337 INFO: calibration group: fragment, predicting mz
2:03:10.131554 PROGRESS: === Epoch 2, step 0, extracting elution groups 0 to 8000 ===
2:03:10.246264 PROGRESS: Extracting batch of 15804 precursors
2:03:10.253086 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:03:10.253195 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:10.253250 INFO: FWHM in RT is 18.85 seconds, sigma is 0.69
2:03:10.253288 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:03:10.253580 INFO: Starting candidate selection
2:03:14.488022 INFO: Starting candidate scoring
2:03:15.864403 INFO: Finished candidate processing
2:03:15.864538 INFO: Collecting candidate features
2:03:17.753670 INFO: Collecting fragment features
2:03:18.200722 INFO: Finished candidate scoring
2:03:18.559886 PROGRESS: === Epoch 2, step 0, extracted 25507 precursors and 152224 fragments ===
2:03:18.560620 INFO: performing precursor FDR with 47 features
2:03:18.560704 INFO: Decoy channel: -1
2:03:18.560744 INFO: Competetive: True
2:03:19.569428 INFO: Test AUC: 0.546
2:03:19.569581 INFO: Train AUC: 0.597
2:03:19.569629 INFO: AUC difference: 8.41%
2:03:19.569670 WARNING: AUC difference > 5%. This may indicate overfitting.
2:03:19.723737 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
2:03:19.724731 PROGRESS: ============================= Precursor FDR =============================
2:03:19.724874 PROGRESS: Total precursors accumulated: 110
2:03:19.724960 PROGRESS: Target precursors: 101 (91.82%)
2:03:19.725035 PROGRESS: Decoy precursors: 9 (8.18%)
2:03:19.725107 PROGRESS: 
2:03:19.725177 PROGRESS: Precursor Summary:
2:03:19.726867 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    42; 0.001 FDR:    42
2:03:19.727006 PROGRESS: 
2:03:19.727100 PROGRESS: Protein Summary:
2:03:19.729010 PROGRESS: Channel   0:	 0.05 FDR:    68; 0.01 FDR:    42; 0.001 FDR:    42
2:03:19.729146 PROGRESS: =========================================================================
2:03:19.730107 PROGRESS: === Epoch 2, step 1, extracting elution groups 8000 to 24000 ===
2:03:19.843574 PROGRESS: Extracting batch of 31612 precursors
2:03:19.853324 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:03:19.853454 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:19.853505 INFO: FWHM in RT is 18.85 seconds, sigma is 0.69
2:03:19.853544 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:03:19.853792 INFO: Starting candidate selection
2:03:24.105956 INFO: Starting candidate scoring
2:03:25.885238 INFO: Finished candidate processing
2:03:25.885372 INFO: Collecting candidate features
2:03:27.853804 INFO: Collecting fragment features
2:03:28.335618 INFO: Finished candidate scoring
2:03:28.628581 PROGRESS: === Epoch 2, step 1, extracted 51401 precursors and 307160 fragments ===
2:03:28.628916 INFO: performing precursor FDR with 47 features
2:03:28.628977 INFO: Decoy channel: -1
2:03:28.629019 INFO: Competetive: True
2:03:32.403123 INFO: Test AUC: 0.556
2:03:32.404140 INFO: Train AUC: 0.593
2:03:32.404241 INFO: AUC difference: 6.23%
2:03:32.404298 WARNING: AUC difference > 5%. This may indicate overfitting.
2:03:32.566383 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
2:03:32.567431 PROGRESS: ============================= Precursor FDR =============================
2:03:32.567585 PROGRESS: Total precursors accumulated: 254
2:03:32.567672 PROGRESS: Target precursors: 231 (90.94%)
2:03:32.567747 PROGRESS: Decoy precursors: 23 (9.06%)
2:03:32.567817 PROGRESS: 
2:03:32.567887 PROGRESS: Precursor Summary:
2:03:32.569674 PROGRESS: Channel   0:	 0.05 FDR:   192; 0.01 FDR:   155; 0.001 FDR:   147
2:03:32.569816 PROGRESS: 
2:03:32.569899 PROGRESS: Protein Summary:
2:03:32.571920 PROGRESS: Channel   0:	 0.05 FDR:   190; 0.01 FDR:   153; 0.001 FDR:   145
2:03:32.572058 PROGRESS: =========================================================================
2:03:32.573066 PROGRESS: === Epoch 2, step 2, extracting elution groups 24000 to 56000 ===
2:03:32.746634 PROGRESS: Extracting batch of 63245 precursors
2:03:32.764660 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:03:32.764802 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:32.764852 INFO: FWHM in RT is 18.85 seconds, sigma is 0.69
2:03:32.764890 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:03:32.765152 INFO: Starting candidate selection
2:03:37.524604 INFO: Starting candidate scoring
2:03:39.925052 INFO: Finished candidate processing
2:03:39.925271 INFO: Collecting candidate features
2:03:42.092632 INFO: Collecting fragment features
2:03:42.680331 INFO: Finished candidate scoring
2:03:43.028923 PROGRESS: === Epoch 2, step 2, extracted 103000 precursors and 616855 fragments ===
2:03:43.029328 INFO: performing precursor FDR with 47 features
2:03:43.029387 INFO: Decoy channel: -1
2:03:43.029436 INFO: Competetive: True
2:03:52.686112 INFO: Test AUC: 0.556
2:03:52.686273 INFO: Train AUC: 0.590
2:03:52.686322 INFO: AUC difference: 5.87%
2:03:52.686360 WARNING: AUC difference > 5%. This may indicate overfitting.
2:03:52.870579 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
2:03:52.871944 PROGRESS: ============================= Precursor FDR =============================
2:03:52.872119 PROGRESS: Total precursors accumulated: 646
2:03:52.872250 PROGRESS: Target precursors: 588 (91.02%)
2:03:52.872347 PROGRESS: Decoy precursors: 58 (8.98%)
2:03:52.872422 PROGRESS: 
2:03:52.872494 PROGRESS: Precursor Summary:
2:03:52.875099 PROGRESS: Channel   0:	 0.05 FDR:   521; 0.01 FDR:   388; 0.001 FDR:   359
2:03:52.875244 PROGRESS: 
2:03:52.875330 PROGRESS: Protein Summary:
2:03:52.877682 PROGRESS: Channel   0:	 0.05 FDR:   497; 0.01 FDR:   370; 0.001 FDR:   342
2:03:52.877813 PROGRESS: =========================================================================
2:03:52.879313 PROGRESS: === Epoch 2, step 3, extracting elution groups 56000 to 120000 ===
2:03:53.038098 PROGRESS: Extracting batch of 126436 precursors
2:03:53.074453 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:03:53.074611 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:53.074666 INFO: FWHM in RT is 18.85 seconds, sigma is 0.69
2:03:53.074705 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:03:53.075008 INFO: Starting candidate selection
2:03:59.842338 INFO: Starting candidate scoring
2:04:03.685721 INFO: Finished candidate processing
2:04:03.685953 INFO: Collecting candidate features
2:04:06.396652 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 204841)
2:04:06.420228 INFO: Collecting fragment features
2:04:07.056131 INFO: Finished candidate scoring
2:04:07.524579 PROGRESS: === Epoch 2, step 3, extracted 204841 precursors and 1224519 fragments ===
2:04:07.525058 INFO: performing precursor FDR with 47 features
2:04:07.525129 INFO: Decoy channel: -1
2:04:07.525166 INFO: Competetive: True
2:04:07.845170 WARNING: dropped 1 target PSMs due to missing features
2:04:07.845325 WARNING: dropped 1 decoy PSMs due to missing features
2:04:28.289093 INFO: Test AUC: 0.560
2:04:28.289328 INFO: Train AUC: 0.583
2:04:28.289381 INFO: AUC difference: 3.92%
2:04:28.478815 PROGRESS: === checking if recalibration conditions were reached, target 600 precursors ===
2:04:28.480202 PROGRESS: ============================= Precursor FDR =============================
2:04:28.480351 PROGRESS: Total precursors accumulated: 1,325
2:04:28.480440 PROGRESS: Target precursors: 1,204 (90.87%)
2:04:28.480527 PROGRESS: Decoy precursors: 121 (9.13%)
2:04:28.480603 PROGRESS: 
2:04:28.480674 PROGRESS: Precursor Summary:
2:04:28.482950 PROGRESS: Channel   0:	 0.05 FDR:   952; 0.01 FDR:   744; 0.001 FDR:   540
2:04:28.483088 PROGRESS: 
2:04:28.483168 PROGRESS: Protein Summary:
2:04:28.485832 PROGRESS: Channel   0:	 0.05 FDR:   859; 0.01 FDR:   669; 0.001 FDR:   503
2:04:28.485972 PROGRESS: =========================================================================
2:04:28.488291 INFO: calibration group: precursor, fitting rt estimator 
2:04:28.622519 INFO: calibration group: fragment, fitting mz estimator 
2:04:29.240270 INFO: === checking if epoch conditions were reached ===
2:04:29.240483 INFO: ✅ ms2_error      : 10.0000 <= 10
2:04:29.240580 INFO: ✅ rt_error       : 300.0000 <= 300
2:04:29.240663 INFO: ✅ current_epoch  : 2 >= 3
2:04:29.240739 INFO: ==============================================
2:04:29.262966 INFO: calibration group: precursor, predicting mz
2:04:29.263298 WARNING: mz prediction was skipped as it has not been fitted yet
2:04:29.263349 INFO: calibration group: precursor, predicting rt
2:04:37.289101 INFO: calibration group: fragment, predicting mz
2:04:57.710106 PROGRESS: Extracting batch of 10696137 precursors
2:05:00.118072 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:05:00.118212 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:05:00.118271 INFO: FWHM in RT is 18.55 seconds, sigma is 0.67
2:05:00.118321 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:05:00.118698 INFO: Starting candidate selection
2:09:37.537111 INFO: Applying score cutoff of 67.85753240203857
2:09:37.862222 INFO: Removed 13231852 precursors with score below cutoff
2:09:41.029385 INFO: Starting candidate scoring
2:11:15.224885 INFO: Finished candidate processing
2:11:15.225127 INFO: Collecting candidate features
2:11:33.351066 INFO: Collecting fragment features
2:11:40.836011 INFO: Finished candidate scoring
2:11:45.771518 INFO: performing precursor FDR with 47 features
2:11:45.771676 INFO: Decoy channel: -1
2:11:45.771718 INFO: Competetive: True
2:18:04.919379 INFO: Test AUC: 0.575
2:18:04.919633 INFO: Train AUC: 0.578
2:18:04.919687 INFO: AUC difference: 0.48%
2:18:05.745188 INFO: Removing fragments below FDR threshold
2:18:06.291598 PROGRESS: ============================= Precursor FDR =============================
2:18:06.291925 PROGRESS: Total precursors accumulated: 40,347
2:18:06.292031 PROGRESS: Target precursors: 39,948 (99.01%)
2:18:06.292109 PROGRESS: Decoy precursors: 399 (0.99%)
2:18:06.292182 PROGRESS: 
2:18:06.292254 PROGRESS: Precursor Summary:
2:18:06.313775 PROGRESS: Channel   0:	 0.05 FDR: 39,948; 0.01 FDR: 39,948; 0.001 FDR: 24,813
2:18:06.314040 PROGRESS: 
2:18:06.314129 PROGRESS: Protein Summary:
2:18:06.343406 PROGRESS: Channel   0:	 0.05 FDR: 7,936; 0.01 FDR: 7,936; 0.001 FDR: 5,670
2:18:06.343681 PROGRESS: =========================================================================
2:18:06.890735 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
2:18:33.503766 PROGRESS: Processing search outputs
2:18:33.503946 PROGRESS: Performing protein grouping and FDR
2:18:33.503998 INFO: Building output for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
2:18:33.592592 INFO: Building output for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
2:18:33.646681 INFO: Building output for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
2:18:33.707552 INFO: Building output for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
2:18:33.779806 INFO: Building output for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
2:18:33.845683 INFO: Building output for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
2:18:33.916261 INFO: Building combined output
2:18:34.354022 INFO: Performing protein inference
2:18:34.829635 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2:18:57.934283 INFO: Performing protein FDR
2:19:04.269948 INFO: Normalizing q-values using 11,016 targets and 1,830 decoys
2:19:04.278212 INFO: Test AUC: 0.886
2:19:04.278324 INFO: Train AUC: 0.879
2:19:04.278373 INFO: AUC difference: 0.77%
2:19:04.772856 PROGRESS: ================ Protein FDR =================
2:19:04.773023 PROGRESS: Unique protein groups in output
2:19:04.773071 PROGRESS:   1% protein FDR: 6,235
2:19:04.773109 PROGRESS: 
2:19:04.773146 PROGRESS: Unique precursor in output
2:19:04.773182 PROGRESS:   1% protein FDR: 64,743
2:19:04.773217 PROGRESS: ================================================
2:19:04.825238 PROGRESS: Building search statistics
2:19:05.046768 INFO: Writing stat output to disk
2:19:05.046921 INFO: Saving /home/robbe/alphadia/Proteobench/stat.tsv to disk
2:19:05.053293 PROGRESS: Performing label free quantification
2:19:05.116934 INFO: Accumulating fragment data
2:19:05.117132 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
2:19:05.360817 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
2:19:05.918634 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
2:19:06.546500 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
2:19:07.191719 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
2:19:07.850628 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
2:19:08.738461 PROGRESS: Performing label free quantification on the pg level
2:19:08.738628 INFO: Filtering fragments by quality
2:19:08.959224 INFO: Performing label-free quantification using directLFQ
2:19:10.669135 INFO: 6235 lfq-groups total
2:19:37.536602 INFO: using 80 processes
2:19:37.571875 INFO: lfq-object 0
2:19:37.678781 INFO: lfq-object 100
2:19:37.781897 INFO: lfq-object 200
2:19:37.863280 INFO: lfq-object 300
2:19:37.982879 INFO: lfq-object 400
2:19:39.007220 INFO: lfq-object 500
2:19:39.109854 INFO: lfq-object 600
2:19:39.260981 INFO: lfq-object 700
2:19:39.398792 INFO: lfq-object 800
2:19:39.463509 INFO: lfq-object 900
2:19:39.520478 INFO: lfq-object 1000
2:19:39.619335 INFO: lfq-object 1100
2:19:39.691159 INFO: lfq-object 1200
2:19:39.765371 INFO: lfq-object 1300
2:19:39.868111 INFO: lfq-object 1400
2:19:39.957378 INFO: lfq-object 1500
2:19:40.016179 INFO: lfq-object 1600
2:19:40.085964 INFO: lfq-object 1700
2:19:40.179680 INFO: lfq-object 1800
2:19:40.272925 INFO: lfq-object 1900
2:19:40.349612 INFO: lfq-object 2000
2:19:40.430711 INFO: lfq-object 2100
2:19:40.504263 INFO: lfq-object 2200
2:19:40.584927 INFO: lfq-object 2300
2:19:40.649068 INFO: lfq-object 2400
2:19:40.711321 INFO: lfq-object 2500
2:19:40.815532 INFO: lfq-object 2600
2:19:40.917024 INFO: lfq-object 2700
2:19:41.013736 INFO: lfq-object 2800
2:19:41.113067 INFO: lfq-object 2900
2:19:41.181536 INFO: lfq-object 3000
2:19:41.267431 INFO: lfq-object 3100
2:19:41.385232 INFO: lfq-object 3200
2:19:41.456539 INFO: lfq-object 3300
2:19:41.528996 INFO: lfq-object 3400
2:19:41.605354 INFO: lfq-object 3500
2:19:41.684088 INFO: lfq-object 3600
2:19:41.755886 INFO: lfq-object 3700
2:19:41.836765 INFO: lfq-object 3800
2:19:41.902344 INFO: lfq-object 3900
2:19:41.982980 INFO: lfq-object 4000
2:19:42.060369 INFO: lfq-object 4100
2:19:42.145073 INFO: lfq-object 4200
2:19:42.264885 INFO: lfq-object 4300
2:19:42.349275 INFO: lfq-object 4400
2:19:42.434335 INFO: lfq-object 4500
2:19:42.510075 INFO: lfq-object 4600
2:19:42.634161 INFO: lfq-object 4700
2:19:42.704746 INFO: lfq-object 4800
2:19:42.779834 INFO: lfq-object 4900
2:19:42.853154 INFO: lfq-object 5000
2:19:42.922121 INFO: lfq-object 5100
2:19:42.992354 INFO: lfq-object 5200
2:19:43.066402 INFO: lfq-object 5300
2:19:43.138916 INFO: lfq-object 5400
2:19:43.222556 INFO: lfq-object 5500
2:19:43.311938 INFO: lfq-object 5600
2:19:43.387178 INFO: lfq-object 5700
2:19:43.481343 INFO: lfq-object 5800
2:19:43.592330 INFO: lfq-object 5900
2:19:43.660273 INFO: lfq-object 6000
2:19:43.759262 INFO: lfq-object 6100
2:19:43.866556 INFO: lfq-object 6200
2:19:45.193197 INFO: Writing pg output to disk
2:19:45.193389 INFO: Saving /home/robbe/alphadia/Proteobench/pg.matrix.tsv to disk
2:19:45.437413 INFO: Writing psm output to disk
2:19:45.437572 INFO: Saving /home/robbe/alphadia/Proteobench/precursors.tsv to disk
2:20:08.262887 PROGRESS: Building spectral library
2:20:08.353691 INFO: Building MBR spectral library
2:20:08.353840 INFO: Running MbrLibraryBuilder
2:20:12.637553 INFO: MBR spectral library contains 64,743 precursors, 6,235 proteins
2:20:12.637701 INFO: Writing MBR spectral library to disk
2:20:13.101694 INFO: Writing MBR spectral library to disk
2:20:13.586876 PROGRESS: =================== Search Finished ===================
2:20:38.984466 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_h958setw. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 2,500,272,189,440
