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0:00:00 PROGRESS: 
0:00:00 PROGRESS: version: 1.8.1
0:00:00 PROGRESS: hostname: Agamemnon
0:00:00 PROGRESS: date: 2024-10-31 20:45:45
0:00:00 PROGRESS: =================== Environment ===================
0:00:00 PROGRESS: alphatims       : 1.0.8
0:00:00 PROGRESS: alpharaw        : 0.4.5
0:00:00 PROGRESS: alphabase       : 1.4.0
0:00:00 PROGRESS: alphapeptdeep   : 1.3.0
0:00:00 PROGRESS: directlfq       : 0.2.19
0:00:00 PROGRESS: ===================================================
0:00:00 INFO: loading default config from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\default.yaml
0:00:00.046872 INFO: ├──version: 1 (default)
0:00:00.046872 INFO: ├──general
0:00:00.046872 INFO: │   ├──thread_count: 10 (default)
0:00:00.046872 INFO: │   ├──reuse_calibration: False (default)
0:00:00.046872 INFO: │   ├──reuse_quant: False (default)
0:00:00.046872 INFO: │   ├──astral_ms1: False (default)
0:00:00.046872 INFO: │   ├──log_level: INFO (default)
0:00:00.046872 INFO: │   ├──wsl: False (default)
0:00:00.046872 INFO: │   ├──mmap_detector_events: False (default)
0:00:00.046872 INFO: │   ├──use_gpu: True (default)
0:00:00.046872 INFO: │   ├──save_library: True (default)
0:00:00.046872 INFO: │   └──save_mbr_library: True (default)
0:00:00.046872 INFO: ├──library_loading
0:00:00.046872 INFO: │   └──rt_heuristic: 180 (default)
0:00:00.046872 INFO: ├──library_prediction
0:00:00.046872 INFO: │   ├──predict: False (default)
0:00:00.046872 INFO: │   ├──[32;20mpredict: True (user defined)[0m
0:00:00.046872 INFO: │   ├──enzyme: trypsin (default)
0:00:00.046872 INFO: │   ├──[32;20menzyme: trypsin/p (user defined)[0m
0:00:00.046872 INFO: │   ├──fixed_modifications: Carbamidomethyl@C (default)
0:00:00.046872 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term (default)
0:00:00.046872 INFO: │   ├──max_var_mod_num: 2 (default)
0:00:00.046872 INFO: │   ├──[32;20mmax_var_mod_num: 1 (user defined)[0m
0:00:00.046872 INFO: │   ├──missed_cleavages: 1 (default)
0:00:00.046872 INFO: │   ├──precursor_len
0:00:00.046872 INFO: │   │   ├──7 (default)
0:00:00.046872 INFO: │   │   ├──[32;20m6 (user defined)[0m
0:00:00.046872 INFO: │   │   └──35 (default)
0:00:00.046872 INFO: │   ├──precursor_charge
0:00:00.046872 INFO: │   │   ├──2 (default)
0:00:00.046872 INFO: │   │   ├──[32;20m1 (user defined)[0m
0:00:00.046872 INFO: │   │   └──4 (default)
0:00:00.046872 INFO: │   ├──precursor_mz
0:00:00.046872 INFO: │   │   ├──400 (default)
0:00:00.046872 INFO: │   │   └──1200 (default)
0:00:00.046872 INFO: │   │   └──[32;20m1000 (user defined)[0m
0:00:00.046872 INFO: │   ├──fragment_mz
0:00:00.046872 INFO: │   │   ├──200 (default)
0:00:00.046872 INFO: │   │   ├──[32;20m50 (user defined)[0m
0:00:00.046872 INFO: │   │   └──2000 (default)
0:00:00.046872 INFO: │   ├──nce: 25.0 (default)
0:00:00.046872 INFO: │   ├──fragment_types: b;y (default)
0:00:00.046872 INFO: │   ├──max_fragment_charge: 2 (default)
0:00:00.046872 INFO: │   ├──instrument: Lumos (default)
0:00:00.046872 INFO: │   ├──[32;20minstrument: QEHFX (user defined)[0m
0:00:00.046872 INFO: │   ├──peptdeep_model_path: None (default)
0:00:00.046872 INFO: │   └──peptdeep_model_type: None (default)
0:00:00.046872 INFO: │   └──[32;20mpeptdeep_model_type: generic (user defined)[0m
0:00:00.046872 INFO: ├──custom_modififcations
0:00:00.046872 INFO: │   ├──Dimethyl:d12@K
0:00:00.046872 INFO: │   │   └──composition: H(-2)2H(8)13C(2) (default)
0:00:00.046872 INFO: │   ├──Dimethyl:d12@Any_N-term
0:00:00.046872 INFO: │   │   └──composition: H(-2)2H(8)13C(2) (default)
0:00:00.046872 INFO: │   ├──Dimethyl:d12@Protein_N-term
0:00:00.046872 INFO: │   │   └──composition: H(-2)2H(8)13C(2) (default)
0:00:00.046872 INFO: │   ├──mTRAQ:d12@K
0:00:00.046872 INFO: │   │   └──composition: H(12)C(1)13C(10)15N(2)O(1) (default)
0:00:00.046872 INFO: │   ├──mTRAQ:d12@Any_N-term
0:00:00.046872 INFO: │   │   └──composition: H(12)C(1)13C(14)15N(2)O(1) (default)
0:00:00.046872 INFO: │   ├──mTRAQ:d12@Protein_N-term
0:00:00.046872 INFO: │   │   └──composition: H(12)C(1)13C(14)15N(2)O(1) (default)
0:00:00.046872 INFO: │   └──Label:13C(12)@K
0:00:00.046872 INFO: │       └──composition: C(12) (default)
0:00:00.046872 INFO: ├──search
0:00:00.046872 INFO: │   ├──channel_filter: 0 (default)
0:00:00.046872 INFO: │   ├──[32;20mchannel_filter:  (user defined)[0m
0:00:00.046872 INFO: │   ├──exclude_shared_ions: True (default)
0:00:00.046872 INFO: │   ├──compete_for_fragments: True (default)
0:00:00.046872 INFO: │   ├──target_num_candidates: 2 (default)
0:00:00.046872 INFO: │   ├──target_ms1_tolerance: 5 (default)
0:00:00.046872 INFO: │   ├──target_ms2_tolerance: 10 (default)
0:00:00.046872 INFO: │   ├──target_mobility_tolerance: 0.0 (default)
0:00:00.046872 INFO: │   ├──target_rt_tolerance: 0.0 (default)
0:00:00.046872 INFO: │   ├──quant_window: 3 (default)
0:00:00.046872 INFO: │   └──quant_all: True (default)
0:00:00.046872 INFO: ├──search_advanced
0:00:00.046872 INFO: │   └──top_k_fragments: 12 (default)
0:00:00.046872 INFO: ├──calibration
0:00:00.046872 INFO: │   ├──batch_size: 8000 (default)
0:00:00.046872 INFO: │   ├──optimization_lock_target: 200 (default)
0:00:00.046872 INFO: │   ├──max_steps: 20 (default)
0:00:00.046872 INFO: │   ├──min_steps: 2 (default)
0:00:00.046872 INFO: │   ├──max_skips: 1 (default)
0:00:00.046872 INFO: │   ├──final_full_calibration: False (default)
0:00:00.046872 INFO: │   ├──norm_rt_mode: linear (default)
0:00:00.046872 INFO: │   ├──max_fragments: 5000 (default)
0:00:00.046872 INFO: │   └──min_correlation: 0.7 (default)
0:00:00.046872 INFO: ├──search_initial
0:00:00.046872 INFO: │   ├──initial_num_candidates: 1 (default)
0:00:00.046872 INFO: │   ├──initial_ms1_tolerance: 30 (default)
0:00:00.046872 INFO: │   ├──initial_ms2_tolerance: 30 (default)
0:00:00.046872 INFO: │   ├──initial_mobility_tolerance: 0.1 (default)
0:00:00.046872 INFO: │   └──initial_rt_tolerance: 0.5 (default)
0:00:00.046872 INFO: ├──selection_config
0:00:00.046872 INFO: │   ├──peak_len_rt: 10.0 (default)
0:00:00.046872 INFO: │   ├──sigma_scale_rt: 0.5 (default)
0:00:00.046872 INFO: │   ├──peak_len_mobility: 0.01 (default)
0:00:00.046872 INFO: │   ├──sigma_scale_mobility: 1.0 (default)
0:00:00.046872 INFO: │   ├──top_k_precursors: 3 (default)
0:00:00.046872 INFO: │   ├──kernel_size: 30 (default)
0:00:00.046872 INFO: │   ├──f_mobility: 1.0 (default)
0:00:00.046872 INFO: │   ├──f_rt: 0.99 (default)
0:00:00.046872 INFO: │   ├──center_fraction: 0.5 (default)
0:00:00.046872 INFO: │   ├──min_size_mobility: 8 (default)
0:00:00.046872 INFO: │   ├──min_size_rt: 3 (default)
0:00:00.046872 INFO: │   ├──max_size_mobility: 20 (default)
0:00:00.046872 INFO: │   ├──max_size_rt: 15 (default)
0:00:00.046872 INFO: │   ├──group_channels: False (default)
0:00:00.046872 INFO: │   ├──use_weighted_score: True (default)
0:00:00.046872 INFO: │   ├──join_close_candidates: False (default)
0:00:00.046872 INFO: │   ├──join_close_candidates_scan_threshold: 0.6 (default)
0:00:00.046872 INFO: │   └──join_close_candidates_cycle_threshold: 0.6 (default)
0:00:00.046872 INFO: ├──scoring_config
0:00:00.046872 INFO: │   ├──score_grouped: False (default)
0:00:00.046872 INFO: │   ├──top_k_isotopes: 3 (default)
0:00:00.046872 INFO: │   ├──reference_channel: -1 (default)
0:00:00.046872 INFO: │   ├──precursor_mz_tolerance: 10 (default)
0:00:00.046872 INFO: │   └──fragment_mz_tolerance: 15 (default)
0:00:00.046872 INFO: ├──library_multiplexing
0:00:00.046872 INFO: │   ├──enabled: False (default)
0:00:00.046872 INFO: │   ├──input_channel: 0 (default)
0:00:00.046872 INFO: │   └──multiplex_mapping
0:00:00.046872 INFO: ├──multiplexing
0:00:00.046872 INFO: │   ├──enabled: False (default)
0:00:00.046872 INFO: │   ├──target_channels: 4,8 (default)
0:00:00.046872 INFO: │   ├──decoy_channel: 12 (default)
0:00:00.046872 INFO: │   ├──reference_channel: 0 (default)
0:00:00.046872 INFO: │   └──competetive_scoring: True (default)
0:00:00.046872 INFO: ├──fdr
0:00:00.046872 INFO: │   ├──fdr: 0.01 (default)
0:00:00.046872 INFO: │   ├──group_level: proteins (default)
0:00:00.046872 INFO: │   ├──competetive_scoring: True (default)
0:00:00.046872 INFO: │   ├──keep_decoys: False (default)
0:00:00.046872 INFO: │   ├──[32;20mkeep_decoys: True (user defined)[0m
0:00:00.046872 INFO: │   ├──channel_wise_fdr: False (default)
0:00:00.060891 INFO: │   └──inference_strategy: heuristic (default)
0:00:00.060891 INFO: ├──search_output
0:00:00.060891 INFO: │   ├──peptide_level_lfq: False (default)
0:00:00.060891 INFO: │   ├──precursor_level_lfq: False (default)
0:00:00.060891 INFO: │   ├──min_k_fragments: 12 (default)
0:00:00.060891 INFO: │   ├──min_correlation: 0.9 (default)
0:00:00.060891 INFO: │   ├──num_samples_quadratic: 50 (default)
0:00:00.060891 INFO: │   ├──min_nonnan: 3 (default)
0:00:00.060891 INFO: │   ├──normalize_lfq: True (default)
0:00:00.060891 INFO: │   └──file_format: tsv (default)
0:00:00.060891 INFO: ├──optimization
0:00:00.060891 INFO: │   ├──order_of_optimization: None (default)
0:00:00.060891 INFO: │   ├──ms2_error
0:00:00.060891 INFO: │   │   ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.060891 INFO: │   │   ├──targeted_update_factor: 1.0 (default)
0:00:00.060891 INFO: │   │   ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.060891 INFO: │   │   ├──automatic_update_factor: 1.1 (default)
0:00:00.060891 INFO: │   │   ├──try_narrower_values: True (default)
0:00:00.060891 INFO: │   │   ├──maximal_decrease: 0.5 (default)
0:00:00.060891 INFO: │   │   ├──favour_narrower_optimum: False (default)
0:00:00.060891 INFO: │   │   └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.060891 INFO: │   ├──ms1_error
0:00:00.060891 INFO: │   │   ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.060891 INFO: │   │   ├──targeted_update_factor: 1.0 (default)
0:00:00.060891 INFO: │   │   ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.060891 INFO: │   │   ├──automatic_update_factor: 1.1 (default)
0:00:00.062901 INFO: │   │   ├──try_narrower_values: False (default)
0:00:00.062901 INFO: │   │   ├──maximal_decrease: 0.2 (default)
0:00:00.062901 INFO: │   │   ├──favour_narrower_optimum: False (default)
0:00:00.062901 INFO: │   │   └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.062901 INFO: │   ├──mobility_error
0:00:00.062901 INFO: │   │   ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.062901 INFO: │   │   ├──targeted_update_factor: 1.0 (default)
0:00:00.062901 INFO: │   │   ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.062901 INFO: │   │   ├──automatic_update_factor: 1.1 (default)
0:00:00.062901 INFO: │   │   ├──try_narrower_values: False (default)
0:00:00.062901 INFO: │   │   ├──maximal_decrease: 0.2 (default)
0:00:00.062901 INFO: │   │   ├──favour_narrower_optimum: False (default)
0:00:00.062901 INFO: │   │   └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.062901 INFO: │   └──rt_error
0:00:00.062901 INFO: │       ├──targeted_update_percentile_range: 0.95 (default)
0:00:00.062901 INFO: │       ├──targeted_update_factor: 1.0 (default)
0:00:00.062901 INFO: │       ├──automatic_update_percentile_range: 0.99 (default)
0:00:00.062901 INFO: │       ├──automatic_update_factor: 1.1 (default)
0:00:00.062901 INFO: │       ├──try_narrower_values: True (default)
0:00:00.062901 INFO: │       ├──maximal_decrease: 0.2 (default)
0:00:00.062901 INFO: │       ├──favour_narrower_optimum: True (default)
0:00:00.062901 INFO: │       └──maximum_decrease_from_maximum: 0.1 (default)
0:00:00.062901 INFO: ├──optimization_manager
0:00:00.062901 INFO: │   ├──fwhm_rt: 5 (default)
0:00:00.062901 INFO: │   ├──fwhm_mobility: 0.01 (default)
0:00:00.062901 INFO: │   └──score_cutoff: 0 (default)
0:00:00.062901 INFO: ├──transfer_library
0:00:00.062901 INFO: │   ├──enabled: False (default)
0:00:00.062901 INFO: │   ├──fragment_types: b;y (default)
0:00:00.062901 INFO: │   ├──max_charge: 2 (default)
0:00:00.062901 INFO: │   ├──top_k_samples: 3 (default)
0:00:00.062901 INFO: │   ├──norm_delta_max: True (default)
0:00:00.062901 INFO: │   ├──precursor_correlation_cutoff: 0.5 (default)
0:00:00.062901 INFO: │   └──fragment_correlation_ratio: 0.75 (default)
0:00:00.062901 INFO: ├──transfer_learning
0:00:00.062901 INFO: │   ├──enabled: False (default)
0:00:00.062901 INFO: │   ├──batch_size: 2000 (default)
0:00:00.062901 INFO: │   ├──max_lr: 0.0001 (default)
0:00:00.062901 INFO: │   ├──train_fraction: 0.7 (default)
0:00:00.062901 INFO: │   ├──validation_fraction: 0.2 (default)
0:00:00.062901 INFO: │   ├──test_fraction: 0.1 (default)
0:00:00.062901 INFO: │   ├──test_interval: 1 (default)
0:00:00.062901 INFO: │   ├──lr_patience: 3 (default)
0:00:00.062901 INFO: │   ├──epochs: 51 (default)
0:00:00.062901 INFO: │   ├──warmup_epochs: 5 (default)
0:00:00.062901 INFO: │   ├──nce: 25 (default)
0:00:00.062901 INFO: │   └──instrument: Lumos (default)
0:00:00.062901 INFO: ├──calibration_manager
0:00:00.062901 INFO: │   ├──0
0:00:00.062901 INFO: │   │   ├──name: fragment (default)
0:00:00.062901 INFO: │   │   └──estimators
0:00:00.062901 INFO: │   │       └──0
0:00:00.062901 INFO: │   │           ├──name: mz (default)
0:00:00.062901 INFO: │   │           ├──model: LOESSRegression (default)
0:00:00.062901 INFO: │   │           ├──model_args
0:00:00.062901 INFO: │   │           │   └──n_kernels: 2 (default)
0:00:00.062901 INFO: │   │           ├──input_columns
0:00:00.062901 INFO: │   │           │   └──mz_library (default)
0:00:00.062901 INFO: │   │           ├──target_columns
0:00:00.062901 INFO: │   │           │   └──mz_observed (default)
0:00:00.062901 INFO: │   │           ├──output_columns
0:00:00.062901 INFO: │   │           │   └──mz_calibrated (default)
0:00:00.062901 INFO: │   │           └──transform_deviation: 1e6 (default)
0:00:00.062901 INFO: │   └──1
0:00:00.062901 INFO: │       ├──name: precursor (default)
0:00:00.062901 INFO: │       └──estimators
0:00:00.062901 INFO: │           ├──0
0:00:00.062901 INFO: │           │   ├──name: mz (default)
0:00:00.062901 INFO: │           │   ├──model: LOESSRegression (default)
0:00:00.062901 INFO: │           │   ├──model_args
0:00:00.062901 INFO: │           │   │   └──n_kernels: 2 (default)
0:00:00.062901 INFO: │           │   ├──input_columns
0:00:00.062901 INFO: │           │   │   └──mz_library (default)
0:00:00.062901 INFO: │           │   ├──target_columns
0:00:00.062901 INFO: │           │   │   └──mz_observed (default)
0:00:00.062901 INFO: │           │   ├──output_columns
0:00:00.062901 INFO: │           │   │   └──mz_calibrated (default)
0:00:00.062901 INFO: │           │   └──transform_deviation: 1e6 (default)
0:00:00.062901 INFO: │           ├──1
0:00:00.062901 INFO: │           │   ├──name: rt (default)
0:00:00.062901 INFO: │           │   ├──model: LOESSRegression (default)
0:00:00.062901 INFO: │           │   ├──model_args
0:00:00.062901 INFO: │           │   │   └──n_kernels: 6 (default)
0:00:00.062901 INFO: │           │   ├──input_columns
0:00:00.062901 INFO: │           │   │   └──rt_library (default)
0:00:00.062901 INFO: │           │   ├──target_columns
0:00:00.062901 INFO: │           │   │   └──rt_observed (default)
0:00:00.062901 INFO: │           │   └──output_columns
0:00:00.062901 INFO: │           │       └──rt_calibrated (default)
0:00:00.062901 INFO: │           └──2
0:00:00.062901 INFO: │               ├──name: mobility (default)
0:00:00.062901 INFO: │               ├──model: LOESSRegression (default)
0:00:00.062901 INFO: │               ├──model_args
0:00:00.062901 INFO: │               │   └──n_kernels: 2 (default)
0:00:00.062901 INFO: │               ├──input_columns
0:00:00.062901 INFO: │               │   └──mobility_library (default)
0:00:00.062901 INFO: │               ├──target_columns
0:00:00.062901 INFO: │               │   └──mobility_observed (default)
0:00:00.062901 INFO: │               └──output_columns
0:00:00.062901 INFO: │                   └──mobility_calibrated (default)
0:00:00.062901 INFO: ├──[32;20mname: PeptideCentric.v1 (user defined)[0m
0:00:00.062901 INFO: ├──[32;20mfasta_list[0m
0:00:00.062901 INFO: │   └──[32;20mD:\Proteobench_manuscript_data\ProteoBenchFASTA_DDAQuantification.fasta (user defined)[0m
0:00:00.062901 INFO: ├──[32;20mraw_path_list[0m
0:00:00.062901 INFO: │   ├──[32;20mD:\Proteobench_manuscript_data\RAW\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw (user defined)[0m
0:00:00.062901 INFO: │   ├──[32;20mD:\Proteobench_manuscript_data\RAW\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw (user defined)[0m
0:00:00.062901 INFO: │   ├──[32;20mD:\Proteobench_manuscript_data\RAW\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw (user defined)[0m
0:00:00.062901 INFO: │   ├──[32;20mD:\Proteobench_manuscript_data\RAW\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw (user defined)[0m
0:00:00.062901 INFO: │   ├──[32;20mD:\Proteobench_manuscript_data\RAW\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw (user defined)[0m
0:00:00.062901 INFO: │   └──[32;20mD:\Proteobench_manuscript_data\RAW\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw (user defined)[0m
0:00:00.062901 INFO: └──[32;20moutput_directory: D:\Proteobench_manuscript_data\run_output\alphadia_default (user defined)[0m
0:00:00.062901 INFO: Registering 7 custom modifications
0:00:00.141038 PROGRESS: No library provided. Building library from fasta files.
0:00:00.141038 INFO: Running FastaDigest
0:00:01.668102 INFO: Digesting fasta file
0:00:16.783818 INFO: Adding modifications
0:04:37.858952 INFO: Removing non-canonical amino acids
0:04:47.998693 INFO: Fasta library contains 5,385,906 precursors
0:04:47.998693 PROGRESS: Predicting library properties.
0:04:47.998693 INFO: Running PeptDeepPrediction
0:04:47.998693 INFO: Device set to cpu
0:04:49.617849 INFO: Loading PeptDeep models of type generic
0:04:50.951688 INFO: Predicting RT, MS2 and mobility
0:04:50.951688 INFO: Using multiprocessing with 10 processes ...
0:04:55.840101 INFO: Predicting rt,ms2,mobility ...
1:05:21.132035 INFO: Adding fragment mz information
1:05:22.066830 INFO: Adding fragment intensity information
1:05:22.647955 INFO: Adding precursor information
1:05:23.625780 INFO: Running PrecursorInitializer
1:05:23.674779 INFO: Running AnnotateFasta
1:05:24.110805 INFO: Dropping decoys from input library before annotation
1:06:12.944755 INFO: Running IsotopeGenerator
1:07:35.412885 INFO: Running RTNormalization
1:07:35.412885 WARNING: Input library already contains normalized RT information. Skipping RT normalization
1:07:35.413885 INFO: Saving library to D:\Proteobench_manuscript_data\run_output\alphadia_default\speclib.hdf
1:08:50.184118 INFO: Running DecoyGenerator
1:10:20.730461 INFO: Running FlattenLibrary
1:10:43.534079 INFO: Running InitFlatColumns
1:10:44.011969 INFO: Running LogFlatLibraryStats
1:10:44.011969 INFO: ============ Library Stats ============
1:10:44.011969 INFO: Number of precursors: 10,742,046
1:10:45.395166 INFO: 	thereof targets:5,385,906
1:10:45.395166 INFO: 	thereof decoys: 5,356,140
1:10:45.480341 INFO: Number of elution groups: 5,385,906
1:10:45.480341 INFO: 	average size: 1.99
1:10:45.714514 INFO: Number of proteins: 118,119
1:10:45.746068 INFO: Number of channels: 1 ([0])
1:10:45.746068 INFO: Isotopes Distribution for 4 isotopes
1:10:45.746068 INFO: =======================================
1:10:45.996226 PROGRESS: Starting Search Workflows
1:10:45.996226 PROGRESS: Loading raw file 1/6: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:10:45.996226 INFO: Creating parent folder for workflows at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress
1:10:45.996226 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01 at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:11:13.154980 INFO: Determining DIA cycle
1:11:13.329889 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
1:11:13.329889 INFO: Determining DIA cycle
1:11:13.457189 INFO: Found cycle with start 0.00 min and length 151.
1:11:13.536521 INFO: ============ Raw file stats ============
1:11:13.536521 INFO: RT (min)            : 0.0 - 150.0
1:11:13.536521 INFO: RT duration (sec)   : 8999.7
1:11:13.536521 INFO: RT duration (min)   : 150.0
1:11:13.536521 INFO: Cycle len (scans)   : 151
1:11:13.536521 INFO: Cycle len (sec)     : 5.83
1:11:13.536521 INFO: Number of cycles    : 1542
1:11:13.536521 INFO: MS2 range (m/z)     : 396.4 - 1004.7
1:11:13.536521 INFO: ========================================
1:11:14.860109 INFO: Initializing CalibrationManager
1:11:14.860109 INFO: Loading calibration config
1:11:14.860109 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']}]}]
1:11:14.860109 INFO: Calibration group :fragment, found 1 estimator(s)
1:11:14.860109 INFO: Calibration group :precursor, found 3 estimator(s)
1:11:14.860109 INFO: Disabling ion mobility calibration
1:11:14.860109 INFO: removed mobility estimator from group precursor
1:11:14.860109 INFO: Initializing OptimizationManager
1:11:14.860109 INFO: initial parameter: ms1_error = 30
1:11:14.860109 INFO: initial parameter: ms2_error = 30
1:11:14.860109 INFO: initial parameter: rt_error = 4500.00927734375
1:11:14.860109 INFO: initial parameter: mobility_error = 0.1
1:11:14.860109 INFO: initial parameter: column_type = library
1:11:14.860109 INFO: initial parameter: num_candidates = 1
1:11:14.860109 INFO: initial parameter: classifier_version = -1
1:11:14.860109 INFO: initial parameter: fwhm_rt = 5
1:11:14.860109 INFO: initial parameter: fwhm_mobility = 0.01
1:11:14.860109 INFO: initial parameter: score_cutoff = 0
1:11:14.860109 INFO: Initializing TimingManager
1:11:14.860109 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
1:11:14.860109 INFO: Initializing FDRManager
1:11:14.860109 INFO: Loading classifier store from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\classifier
1:11:16.105668 PROGRESS: 5,385,906 target precursors potentially observable (0 removed)
1:11:17.996588 PROGRESS: Starting initial search for precursors.
1:11:18.739434 INFO: Starting optimization step 0.
1:11:18.739434 PROGRESS: === Extracting elution groups 0 to 8000 ===
1:11:18.739434 PROGRESS: Extracting batch of 15803 precursors
1:11:20.611102 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:11:20.611102 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:11:20.611102 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:11:20.611102 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:11:21.867539 INFO: Starting candidate selection
1:12:29.395127 INFO: Starting candidate scoring
1:15:55.897818 INFO: Finished candidate processing
1:15:55.897818 INFO: Collecting candidate features
1:15:56.602240 INFO: Collecting fragment features
1:15:59.773311 INFO: Finished candidate scoring
1:15:59.793338 PROGRESS: === Extracted 15797 precursors and 135899 fragments ===
1:15:59.793338 INFO: performing precursor FDR with 47 features
1:15:59.793338 INFO: Decoy channel: -1
1:15:59.793338 INFO: Competetive: True
1:16:04.131439 INFO: Test AUC: 0.520
1:16:04.132438 INFO: Train AUC: 0.527
1:16:04.132438 INFO: AUC difference: 1.35%
1:16:04.362284 INFO: === FDR correction performed with classifier version -1 ===
1:16:04.364330 PROGRESS: ============================= Precursor FDR =============================
1:16:04.364330 PROGRESS: Total precursors accumulated: 1
1:16:04.364330 PROGRESS: Target precursors: 1 (100.00%)
1:16:04.364330 PROGRESS: Decoy precursors: 0 (0.00%)
1:16:04.364330 PROGRESS: 
1:16:04.365285 PROGRESS: Precursor Summary:
1:16:04.366292 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:16:04.367285 PROGRESS: 
1:16:04.367285 PROGRESS: Protein Summary:
1:16:04.371289 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:16:04.371289 PROGRESS: =========================================================================
1:16:04.699745 INFO: Starting optimization step 1.
1:16:04.699745 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1:16:04.699745 PROGRESS: Extracting batch of 31592 precursors
1:16:04.715401 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:16:04.715401 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:04.715401 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:16:04.715401 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:04.715401 INFO: Starting candidate selection
1:16:24.488216 INFO: Starting candidate scoring
1:16:25.791506 INFO: Finished candidate processing
1:16:25.791506 INFO: Collecting candidate features
1:16:25.988298 INFO: Collecting fragment features
1:16:26.051466 INFO: Finished candidate scoring
1:16:26.149489 PROGRESS: === Extracted 47345 precursors and 407903 fragments ===
1:16:26.165118 INFO: performing precursor FDR with 47 features
1:16:26.165118 INFO: Decoy channel: -1
1:16:26.165118 INFO: Competetive: True
1:16:27.443538 INFO: Test AUC: 0.552
1:16:27.443538 INFO: Train AUC: 0.564
1:16:27.443538 INFO: AUC difference: 2.11%
1:16:27.614920 INFO: === FDR correction performed with classifier version -1 ===
1:16:27.616925 PROGRESS: ============================= Precursor FDR =============================
1:16:27.616925 PROGRESS: Total precursors accumulated: 1
1:16:27.616925 PROGRESS: Target precursors: 1 (100.00%)
1:16:27.617924 PROGRESS: Decoy precursors: 0 (0.00%)
1:16:27.617924 PROGRESS: 
1:16:27.617924 PROGRESS: Precursor Summary:
1:16:27.620224 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:16:27.621220 PROGRESS: 
1:16:27.621220 PROGRESS: Protein Summary:
1:16:27.624222 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
1:16:27.624222 PROGRESS: =========================================================================
1:16:28.035071 INFO: Starting optimization step 2.
1:16:28.035071 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1:16:28.035071 PROGRESS: Extracting batch of 63206 precursors
1:16:28.065230 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:16:28.065230 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:16:28.065230 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:16:28.065230 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:16:28.065230 INFO: Starting candidate selection
1:18:16.507846 INFO: Starting candidate scoring
1:18:19.095424 INFO: Finished candidate processing
1:18:19.095424 INFO: Collecting candidate features
1:18:19.395219 INFO: Collecting fragment features
1:18:19.531490 INFO: Finished candidate scoring
1:18:19.724932 PROGRESS: === Extracted 110504 precursors and 953068 fragments ===
1:18:19.775558 INFO: performing precursor FDR with 47 features
1:18:19.775558 INFO: Decoy channel: -1
1:18:19.775558 INFO: Competetive: True
1:18:24.118729 INFO: Test AUC: 0.566
1:18:24.118729 INFO: Train AUC: 0.575
1:18:24.118729 INFO: AUC difference: 1.51%
1:18:24.340421 INFO: === FDR correction performed with classifier version -1 ===
1:18:24.342423 PROGRESS: ============================= Precursor FDR =============================
1:18:24.342423 PROGRESS: Total precursors accumulated: 356
1:18:24.343431 PROGRESS: Target precursors: 326 (91.57%)
1:18:24.343431 PROGRESS: Decoy precursors: 30 (8.43%)
1:18:24.343431 PROGRESS: 
1:18:24.343431 PROGRESS: Precursor Summary:
1:18:24.346461 PROGRESS: Channel   0:	 0.05 FDR:   253; 0.01 FDR:    13; 0.001 FDR:    13
1:18:24.346461 PROGRESS: 
1:18:24.346461 PROGRESS: Protein Summary:
1:18:24.349460 PROGRESS: Channel   0:	 0.05 FDR:   244; 0.01 FDR:    13; 0.001 FDR:    13
1:18:24.350461 PROGRESS: =========================================================================
1:18:24.913632 INFO: Starting optimization step 3.
1:18:24.914629 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:18:24.914629 PROGRESS: Extracting batch of 126403 precursors
1:18:24.957820 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:18:24.957820 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:18:24.957820 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
1:18:24.957820 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
1:18:24.957820 INFO: Starting candidate selection
1:19:41.533703 INFO: Starting candidate scoring
1:19:46.343021 INFO: Finished candidate processing
1:19:46.343021 INFO: Collecting candidate features
1:19:46.891675 INFO: Collecting fragment features
1:19:47.119860 INFO: Finished candidate scoring
1:19:47.453630 PROGRESS: === Extracted 236800 precursors and 2042688 fragments ===
1:19:47.516565 INFO: performing precursor FDR with 47 features
1:19:47.516565 INFO: Decoy channel: -1
1:19:47.516565 INFO: Competetive: True
1:19:54.501858 INFO: Test AUC: 0.569
1:19:54.501858 INFO: Train AUC: 0.582
1:19:54.501858 INFO: AUC difference: 2.19%
1:19:54.758753 INFO: === FDR correction performed with classifier version -1 ===
1:19:54.758753 PROGRESS: ============================= Precursor FDR =============================
1:19:54.758753 PROGRESS: Total precursors accumulated: 1,058
1:19:54.758753 PROGRESS: Target precursors: 963 (91.02%)
1:19:54.758753 PROGRESS: Decoy precursors: 95 (8.98%)
1:19:54.774799 PROGRESS: 
1:19:54.775030 PROGRESS: Precursor Summary:
1:19:54.778040 PROGRESS: Channel   0:	 0.05 FDR:   796; 0.01 FDR:   518; 0.001 FDR:   244
1:19:54.778040 PROGRESS: 
1:19:54.778040 PROGRESS: Protein Summary:
1:19:54.779381 PROGRESS: Channel   0:	 0.05 FDR:   700; 0.01 FDR:   468; 0.001 FDR:   234
1:19:54.779381 PROGRESS: =========================================================================
1:19:54.815423 INFO: fragments_df_filtered: 3821
1:19:55.282444 INFO: calibration group: precursor, fitting rt estimator 
1:19:55.412237 INFO: calibration group: fragment, fitting mz estimator 
1:19:58.845867 INFO: calibration group: precursor, predicting mz
1:19:58.845867 WARNING: mz prediction was skipped as it has not been fitted yet
1:19:58.845867 INFO: calibration group: precursor, predicting rt
1:19:58.920763 INFO: calibration group: fragment, predicting mz
1:19:59.304400 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:19:59.304400 INFO: Starting optimization step 4.
1:19:59.304400 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:19:59.304400 PROGRESS: Extracting batch of 110601 precursors
1:19:59.364254 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:19:59.364254 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:19:59.364254 INFO: FWHM in RT is 18.94 seconds, sigma is 0.69
1:19:59.364254 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:19:59.364254 INFO: Starting candidate selection
1:21:09.614461 INFO: Starting candidate scoring
1:21:17.506581 INFO: Finished candidate processing
1:21:17.506581 INFO: Collecting candidate features
1:21:18.293297 INFO: Collecting fragment features
1:21:18.664493 INFO: Finished candidate scoring
1:21:18.848184 PROGRESS: === Extracted 221025 precursors and 1961676 fragments ===
1:21:18.848184 INFO: performing precursor FDR with 47 features
1:21:18.848184 INFO: Decoy channel: -1
1:21:18.848184 INFO: Competetive: True
1:21:25.197284 INFO: Test AUC: 0.572
1:21:25.197284 INFO: Train AUC: 0.585
1:21:25.197284 INFO: AUC difference: 2.23%
1:21:25.437450 INFO: === FDR correction performed with classifier version 3 ===
1:21:25.437450 PROGRESS: ============================= Precursor FDR =============================
1:21:25.437450 PROGRESS: Total precursors accumulated: 452
1:21:25.437450 PROGRESS: Target precursors: 411 (90.93%)
1:21:25.437450 PROGRESS: Decoy precursors: 41 (9.07%)
1:21:25.437450 PROGRESS: 
1:21:25.437450 PROGRESS: Precursor Summary:
1:21:25.444263 PROGRESS: Channel   0:	 0.05 FDR:   346; 0.01 FDR:   211; 0.001 FDR:   148
1:21:25.444263 PROGRESS: 
1:21:25.444263 PROGRESS: Protein Summary:
1:21:25.444263 PROGRESS: Channel   0:	 0.05 FDR:   331; 0.01 FDR:   204; 0.001 FDR:   143
1:21:25.444263 PROGRESS: =========================================================================
1:21:25.469235 INFO: fragments_df_filtered: 1806
1:21:25.928303 INFO: calibration group: precursor, fitting rt estimator 
1:21:26.022470 INFO: calibration group: fragment, fitting mz estimator 
1:21:26.680439 INFO: calibration group: precursor, predicting mz
1:21:26.680439 WARNING: mz prediction was skipped as it has not been fitted yet
1:21:26.680439 INFO: calibration group: precursor, predicting rt
1:21:26.775002 INFO: calibration group: fragment, predicting mz
1:21:27.141732 INFO: === checking if optimization conditions were reached ===
1:21:27.143731 PROGRESS: ❌ ms2_error      : 10.0171 > 10.0000 or insufficient steps taken.
1:21:27.143731 INFO: ==============================================
1:21:27.143731 INFO: Starting optimization step 5.
1:21:27.146790 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:21:27.146790 PROGRESS: Extracting batch of 110601 precursors
1:21:27.191925 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:21:27.191925 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:21:27.191925 INFO: FWHM in RT is 19.49 seconds, sigma is 0.71
1:21:27.191925 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:21:27.207568 INFO: Starting candidate selection
1:22:24.314326 INFO: Starting candidate scoring
1:22:28.393953 INFO: Finished candidate processing
1:22:28.393953 INFO: Collecting candidate features
1:22:28.720613 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 220888)
1:22:28.736359 INFO: Collecting fragment features
1:22:28.887707 INFO: Finished candidate scoring
1:22:28.960118 PROGRESS: === Extracted 220888 precursors and 1629984 fragments ===
1:22:28.960118 INFO: performing precursor FDR with 47 features
1:22:28.960118 INFO: Decoy channel: -1
1:22:28.960118 INFO: Competetive: True
1:22:29.099399 WARNING: dropped 6 target PSMs due to missing features
1:22:29.099399 WARNING: dropped 11 decoy PSMs due to missing features
1:22:31.328813 INFO: Test AUC: 0.571
1:22:31.328813 INFO: Train AUC: 0.587
1:22:31.328813 INFO: AUC difference: 2.72%
1:22:31.426519 INFO: === FDR correction performed with classifier version 4 ===
1:22:31.426519 PROGRESS: ============================= Precursor FDR =============================
1:22:31.426519 PROGRESS: Total precursors accumulated: 566
1:22:31.426519 PROGRESS: Target precursors: 515 (90.99%)
1:22:31.426519 PROGRESS: Decoy precursors: 51 (9.01%)
1:22:31.426519 PROGRESS: 
1:22:31.426519 PROGRESS: Precursor Summary:
1:22:31.426519 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   205; 0.001 FDR:   183
1:22:31.426519 PROGRESS: 
1:22:31.426519 PROGRESS: Protein Summary:
1:22:31.426519 PROGRESS: Channel   0:	 0.05 FDR:   408; 0.01 FDR:   199; 0.001 FDR:   178
1:22:31.426519 PROGRESS: =========================================================================
1:22:31.442200 INFO: fragments_df_filtered: 1402
1:22:31.658237 INFO: calibration group: precursor, fitting rt estimator 
1:22:31.696929 INFO: calibration group: fragment, fitting mz estimator 
1:22:31.844817 INFO: calibration group: precursor, predicting mz
1:22:31.844817 WARNING: mz prediction was skipped as it has not been fitted yet
1:22:31.844817 INFO: calibration group: precursor, predicting rt
1:22:31.878070 INFO: calibration group: fragment, predicting mz
1:22:32.031313 INFO: === checking if optimization conditions were reached ===
1:22:32.031313 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:22:32.031313 INFO: ==============================================
1:22:32.031313 PROGRESS: Optimization finished for ms2_error.
1:22:32.224291 INFO: calibration group: precursor, predicting mz
1:22:32.224291 WARNING: mz prediction was skipped as it has not been fitted yet
1:22:32.224291 INFO: calibration group: precursor, predicting rt
1:22:32.255594 INFO: calibration group: fragment, predicting mz
1:22:32.432618 INFO: Starting optimization step 0.
1:22:32.432618 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:22:32.432618 PROGRESS: Extracting batch of 110601 precursors
1:22:32.448323 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:22:32.448323 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:22:32.448323 INFO: FWHM in RT is 17.60 seconds, sigma is 0.64
1:22:32.448323 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:22:32.448323 INFO: Starting candidate selection
1:23:17.127098 INFO: Starting candidate scoring
1:23:25.723701 INFO: Finished candidate processing
1:23:25.723701 INFO: Collecting candidate features
1:23:27.101449 WARNING: intensity_correlation has 14 NaNs ( 0.01 % out of 220890)
1:23:27.151078 INFO: Collecting fragment features
1:23:27.824521 INFO: Finished candidate scoring
1:23:28.366332 PROGRESS: === Extracted 220890 precursors and 1621344 fragments ===
1:23:28.368329 INFO: performing precursor FDR with 47 features
1:23:28.369334 INFO: Decoy channel: -1
1:23:28.369462 INFO: Competetive: True
1:23:28.986981 WARNING: dropped 6 target PSMs due to missing features
1:23:28.986981 WARNING: dropped 8 decoy PSMs due to missing features
1:23:38.583351 INFO: Test AUC: 0.575
1:23:38.583351 INFO: Train AUC: 0.593
1:23:38.583351 INFO: AUC difference: 3.15%
1:23:39.099338 INFO: === FDR correction performed with classifier version 5 ===
1:23:39.102335 PROGRESS: ============================= Precursor FDR =============================
1:23:39.102335 PROGRESS: Total precursors accumulated: 584
1:23:39.103851 PROGRESS: Target precursors: 532 (91.10%)
1:23:39.103851 PROGRESS: Decoy precursors: 52 (8.90%)
1:23:39.103851 PROGRESS: 
1:23:39.103851 PROGRESS: Precursor Summary:
1:23:39.112298 PROGRESS: Channel   0:	 0.05 FDR:   467; 0.01 FDR:   302; 0.001 FDR:   229
1:23:39.113298 PROGRESS: 
1:23:39.114526 PROGRESS: Protein Summary:
1:23:39.127203 PROGRESS: Channel   0:	 0.05 FDR:   441; 0.01 FDR:   289; 0.001 FDR:   222
1:23:39.128205 PROGRESS: =========================================================================
1:23:39.145647 INFO: fragments_df_filtered: 1536
1:23:40.032866 INFO: calibration group: precursor, fitting rt estimator 
1:23:40.225522 INFO: calibration group: fragment, fitting mz estimator 
1:23:40.903845 INFO: calibration group: precursor, predicting mz
1:23:40.906360 WARNING: mz prediction was skipped as it has not been fitted yet
1:23:40.906360 INFO: calibration group: precursor, predicting rt
1:23:41.029739 INFO: calibration group: fragment, predicting mz
1:23:41.613493 INFO: === checking if optimization conditions were reached ===
1:23:41.614487 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:23:41.622339 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 818.6986.
1:23:41.622339 INFO: ==============================================
1:23:41.623355 INFO: Starting optimization step 1.
1:23:41.624354 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:23:41.624354 PROGRESS: Extracting batch of 110601 precursors
1:23:41.733195 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:23:41.733195 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:23:41.733195 INFO: FWHM in RT is 17.30 seconds, sigma is 0.63
1:23:41.733195 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:23:41.733195 INFO: Starting candidate selection
1:23:51.758008 INFO: Starting candidate scoring
1:23:58.657535 INFO: Finished candidate processing
1:23:58.657535 INFO: Collecting candidate features
1:23:59.292247 WARNING: intensity_correlation has 311 NaNs ( 0.15 % out of 212744)
1:23:59.327434 INFO: Collecting fragment features
1:23:59.608662 INFO: Finished candidate scoring
1:23:59.896096 PROGRESS: === Extracted 212744 precursors and 1330980 fragments ===
1:23:59.898089 INFO: performing precursor FDR with 47 features
1:23:59.898089 INFO: Decoy channel: -1
1:23:59.898089 INFO: Competetive: True
1:24:00.212173 WARNING: dropped 177 target PSMs due to missing features
1:24:00.212173 WARNING: dropped 134 decoy PSMs due to missing features
1:24:06.238866 INFO: Test AUC: 0.561
1:24:06.238866 INFO: Train AUC: 0.580
1:24:06.238866 INFO: AUC difference: 3.27%
1:24:06.474660 INFO: === FDR correction performed with classifier version 5 ===
1:24:06.479123 PROGRESS: ============================= Precursor FDR =============================
1:24:06.482696 PROGRESS: Total precursors accumulated: 803
1:24:06.482696 PROGRESS: Target precursors: 733 (91.28%)
1:24:06.482696 PROGRESS: Decoy precursors: 70 (8.72%)
1:24:06.482696 PROGRESS: 
1:24:06.482696 PROGRESS: Precursor Summary:
1:24:06.488351 PROGRESS: Channel   0:	 0.05 FDR:   580; 0.01 FDR:   337; 0.001 FDR:   178
1:24:06.488351 PROGRESS: 
1:24:06.488351 PROGRESS: Protein Summary:
1:24:06.494519 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   320; 0.001 FDR:   173
1:24:06.494519 PROGRESS: =========================================================================
1:24:06.504003 INFO: fragments_df_filtered: 1636
1:24:06.999817 INFO: calibration group: precursor, fitting rt estimator 
1:24:07.125365 INFO: calibration group: fragment, fitting mz estimator 
1:24:07.684918 INFO: calibration group: precursor, predicting mz
1:24:07.684918 WARNING: mz prediction was skipped as it has not been fitted yet
1:24:07.684918 INFO: calibration group: precursor, predicting rt
1:24:07.763613 INFO: calibration group: fragment, predicting mz
1:24:08.135536 INFO: === checking if optimization conditions were reached ===
1:24:08.136545 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:24:08.140079 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 520.3276.
1:24:08.141086 INFO: ==============================================
1:24:08.141086 INFO: Starting optimization step 2.
1:24:08.141086 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:24:08.142334 PROGRESS: Extracting batch of 110601 precursors
1:24:08.198770 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:24:08.198770 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:24:08.198770 INFO: FWHM in RT is 17.47 seconds, sigma is 0.64
1:24:08.198770 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:24:08.198770 INFO: Starting candidate selection
1:24:21.471167 INFO: Starting candidate scoring
1:24:27.116098 INFO: Finished candidate processing
1:24:27.116098 INFO: Collecting candidate features
1:24:27.727679 WARNING: intensity_correlation has 373 NaNs ( 0.18 % out of 209478)
1:24:27.775279 INFO: Collecting fragment features
1:24:28.101812 INFO: Finished candidate scoring
1:24:28.221884 PROGRESS: === Extracted 209478 precursors and 1252718 fragments ===
1:24:28.221884 INFO: performing precursor FDR with 47 features
1:24:28.221884 INFO: Decoy channel: -1
1:24:28.221884 INFO: Competetive: True
1:24:28.415296 WARNING: dropped 201 target PSMs due to missing features
1:24:28.415296 WARNING: dropped 172 decoy PSMs due to missing features
1:24:33.501785 INFO: Test AUC: 0.558
1:24:33.501785 INFO: Train AUC: 0.576
1:24:33.501785 INFO: AUC difference: 3.11%
1:24:33.774554 INFO: === FDR correction performed with classifier version 5 ===
1:24:33.774554 PROGRESS: ============================= Precursor FDR =============================
1:24:33.774554 PROGRESS: Total precursors accumulated: 853
1:24:33.774554 PROGRESS: Target precursors: 778 (91.21%)
1:24:33.774554 PROGRESS: Decoy precursors: 75 (8.79%)
1:24:33.774554 PROGRESS: 
1:24:33.774554 PROGRESS: Precursor Summary:
1:24:33.774554 PROGRESS: Channel   0:	 0.05 FDR:   645; 0.01 FDR:   352; 0.001 FDR:   301
1:24:33.774554 PROGRESS: 
1:24:33.774554 PROGRESS: Protein Summary:
1:24:33.788976 PROGRESS: Channel   0:	 0.05 FDR:   606; 0.01 FDR:   332; 0.001 FDR:   286
1:24:33.789829 PROGRESS: =========================================================================
1:24:33.804706 INFO: fragments_df_filtered: 1643
1:24:34.285712 INFO: calibration group: precursor, fitting rt estimator 
1:24:34.429264 INFO: calibration group: fragment, fitting mz estimator 
1:24:34.900528 INFO: calibration group: precursor, predicting mz
1:24:34.900528 WARNING: mz prediction was skipped as it has not been fitted yet
1:24:34.900528 INFO: calibration group: precursor, predicting rt
1:24:34.967673 INFO: calibration group: fragment, predicting mz
1:24:35.333462 INFO: === checking if optimization conditions were reached ===
1:24:35.333462 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:24:35.349600 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 500.5970.
1:24:35.349600 INFO: ==============================================
1:24:35.349600 INFO: Starting optimization step 3.
1:24:35.350602 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:24:35.350602 PROGRESS: Extracting batch of 110601 precursors
1:24:35.411433 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:24:35.411433 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:24:35.411433 INFO: FWHM in RT is 17.45 seconds, sigma is 0.64
1:24:35.411433 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:24:35.411433 INFO: Starting candidate selection
1:24:47.439124 INFO: Starting candidate scoring
1:24:54.119674 INFO: Finished candidate processing
1:24:54.119674 INFO: Collecting candidate features
1:24:54.851270 WARNING: intensity_correlation has 365 NaNs ( 0.18 % out of 207811)
1:24:54.870045 INFO: Collecting fragment features
1:24:55.124210 INFO: Finished candidate scoring
1:24:55.361390 PROGRESS: === Extracted 207811 precursors and 1232237 fragments ===
1:24:55.363384 INFO: performing precursor FDR with 47 features
1:24:55.363384 INFO: Decoy channel: -1
1:24:55.363384 INFO: Competetive: True
1:24:55.609746 WARNING: dropped 187 target PSMs due to missing features
1:24:55.609746 WARNING: dropped 178 decoy PSMs due to missing features
1:25:01.724690 INFO: Test AUC: 0.558
1:25:01.724690 INFO: Train AUC: 0.575
1:25:01.724690 INFO: AUC difference: 3.04%
1:25:01.965857 INFO: === FDR correction performed with classifier version 5 ===
1:25:01.981680 PROGRESS: ============================= Precursor FDR =============================
1:25:01.981680 PROGRESS: Total precursors accumulated: 807
1:25:01.981680 PROGRESS: Target precursors: 737 (91.33%)
1:25:01.981680 PROGRESS: Decoy precursors: 70 (8.67%)
1:25:01.981680 PROGRESS: 
1:25:01.981680 PROGRESS: Precursor Summary:
1:25:01.981680 PROGRESS: Channel   0:	 0.05 FDR:   630; 0.01 FDR:   432; 0.001 FDR:   258
1:25:01.981680 PROGRESS: 
1:25:01.981680 PROGRESS: Protein Summary:
1:25:01.981680 PROGRESS: Channel   0:	 0.05 FDR:   589; 0.01 FDR:   406; 0.001 FDR:   244
1:25:01.981680 PROGRESS: =========================================================================
1:25:01.997360 INFO: fragments_df_filtered: 1765
1:25:02.430329 INFO: calibration group: precursor, fitting rt estimator 
1:25:02.536738 INFO: calibration group: fragment, fitting mz estimator 
1:25:03.561992 INFO: calibration group: precursor, predicting mz
1:25:03.561992 WARNING: mz prediction was skipped as it has not been fitted yet
1:25:03.561992 INFO: calibration group: precursor, predicting rt
1:25:03.627571 INFO: calibration group: fragment, predicting mz
1:25:03.963100 INFO: === checking if optimization conditions were reached ===
1:25:03.963100 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:25:03.963100 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 500.5970 found after 4 searches.
1:25:03.963100 INFO: ==============================================
1:25:03.963100 PROGRESS: Optimization finished for rt_error.
1:25:04.387970 INFO: calibration group: precursor, predicting mz
1:25:04.388965 WARNING: mz prediction was skipped as it has not been fitted yet
1:25:04.388965 INFO: calibration group: precursor, predicting rt
1:25:04.458481 INFO: calibration group: fragment, predicting mz
1:25:04.866998 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:25:04.867997 PROGRESS: ==============================================
1:25:04.867997 PROGRESS: ms2_error      : 10.0000
1:25:04.867997 PROGRESS: rt_error       : 500.5970
1:25:04.867997 PROGRESS: ==============================================
1:25:04.872611 INFO: calibration group: precursor, predicting mz
1:25:04.872611 WARNING: mz prediction was skipped as it has not been fitted yet
1:25:04.872611 INFO: calibration group: precursor, predicting rt
1:25:12.092944 INFO: calibration group: fragment, predicting mz
1:25:46.269877 PROGRESS: Extracting batch of 10640830 precursors
1:25:49.025175 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
1:25:49.025175 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
1:25:49.025175 INFO: FWHM in RT is 17.40 seconds, sigma is 0.63
1:25:49.025175 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
1:25:49.025175 INFO: Starting candidate selection
1:52:10.054483 INFO: Applying score cutoff of 69.96586288452148
1:52:11.072933 INFO: Removed 14741319 precursors with score below cutoff
1:52:17.168040 INFO: Starting candidate scoring
1:57:05.736297 INFO: Finished candidate processing
1:57:05.736297 INFO: Collecting candidate features
1:57:30.870845 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 6347656)
1:57:31.730188 INFO: Collecting fragment features
1:57:42.931040 INFO: Finished candidate scoring
1:57:54.876776 INFO: === FDR correction performed with classifier version 9 ===
1:57:54.876776 INFO: performing precursor FDR with 47 features
1:57:54.876776 INFO: Decoy channel: -1
1:57:54.876776 INFO: Competetive: True
1:58:02.280416 WARNING: dropped 1 decoy PSMs due to missing features
2:01:45.035381 INFO: Test AUC: 0.583
2:01:45.035381 INFO: Train AUC: 0.586
2:01:45.035381 INFO: AUC difference: 0.48%
2:01:46.128181 INFO: Removing fragments below FDR threshold
2:01:47.168574 PROGRESS: ============================= Precursor FDR =============================
2:01:47.168574 PROGRESS: Total precursors accumulated: 52,899
2:01:47.168574 PROGRESS: Target precursors: 52,376 (99.01%)
2:01:47.168574 PROGRESS: Decoy precursors: 523 (0.99%)
2:01:47.168574 PROGRESS: 
2:01:47.168574 PROGRESS: Precursor Summary:
2:01:47.222775 PROGRESS: Channel   0:	 0.05 FDR: 52,376; 0.01 FDR: 52,376; 0.001 FDR: 35,431
2:01:47.222775 PROGRESS: 
2:01:47.222775 PROGRESS: Protein Summary:
2:01:47.333078 PROGRESS: Channel   0:	 0.05 FDR: 8,884; 0.01 FDR: 8,884; 0.001 FDR: 6,691
2:01:47.333078 PROGRESS: =========================================================================
2:01:49.048861 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
2:01:50.908121 PROGRESS: Loading raw file 2/6: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
2:01:50.908121 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02 at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
2:03:01.674623 INFO: Determining DIA cycle
2:03:01.705871 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
2:03:01.721494 INFO: Determining DIA cycle
2:03:01.755455 INFO: Found cycle with start 0.00 min and length 151.
2:03:01.942229 INFO: ============ Raw file stats ============
2:03:01.942229 INFO: RT (min)            : 0.0 - 150.0
2:03:01.942229 INFO: RT duration (sec)   : 8999.7
2:03:01.942229 INFO: RT duration (min)   : 150.0
2:03:01.942229 INFO: Cycle len (scans)   : 151
2:03:01.942229 INFO: Cycle len (sec)     : 5.84
2:03:01.942229 INFO: Number of cycles    : 1542
2:03:01.942229 INFO: MS2 range (m/z)     : 396.4 - 1004.7
2:03:01.942229 INFO: ========================================
2:03:10.138680 INFO: Initializing CalibrationManager
2:03:10.138680 INFO: Loading calibration config
2:03:10.138680 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)}]}]
2:03:10.138680 INFO: Calibration group :fragment, found 1 estimator(s)
2:03:10.138680 INFO: Calibration group :precursor, found 3 estimator(s)
2:03:10.138680 INFO: Disabling ion mobility calibration
2:03:10.138680 INFO: removed mobility estimator from group precursor
2:03:10.138680 INFO: Initializing OptimizationManager
2:03:10.138680 INFO: initial parameter: ms1_error = 30
2:03:10.138680 INFO: initial parameter: ms2_error = 30
2:03:10.138680 INFO: initial parameter: rt_error = 4499.99560546875
2:03:10.138680 INFO: initial parameter: mobility_error = 0.1
2:03:10.138680 INFO: initial parameter: column_type = library
2:03:10.138680 INFO: initial parameter: num_candidates = 1
2:03:10.154323 INFO: initial parameter: classifier_version = -1
2:03:10.154323 INFO: initial parameter: fwhm_rt = 5
2:03:10.154834 INFO: initial parameter: fwhm_mobility = 0.01
2:03:10.154834 INFO: initial parameter: score_cutoff = 0
2:03:10.154834 INFO: Initializing TimingManager
2:03:10.154834 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
2:03:10.154834 INFO: Initializing FDRManager
2:03:10.154834 INFO: Loading classifier store from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\classifier
2:03:13.442248 PROGRESS: 5,385,906 target precursors potentially observable (0 removed)
2:03:18.175461 PROGRESS: Starting initial search for precursors.
2:03:18.918153 INFO: Starting optimization step 0.
2:03:18.918153 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:03:18.918153 PROGRESS: Extracting batch of 15803 precursors
2:03:18.937533 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:03:18.937533 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:18.937533 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:03:18.937533 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:03:18.937533 INFO: Starting candidate selection
2:03:31.141790 INFO: Starting candidate scoring
2:03:31.812359 INFO: Finished candidate processing
2:03:31.812359 INFO: Collecting candidate features
2:03:31.918563 INFO: Collecting fragment features
2:03:31.978198 INFO: Finished candidate scoring
2:03:31.999165 PROGRESS: === Extracted 15796 precursors and 140309 fragments ===
2:03:31.999165 INFO: performing precursor FDR with 47 features
2:03:31.999165 INFO: Decoy channel: -1
2:03:31.999165 INFO: Competetive: True
2:03:32.491536 INFO: Test AUC: 0.491
2:03:32.491536 INFO: Train AUC: 0.500
2:03:32.491536 INFO: AUC difference: 1.82%
2:03:32.724079 INFO: === FDR correction performed with classifier version -1 ===
2:03:32.724079 PROGRESS: ============================= Precursor FDR =============================
2:03:32.724079 PROGRESS: Total precursors accumulated: 2
2:03:32.724079 PROGRESS: Target precursors: 2 (100.00%)
2:03:32.724079 PROGRESS: Decoy precursors: 0 (0.00%)
2:03:32.724079 PROGRESS: 
2:03:32.724079 PROGRESS: Precursor Summary:
2:03:32.724079 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:03:32.724079 PROGRESS: 
2:03:32.724079 PROGRESS: Protein Summary:
2:03:32.724079 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
2:03:32.724079 PROGRESS: =========================================================================
2:03:33.000341 INFO: Starting optimization step 1.
2:03:33.000341 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:03:33.000341 PROGRESS: Extracting batch of 31592 precursors
2:03:33.039293 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:03:33.039293 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:03:33.039293 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:03:33.039293 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:03:33.039293 INFO: Starting candidate selection
2:03:58.279043 INFO: Starting candidate scoring
2:03:59.837951 INFO: Finished candidate processing
2:03:59.837951 INFO: Collecting candidate features
2:04:00.070784 INFO: Collecting fragment features
2:04:00.165389 INFO: Finished candidate scoring
2:04:00.259617 PROGRESS: === Extracted 47346 precursors and 421538 fragments ===
2:04:00.276317 INFO: performing precursor FDR with 47 features
2:04:00.276317 INFO: Decoy channel: -1
2:04:00.276317 INFO: Competetive: True
2:04:01.855734 INFO: Test AUC: 0.542
2:04:01.855734 INFO: Train AUC: 0.550
2:04:01.855734 INFO: AUC difference: 1.45%
2:04:02.091687 INFO: === FDR correction performed with classifier version -1 ===
2:04:02.091687 PROGRESS: ============================= Precursor FDR =============================
2:04:02.091687 PROGRESS: Total precursors accumulated: 1
2:04:02.091687 PROGRESS: Target precursors: 1 (100.00%)
2:04:02.091687 PROGRESS: Decoy precursors: 0 (0.00%)
2:04:02.091687 PROGRESS: 
2:04:02.091687 PROGRESS: Precursor Summary:
2:04:02.091687 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:04:02.091687 PROGRESS: 
2:04:02.091687 PROGRESS: Protein Summary:
2:04:02.107348 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
2:04:02.107348 PROGRESS: =========================================================================
2:04:02.471232 INFO: Starting optimization step 2.
2:04:02.471232 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:04:02.471232 PROGRESS: Extracting batch of 63206 precursors
2:04:02.525296 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:04:02.525296 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:04:02.525296 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:04:02.525296 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:04:02.525296 INFO: Starting candidate selection
2:04:51.937980 INFO: Starting candidate scoring
2:04:54.697021 INFO: Finished candidate processing
2:04:54.697021 INFO: Collecting candidate features
2:04:55.033960 INFO: Collecting fragment features
2:04:55.221335 INFO: Finished candidate scoring
2:04:55.426382 PROGRESS: === Extracted 110503 precursors and 985014 fragments ===
2:04:55.473818 INFO: performing precursor FDR with 47 features
2:04:55.473818 INFO: Decoy channel: -1
2:04:55.473818 INFO: Competetive: True
2:04:59.245520 INFO: Test AUC: 0.562
2:04:59.245520 INFO: Train AUC: 0.568
2:04:59.245520 INFO: AUC difference: 0.97%
2:04:59.481654 INFO: === FDR correction performed with classifier version -1 ===
2:04:59.481654 PROGRESS: ============================= Precursor FDR =============================
2:04:59.481654 PROGRESS: Total precursors accumulated: 143
2:04:59.481654 PROGRESS: Target precursors: 131 (91.61%)
2:04:59.481654 PROGRESS: Decoy precursors: 12 (8.39%)
2:04:59.481654 PROGRESS: 
2:04:59.481654 PROGRESS: Precursor Summary:
2:04:59.481654 PROGRESS: Channel   0:	 0.05 FDR:    25; 0.01 FDR:    19; 0.001 FDR:    19
2:04:59.481654 PROGRESS: 
2:04:59.481654 PROGRESS: Protein Summary:
2:04:59.492886 PROGRESS: Channel   0:	 0.05 FDR:    25; 0.01 FDR:    19; 0.001 FDR:    19
2:04:59.492886 PROGRESS: =========================================================================
2:05:00.048480 INFO: Starting optimization step 3.
2:05:00.048480 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:05:00.048480 PROGRESS: Extracting batch of 126403 precursors
2:05:00.127373 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:05:00.127373 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:05:00.127373 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:05:00.127373 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:05:00.127373 INFO: Starting candidate selection
2:06:26.172458 INFO: Starting candidate scoring
2:06:31.806249 INFO: Finished candidate processing
2:06:31.806249 INFO: Collecting candidate features
2:06:32.405901 INFO: Collecting fragment features
2:06:32.657711 INFO: Finished candidate scoring
2:06:33.019262 PROGRESS: === Extracted 236800 precursors and 2111207 fragments ===
2:06:33.097791 INFO: performing precursor FDR with 47 features
2:06:33.097791 INFO: Decoy channel: -1
2:06:33.097791 INFO: Competetive: True
2:06:41.730662 INFO: Test AUC: 0.569
2:06:41.730662 INFO: Train AUC: 0.578
2:06:41.730662 INFO: AUC difference: 1.56%
2:06:42.029625 INFO: === FDR correction performed with classifier version -1 ===
2:06:42.029625 PROGRESS: ============================= Precursor FDR =============================
2:06:42.029625 PROGRESS: Total precursors accumulated: 1,016
2:06:42.029625 PROGRESS: Target precursors: 927 (91.24%)
2:06:42.029625 PROGRESS: Decoy precursors: 89 (8.76%)
2:06:42.029625 PROGRESS: 
2:06:42.029625 PROGRESS: Precursor Summary:
2:06:42.045245 PROGRESS: Channel   0:	 0.05 FDR:   749; 0.01 FDR:   367; 0.001 FDR:   247
2:06:42.045245 PROGRESS: 
2:06:42.045245 PROGRESS: Protein Summary:
2:06:42.045245 PROGRESS: Channel   0:	 0.05 FDR:   658; 0.01 FDR:   336; 0.001 FDR:   234
2:06:42.045245 PROGRESS: =========================================================================
2:06:42.108503 INFO: fragments_df_filtered: 3227
2:06:43.192472 INFO: calibration group: precursor, fitting rt estimator 
2:06:43.350299 INFO: calibration group: fragment, fitting mz estimator 
2:06:45.035289 INFO: calibration group: precursor, predicting mz
2:06:45.035289 WARNING: mz prediction was skipped as it has not been fitted yet
2:06:45.035289 INFO: calibration group: precursor, predicting rt
2:06:45.239750 INFO: calibration group: fragment, predicting mz
2:06:46.121083 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:06:46.121083 INFO: Starting optimization step 4.
2:06:46.121083 PROGRESS: === Extracting elution groups 0 to 120000 ===
2:06:46.134742 PROGRESS: Extracting batch of 237004 precursors
2:06:46.262448 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:06:46.262448 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:06:46.262448 INFO: FWHM in RT is 20.21 seconds, sigma is 0.74
2:06:46.262448 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:06:46.262448 INFO: Starting candidate selection
2:08:17.923274 INFO: Starting candidate scoring
2:08:28.441115 INFO: Finished candidate processing
2:08:28.441115 INFO: Collecting candidate features
2:08:29.778857 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 473647)
2:08:29.835404 INFO: Collecting fragment features
2:08:30.436568 INFO: Finished candidate scoring
2:08:30.839572 PROGRESS: === Extracted 473647 precursors and 4352329 fragments ===
2:08:30.839572 INFO: performing precursor FDR with 47 features
2:08:30.839572 INFO: Decoy channel: -1
2:08:30.839572 INFO: Competetive: True
2:08:31.294593 WARNING: dropped 2 target PSMs due to missing features
2:08:31.294593 WARNING: dropped 4 decoy PSMs due to missing features
2:08:40.042972 INFO: Test AUC: 0.575
2:08:40.042972 INFO: Train AUC: 0.581
2:08:40.042972 INFO: AUC difference: 1.04%
2:08:40.460223 INFO: === FDR correction performed with classifier version 3 ===
2:08:40.475853 PROGRESS: ============================= Precursor FDR =============================
2:08:40.475853 PROGRESS: Total precursors accumulated: 1,168
2:08:40.475853 PROGRESS: Target precursors: 1,063 (91.01%)
2:08:40.475853 PROGRESS: Decoy precursors: 105 (8.99%)
2:08:40.475853 PROGRESS: 
2:08:40.475853 PROGRESS: Precursor Summary:
2:08:40.491469 PROGRESS: Channel   0:	 0.05 FDR:   868; 0.01 FDR:   570; 0.001 FDR:   451
2:08:40.491469 PROGRESS: 
2:08:40.491469 PROGRESS: Protein Summary:
2:08:40.507257 PROGRESS: Channel   0:	 0.05 FDR:   757; 0.01 FDR:   512; 0.001 FDR:   406
2:08:40.507257 PROGRESS: =========================================================================
2:08:40.554797 INFO: fragments_df_filtered: 4144
2:08:41.473337 INFO: calibration group: precursor, fitting rt estimator 
2:08:41.713737 INFO: calibration group: fragment, fitting mz estimator 
2:08:45.747713 INFO: calibration group: precursor, predicting mz
2:08:45.748411 WARNING: mz prediction was skipped as it has not been fitted yet
2:08:45.748411 INFO: calibration group: precursor, predicting rt
2:08:45.814733 INFO: calibration group: fragment, predicting mz
2:08:46.423709 INFO: === checking if optimization conditions were reached ===
2:08:46.423709 PROGRESS: ❌ ms2_error      : 10.1500 > 10.0000 or insufficient steps taken.
2:08:46.423709 INFO: ==============================================
2:08:46.423709 INFO: Starting optimization step 5.
2:08:46.423709 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:08:46.423709 PROGRESS: Extracting batch of 110601 precursors
2:08:46.587834 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:08:46.589089 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:08:46.589089 INFO: FWHM in RT is 20.62 seconds, sigma is 0.75
2:08:46.589089 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:08:46.589089 INFO: Starting candidate selection
2:10:22.108122 INFO: Starting candidate scoring
2:10:30.371129 INFO: Finished candidate processing
2:10:30.371129 INFO: Collecting candidate features
2:10:31.014343 WARNING: intensity_correlation has 22 NaNs ( 0.01 % out of 220947)
2:10:31.046659 INFO: Collecting fragment features
2:10:31.333012 INFO: Finished candidate scoring
2:10:31.522504 PROGRESS: === Extracted 220947 precursors and 1711763 fragments ===
2:10:31.522504 INFO: performing precursor FDR with 47 features
2:10:31.522504 INFO: Decoy channel: -1
2:10:31.522504 INFO: Competetive: True
2:10:31.761610 WARNING: dropped 9 target PSMs due to missing features
2:10:31.761610 WARNING: dropped 13 decoy PSMs due to missing features
2:10:36.624278 INFO: Test AUC: 0.573
2:10:36.624278 INFO: Train AUC: 0.587
2:10:36.624278 INFO: AUC difference: 2.44%
2:10:36.844455 INFO: === FDR correction performed with classifier version 4 ===
2:10:36.860048 PROGRESS: ============================= Precursor FDR =============================
2:10:36.860048 PROGRESS: Total precursors accumulated: 604
2:10:36.860048 PROGRESS: Target precursors: 549 (90.89%)
2:10:36.860048 PROGRESS: Decoy precursors: 55 (9.11%)
2:10:36.860048 PROGRESS: 
2:10:36.860048 PROGRESS: Precursor Summary:
2:10:36.860048 PROGRESS: Channel   0:	 0.05 FDR:   451; 0.01 FDR:   324; 0.001 FDR:   180
2:10:36.860048 PROGRESS: 
2:10:36.860048 PROGRESS: Protein Summary:
2:10:36.860048 PROGRESS: Channel   0:	 0.05 FDR:   425; 0.01 FDR:   306; 0.001 FDR:   175
2:10:36.860048 PROGRESS: =========================================================================
2:10:36.875674 INFO: fragments_df_filtered: 1619
2:10:37.252969 INFO: calibration group: precursor, fitting rt estimator 
2:10:37.362907 INFO: calibration group: fragment, fitting mz estimator 
2:10:38.056051 INFO: calibration group: precursor, predicting mz
2:10:38.056051 WARNING: mz prediction was skipped as it has not been fitted yet
2:10:38.056051 INFO: calibration group: precursor, predicting rt
2:10:38.150664 INFO: calibration group: fragment, predicting mz
2:10:38.574984 INFO: === checking if optimization conditions were reached ===
2:10:38.574984 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:10:38.590610 INFO: ==============================================
2:10:38.590610 PROGRESS: Optimization finished for ms2_error.
2:10:39.380034 INFO: calibration group: precursor, predicting mz
2:10:39.380034 WARNING: mz prediction was skipped as it has not been fitted yet
2:10:39.380034 INFO: calibration group: precursor, predicting rt
2:10:39.538291 INFO: calibration group: fragment, predicting mz
2:10:40.041978 INFO: Starting optimization step 0.
2:10:40.041978 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:10:40.041978 PROGRESS: Extracting batch of 110601 precursors
2:10:40.168228 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:10:40.168228 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:10:40.168228 INFO: FWHM in RT is 18.20 seconds, sigma is 0.66
2:10:40.168228 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:10:40.168228 INFO: Starting candidate selection
2:12:18.765261 INFO: Starting candidate scoring
2:12:25.174484 INFO: Finished candidate processing
2:12:25.174484 INFO: Collecting candidate features
2:12:25.850080 WARNING: intensity_correlation has 14 NaNs ( 0.01 % out of 220946)
2:12:25.881338 INFO: Collecting fragment features
2:12:26.196555 INFO: Finished candidate scoring
2:12:26.369022 PROGRESS: === Extracted 220946 precursors and 1702594 fragments ===
2:12:26.369022 INFO: performing precursor FDR with 47 features
2:12:26.369022 INFO: Decoy channel: -1
2:12:26.369022 INFO: Competetive: True
2:12:26.635855 WARNING: dropped 6 target PSMs due to missing features
2:12:26.635855 WARNING: dropped 8 decoy PSMs due to missing features
2:12:31.591030 INFO: Test AUC: 0.583
2:12:31.591030 INFO: Train AUC: 0.591
2:12:31.591030 INFO: AUC difference: 1.36%
2:12:32.600269 INFO: === FDR correction performed with classifier version 5 ===
2:12:32.600269 PROGRESS: ============================= Precursor FDR =============================
2:12:32.600269 PROGRESS: Total precursors accumulated: 659
2:12:32.600269 PROGRESS: Target precursors: 598 (90.74%)
2:12:32.600269 PROGRESS: Decoy precursors: 61 (9.26%)
2:12:32.600269 PROGRESS: 
2:12:32.600269 PROGRESS: Precursor Summary:
2:12:32.615895 PROGRESS: Channel   0:	 0.05 FDR:   473; 0.01 FDR:   372; 0.001 FDR:   237
2:12:32.615895 PROGRESS: 
2:12:32.615895 PROGRESS: Protein Summary:
2:12:32.615895 PROGRESS: Channel   0:	 0.05 FDR:   446; 0.01 FDR:   349; 0.001 FDR:   228
2:12:32.615895 PROGRESS: =========================================================================
2:12:32.642576 INFO: fragments_df_filtered: 1643
2:12:33.071856 INFO: calibration group: precursor, fitting rt estimator 
2:12:33.182584 INFO: calibration group: fragment, fitting mz estimator 
2:12:33.967939 INFO: calibration group: precursor, predicting mz
2:12:33.967939 WARNING: mz prediction was skipped as it has not been fitted yet
2:12:33.967939 INFO: calibration group: precursor, predicting rt
2:12:34.062384 INFO: calibration group: fragment, predicting mz
2:12:34.518653 INFO: === checking if optimization conditions were reached ===
2:12:34.518653 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:12:34.534564 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 616.7899.
2:12:34.534564 INFO: ==============================================
2:12:34.534564 INFO: Starting optimization step 1.
2:12:34.534564 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:12:34.534564 PROGRESS: Extracting batch of 110601 precursors
2:12:34.629494 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:12:34.631176 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:12:34.631176 INFO: FWHM in RT is 18.01 seconds, sigma is 0.66
2:12:34.631176 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:12:34.631745 INFO: Starting candidate selection
2:12:53.848276 INFO: Starting candidate scoring
2:13:02.536511 INFO: Finished candidate processing
2:13:02.536511 INFO: Collecting candidate features
2:13:04.098637 WARNING: intensity_correlation has 319 NaNs ( 0.15 % out of 212354)
2:13:04.177221 INFO: Collecting fragment features
2:13:04.903215 INFO: Finished candidate scoring
2:13:05.579458 PROGRESS: === Extracted 212354 precursors and 1380531 fragments ===
2:13:05.579458 INFO: performing precursor FDR with 47 features
2:13:05.579458 INFO: Decoy channel: -1
2:13:05.579458 INFO: Competetive: True
2:13:06.399449 WARNING: dropped 171 target PSMs due to missing features
2:13:06.399449 WARNING: dropped 148 decoy PSMs due to missing features
2:13:11.586009 INFO: Test AUC: 0.561
2:13:11.586009 INFO: Train AUC: 0.576
2:13:11.586009 INFO: AUC difference: 2.59%
2:13:11.903570 INFO: === FDR correction performed with classifier version 5 ===
2:13:11.903570 PROGRESS: ============================= Precursor FDR =============================
2:13:11.903570 PROGRESS: Total precursors accumulated: 718
2:13:11.903570 PROGRESS: Target precursors: 652 (90.81%)
2:13:11.903570 PROGRESS: Decoy precursors: 66 (9.19%)
2:13:11.903570 PROGRESS: 
2:13:11.903570 PROGRESS: Precursor Summary:
2:13:11.918773 PROGRESS: Channel   0:	 0.05 FDR:   546; 0.01 FDR:   408; 0.001 FDR:   355
2:13:11.918773 PROGRESS: 
2:13:11.918773 PROGRESS: Protein Summary:
2:13:11.918773 PROGRESS: Channel   0:	 0.05 FDR:   512; 0.01 FDR:   382; 0.001 FDR:   334
2:13:11.918773 PROGRESS: =========================================================================
2:13:11.934414 INFO: fragments_df_filtered: 1719
2:13:12.532176 INFO: calibration group: precursor, fitting rt estimator 
2:13:12.690152 INFO: calibration group: fragment, fitting mz estimator 
2:13:13.396335 INFO: calibration group: precursor, predicting mz
2:13:13.396335 WARNING: mz prediction was skipped as it has not been fitted yet
2:13:13.396335 INFO: calibration group: precursor, predicting rt
2:13:13.490582 INFO: calibration group: fragment, predicting mz
2:13:13.947776 INFO: === checking if optimization conditions were reached ===
2:13:13.947776 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:13:13.947776 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 478.0389.
2:13:13.947776 INFO: ==============================================
2:13:13.963874 INFO: Starting optimization step 2.
2:13:13.963874 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:13:13.963874 PROGRESS: Extracting batch of 110601 precursors
2:13:14.027267 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:13:14.027267 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:13:14.027267 INFO: FWHM in RT is 18.11 seconds, sigma is 0.66
2:13:14.027267 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:13:14.027267 INFO: Starting candidate selection
2:13:26.287827 INFO: Starting candidate scoring
2:13:31.940816 INFO: Finished candidate processing
2:13:31.940816 INFO: Collecting candidate features
2:13:33.231195 WARNING: intensity_correlation has 327 NaNs ( 0.16 % out of 209741)
2:13:33.294163 INFO: Collecting fragment features
2:13:33.894866 INFO: Finished candidate scoring
2:13:34.474196 PROGRESS: === Extracted 209741 precursors and 1332321 fragments ===
2:13:34.474196 INFO: performing precursor FDR with 47 features
2:13:34.474196 INFO: Decoy channel: -1
2:13:34.474196 INFO: Competetive: True
2:13:35.205683 WARNING: dropped 169 target PSMs due to missing features
2:13:35.205683 WARNING: dropped 158 decoy PSMs due to missing features
2:13:44.641085 INFO: Test AUC: 0.562
2:13:44.641085 INFO: Train AUC: 0.575
2:13:44.641085 INFO: AUC difference: 2.33%
2:13:45.163182 INFO: === FDR correction performed with classifier version 5 ===
2:13:45.163182 PROGRESS: ============================= Precursor FDR =============================
2:13:45.178843 PROGRESS: Total precursors accumulated: 747
2:13:45.178843 PROGRESS: Target precursors: 680 (91.03%)
2:13:45.178843 PROGRESS: Decoy precursors: 67 (8.97%)
2:13:45.178843 PROGRESS: 
2:13:45.178843 PROGRESS: Precursor Summary:
2:13:45.182360 PROGRESS: Channel   0:	 0.05 FDR:   583; 0.01 FDR:   357; 0.001 FDR:   298
2:13:45.182360 PROGRESS: 
2:13:45.182360 PROGRESS: Protein Summary:
2:13:45.194874 PROGRESS: Channel   0:	 0.05 FDR:   548; 0.01 FDR:   334; 0.001 FDR:   281
2:13:45.198667 PROGRESS: =========================================================================
2:13:45.228983 INFO: fragments_df_filtered: 1686
2:13:46.442679 INFO: calibration group: precursor, fitting rt estimator 
2:13:46.662599 INFO: calibration group: fragment, fitting mz estimator 
2:13:47.496365 INFO: calibration group: precursor, predicting mz
2:13:47.496365 WARNING: mz prediction was skipped as it has not been fitted yet
2:13:47.496365 INFO: calibration group: precursor, predicting rt
2:13:47.669635 INFO: calibration group: fragment, predicting mz
2:13:48.268807 INFO: === checking if optimization conditions were reached ===
2:13:48.268807 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:13:48.284508 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 450.0291.
2:13:48.284508 INFO: ==============================================
2:13:48.284508 INFO: Starting optimization step 3.
2:13:48.284508 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:13:48.284508 PROGRESS: Extracting batch of 110601 precursors
2:13:48.442340 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:13:48.442340 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:13:48.442340 INFO: FWHM in RT is 18.01 seconds, sigma is 0.66
2:13:48.442340 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:13:48.442340 INFO: Starting candidate selection
2:14:03.283301 INFO: Starting candidate scoring
2:14:10.054238 INFO: Finished candidate processing
2:14:10.054238 INFO: Collecting candidate features
2:14:10.905416 WARNING: intensity_correlation has 345 NaNs ( 0.16 % out of 209231)
2:14:10.936735 INFO: Collecting fragment features
2:14:11.204246 INFO: Finished candidate scoring
2:14:11.393418 PROGRESS: === Extracted 209231 precursors and 1316575 fragments ===
2:14:11.393418 INFO: performing precursor FDR with 47 features
2:14:11.393418 INFO: Decoy channel: -1
2:14:11.393418 INFO: Competetive: True
2:14:11.645104 WARNING: dropped 176 target PSMs due to missing features
2:14:11.645104 WARNING: dropped 169 decoy PSMs due to missing features
2:14:16.699426 INFO: Test AUC: 0.556
2:14:16.699426 INFO: Train AUC: 0.578
2:14:16.699426 INFO: AUC difference: 3.76%
2:14:16.949385 INFO: === FDR correction performed with classifier version 5 ===
2:14:16.949385 PROGRESS: ============================= Precursor FDR =============================
2:14:16.949385 PROGRESS: Total precursors accumulated: 798
2:14:16.949385 PROGRESS: Target precursors: 726 (90.98%)
2:14:16.949385 PROGRESS: Decoy precursors: 72 (9.02%)
2:14:16.949385 PROGRESS: 
2:14:16.949385 PROGRESS: Precursor Summary:
2:14:16.949385 PROGRESS: Channel   0:	 0.05 FDR:   612; 0.01 FDR:   328; 0.001 FDR:   272
2:14:16.949385 PROGRESS: 
2:14:16.949385 PROGRESS: Protein Summary:
2:14:16.949385 PROGRESS: Channel   0:	 0.05 FDR:   574; 0.01 FDR:   306; 0.001 FDR:   258
2:14:16.949385 PROGRESS: =========================================================================
2:14:16.964456 INFO: fragments_df_filtered: 1671
2:14:17.386804 INFO: calibration group: precursor, fitting rt estimator 
2:14:17.503860 INFO: calibration group: fragment, fitting mz estimator 
2:14:18.296626 INFO: calibration group: precursor, predicting mz
2:14:18.296626 WARNING: mz prediction was skipped as it has not been fitted yet
2:14:18.296626 INFO: calibration group: precursor, predicting rt
2:14:18.386602 INFO: calibration group: fragment, predicting mz
2:14:18.709568 INFO: === checking if optimization conditions were reached ===
2:14:18.709568 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:14:18.709568 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 445.7574.
2:14:18.709568 INFO: ==============================================
2:14:18.709568 INFO: Starting optimization step 4.
2:14:18.709568 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:14:18.709568 PROGRESS: Extracting batch of 110601 precursors
2:14:18.741224 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:14:18.741224 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:14:18.741224 INFO: FWHM in RT is 18.08 seconds, sigma is 0.66
2:14:18.741224 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:14:18.741224 INFO: Starting candidate selection
2:14:27.023797 INFO: Starting candidate scoring
2:14:32.173709 INFO: Finished candidate processing
2:14:32.173709 INFO: Collecting candidate features
2:14:32.786890 WARNING: intensity_correlation has 343 NaNs ( 0.16 % out of 209179)
2:14:32.799869 INFO: Collecting fragment features
2:14:33.060686 INFO: Finished candidate scoring
2:14:33.250425 PROGRESS: === Extracted 209179 precursors and 1316467 fragments ===
2:14:33.250425 INFO: performing precursor FDR with 47 features
2:14:33.250425 INFO: Decoy channel: -1
2:14:33.250425 INFO: Competetive: True
2:14:33.457133 WARNING: dropped 178 target PSMs due to missing features
2:14:33.457133 WARNING: dropped 165 decoy PSMs due to missing features
2:14:38.105697 INFO: Test AUC: 0.556
2:14:38.105697 INFO: Train AUC: 0.576
2:14:38.105697 INFO: AUC difference: 3.60%
2:14:38.304954 INFO: === FDR correction performed with classifier version 5 ===
2:14:38.320572 PROGRESS: ============================= Precursor FDR =============================
2:14:38.320572 PROGRESS: Total precursors accumulated: 781
2:14:38.320572 PROGRESS: Target precursors: 711 (91.04%)
2:14:38.320572 PROGRESS: Decoy precursors: 70 (8.96%)
2:14:38.320572 PROGRESS: 
2:14:38.320572 PROGRESS: Precursor Summary:
2:14:38.320572 PROGRESS: Channel   0:	 0.05 FDR:   606; 0.01 FDR:   405; 0.001 FDR:   360
2:14:38.320572 PROGRESS: 
2:14:38.320572 PROGRESS: Protein Summary:
2:14:38.324122 PROGRESS: Channel   0:	 0.05 FDR:   571; 0.01 FDR:   379; 0.001 FDR:   336
2:14:38.324122 PROGRESS: =========================================================================
2:14:38.324122 INFO: fragments_df_filtered: 1700
2:14:38.686683 INFO: calibration group: precursor, fitting rt estimator 
2:14:38.813539 INFO: calibration group: fragment, fitting mz estimator 
2:14:39.528058 INFO: calibration group: precursor, predicting mz
2:14:39.528058 WARNING: mz prediction was skipped as it has not been fitted yet
2:14:39.528058 INFO: calibration group: precursor, predicting rt
2:14:39.621825 INFO: calibration group: fragment, predicting mz
2:14:39.983060 INFO: === checking if optimization conditions were reached ===
2:14:39.983060 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:14:39.983060 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 445.7574 found after 5 searches.
2:14:39.983060 INFO: ==============================================
2:14:39.983060 PROGRESS: Optimization finished for rt_error.
2:14:40.333027 INFO: calibration group: precursor, predicting mz
2:14:40.333027 WARNING: mz prediction was skipped as it has not been fitted yet
2:14:40.333027 INFO: calibration group: precursor, predicting rt
2:14:40.408353 INFO: calibration group: fragment, predicting mz
2:14:40.618638 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:14:40.618638 PROGRESS: ==============================================
2:14:40.618638 PROGRESS: ms2_error      : 10.0000
2:14:40.618638 PROGRESS: rt_error       : 445.7574
2:14:40.618638 PROGRESS: ==============================================
2:14:40.662638 INFO: calibration group: precursor, predicting mz
2:14:40.662638 WARNING: mz prediction was skipped as it has not been fitted yet
2:14:40.662638 INFO: calibration group: precursor, predicting rt
2:14:44.998484 INFO: calibration group: fragment, predicting mz
2:15:15.605464 PROGRESS: Extracting batch of 10640830 precursors
2:15:18.000052 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:15:18.000052 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:15:18.000052 INFO: FWHM in RT is 18.12 seconds, sigma is 0.66
2:15:18.000052 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:15:18.000052 INFO: Starting candidate selection
2:34:20.994321 INFO: Applying score cutoff of 80.17851248168945
2:34:21.715071 INFO: Removed 16341084 precursors with score below cutoff
2:34:27.262132 INFO: Starting candidate scoring
2:37:51.023457 INFO: Finished candidate processing
2:37:51.023457 INFO: Collecting candidate features
2:38:11.456198 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 4673523)
2:38:12.346627 INFO: Collecting fragment features
2:38:23.445028 INFO: Finished candidate scoring
2:38:34.419601 INFO: === FDR correction performed with classifier version 10 ===
2:38:34.419601 INFO: performing precursor FDR with 47 features
2:38:34.419601 INFO: Decoy channel: -1
2:38:34.419601 INFO: Competetive: True
2:38:40.910322 WARNING: dropped 1 target PSMs due to missing features
2:42:35.239322 INFO: Test AUC: 0.583
2:42:35.239322 INFO: Train AUC: 0.586
2:42:35.239322 INFO: AUC difference: 0.48%
2:42:36.418108 INFO: Removing fragments below FDR threshold
2:42:37.420982 PROGRESS: ============================= Precursor FDR =============================
2:42:37.420982 PROGRESS: Total precursors accumulated: 53,302
2:42:37.420982 PROGRESS: Target precursors: 52,775 (99.01%)
2:42:37.420982 PROGRESS: Decoy precursors: 527 (0.99%)
2:42:37.421979 PROGRESS: 
2:42:37.421979 PROGRESS: Precursor Summary:
2:42:37.499670 PROGRESS: Channel   0:	 0.05 FDR: 52,775; 0.01 FDR: 52,775; 0.001 FDR: 33,705
2:42:37.499670 PROGRESS: 
2:42:37.500660 PROGRESS: Protein Summary:
2:42:37.603189 PROGRESS: Channel   0:	 0.05 FDR: 8,907; 0.01 FDR: 8,907; 0.001 FDR: 6,512
2:42:37.603189 PROGRESS: =========================================================================
2:42:39.228438 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
2:42:41.388493 PROGRESS: Loading raw file 3/6: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
2:42:41.389491 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03 at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
2:43:40.517130 INFO: Determining DIA cycle
2:43:40.530130 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
2:43:40.537130 INFO: Determining DIA cycle
2:43:40.549259 INFO: Found cycle with start 0.00 min and length 151.
2:43:40.644009 INFO: ============ Raw file stats ============
2:43:40.645009 INFO: RT (min)            : 0.0 - 150.0
2:43:40.645009 INFO: RT duration (sec)   : 8999.7
2:43:40.645009 INFO: RT duration (min)   : 150.0
2:43:40.646009 INFO: Cycle len (scans)   : 151
2:43:40.646009 INFO: Cycle len (sec)     : 5.84
2:43:40.646009 INFO: Number of cycles    : 1542
2:43:40.646009 INFO: MS2 range (m/z)     : 396.4 - 1004.7
2:43:40.646009 INFO: ========================================
2:43:48.601701 INFO: Initializing CalibrationManager
2:43:48.603702 INFO: Loading calibration config
2:43:48.606710 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)}]}]
2:43:48.607891 INFO: Calibration group :fragment, found 1 estimator(s)
2:43:48.608899 INFO: Calibration group :precursor, found 3 estimator(s)
2:43:48.609898 INFO: Disabling ion mobility calibration
2:43:48.609898 INFO: removed mobility estimator from group precursor
2:43:48.610894 INFO: Initializing OptimizationManager
2:43:48.612898 INFO: initial parameter: ms1_error = 30
2:43:48.613897 INFO: initial parameter: ms2_error = 30
2:43:48.613897 INFO: initial parameter: rt_error = 4500.001953125
2:43:48.614897 INFO: initial parameter: mobility_error = 0.1
2:43:48.614897 INFO: initial parameter: column_type = library
2:43:48.615901 INFO: initial parameter: num_candidates = 1
2:43:48.616900 INFO: initial parameter: classifier_version = -1
2:43:48.617904 INFO: initial parameter: fwhm_rt = 5
2:43:48.617904 INFO: initial parameter: fwhm_mobility = 0.01
2:43:48.618896 INFO: initial parameter: score_cutoff = 0
2:43:48.618896 INFO: Initializing TimingManager
2:43:48.619897 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
2:43:48.620899 INFO: Initializing FDRManager
2:43:48.620899 INFO: Loading classifier store from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\classifier
2:43:54.120219 PROGRESS: 5,385,906 target precursors potentially observable (0 removed)
2:44:01.332646 PROGRESS: Starting initial search for precursors.
2:44:01.939123 INFO: Starting optimization step 0.
2:44:01.986227 PROGRESS: === Extracting elution groups 0 to 8000 ===
2:44:01.991233 PROGRESS: Extracting batch of 15803 precursors
2:44:02.035023 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:44:02.036022 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:44:02.036022 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:44:02.036022 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:44:02.036022 INFO: Starting candidate selection
2:44:15.758254 INFO: Starting candidate scoring
2:44:16.672097 INFO: Finished candidate processing
2:44:16.672097 INFO: Collecting candidate features
2:44:16.923500 INFO: Collecting fragment features
2:44:17.065293 INFO: Finished candidate scoring
2:44:17.147363 PROGRESS: === Extracted 15795 precursors and 133329 fragments ===
2:44:17.149360 INFO: performing precursor FDR with 47 features
2:44:17.149360 INFO: Decoy channel: -1
2:44:17.149360 INFO: Competetive: True
2:44:17.525715 INFO: Test AUC: 0.506
2:44:17.525715 INFO: Train AUC: 0.530
2:44:17.525715 INFO: AUC difference: 4.47%
2:44:17.604304 INFO: === FDR correction performed with classifier version -1 ===
2:44:17.605304 PROGRESS: ============================= Precursor FDR =============================
2:44:17.605304 PROGRESS: Total precursors accumulated: 3
2:44:17.605304 PROGRESS: Target precursors: 3 (100.00%)
2:44:17.605304 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:17.605304 PROGRESS: 
2:44:17.606304 PROGRESS: Precursor Summary:
2:44:17.606304 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:44:17.607305 PROGRESS: 
2:44:17.607305 PROGRESS: Protein Summary:
2:44:17.608304 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
2:44:17.608304 PROGRESS: =========================================================================
2:44:17.730453 INFO: Starting optimization step 1.
2:44:17.730453 PROGRESS: === Extracting elution groups 8000 to 24000 ===
2:44:17.730973 PROGRESS: Extracting batch of 31592 precursors
2:44:17.740978 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:44:17.740978 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:44:17.740978 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:44:17.740978 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:44:17.740978 INFO: Starting candidate selection
2:44:29.763852 INFO: Starting candidate scoring
2:44:30.961856 INFO: Finished candidate processing
2:44:30.961856 INFO: Collecting candidate features
2:44:31.180134 INFO: Collecting fragment features
2:44:31.264986 INFO: Finished candidate scoring
2:44:31.363973 PROGRESS: === Extracted 47346 precursors and 400518 fragments ===
2:44:31.386964 INFO: performing precursor FDR with 47 features
2:44:31.386964 INFO: Decoy channel: -1
2:44:31.386964 INFO: Competetive: True
2:44:32.564995 INFO: Test AUC: 0.544
2:44:32.565108 INFO: Train AUC: 0.560
2:44:32.565108 INFO: AUC difference: 2.76%
2:44:32.753058 INFO: === FDR correction performed with classifier version -1 ===
2:44:32.754057 PROGRESS: ============================= Precursor FDR =============================
2:44:32.755056 PROGRESS: Total precursors accumulated: 4
2:44:32.755056 PROGRESS: Target precursors: 4 (100.00%)
2:44:32.755056 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:32.755056 PROGRESS: 
2:44:32.755056 PROGRESS: Precursor Summary:
2:44:32.757059 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
2:44:32.757059 PROGRESS: 
2:44:32.757059 PROGRESS: Protein Summary:
2:44:32.759058 PROGRESS: Channel   0:	 0.05 FDR:     4; 0.01 FDR:     4; 0.001 FDR:     4
2:44:32.759058 PROGRESS: =========================================================================
2:44:33.134326 INFO: Starting optimization step 2.
2:44:33.134326 PROGRESS: === Extracting elution groups 24000 to 56000 ===
2:44:33.135324 PROGRESS: Extracting batch of 63206 precursors
2:44:33.183151 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:44:33.184147 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:44:33.184147 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:44:33.184147 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:44:33.184147 INFO: Starting candidate selection
2:45:16.367948 INFO: Starting candidate scoring
2:45:18.951083 INFO: Finished candidate processing
2:45:18.951083 INFO: Collecting candidate features
2:45:19.270172 INFO: Collecting fragment features
2:45:19.379080 INFO: Finished candidate scoring
2:45:19.580458 PROGRESS: === Extracted 110502 precursors and 936398 fragments ===
2:45:19.617060 INFO: performing precursor FDR with 47 features
2:45:19.617060 INFO: Decoy channel: -1
2:45:19.617060 INFO: Competetive: True
2:45:20.998287 INFO: Test AUC: 0.561
2:45:20.998287 INFO: Train AUC: 0.576
2:45:20.998287 INFO: AUC difference: 2.53%
2:45:21.095205 INFO: === FDR correction performed with classifier version -1 ===
2:45:21.096221 PROGRESS: ============================= Precursor FDR =============================
2:45:21.096221 PROGRESS: Total precursors accumulated: 389
2:45:21.096221 PROGRESS: Target precursors: 354 (91.00%)
2:45:21.096221 PROGRESS: Decoy precursors: 35 (9.00%)
2:45:21.096221 PROGRESS: 
2:45:21.097127 PROGRESS: Precursor Summary:
2:45:21.098223 PROGRESS: Channel   0:	 0.05 FDR:   248; 0.01 FDR:    36; 0.001 FDR:    36
2:45:21.098223 PROGRESS: 
2:45:21.098223 PROGRESS: Protein Summary:
2:45:21.099127 PROGRESS: Channel   0:	 0.05 FDR:   240; 0.01 FDR:    36; 0.001 FDR:    36
2:45:21.099127 PROGRESS: =========================================================================
2:45:21.362256 INFO: Starting optimization step 3.
2:45:21.362256 PROGRESS: === Extracting elution groups 56000 to 120000 ===
2:45:21.362256 PROGRESS: Extracting batch of 126403 precursors
2:45:21.390376 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:45:21.390376 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:45:21.390376 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
2:45:21.390376 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
2:45:21.390376 INFO: Starting candidate selection
2:46:55.843538 INFO: Starting candidate scoring
2:47:02.161052 INFO: Finished candidate processing
2:47:02.161052 INFO: Collecting candidate features
2:47:02.968501 INFO: Collecting fragment features
2:47:03.293236 INFO: Finished candidate scoring
2:47:03.816144 PROGRESS: === Extracted 236805 precursors and 2006112 fragments ===
2:47:03.938484 INFO: performing precursor FDR with 47 features
2:47:03.938484 INFO: Decoy channel: -1
2:47:03.938484 INFO: Competetive: True
2:47:12.701278 INFO: Test AUC: 0.566
2:47:12.701278 INFO: Train AUC: 0.579
2:47:12.701278 INFO: AUC difference: 2.33%
2:47:13.057260 INFO: === FDR correction performed with classifier version -1 ===
2:47:13.057260 PROGRESS: ============================= Precursor FDR =============================
2:47:13.073396 PROGRESS: Total precursors accumulated: 1,137
2:47:13.073396 PROGRESS: Target precursors: 1,036 (91.12%)
2:47:13.073396 PROGRESS: Decoy precursors: 101 (8.88%)
2:47:13.073396 PROGRESS: 
2:47:13.073396 PROGRESS: Precursor Summary:
2:47:13.073396 PROGRESS: Channel   0:	 0.05 FDR:   871; 0.01 FDR:   661; 0.001 FDR:   445
2:47:13.073396 PROGRESS: 
2:47:13.073396 PROGRESS: Protein Summary:
2:47:13.073396 PROGRESS: Channel   0:	 0.05 FDR:   755; 0.01 FDR:   586; 0.001 FDR:   409
2:47:13.073396 PROGRESS: =========================================================================
2:47:13.151871 INFO: fragments_df_filtered: 3967
2:47:13.790608 INFO: calibration group: precursor, fitting rt estimator 
2:47:14.022881 INFO: calibration group: fragment, fitting mz estimator 
2:47:18.277637 INFO: calibration group: precursor, predicting mz
2:47:18.293259 WARNING: mz prediction was skipped as it has not been fitted yet
2:47:18.293259 INFO: calibration group: precursor, predicting rt
2:47:18.416704 INFO: calibration group: fragment, predicting mz
2:47:18.874610 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:47:18.874610 INFO: Starting optimization step 4.
2:47:18.874610 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:47:18.874610 PROGRESS: Extracting batch of 110601 precursors
2:47:18.955022 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:47:18.955022 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:47:18.955022 INFO: FWHM in RT is 18.94 seconds, sigma is 0.69
2:47:18.955022 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:47:18.955022 INFO: Starting candidate selection
2:49:20.010847 INFO: Starting candidate scoring
2:49:29.308735 INFO: Finished candidate processing
2:49:29.308735 INFO: Collecting candidate features
2:49:30.272991 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 221024)
2:49:30.304646 INFO: Collecting fragment features
2:49:30.798531 INFO: Finished candidate scoring
2:49:31.133856 PROGRESS: === Extracted 221024 precursors and 1929872 fragments ===
2:49:31.133856 INFO: performing precursor FDR with 47 features
2:49:31.133856 INFO: Decoy channel: -1
2:49:31.133856 INFO: Competetive: True
2:49:31.544894 WARNING: dropped 2 decoy PSMs due to missing features
2:49:39.013422 INFO: Test AUC: 0.572
2:49:39.013422 INFO: Train AUC: 0.582
2:49:39.013422 INFO: AUC difference: 1.86%
2:49:39.347018 INFO: === FDR correction performed with classifier version 3 ===
2:49:39.350018 PROGRESS: ============================= Precursor FDR =============================
2:49:39.350018 PROGRESS: Total precursors accumulated: 528
2:49:39.351017 PROGRESS: Target precursors: 482 (91.29%)
2:49:39.351017 PROGRESS: Decoy precursors: 46 (8.71%)
2:49:39.351017 PROGRESS: 
2:49:39.351017 PROGRESS: Precursor Summary:
2:49:39.355021 PROGRESS: Channel   0:	 0.05 FDR:   372; 0.01 FDR:   272; 0.001 FDR:   135
2:49:39.356022 PROGRESS: 
2:49:39.356022 PROGRESS: Protein Summary:
2:49:39.360072 PROGRESS: Channel   0:	 0.05 FDR:   351; 0.01 FDR:   261; 0.001 FDR:   133
2:49:39.360072 PROGRESS: =========================================================================
2:49:39.380835 INFO: fragments_df_filtered: 1899
2:49:40.103924 INFO: calibration group: precursor, fitting rt estimator 
2:49:40.231146 INFO: calibration group: fragment, fitting mz estimator 
2:49:41.301225 INFO: calibration group: precursor, predicting mz
2:49:41.301225 WARNING: mz prediction was skipped as it has not been fitted yet
2:49:41.301225 INFO: calibration group: precursor, predicting rt
2:49:41.425519 INFO: calibration group: fragment, predicting mz
2:49:41.775192 INFO: === checking if optimization conditions were reached ===
2:49:41.775192 PROGRESS: ❌ ms2_error      : 10.3350 > 10.0000 or insufficient steps taken.
2:49:41.775192 INFO: ==============================================
2:49:41.775192 INFO: Starting optimization step 5.
2:49:41.775192 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:49:41.775192 PROGRESS: Extracting batch of 110601 precursors
2:49:41.821996 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:49:41.821996 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:49:41.821996 INFO: FWHM in RT is 19.52 seconds, sigma is 0.71
2:49:41.821996 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:49:41.821996 INFO: Starting candidate selection
2:51:10.547936 INFO: Starting candidate scoring
2:51:19.098112 INFO: Finished candidate processing
2:51:19.098112 INFO: Collecting candidate features
2:51:19.964567 WARNING: intensity_correlation has 22 NaNs ( 0.01 % out of 220899)
2:51:20.011445 INFO: Collecting fragment features
2:51:20.283230 INFO: Finished candidate scoring
2:51:20.573066 PROGRESS: === Extracted 220899 precursors and 1589671 fragments ===
2:51:20.573066 INFO: performing precursor FDR with 47 features
2:51:20.573066 INFO: Decoy channel: -1
2:51:20.573066 INFO: Competetive: True
2:51:20.960623 WARNING: dropped 12 target PSMs due to missing features
2:51:20.960623 WARNING: dropped 10 decoy PSMs due to missing features
2:51:28.442199 INFO: Test AUC: 0.571
2:51:28.442199 INFO: Train AUC: 0.587
2:51:28.443711 INFO: AUC difference: 2.76%
2:51:28.757376 INFO: === FDR correction performed with classifier version 4 ===
2:51:28.773017 PROGRESS: ============================= Precursor FDR =============================
2:51:28.773017 PROGRESS: Total precursors accumulated: 676
2:51:28.773017 PROGRESS: Target precursors: 614 (90.83%)
2:51:28.773017 PROGRESS: Decoy precursors: 62 (9.17%)
2:51:28.773017 PROGRESS: 
2:51:28.773017 PROGRESS: Precursor Summary:
2:51:28.773017 PROGRESS: Channel   0:	 0.05 FDR:   448; 0.01 FDR:   313; 0.001 FDR:   193
2:51:28.773017 PROGRESS: 
2:51:28.773017 PROGRESS: Protein Summary:
2:51:28.788646 PROGRESS: Channel   0:	 0.05 FDR:   421; 0.01 FDR:   295; 0.001 FDR:   188
2:51:28.788646 PROGRESS: =========================================================================
2:51:28.804267 INFO: fragments_df_filtered: 1515
2:51:29.423082 INFO: calibration group: precursor, fitting rt estimator 
2:51:29.564539 INFO: calibration group: fragment, fitting mz estimator 
2:51:30.303595 INFO: calibration group: precursor, predicting mz
2:51:30.303595 WARNING: mz prediction was skipped as it has not been fitted yet
2:51:30.303595 INFO: calibration group: precursor, predicting rt
2:51:30.423513 INFO: calibration group: fragment, predicting mz
2:51:30.873930 INFO: === checking if optimization conditions were reached ===
2:51:30.873930 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:51:30.873930 INFO: ==============================================
2:51:30.873930 PROGRESS: Optimization finished for ms2_error.
2:51:31.453285 INFO: calibration group: precursor, predicting mz
2:51:31.453285 WARNING: mz prediction was skipped as it has not been fitted yet
2:51:31.453285 INFO: calibration group: precursor, predicting rt
2:51:31.577127 INFO: calibration group: fragment, predicting mz
2:51:32.047379 INFO: Starting optimization step 0.
2:51:32.047379 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:51:32.047379 PROGRESS: Extracting batch of 110601 precursors
2:51:32.110294 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:51:32.110294 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:51:32.125919 INFO: FWHM in RT is 17.09 seconds, sigma is 0.62
2:51:32.125919 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:51:32.125919 INFO: Starting candidate selection
2:53:34.929878 INFO: Starting candidate scoring
2:53:45.030562 INFO: Finished candidate processing
2:53:45.030562 INFO: Collecting candidate features
2:53:46.039983 WARNING: intensity_correlation has 13 NaNs ( 0.01 % out of 220908)
2:53:46.086857 INFO: Collecting fragment features
2:53:46.522138 INFO: Finished candidate scoring
2:53:46.862359 PROGRESS: === Extracted 220908 precursors and 1581510 fragments ===
2:53:46.863359 INFO: performing precursor FDR with 47 features
2:53:46.863359 INFO: Decoy channel: -1
2:53:46.863359 INFO: Competetive: True
2:53:47.286476 WARNING: dropped 6 target PSMs due to missing features
2:53:47.286476 WARNING: dropped 7 decoy PSMs due to missing features
2:53:55.082407 INFO: Test AUC: 0.578
2:53:55.082407 INFO: Train AUC: 0.592
2:53:55.082407 INFO: AUC difference: 2.28%
2:53:55.400604 INFO: === FDR correction performed with classifier version 5 ===
2:53:55.402607 PROGRESS: ============================= Precursor FDR =============================
2:53:55.403605 PROGRESS: Total precursors accumulated: 660
2:53:55.403605 PROGRESS: Target precursors: 600 (90.91%)
2:53:55.404606 PROGRESS: Decoy precursors: 60 (9.09%)
2:53:55.404606 PROGRESS: 
2:53:55.404606 PROGRESS: Precursor Summary:
2:53:55.409133 PROGRESS: Channel   0:	 0.05 FDR:   462; 0.01 FDR:   335; 0.001 FDR:   229
2:53:55.410151 PROGRESS: 
2:53:55.410151 PROGRESS: Protein Summary:
2:53:55.412244 PROGRESS: Channel   0:	 0.05 FDR:   434; 0.01 FDR:   314; 0.001 FDR:   218
2:53:55.412244 PROGRESS: =========================================================================
2:53:55.427888 INFO: fragments_df_filtered: 1536
2:53:56.067850 INFO: calibration group: precursor, fitting rt estimator 
2:53:56.224926 INFO: calibration group: fragment, fitting mz estimator 
2:53:56.955126 INFO: calibration group: precursor, predicting mz
2:53:56.955126 WARNING: mz prediction was skipped as it has not been fitted yet
2:53:56.955126 INFO: calibration group: precursor, predicting rt
2:53:57.080539 INFO: calibration group: fragment, predicting mz
2:53:57.531462 INFO: === checking if optimization conditions were reached ===
2:53:57.531462 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:53:57.531462 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 785.3768.
2:53:57.531462 INFO: ==============================================
2:53:57.531462 INFO: Starting optimization step 1.
2:53:57.531462 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:53:57.531462 PROGRESS: Extracting batch of 110601 precursors
2:53:57.612132 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:53:57.612132 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:53:57.612132 INFO: FWHM in RT is 17.03 seconds, sigma is 0.62
2:53:57.612132 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:53:57.612132 INFO: Starting candidate selection
2:54:26.460137 INFO: Starting candidate scoring
2:54:35.534166 INFO: Finished candidate processing
2:54:35.534166 INFO: Collecting candidate features
2:54:36.491544 WARNING: intensity_correlation has 291 NaNs ( 0.14 % out of 213236)
2:54:36.538418 INFO: Collecting fragment features
2:54:36.926938 INFO: Finished candidate scoring
2:54:37.232341 PROGRESS: === Extracted 213236 precursors and 1275890 fragments ===
2:54:37.232341 INFO: performing precursor FDR with 47 features
2:54:37.232341 INFO: Decoy channel: -1
2:54:37.232341 INFO: Competetive: True
2:54:37.657967 WARNING: dropped 162 target PSMs due to missing features
2:54:37.657967 WARNING: dropped 129 decoy PSMs due to missing features
2:54:42.931690 INFO: Test AUC: 0.562
2:54:42.931690 INFO: Train AUC: 0.579
2:54:42.931690 INFO: AUC difference: 2.99%
2:54:43.247609 INFO: === FDR correction performed with classifier version 5 ===
2:54:43.247609 PROGRESS: ============================= Precursor FDR =============================
2:54:43.247609 PROGRESS: Total precursors accumulated: 774
2:54:43.247609 PROGRESS: Target precursors: 703 (90.83%)
2:54:43.247609 PROGRESS: Decoy precursors: 71 (9.17%)
2:54:43.247609 PROGRESS: 
2:54:43.247609 PROGRESS: Precursor Summary:
2:54:43.267256 PROGRESS: Channel   0:	 0.05 FDR:   547; 0.01 FDR:   352; 0.001 FDR:   103
2:54:43.267256 PROGRESS: 
2:54:43.267256 PROGRESS: Protein Summary:
2:54:43.267256 PROGRESS: Channel   0:	 0.05 FDR:   514; 0.01 FDR:   332; 0.001 FDR:   101
2:54:43.267256 PROGRESS: =========================================================================
2:54:43.294928 INFO: fragments_df_filtered: 1535
2:54:43.900820 INFO: calibration group: precursor, fitting rt estimator 
2:54:44.059261 INFO: calibration group: fragment, fitting mz estimator 
2:54:44.801551 INFO: calibration group: precursor, predicting mz
2:54:44.801551 WARNING: mz prediction was skipped as it has not been fitted yet
2:54:44.801551 INFO: calibration group: precursor, predicting rt
2:54:44.928941 INFO: calibration group: fragment, predicting mz
2:54:45.383160 INFO: === checking if optimization conditions were reached ===
2:54:45.383160 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:54:45.383160 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 491.3373.
2:54:45.383160 INFO: ==============================================
2:54:45.383160 INFO: Starting optimization step 2.
2:54:45.383160 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:54:45.383160 PROGRESS: Extracting batch of 110601 precursors
2:54:45.470164 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:54:45.470164 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:54:45.470164 INFO: FWHM in RT is 16.91 seconds, sigma is 0.62
2:54:45.470164 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:54:45.470164 INFO: Starting candidate selection
2:55:00.820972 INFO: Starting candidate scoring
2:55:08.660118 INFO: Finished candidate processing
2:55:08.660118 INFO: Collecting candidate features
2:55:09.575974 WARNING: intensity_correlation has 309 NaNs ( 0.15 % out of 208144)
2:55:09.618106 INFO: Collecting fragment features
2:55:09.982151 INFO: Finished candidate scoring
2:55:10.300248 PROGRESS: === Extracted 208144 precursors and 1181631 fragments ===
2:55:10.300248 INFO: performing precursor FDR with 47 features
2:55:10.300248 INFO: Decoy channel: -1
2:55:10.300248 INFO: Competetive: True
2:55:10.731855 WARNING: dropped 178 target PSMs due to missing features
2:55:10.731855 WARNING: dropped 131 decoy PSMs due to missing features
2:55:18.048605 INFO: Test AUC: 0.558
2:55:18.048605 INFO: Train AUC: 0.577
2:55:18.048605 INFO: AUC difference: 3.19%
2:55:18.365097 INFO: === FDR correction performed with classifier version 5 ===
2:55:18.369089 PROGRESS: ============================= Precursor FDR =============================
2:55:18.369089 PROGRESS: Total precursors accumulated: 767
2:55:18.370090 PROGRESS: Target precursors: 695 (90.61%)
2:55:18.370090 PROGRESS: Decoy precursors: 72 (9.39%)
2:55:18.370090 PROGRESS: 
2:55:18.371091 PROGRESS: Precursor Summary:
2:55:18.372079 PROGRESS: Channel   0:	 0.05 FDR:   557; 0.01 FDR:   377; 0.001 FDR:   252
2:55:18.372079 PROGRESS: 
2:55:18.372079 PROGRESS: Protein Summary:
2:55:18.372079 PROGRESS: Channel   0:	 0.05 FDR:   524; 0.01 FDR:   355; 0.001 FDR:   240
2:55:18.372079 PROGRESS: =========================================================================
2:55:18.387104 INFO: fragments_df_filtered: 1596
2:55:18.986143 INFO: calibration group: precursor, fitting rt estimator 
2:55:19.143254 INFO: calibration group: fragment, fitting mz estimator 
2:55:19.941008 INFO: calibration group: precursor, predicting mz
2:55:19.941008 WARNING: mz prediction was skipped as it has not been fitted yet
2:55:19.941008 INFO: calibration group: precursor, predicting rt
2:55:20.062902 INFO: calibration group: fragment, predicting mz
2:55:20.526819 INFO: === checking if optimization conditions were reached ===
2:55:20.526819 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:55:20.526819 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 485.5165.
2:55:20.526819 INFO: ==============================================
2:55:20.526819 INFO: Starting optimization step 3.
2:55:20.526819 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:55:20.526819 PROGRESS: Extracting batch of 110601 precursors
2:55:20.605386 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:55:20.605386 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:55:20.605386 INFO: FWHM in RT is 16.93 seconds, sigma is 0.62
2:55:20.605386 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:55:20.605386 INFO: Starting candidate selection
2:55:35.698733 INFO: Starting candidate scoring
2:55:43.527884 INFO: Finished candidate processing
2:55:43.527884 INFO: Collecting candidate features
2:55:44.454657 WARNING: intensity_correlation has 312 NaNs ( 0.15 % out of 208384)
2:55:44.501543 INFO: Collecting fragment features
2:55:44.875348 INFO: Finished candidate scoring
2:55:45.179136 PROGRESS: === Extracted 208384 precursors and 1183148 fragments ===
2:55:45.179136 INFO: performing precursor FDR with 47 features
2:55:45.179136 INFO: Decoy channel: -1
2:55:45.179136 INFO: Competetive: True
2:55:45.596527 WARNING: dropped 170 target PSMs due to missing features
2:55:45.596527 WARNING: dropped 142 decoy PSMs due to missing features
2:55:52.754343 INFO: Test AUC: 0.556
2:55:52.754343 INFO: Train AUC: 0.576
2:55:52.754343 INFO: AUC difference: 3.39%
2:55:53.077365 INFO: === FDR correction performed with classifier version 5 ===
2:55:53.077365 PROGRESS: ============================= Precursor FDR =============================
2:55:53.077365 PROGRESS: Total precursors accumulated: 782
2:55:53.077365 PROGRESS: Target precursors: 713 (91.18%)
2:55:53.077365 PROGRESS: Decoy precursors: 69 (8.82%)
2:55:53.092991 PROGRESS: 
2:55:53.092991 PROGRESS: Precursor Summary:
2:55:53.092991 PROGRESS: Channel   0:	 0.05 FDR:   556; 0.01 FDR:   378; 0.001 FDR:   270
2:55:53.092991 PROGRESS: 
2:55:53.092991 PROGRESS: Protein Summary:
2:55:53.092991 PROGRESS: Channel   0:	 0.05 FDR:   520; 0.01 FDR:   355; 0.001 FDR:   257
2:55:53.092991 PROGRESS: =========================================================================
2:55:53.124239 INFO: fragments_df_filtered: 1610
2:55:53.736454 INFO: calibration group: precursor, fitting rt estimator 
2:55:53.889793 INFO: calibration group: fragment, fitting mz estimator 
2:55:54.682177 INFO: calibration group: precursor, predicting mz
2:55:54.682177 WARNING: mz prediction was skipped as it has not been fitted yet
2:55:54.682177 INFO: calibration group: precursor, predicting rt
2:55:54.817393 INFO: calibration group: fragment, predicting mz
2:55:55.267802 INFO: === checking if optimization conditions were reached ===
2:55:55.267802 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:55:55.283442 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 485.5165 found after 4 searches.
2:55:55.283442 INFO: ==============================================
2:55:55.283442 PROGRESS: Optimization finished for rt_error.
2:55:55.864665 INFO: calibration group: precursor, predicting mz
2:55:55.864665 WARNING: mz prediction was skipped as it has not been fitted yet
2:55:55.864665 INFO: calibration group: precursor, predicting rt
2:55:55.983478 INFO: calibration group: fragment, predicting mz
2:55:56.512497 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:55:56.528121 PROGRESS: ==============================================
2:55:56.528121 PROGRESS: ms2_error      : 10.0000
2:55:56.528121 PROGRESS: rt_error       : 485.5165
2:55:56.528121 PROGRESS: ==============================================
2:55:56.543745 INFO: calibration group: precursor, predicting mz
2:55:56.543745 WARNING: mz prediction was skipped as it has not been fitted yet
2:55:56.543745 INFO: calibration group: precursor, predicting rt
2:56:06.358941 INFO: calibration group: fragment, predicting mz
2:56:55.007019 PROGRESS: Extracting batch of 10640830 precursors
2:56:59.701874 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
2:56:59.701874 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
2:56:59.701874 INFO: FWHM in RT is 16.95 seconds, sigma is 0.62
2:56:59.701874 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
2:56:59.701874 INFO: Starting candidate selection
3:18:15.985690 INFO: Applying score cutoff of 68.0940083694458
3:18:16.465856 INFO: Removed 15536815 precursors with score below cutoff
3:18:19.574358 INFO: Starting candidate scoring
3:20:42.310696 INFO: Finished candidate processing
3:20:42.310696 INFO: Collecting candidate features
3:21:00.061808 INFO: Collecting fragment features
3:21:07.883496 INFO: Finished candidate scoring
3:21:16.884581 INFO: === FDR correction performed with classifier version 9 ===
3:21:16.884581 INFO: performing precursor FDR with 47 features
3:21:16.884581 INFO: Decoy channel: -1
3:21:16.884581 INFO: Competetive: True
3:23:28.102842 INFO: Test AUC: 0.581
3:23:28.102842 INFO: Train AUC: 0.583
3:23:28.102842 INFO: AUC difference: 0.41%
3:23:29.164620 INFO: Removing fragments below FDR threshold
3:23:29.915045 PROGRESS: ============================= Precursor FDR =============================
3:23:29.915045 PROGRESS: Total precursors accumulated: 51,312
3:23:29.915045 PROGRESS: Target precursors: 50,804 (99.01%)
3:23:29.916041 PROGRESS: Decoy precursors: 508 (0.99%)
3:23:29.916041 PROGRESS: 
3:23:29.916041 PROGRESS: Precursor Summary:
3:23:29.981894 PROGRESS: Channel   0:	 0.05 FDR: 50,804; 0.01 FDR: 50,804; 0.001 FDR: 36,176
3:23:29.981894 PROGRESS: 
3:23:29.981894 PROGRESS: Protein Summary:
3:23:30.045270 PROGRESS: Channel   0:	 0.05 FDR: 8,754; 0.01 FDR: 8,754; 0.001 FDR: 6,785
3:23:30.045270 PROGRESS: =========================================================================
3:23:31.276971 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
3:23:32.069190 PROGRESS: Loading raw file 4/6: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
3:23:32.069190 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01 at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
3:24:05.745998 INFO: Determining DIA cycle
3:24:05.781884 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
3:24:05.781884 INFO: Determining DIA cycle
3:24:05.820087 INFO: Found cycle with start 0.00 min and length 151.
3:24:05.936609 INFO: ============ Raw file stats ============
3:24:05.937609 INFO: RT (min)            : 0.0 - 150.0
3:24:05.937609 INFO: RT duration (sec)   : 8999.7
3:24:05.937609 INFO: RT duration (min)   : 150.0
3:24:05.937609 INFO: Cycle len (scans)   : 151
3:24:05.937609 INFO: Cycle len (sec)     : 5.83
3:24:05.937609 INFO: Number of cycles    : 1542
3:24:05.937609 INFO: MS2 range (m/z)     : 396.4 - 1004.7
3:24:05.937609 INFO: ========================================
3:24:08.569178 INFO: Initializing CalibrationManager
3:24:08.569178 INFO: Loading calibration config
3:24:08.571040 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)}]}]
3:24:08.571040 INFO: Calibration group :fragment, found 1 estimator(s)
3:24:08.571040 INFO: Calibration group :precursor, found 3 estimator(s)
3:24:08.571040 INFO: Disabling ion mobility calibration
3:24:08.571040 INFO: removed mobility estimator from group precursor
3:24:08.571040 INFO: Initializing OptimizationManager
3:24:08.571040 INFO: initial parameter: ms1_error = 30
3:24:08.571040 INFO: initial parameter: ms2_error = 30
3:24:08.571040 INFO: initial parameter: rt_error = 4500.00048828125
3:24:08.571040 INFO: initial parameter: mobility_error = 0.1
3:24:08.571040 INFO: initial parameter: column_type = library
3:24:08.571040 INFO: initial parameter: num_candidates = 1
3:24:08.571040 INFO: initial parameter: classifier_version = -1
3:24:08.571040 INFO: initial parameter: fwhm_rt = 5
3:24:08.571040 INFO: initial parameter: fwhm_mobility = 0.01
3:24:08.571040 INFO: initial parameter: score_cutoff = 0
3:24:08.571040 INFO: Initializing TimingManager
3:24:08.571040 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
3:24:08.571040 INFO: Initializing FDRManager
3:24:08.571040 INFO: Loading classifier store from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\classifier
3:24:10.892034 PROGRESS: 5,385,906 target precursors potentially observable (0 removed)
3:24:13.968780 PROGRESS: Starting initial search for precursors.
3:24:14.383351 INFO: Starting optimization step 0.
3:24:14.384332 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:24:14.384473 PROGRESS: Extracting batch of 15803 precursors
3:24:14.400144 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:24:14.400144 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:14.400144 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:24:14.400144 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:14.400144 INFO: Starting candidate selection
3:24:20.918459 INFO: Starting candidate scoring
3:24:21.240324 INFO: Finished candidate processing
3:24:21.240324 INFO: Collecting candidate features
3:24:21.298442 INFO: Collecting fragment features
3:24:21.317886 INFO: Finished candidate scoring
3:24:21.349878 PROGRESS: === Extracted 15796 precursors and 134316 fragments ===
3:24:21.350946 INFO: performing precursor FDR with 47 features
3:24:21.350946 INFO: Decoy channel: -1
3:24:21.350946 INFO: Competetive: True
3:24:21.573745 INFO: Test AUC: 0.514
3:24:21.573745 INFO: Train AUC: 0.517
3:24:21.573745 INFO: AUC difference: 0.59%
3:24:21.688654 INFO: === FDR correction performed with classifier version -1 ===
3:24:21.688654 PROGRESS: ============================= Precursor FDR =============================
3:24:21.688654 PROGRESS: Total precursors accumulated: 3
3:24:21.688654 PROGRESS: Target precursors: 3 (100.00%)
3:24:21.688654 PROGRESS: Decoy precursors: 0 (0.00%)
3:24:21.688654 PROGRESS: 
3:24:21.688654 PROGRESS: Precursor Summary:
3:24:21.688654 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
3:24:21.688654 PROGRESS: 
3:24:21.688654 PROGRESS: Protein Summary:
3:24:21.704216 PROGRESS: Channel   0:	 0.05 FDR:     3; 0.01 FDR:     3; 0.001 FDR:     3
3:24:21.704216 PROGRESS: =========================================================================
3:24:21.885293 INFO: Starting optimization step 1.
3:24:21.885293 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:24:21.885293 PROGRESS: Extracting batch of 31592 precursors
3:24:21.906366 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:24:21.907368 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:21.907368 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:24:21.907368 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:21.907368 INFO: Starting candidate selection
3:24:34.685515 INFO: Starting candidate scoring
3:24:35.282599 INFO: Finished candidate processing
3:24:35.282599 INFO: Collecting candidate features
3:24:35.380182 INFO: Collecting fragment features
3:24:35.427166 INFO: Finished candidate scoring
3:24:35.492651 PROGRESS: === Extracted 47342 precursors and 403372 fragments ===
3:24:35.508264 INFO: performing precursor FDR with 47 features
3:24:35.508264 INFO: Decoy channel: -1
3:24:35.508264 INFO: Competetive: True
3:24:36.459564 INFO: Test AUC: 0.565
3:24:36.459564 INFO: Train AUC: 0.565
3:24:36.459564 INFO: AUC difference: 0.00%
3:24:36.621321 INFO: === FDR correction performed with classifier version -1 ===
3:24:36.621321 PROGRESS: ============================= Precursor FDR =============================
3:24:36.621321 PROGRESS: Total precursors accumulated: 6
3:24:36.621321 PROGRESS: Target precursors: 6 (100.00%)
3:24:36.621321 PROGRESS: Decoy precursors: 0 (0.00%)
3:24:36.621321 PROGRESS: 
3:24:36.621321 PROGRESS: Precursor Summary:
3:24:36.621321 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
3:24:36.621321 PROGRESS: 
3:24:36.621321 PROGRESS: Protein Summary:
3:24:36.621321 PROGRESS: Channel   0:	 0.05 FDR:     6; 0.01 FDR:     6; 0.001 FDR:     6
3:24:36.621321 PROGRESS: =========================================================================
3:24:36.877681 INFO: Starting optimization step 2.
3:24:36.877681 PROGRESS: === Extracting elution groups 24000 to 56000 ===
3:24:36.877681 PROGRESS: Extracting batch of 63206 precursors
3:24:36.908874 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:24:36.908874 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:24:36.908874 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:24:36.908874 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:24:36.908874 INFO: Starting candidate selection
3:25:02.561800 INFO: Starting candidate scoring
3:25:03.755412 INFO: Finished candidate processing
3:25:03.755412 INFO: Collecting candidate features
3:25:03.975242 INFO: Collecting fragment features
3:25:04.085217 INFO: Finished candidate scoring
3:25:04.211439 PROGRESS: === Extracted 110493 precursors and 941603 fragments ===
3:25:04.258531 INFO: performing precursor FDR with 47 features
3:25:04.258531 INFO: Decoy channel: -1
3:25:04.258531 INFO: Competetive: True
3:25:06.553205 INFO: Test AUC: 0.560
3:25:06.553205 INFO: Train AUC: 0.579
3:25:06.553205 INFO: AUC difference: 3.37%
3:25:06.714933 INFO: === FDR correction performed with classifier version -1 ===
3:25:06.714933 PROGRESS: ============================= Precursor FDR =============================
3:25:06.714933 PROGRESS: Total precursors accumulated: 390
3:25:06.714933 PROGRESS: Target precursors: 357 (91.54%)
3:25:06.714933 PROGRESS: Decoy precursors: 33 (8.46%)
3:25:06.714933 PROGRESS: 
3:25:06.714933 PROGRESS: Precursor Summary:
3:25:06.714933 PROGRESS: Channel   0:	 0.05 FDR:   267; 0.01 FDR:   221; 0.001 FDR:    49
3:25:06.714933 PROGRESS: 
3:25:06.714933 PROGRESS: Protein Summary:
3:25:06.714933 PROGRESS: Channel   0:	 0.05 FDR:   257; 0.01 FDR:   216; 0.001 FDR:    49
3:25:06.714933 PROGRESS: =========================================================================
3:25:06.746297 INFO: fragments_df_filtered: 1596
3:25:07.102270 INFO: calibration group: precursor, fitting rt estimator 
3:25:07.196678 INFO: calibration group: fragment, fitting mz estimator 
3:25:07.742357 INFO: calibration group: precursor, predicting mz
3:25:07.742357 WARNING: mz prediction was skipped as it has not been fitted yet
3:25:07.742357 INFO: calibration group: precursor, predicting rt
3:25:07.822194 INFO: calibration group: fragment, predicting mz
3:25:08.130581 PROGRESS: Required number of precursors found. Starting search parameter optimization.
3:25:08.130581 INFO: Starting optimization step 3.
3:25:08.130581 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:25:08.130581 PROGRESS: Extracting batch of 110601 precursors
3:25:08.161833 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:25:08.161833 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:25:08.161833 INFO: FWHM in RT is 18.03 seconds, sigma is 0.66
3:25:08.161833 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:25:08.161833 INFO: Starting candidate selection
3:25:54.745620 INFO: Starting candidate scoring
3:25:59.383438 INFO: Finished candidate processing
3:25:59.383438 INFO: Collecting candidate features
3:25:59.972597 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 221021)
3:26:00.004316 INFO: Collecting fragment features
3:26:00.300216 INFO: Finished candidate scoring
3:26:00.471833 PROGRESS: === Extracted 221021 precursors and 1938830 fragments ===
3:26:00.471833 INFO: performing precursor FDR with 47 features
3:26:00.471833 INFO: Decoy channel: -1
3:26:00.471833 INFO: Competetive: True
3:26:00.723421 WARNING: dropped 1 target PSMs due to missing features
3:26:00.723421 WARNING: dropped 2 decoy PSMs due to missing features
3:26:05.016202 INFO: Test AUC: 0.569
3:26:05.016202 INFO: Train AUC: 0.583
3:26:05.016202 INFO: AUC difference: 2.38%
3:26:05.241029 INFO: === FDR correction performed with classifier version 2 ===
3:26:05.241029 PROGRESS: ============================= Precursor FDR =============================
3:26:05.241029 PROGRESS: Total precursors accumulated: 465
3:26:05.241029 PROGRESS: Target precursors: 426 (91.61%)
3:26:05.241029 PROGRESS: Decoy precursors: 39 (8.39%)
3:26:05.241029 PROGRESS: 
3:26:05.241029 PROGRESS: Precursor Summary:
3:26:05.241029 PROGRESS: Channel   0:	 0.05 FDR:   352; 0.01 FDR:   259; 0.001 FDR:   179
3:26:05.241029 PROGRESS: 
3:26:05.241029 PROGRESS: Protein Summary:
3:26:05.241029 PROGRESS: Channel   0:	 0.05 FDR:   336; 0.01 FDR:   251; 0.001 FDR:   176
3:26:05.241029 PROGRESS: =========================================================================
3:26:05.272277 INFO: fragments_df_filtered: 1718
3:26:05.638843 INFO: calibration group: precursor, fitting rt estimator 
3:26:05.717632 INFO: calibration group: fragment, fitting mz estimator 
3:26:06.412202 INFO: calibration group: precursor, predicting mz
3:26:06.414751 WARNING: mz prediction was skipped as it has not been fitted yet
3:26:06.414751 INFO: calibration group: precursor, predicting rt
3:26:06.479619 INFO: calibration group: fragment, predicting mz
3:26:06.798890 INFO: === checking if optimization conditions were reached ===
3:26:06.798890 PROGRESS: ❌ ms2_error      : 10.3235 > 10.0000 or insufficient steps taken.
3:26:06.798890 INFO: ==============================================
3:26:06.798890 INFO: Starting optimization step 4.
3:26:06.798890 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:26:06.798890 PROGRESS: Extracting batch of 110601 precursors
3:26:06.857399 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:26:06.857399 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:26:06.857399 INFO: FWHM in RT is 18.95 seconds, sigma is 0.69
3:26:06.857399 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:26:06.858428 INFO: Starting candidate selection
3:26:52.116708 INFO: Starting candidate scoring
3:26:56.329773 INFO: Finished candidate processing
3:26:56.329773 INFO: Collecting candidate features
3:26:56.947161 WARNING: intensity_correlation has 20 NaNs ( 0.01 % out of 220855)
3:26:56.963229 INFO: Collecting fragment features
3:26:57.231692 INFO: Finished candidate scoring
3:26:57.412495 PROGRESS: === Extracted 220855 precursors and 1598432 fragments ===
3:26:57.412495 INFO: performing precursor FDR with 47 features
3:26:57.412495 INFO: Decoy channel: -1
3:26:57.412495 INFO: Competetive: True
3:26:57.664794 WARNING: dropped 10 target PSMs due to missing features
3:26:57.664794 WARNING: dropped 10 decoy PSMs due to missing features
3:27:01.941835 INFO: Test AUC: 0.572
3:27:01.941835 INFO: Train AUC: 0.586
3:27:01.941835 INFO: AUC difference: 2.43%
3:27:02.130748 INFO: === FDR correction performed with classifier version 3 ===
3:27:02.146418 PROGRESS: ============================= Precursor FDR =============================
3:27:02.146418 PROGRESS: Total precursors accumulated: 617
3:27:02.146418 PROGRESS: Target precursors: 564 (91.41%)
3:27:02.146418 PROGRESS: Decoy precursors: 53 (8.59%)
3:27:02.146418 PROGRESS: 
3:27:02.146418 PROGRESS: Precursor Summary:
3:27:02.146418 PROGRESS: Channel   0:	 0.05 FDR:   439; 0.01 FDR:   306; 0.001 FDR:   136
3:27:02.146418 PROGRESS: 
3:27:02.146418 PROGRESS: Protein Summary:
3:27:02.146418 PROGRESS: Channel   0:	 0.05 FDR:   416; 0.01 FDR:   292; 0.001 FDR:   131
3:27:02.146418 PROGRESS: =========================================================================
3:27:02.161989 INFO: fragments_df_filtered: 1321
3:27:02.550304 INFO: calibration group: precursor, fitting rt estimator 
3:27:02.644589 INFO: calibration group: fragment, fitting mz estimator 
3:27:03.089583 INFO: calibration group: precursor, predicting mz
3:27:03.089583 WARNING: mz prediction was skipped as it has not been fitted yet
3:27:03.089583 INFO: calibration group: precursor, predicting rt
3:27:03.164617 INFO: calibration group: fragment, predicting mz
3:27:03.456578 INFO: === checking if optimization conditions were reached ===
3:27:03.456578 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
3:27:03.472139 INFO: ==============================================
3:27:03.472139 PROGRESS: Optimization finished for ms2_error.
3:27:03.805928 INFO: calibration group: precursor, predicting mz
3:27:03.805928 WARNING: mz prediction was skipped as it has not been fitted yet
3:27:03.805928 INFO: calibration group: precursor, predicting rt
3:27:03.906878 INFO: calibration group: fragment, predicting mz
3:27:04.206404 INFO: Starting optimization step 0.
3:27:04.206404 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:27:04.206404 PROGRESS: Extracting batch of 110601 precursors
3:27:04.253284 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:27:04.253284 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:27:04.253284 INFO: FWHM in RT is 17.59 seconds, sigma is 0.64
3:27:04.253284 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:27:04.253284 INFO: Starting candidate selection
3:27:49.428432 INFO: Starting candidate scoring
3:27:53.927391 INFO: Finished candidate processing
3:27:53.927391 INFO: Collecting candidate features
3:27:54.496225 WARNING: intensity_correlation has 15 NaNs ( 0.01 % out of 220870)
3:27:54.511850 INFO: Collecting fragment features
3:27:54.781838 INFO: Finished candidate scoring
3:27:54.952662 PROGRESS: === Extracted 220870 precursors and 1593687 fragments ===
3:27:54.952662 INFO: performing precursor FDR with 47 features
3:27:54.952662 INFO: Decoy channel: -1
3:27:54.952662 INFO: Competetive: True
3:27:55.193346 WARNING: dropped 7 target PSMs due to missing features
3:27:55.193346 WARNING: dropped 8 decoy PSMs due to missing features
3:27:59.662542 INFO: Test AUC: 0.572
3:27:59.662542 INFO: Train AUC: 0.591
3:27:59.662542 INFO: AUC difference: 3.35%
3:27:59.860881 INFO: === FDR correction performed with classifier version 4 ===
3:27:59.862876 PROGRESS: ============================= Precursor FDR =============================
3:27:59.862876 PROGRESS: Total precursors accumulated: 657
3:27:59.863876 PROGRESS: Target precursors: 604 (91.93%)
3:27:59.863876 PROGRESS: Decoy precursors: 53 (8.07%)
3:27:59.863876 PROGRESS: 
3:27:59.863876 PROGRESS: Precursor Summary:
3:27:59.866892 PROGRESS: Channel   0:	 0.05 FDR:   455; 0.01 FDR:   349; 0.001 FDR:   176
3:27:59.866892 PROGRESS: 
3:27:59.866892 PROGRESS: Protein Summary:
3:27:59.869884 PROGRESS: Channel   0:	 0.05 FDR:   431; 0.01 FDR:   332; 0.001 FDR:   171
3:27:59.869884 PROGRESS: =========================================================================
3:27:59.880400 INFO: fragments_df_filtered: 1433
3:28:00.260790 INFO: calibration group: precursor, fitting rt estimator 
3:28:00.354519 INFO: calibration group: fragment, fitting mz estimator 
3:28:00.840693 INFO: calibration group: precursor, predicting mz
3:28:00.840693 WARNING: mz prediction was skipped as it has not been fitted yet
3:28:00.840693 INFO: calibration group: precursor, predicting rt
3:28:00.909103 INFO: calibration group: fragment, predicting mz
3:28:01.238498 INFO: === checking if optimization conditions were reached ===
3:28:01.254115 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
3:28:01.254115 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 775.4718.
3:28:01.254115 INFO: ==============================================
3:28:01.254115 INFO: Starting optimization step 1.
3:28:01.254115 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:28:01.254115 PROGRESS: Extracting batch of 110601 precursors
3:28:01.285785 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:28:01.301434 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:28:01.301434 INFO: FWHM in RT is 17.37 seconds, sigma is 0.63
3:28:01.301434 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:28:01.301434 INFO: Starting candidate selection
3:28:11.710570 INFO: Starting candidate scoring
3:28:15.365312 INFO: Finished candidate processing
3:28:15.365312 INFO: Collecting candidate features
3:28:15.926876 WARNING: intensity_correlation has 339 NaNs ( 0.16 % out of 212512)
3:28:15.971735 INFO: Collecting fragment features
3:28:16.208675 INFO: Finished candidate scoring
3:28:16.399362 PROGRESS: === Extracted 212512 precursors and 1292818 fragments ===
3:28:16.401246 INFO: performing precursor FDR with 47 features
3:28:16.401246 INFO: Decoy channel: -1
3:28:16.401246 INFO: Competetive: True
3:28:16.650005 WARNING: dropped 166 target PSMs due to missing features
3:28:16.650005 WARNING: dropped 173 decoy PSMs due to missing features
3:28:20.669051 INFO: Test AUC: 0.561
3:28:20.669051 INFO: Train AUC: 0.577
3:28:20.669051 INFO: AUC difference: 2.69%
3:28:20.863167 INFO: === FDR correction performed with classifier version 4 ===
3:28:20.863167 PROGRESS: ============================= Precursor FDR =============================
3:28:20.863167 PROGRESS: Total precursors accumulated: 680
3:28:20.863167 PROGRESS: Target precursors: 622 (91.47%)
3:28:20.863167 PROGRESS: Decoy precursors: 58 (8.53%)
3:28:20.863167 PROGRESS: 
3:28:20.863167 PROGRESS: Precursor Summary:
3:28:20.863167 PROGRESS: Channel   0:	 0.05 FDR:   570; 0.01 FDR:   430; 0.001 FDR:   268
3:28:20.863167 PROGRESS: 
3:28:20.863167 PROGRESS: Protein Summary:
3:28:20.880401 PROGRESS: Channel   0:	 0.05 FDR:   538; 0.01 FDR:   409; 0.001 FDR:   257
3:28:20.880401 PROGRESS: =========================================================================
3:28:20.880401 INFO: fragments_df_filtered: 1509
3:28:21.259499 INFO: calibration group: precursor, fitting rt estimator 
3:28:21.368587 INFO: calibration group: fragment, fitting mz estimator 
3:28:21.846422 INFO: calibration group: precursor, predicting mz
3:28:21.846422 WARNING: mz prediction was skipped as it has not been fitted yet
3:28:21.846422 INFO: calibration group: precursor, predicting rt
3:28:21.910671 INFO: calibration group: fragment, predicting mz
3:28:22.227260 INFO: === checking if optimization conditions were reached ===
3:28:22.227260 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
3:28:22.227260 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 709.1761.
3:28:22.227260 INFO: ==============================================
3:28:22.227260 INFO: Starting optimization step 2.
3:28:22.227260 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:28:22.227260 PROGRESS: Extracting batch of 110601 precursors
3:28:22.274174 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:28:22.274174 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:28:22.274174 INFO: FWHM in RT is 17.46 seconds, sigma is 0.64
3:28:22.274174 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:28:22.274174 INFO: Starting candidate selection
3:28:31.866514 INFO: Starting candidate scoring
3:28:35.825042 INFO: Finished candidate processing
3:28:35.825042 INFO: Collecting candidate features
3:28:36.409602 WARNING: intensity_correlation has 347 NaNs ( 0.16 % out of 212008)
3:28:36.434091 INFO: Collecting fragment features
3:28:36.766126 INFO: Finished candidate scoring
3:28:36.992676 PROGRESS: === Extracted 212008 precursors and 1282442 fragments ===
3:28:36.992676 INFO: performing precursor FDR with 47 features
3:28:36.992676 INFO: Decoy channel: -1
3:28:36.992676 INFO: Competetive: True
3:28:37.395242 WARNING: dropped 171 target PSMs due to missing features
3:28:37.395242 WARNING: dropped 176 decoy PSMs due to missing features
3:28:41.428376 INFO: Test AUC: 0.561
3:28:41.428376 INFO: Train AUC: 0.577
3:28:41.428376 INFO: AUC difference: 2.84%
3:28:41.622426 INFO: === FDR correction performed with classifier version 4 ===
3:28:41.622426 PROGRESS: ============================= Precursor FDR =============================
3:28:41.622426 PROGRESS: Total precursors accumulated: 725
3:28:41.638173 PROGRESS: Target precursors: 663 (91.45%)
3:28:41.638173 PROGRESS: Decoy precursors: 62 (8.55%)
3:28:41.638173 PROGRESS: 
3:28:41.638173 PROGRESS: Precursor Summary:
3:28:41.638173 PROGRESS: Channel   0:	 0.05 FDR:   543; 0.01 FDR:   363; 0.001 FDR:   342
3:28:41.638173 PROGRESS: 
3:28:41.638173 PROGRESS: Protein Summary:
3:28:41.643754 PROGRESS: Channel   0:	 0.05 FDR:   511; 0.01 FDR:   347; 0.001 FDR:   327
3:28:41.643754 PROGRESS: =========================================================================
3:28:41.654361 INFO: fragments_df_filtered: 1471
3:28:42.022696 INFO: calibration group: precursor, fitting rt estimator 
3:28:42.149114 INFO: calibration group: fragment, fitting mz estimator 
3:28:42.662098 INFO: calibration group: precursor, predicting mz
3:28:42.662098 WARNING: mz prediction was skipped as it has not been fitted yet
3:28:42.662098 INFO: calibration group: precursor, predicting rt
3:28:42.745346 INFO: calibration group: fragment, predicting mz
3:28:43.049705 INFO: === checking if optimization conditions were reached ===
3:28:43.049705 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
3:28:43.049705 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 567.3309.
3:28:43.049705 INFO: ==============================================
3:28:43.049705 INFO: Starting optimization step 3.
3:28:43.049705 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:28:43.049705 PROGRESS: Extracting batch of 110601 precursors
3:28:43.096713 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:28:43.096713 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:28:43.096713 INFO: FWHM in RT is 17.50 seconds, sigma is 0.64
3:28:43.096713 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:28:43.096713 INFO: Starting candidate selection
3:28:52.102182 INFO: Starting candidate scoring
3:28:55.731591 INFO: Finished candidate processing
3:28:55.731591 INFO: Collecting candidate features
3:28:56.264787 WARNING: intensity_correlation has 401 NaNs ( 0.19 % out of 209743)
3:28:56.295135 INFO: Collecting fragment features
3:28:56.530399 INFO: Finished candidate scoring
3:28:56.690262 PROGRESS: === Extracted 209743 precursors and 1236833 fragments ===
3:28:56.690262 INFO: performing precursor FDR with 47 features
3:28:56.690262 INFO: Decoy channel: -1
3:28:56.690262 INFO: Competetive: True
3:28:56.935574 WARNING: dropped 202 target PSMs due to missing features
3:28:56.935574 WARNING: dropped 199 decoy PSMs due to missing features
3:29:01.062530 INFO: Test AUC: 0.549
3:29:01.062530 INFO: Train AUC: 0.576
3:29:01.062530 INFO: AUC difference: 4.65%
3:29:01.242776 INFO: === FDR correction performed with classifier version 4 ===
3:29:01.242776 PROGRESS: ============================= Precursor FDR =============================
3:29:01.242776 PROGRESS: Total precursors accumulated: 679
3:29:01.242776 PROGRESS: Target precursors: 619 (91.16%)
3:29:01.242776 PROGRESS: Decoy precursors: 60 (8.84%)
3:29:01.242776 PROGRESS: 
3:29:01.242776 PROGRESS: Precursor Summary:
3:29:01.258395 PROGRESS: Channel   0:	 0.05 FDR:   545; 0.01 FDR:   425; 0.001 FDR:   265
3:29:01.258395 PROGRESS: 
3:29:01.258395 PROGRESS: Protein Summary:
3:29:01.258395 PROGRESS: Channel   0:	 0.05 FDR:   513; 0.01 FDR:   406; 0.001 FDR:   253
3:29:01.258395 PROGRESS: =========================================================================
3:29:01.274521 INFO: fragments_df_filtered: 1548
3:29:01.604828 INFO: calibration group: precursor, fitting rt estimator 
3:29:01.698642 INFO: calibration group: fragment, fitting mz estimator 
3:29:02.228740 INFO: calibration group: precursor, predicting mz
3:29:02.228740 WARNING: mz prediction was skipped as it has not been fitted yet
3:29:02.228740 INFO: calibration group: precursor, predicting rt
3:29:02.291370 INFO: calibration group: fragment, predicting mz
3:29:02.600784 INFO: === checking if optimization conditions were reached ===
3:29:02.600784 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
3:29:02.600784 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 502.4584.
3:29:02.600784 INFO: ==============================================
3:29:02.600784 INFO: Starting optimization step 4.
3:29:02.600784 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:29:02.600784 PROGRESS: Extracting batch of 110601 precursors
3:29:02.648491 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:29:02.648491 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:29:02.648491 INFO: FWHM in RT is 17.50 seconds, sigma is 0.64
3:29:02.648491 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:29:02.648491 INFO: Starting candidate selection
3:29:10.694094 INFO: Starting candidate scoring
3:29:14.385178 INFO: Finished candidate processing
3:29:14.385178 INFO: Collecting candidate features
3:29:14.945870 WARNING: intensity_correlation has 399 NaNs ( 0.19 % out of 206582)
3:29:14.961482 INFO: Collecting fragment features
3:29:15.191972 INFO: Finished candidate scoring
3:29:15.380813 PROGRESS: === Extracted 206582 precursors and 1194494 fragments ===
3:29:15.380813 INFO: performing precursor FDR with 47 features
3:29:15.380813 INFO: Decoy channel: -1
3:29:15.380813 INFO: Competetive: True
3:29:15.618556 WARNING: dropped 204 target PSMs due to missing features
3:29:15.618556 WARNING: dropped 195 decoy PSMs due to missing features
3:29:19.648855 INFO: Test AUC: 0.555
3:29:19.648855 INFO: Train AUC: 0.575
3:29:19.648855 INFO: AUC difference: 3.46%
3:29:19.828396 INFO: === FDR correction performed with classifier version 4 ===
3:29:19.844572 PROGRESS: ============================= Precursor FDR =============================
3:29:19.844572 PROGRESS: Total precursors accumulated: 720
3:29:19.844572 PROGRESS: Target precursors: 658 (91.39%)
3:29:19.845628 PROGRESS: Decoy precursors: 62 (8.61%)
3:29:19.845628 PROGRESS: 
3:29:19.845628 PROGRESS: Precursor Summary:
3:29:19.848619 PROGRESS: Channel   0:	 0.05 FDR:   567; 0.01 FDR:   422; 0.001 FDR:   319
3:29:19.849614 PROGRESS: 
3:29:19.849614 PROGRESS: Protein Summary:
3:29:19.852617 PROGRESS: Channel   0:	 0.05 FDR:   533; 0.01 FDR:   403; 0.001 FDR:   307
3:29:19.852617 PROGRESS: =========================================================================
3:29:19.861805 INFO: fragments_df_filtered: 1541
3:29:20.217807 INFO: calibration group: precursor, fitting rt estimator 
3:29:20.328711 INFO: calibration group: fragment, fitting mz estimator 
3:29:20.913064 INFO: calibration group: precursor, predicting mz
3:29:20.913064 WARNING: mz prediction was skipped as it has not been fitted yet
3:29:20.913064 INFO: calibration group: precursor, predicting rt
3:29:21.007451 INFO: calibration group: fragment, predicting mz
3:29:21.306510 INFO: === checking if optimization conditions were reached ===
3:29:21.322185 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
3:29:21.325432 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 506.7820.
3:29:21.325432 INFO: ==============================================
3:29:21.325432 INFO: Starting optimization step 5.
3:29:21.326330 PROGRESS: === Extracting elution groups 0 to 56000 ===
3:29:21.326330 PROGRESS: Extracting batch of 110601 precursors
3:29:21.362552 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:29:21.362552 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:29:21.362552 INFO: FWHM in RT is 17.45 seconds, sigma is 0.63
3:29:21.362552 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:29:21.362552 INFO: Starting candidate selection
3:29:29.432432 INFO: Starting candidate scoring
3:29:33.044792 INFO: Finished candidate processing
3:29:33.044792 INFO: Collecting candidate features
3:29:33.588964 WARNING: intensity_correlation has 422 NaNs ( 0.20 % out of 207346)
3:29:33.604070 INFO: Collecting fragment features
3:29:33.843008 INFO: Finished candidate scoring
3:29:34.005927 PROGRESS: === Extracted 207346 precursors and 1201338 fragments ===
3:29:34.005927 INFO: performing precursor FDR with 47 features
3:29:34.005927 INFO: Decoy channel: -1
3:29:34.005927 INFO: Competetive: True
3:29:34.242413 WARNING: dropped 210 target PSMs due to missing features
3:29:34.242413 WARNING: dropped 212 decoy PSMs due to missing features
3:29:38.228483 INFO: Test AUC: 0.556
3:29:38.228483 INFO: Train AUC: 0.576
3:29:38.228483 INFO: AUC difference: 3.37%
3:29:38.428942 INFO: === FDR correction performed with classifier version 4 ===
3:29:38.428942 PROGRESS: ============================= Precursor FDR =============================
3:29:38.428942 PROGRESS: Total precursors accumulated: 725
3:29:38.428942 PROGRESS: Target precursors: 661 (91.17%)
3:29:38.428942 PROGRESS: Decoy precursors: 64 (8.83%)
3:29:38.428942 PROGRESS: 
3:29:38.428942 PROGRESS: Precursor Summary:
3:29:38.428942 PROGRESS: Channel   0:	 0.05 FDR:   569; 0.01 FDR:   428; 0.001 FDR:   357
3:29:38.428942 PROGRESS: 
3:29:38.428942 PROGRESS: Protein Summary:
3:29:38.428942 PROGRESS: Channel   0:	 0.05 FDR:   536; 0.01 FDR:   407; 0.001 FDR:   340
3:29:38.428942 PROGRESS: =========================================================================
3:29:38.443948 INFO: fragments_df_filtered: 1549
3:29:38.827265 INFO: calibration group: precursor, fitting rt estimator 
3:29:38.930249 INFO: calibration group: fragment, fitting mz estimator 
3:29:39.489418 INFO: calibration group: precursor, predicting mz
3:29:39.489418 WARNING: mz prediction was skipped as it has not been fitted yet
3:29:39.489418 INFO: calibration group: precursor, predicting rt
3:29:39.572623 INFO: calibration group: fragment, predicting mz
3:29:39.890755 INFO: === checking if optimization conditions were reached ===
3:29:39.890755 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
3:29:39.890755 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 502.4584 found after 6 searches.
3:29:39.890755 INFO: ==============================================
3:29:39.890755 PROGRESS: Optimization finished for rt_error.
3:29:40.231545 INFO: calibration group: precursor, predicting mz
3:29:40.236106 WARNING: mz prediction was skipped as it has not been fitted yet
3:29:40.236106 INFO: calibration group: precursor, predicting rt
3:29:40.325008 INFO: calibration group: fragment, predicting mz
3:29:40.680946 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
3:29:40.680946 PROGRESS: ==============================================
3:29:40.680946 PROGRESS: ms2_error      : 10.0000
3:29:40.680946 PROGRESS: rt_error       : 502.4584
3:29:40.680946 PROGRESS: ==============================================
3:29:40.775300 INFO: calibration group: precursor, predicting mz
3:29:40.775300 WARNING: mz prediction was skipped as it has not been fitted yet
3:29:40.775300 INFO: calibration group: precursor, predicting rt
3:29:47.621953 INFO: calibration group: fragment, predicting mz
3:30:19.235584 PROGRESS: Extracting batch of 10640830 precursors
3:30:21.515821 INFO: Duty cycle consists of 151 frames, 5.83 seconds cycle time
3:30:21.515821 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:30:21.515821 INFO: FWHM in RT is 17.45 seconds, sigma is 0.63
3:30:21.515821 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
3:30:21.515821 INFO: Starting candidate selection
3:42:52.046100 INFO: Applying score cutoff of 71.76372343444824
3:42:52.515627 INFO: Removed 15821556 precursors with score below cutoff
3:42:55.629804 INFO: Starting candidate scoring
3:44:41.865476 INFO: Finished candidate processing
3:44:41.865476 INFO: Collecting candidate features
3:44:57.433254 INFO: Collecting fragment features
3:45:04.306756 INFO: Finished candidate scoring
3:45:14.295992 INFO: === FDR correction performed with classifier version 9 ===
3:45:14.295992 INFO: performing precursor FDR with 47 features
3:45:14.295992 INFO: Decoy channel: -1
3:45:14.295992 INFO: Competetive: True
3:47:26.100909 INFO: Test AUC: 0.581
3:47:26.100909 INFO: Train AUC: 0.585
3:47:26.100909 INFO: AUC difference: 0.57%
3:47:27.138561 INFO: Removing fragments below FDR threshold
3:47:27.956106 PROGRESS: ============================= Precursor FDR =============================
3:47:27.956106 PROGRESS: Total precursors accumulated: 47,388
3:47:27.957058 PROGRESS: Target precursors: 46,919 (99.01%)
3:47:27.957058 PROGRESS: Decoy precursors: 469 (0.99%)
3:47:27.957058 PROGRESS: 
3:47:27.957058 PROGRESS: Precursor Summary:
3:47:28.027256 PROGRESS: Channel   0:	 0.05 FDR: 46,919; 0.01 FDR: 46,919; 0.001 FDR: 33,220
3:47:28.027256 PROGRESS: 
3:47:28.027256 PROGRESS: Protein Summary:
3:47:28.104326 PROGRESS: Channel   0:	 0.05 FDR: 8,540; 0.01 FDR: 8,540; 0.001 FDR: 6,724
3:47:28.104326 PROGRESS: =========================================================================
3:47:29.132055 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
3:47:30.008942 PROGRESS: Loading raw file 5/6: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
3:47:30.008942 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02 at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
3:48:03.969436 INFO: Determining DIA cycle
3:48:03.984949 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
3:48:04.000583 INFO: Determining DIA cycle
3:48:04.031836 INFO: Found cycle with start 0.00 min and length 151.
3:48:04.204646 INFO: ============ Raw file stats ============
3:48:04.204646 INFO: RT (min)            : 0.0 - 150.0
3:48:04.204646 INFO: RT duration (sec)   : 8999.7
3:48:04.204646 INFO: RT duration (min)   : 150.0
3:48:04.204646 INFO: Cycle len (scans)   : 151
3:48:04.204646 INFO: Cycle len (sec)     : 5.84
3:48:04.204646 INFO: Number of cycles    : 1541
3:48:04.204646 INFO: MS2 range (m/z)     : 396.4 - 1004.7
3:48:04.204646 INFO: ========================================
3:48:06.282202 INFO: Initializing CalibrationManager
3:48:06.282202 INFO: Loading calibration config
3:48:06.282202 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)}]}]
3:48:06.282202 INFO: Calibration group :fragment, found 1 estimator(s)
3:48:06.282202 INFO: Calibration group :precursor, found 3 estimator(s)
3:48:06.282202 INFO: Disabling ion mobility calibration
3:48:06.282202 INFO: removed mobility estimator from group precursor
3:48:06.282202 INFO: Initializing OptimizationManager
3:48:06.282202 INFO: initial parameter: ms1_error = 30
3:48:06.282202 INFO: initial parameter: ms2_error = 30
3:48:06.282202 INFO: initial parameter: rt_error = 4499.99609375
3:48:06.282202 INFO: initial parameter: mobility_error = 0.1
3:48:06.282202 INFO: initial parameter: column_type = library
3:48:06.282202 INFO: initial parameter: num_candidates = 1
3:48:06.282202 INFO: initial parameter: classifier_version = -1
3:48:06.282202 INFO: initial parameter: fwhm_rt = 5
3:48:06.282202 INFO: initial parameter: fwhm_mobility = 0.01
3:48:06.282202 INFO: initial parameter: score_cutoff = 0
3:48:06.282202 INFO: Initializing TimingManager
3:48:06.282202 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
3:48:06.282202 INFO: Initializing FDRManager
3:48:06.282202 INFO: Loading classifier store from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\classifier
3:48:08.693701 PROGRESS: 5,385,906 target precursors potentially observable (0 removed)
3:48:11.804444 PROGRESS: Starting initial search for precursors.
3:48:12.224418 INFO: Starting optimization step 0.
3:48:12.224418 PROGRESS: === Extracting elution groups 0 to 8000 ===
3:48:12.240035 PROGRESS: Extracting batch of 15803 precursors
3:48:12.240035 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:48:12.240035 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:12.240035 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:48:12.240035 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:48:12.240035 INFO: Starting candidate selection
3:48:18.933222 INFO: Starting candidate scoring
3:48:19.247665 INFO: Finished candidate processing
3:48:19.247665 INFO: Collecting candidate features
3:48:19.301342 INFO: Collecting fragment features
3:48:19.331178 INFO: Finished candidate scoring
3:48:19.346809 PROGRESS: === Extracted 15796 precursors and 140000 fragments ===
3:48:19.346809 INFO: performing precursor FDR with 47 features
3:48:19.346809 INFO: Decoy channel: -1
3:48:19.346809 INFO: Competetive: True
3:48:19.679298 INFO: Test AUC: 0.505
3:48:19.679298 INFO: Train AUC: 0.518
3:48:19.679298 INFO: AUC difference: 2.57%
3:48:19.830780 INFO: === FDR correction performed with classifier version -1 ===
3:48:19.855878 PROGRESS: ============================= Precursor FDR =============================
3:48:19.855878 PROGRESS: Total precursors accumulated: 7,994
3:48:19.855878 PROGRESS: Target precursors: 4,255 (53.23%)
3:48:19.856879 PROGRESS: Decoy precursors: 3,739 (46.77%)
3:48:19.856879 PROGRESS: 
3:48:19.856879 PROGRESS: Precursor Summary:
3:48:19.859878 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:48:19.859878 PROGRESS: 
3:48:19.859878 PROGRESS: Protein Summary:
3:48:19.862870 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:48:19.862870 PROGRESS: =========================================================================
3:48:20.042053 INFO: Starting optimization step 1.
3:48:20.042053 PROGRESS: === Extracting elution groups 8000 to 24000 ===
3:48:20.057692 PROGRESS: Extracting batch of 31592 precursors
3:48:20.073302 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:48:20.073302 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:20.073302 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:48:20.073302 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:48:20.073302 INFO: Starting candidate selection
3:48:32.999630 INFO: Starting candidate scoring
3:48:33.600217 INFO: Finished candidate processing
3:48:33.600217 INFO: Collecting candidate features
3:48:33.704426 INFO: Collecting fragment features
3:48:33.767487 INFO: Finished candidate scoring
3:48:33.850956 PROGRESS: === Extracted 47346 precursors and 420294 fragments ===
3:48:33.872508 INFO: performing precursor FDR with 47 features
3:48:33.872508 INFO: Decoy channel: -1
3:48:33.872508 INFO: Competetive: True
3:48:34.769949 INFO: Test AUC: 0.500
3:48:34.769949 INFO: Train AUC: 0.500
3:48:34.769949 INFO: AUC difference: 0.01%
3:48:34.910119 INFO: === FDR correction performed with classifier version -1 ===
3:48:34.911123 PROGRESS: ============================= Precursor FDR =============================
3:48:34.912133 PROGRESS: Total precursors accumulated: 1
3:48:34.912133 PROGRESS: Target precursors: 1 (100.00%)
3:48:34.912133 PROGRESS: Decoy precursors: 0 (0.00%)
3:48:34.912133 PROGRESS: 
3:48:34.912133 PROGRESS: Precursor Summary:
3:48:34.913227 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:48:34.913227 PROGRESS: 
3:48:34.913227 PROGRESS: Protein Summary:
3:48:34.914232 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:48:34.914232 PROGRESS: =========================================================================
3:48:35.179654 INFO: Starting optimization step 2.
3:48:35.179654 PROGRESS: === Extracting elution groups 24000 to 56000 ===
3:48:35.195349 PROGRESS: Extracting batch of 63206 precursors
3:48:35.210993 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:48:35.210993 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:48:35.210993 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:48:35.210993 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:48:35.210993 INFO: Starting candidate selection
3:49:01.262119 INFO: Starting candidate scoring
3:49:02.460432 INFO: Finished candidate processing
3:49:02.460432 INFO: Collecting candidate features
3:49:02.666720 INFO: Collecting fragment features
3:49:02.784045 INFO: Finished candidate scoring
3:49:02.926306 PROGRESS: === Extracted 110506 precursors and 981591 fragments ===
3:49:02.959493 INFO: performing precursor FDR with 47 features
3:49:02.959493 INFO: Decoy channel: -1
3:49:02.959493 INFO: Competetive: True
3:49:05.128046 INFO: Test AUC: 0.558
3:49:05.128046 INFO: Train AUC: 0.564
3:49:05.128046 INFO: AUC difference: 1.14%
3:49:05.305170 INFO: === FDR correction performed with classifier version -1 ===
3:49:05.305170 PROGRESS: ============================= Precursor FDR =============================
3:49:05.305170 PROGRESS: Total precursors accumulated: 1
3:49:05.305170 PROGRESS: Target precursors: 1 (100.00%)
3:49:05.305170 PROGRESS: Decoy precursors: 0 (0.00%)
3:49:05.305170 PROGRESS: 
3:49:05.305170 PROGRESS: Precursor Summary:
3:49:05.305170 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:49:05.305170 PROGRESS: 
3:49:05.320799 PROGRESS: Protein Summary:
3:49:05.322894 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
3:49:05.322894 PROGRESS: =========================================================================
3:49:05.738785 INFO: Starting optimization step 3.
3:49:05.738785 PROGRESS: === Extracting elution groups 56000 to 120000 ===
3:49:05.738785 PROGRESS: Extracting batch of 126403 precursors
3:49:05.790329 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:49:05.790329 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:49:05.790329 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:49:05.790329 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:49:05.790329 INFO: Starting candidate selection
3:49:57.368807 INFO: Starting candidate scoring
3:50:00.390762 INFO: Finished candidate processing
3:50:00.390762 INFO: Collecting candidate features
3:50:00.856245 INFO: Collecting fragment features
3:50:01.040956 INFO: Finished candidate scoring
3:50:01.277043 PROGRESS: === Extracted 236806 precursors and 2102170 fragments ===
3:50:01.359091 INFO: performing precursor FDR with 47 features
3:50:01.360086 INFO: Decoy channel: -1
3:50:01.360086 INFO: Competetive: True
3:50:06.265032 INFO: Test AUC: 0.564
3:50:06.265032 INFO: Train AUC: 0.577
3:50:06.265032 INFO: AUC difference: 2.23%
3:50:06.448990 INFO: === FDR correction performed with classifier version -1 ===
3:50:06.464715 PROGRESS: ============================= Precursor FDR =============================
3:50:06.464715 PROGRESS: Total precursors accumulated: 8
3:50:06.464715 PROGRESS: Target precursors: 8 (100.00%)
3:50:06.464715 PROGRESS: Decoy precursors: 0 (0.00%)
3:50:06.464715 PROGRESS: 
3:50:06.464715 PROGRESS: Precursor Summary:
3:50:06.464715 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
3:50:06.464715 PROGRESS: 
3:50:06.464715 PROGRESS: Protein Summary:
3:50:06.464715 PROGRESS: Channel   0:	 0.05 FDR:     8; 0.01 FDR:     8; 0.001 FDR:     8
3:50:06.464715 PROGRESS: =========================================================================
3:50:07.094409 INFO: Starting optimization step 4.
3:50:07.094409 PROGRESS: === Extracting elution groups 120000 to 248000 ===
3:50:07.094409 PROGRESS: Extracting batch of 252949 precursors
3:50:07.169147 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:50:07.177658 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:50:07.177658 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:50:07.177658 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:50:07.177658 INFO: Starting candidate selection
3:53:13.585517 INFO: Starting candidate scoring
3:53:19.768247 INFO: Finished candidate processing
3:53:19.768247 INFO: Collecting candidate features
3:53:20.570453 INFO: Collecting fragment features
3:53:20.929494 INFO: Finished candidate scoring
3:53:21.456831 PROGRESS: === Extracted 489535 precursors and 4342589 fragments ===
3:53:21.572178 INFO: performing precursor FDR with 47 features
3:53:21.572178 INFO: Decoy channel: -1
3:53:21.572178 INFO: Competetive: True
3:53:32.011382 INFO: Test AUC: 0.570
3:53:32.011382 INFO: Train AUC: 0.583
3:53:32.011382 INFO: AUC difference: 2.39%
3:53:32.295205 INFO: === FDR correction performed with classifier version -1 ===
3:53:32.295205 PROGRESS: ============================= Precursor FDR =============================
3:53:32.295205 PROGRESS: Total precursors accumulated: 2
3:53:32.295205 PROGRESS: Target precursors: 2 (100.00%)
3:53:32.295205 PROGRESS: Decoy precursors: 0 (0.00%)
3:53:32.295205 PROGRESS: 
3:53:32.295205 PROGRESS: Precursor Summary:
3:53:32.295205 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
3:53:32.295205 PROGRESS: 
3:53:32.295205 PROGRESS: Protein Summary:
3:53:32.295205 PROGRESS: Channel   0:	 0.05 FDR:     2; 0.01 FDR:     2; 0.001 FDR:     2
3:53:32.295205 PROGRESS: =========================================================================
3:53:33.343378 INFO: Starting optimization step 5.
3:53:33.343378 PROGRESS: === Extracting elution groups 248000 to 504000 ===
3:53:33.344525 PROGRESS: Extracting batch of 505702 precursors
3:53:33.491797 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:53:33.491797 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:53:33.491797 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:53:33.491797 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:53:33.491797 INFO: Starting candidate selection
3:56:59.527295 INFO: Starting candidate scoring
3:57:08.796430 INFO: Finished candidate processing
3:57:08.796430 INFO: Collecting candidate features
3:57:10.373145 INFO: Collecting fragment features
3:57:11.062182 INFO: Finished candidate scoring
3:57:12.030791 PROGRESS: === Extracted 994819 precursors and 8825768 fragments ===
3:57:12.235042 INFO: performing precursor FDR with 47 features
3:57:12.235042 INFO: Decoy channel: -1
3:57:12.235042 INFO: Competetive: True
3:57:34.441232 INFO: Test AUC: 0.575
3:57:34.441232 INFO: Train AUC: 0.583
3:57:34.441232 INFO: AUC difference: 1.37%
3:57:34.840238 INFO: === FDR correction performed with classifier version -1 ===
3:57:34.856246 PROGRESS: ============================= Precursor FDR =============================
3:57:34.856614 PROGRESS: Total precursors accumulated: 4,561
3:57:34.856614 PROGRESS: Target precursors: 4,163 (91.27%)
3:57:34.856614 PROGRESS: Decoy precursors: 398 (8.73%)
3:57:34.856614 PROGRESS: 
3:57:34.857616 PROGRESS: Precursor Summary:
3:57:34.859622 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:57:34.859622 PROGRESS: 
3:57:34.859622 PROGRESS: Protein Summary:
3:57:34.861622 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
3:57:34.861622 PROGRESS: =========================================================================
3:57:36.717051 INFO: Starting optimization step 6.
3:57:36.717051 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
3:57:36.717051 PROGRESS: Extracting batch of 1011429 precursors
3:57:37.007010 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
3:57:37.007010 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
3:57:37.007010 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
3:57:37.007010 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
3:57:37.007010 INFO: Starting candidate selection
4:04:26.008527 INFO: Starting candidate scoring
4:04:46.193240 INFO: Finished candidate processing
4:04:46.193240 INFO: Collecting candidate features
4:04:49.261396 INFO: Collecting fragment features
4:04:50.606736 INFO: Finished candidate scoring
4:04:52.872104 PROGRESS: === Extracted 2005479 precursors and 17793117 fragments ===
4:04:53.283998 INFO: performing precursor FDR with 47 features
4:04:53.283998 INFO: Decoy channel: -1
4:04:53.283998 INFO: Competetive: True
4:05:50.922648 INFO: Test AUC: 0.578
4:05:50.922648 INFO: Train AUC: 0.583
4:05:50.922648 INFO: AUC difference: 0.91%
4:05:52.481908 INFO: === FDR correction performed with classifier version -1 ===
4:05:52.497468 PROGRESS: ============================= Precursor FDR =============================
4:05:52.497468 PROGRESS: Total precursors accumulated: 11,011
4:05:52.497468 PROGRESS: Target precursors: 10,054 (91.31%)
4:05:52.497468 PROGRESS: Decoy precursors: 957 (8.69%)
4:05:52.497468 PROGRESS: 
4:05:52.497468 PROGRESS: Precursor Summary:
4:05:52.497468 PROGRESS: Channel   0:	 0.05 FDR: 8,238; 0.01 FDR:    18; 0.001 FDR:    18
4:05:52.497468 PROGRESS: 
4:05:52.497468 PROGRESS: Protein Summary:
4:05:52.513054 PROGRESS: Channel   0:	 0.05 FDR: 4,305; 0.01 FDR:    18; 0.001 FDR:    18
4:05:52.513054 PROGRESS: =========================================================================
4:05:55.765723 INFO: Starting optimization step 7.
4:05:55.765723 PROGRESS: === Extracting elution groups 1016000 to 2040000 ===
4:05:55.765723 PROGRESS: Extracting batch of 2023223 precursors
4:05:56.246990 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
4:05:56.246990 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:05:56.246990 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
4:05:56.246990 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
4:05:56.246990 INFO: Starting candidate selection
4:19:44.827657 INFO: Starting candidate scoring
4:20:29.157004 INFO: Finished candidate processing
4:20:29.157004 INFO: Collecting candidate features
4:20:35.368240 INFO: Collecting fragment features
4:20:38.152928 INFO: Finished candidate scoring
4:20:43.583602 PROGRESS: === Extracted 4027142 precursors and 35721118 fragments ===
4:20:44.356248 INFO: performing precursor FDR with 47 features
4:20:44.356248 INFO: Decoy channel: -1
4:20:44.356248 INFO: Competetive: True
4:23:27.332571 INFO: Test AUC: 0.581
4:23:27.332571 INFO: Train AUC: 0.585
4:23:27.332571 INFO: AUC difference: 0.66%
4:23:28.462856 INFO: === FDR correction performed with classifier version -1 ===
4:23:28.478599 PROGRESS: ============================= Precursor FDR =============================
4:23:28.478599 PROGRESS: Total precursors accumulated: 24,390
4:23:28.478599 PROGRESS: Target precursors: 22,324 (91.53%)
4:23:28.478599 PROGRESS: Decoy precursors: 2,066 (8.47%)
4:23:28.478599 PROGRESS: 
4:23:28.478599 PROGRESS: Precursor Summary:
4:23:28.478599 PROGRESS: Channel   0:	 0.05 FDR: 18,425; 0.01 FDR:     5; 0.001 FDR:     5
4:23:28.478599 PROGRESS: 
4:23:28.478599 PROGRESS: Protein Summary:
4:23:28.494123 PROGRESS: Channel   0:	 0.05 FDR: 6,864; 0.01 FDR:     5; 0.001 FDR:     5
4:23:28.494123 PROGRESS: =========================================================================
4:23:34.617695 INFO: Starting optimization step 8.
4:23:34.617695 PROGRESS: === Extracting elution groups 2040000 to 4088000 ===
4:23:34.617695 PROGRESS: Extracting batch of 4046233 precursors
4:23:35.587129 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
4:23:35.587129 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
4:23:35.587129 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
4:23:35.587129 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
4:23:35.587129 INFO: Starting candidate selection
4:51:13.569319 INFO: Starting candidate scoring
4:52:32.715981 INFO: Finished candidate processing
4:52:32.715981 INFO: Collecting candidate features
4:52:44.097289 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 4043123)
4:52:44.584640 INFO: Collecting fragment features
4:52:50.077013 INFO: Finished candidate scoring
4:53:02.324225 PROGRESS: === Extracted 8070265 precursors and 71585809 fragments ===
4:53:03.890074 INFO: performing precursor FDR with 47 features
4:53:03.890074 INFO: Decoy channel: -1
4:53:03.890074 INFO: Competetive: True
4:53:13.433232 WARNING: dropped 1 decoy PSMs due to missing features
5:00:22.495732 INFO: Test AUC: 0.584
5:00:22.495732 INFO: Train AUC: 0.586
5:00:22.495732 INFO: AUC difference: 0.44%
5:00:24.471616 INFO: === FDR correction performed with classifier version -1 ===
5:00:24.518498 PROGRESS: ============================= Precursor FDR =============================
5:00:24.518498 PROGRESS: Total precursors accumulated: 55,700
5:00:24.518498 PROGRESS: Target precursors: 51,246 (92.00%)
5:00:24.518498 PROGRESS: Decoy precursors: 4,454 (8.00%)
5:00:24.518498 PROGRESS: 
5:00:24.518498 PROGRESS: Precursor Summary:
5:00:24.550353 PROGRESS: Channel   0:	 0.05 FDR: 42,389; 0.01 FDR: 31,311; 0.001 FDR:    18
5:00:24.550353 PROGRESS: 
5:00:24.550353 PROGRESS: Protein Summary:
5:00:24.588136 PROGRESS: Channel   0:	 0.05 FDR: 11,412; 0.01 FDR: 7,167; 0.001 FDR:    18
5:00:24.588136 PROGRESS: =========================================================================
5:00:25.972640 INFO: fragments_df_filtered: 5000
5:00:27.155870 INFO: calibration group: precursor, fitting rt estimator 
5:03:43.109938 INFO: calibration group: fragment, fitting mz estimator 
5:03:48.183292 INFO: calibration group: precursor, predicting mz
5:03:48.183292 WARNING: mz prediction was skipped as it has not been fitted yet
5:03:48.183292 INFO: calibration group: precursor, predicting rt
5:03:48.277683 INFO: calibration group: fragment, predicting mz
5:03:48.589065 PROGRESS: Required number of precursors found. Starting search parameter optimization.
5:03:48.589065 INFO: Starting optimization step 9.
5:03:48.589065 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:03:48.589065 PROGRESS: Extracting batch of 110601 precursors
5:03:48.620329 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:03:48.620329 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:03:48.620329 INFO: FWHM in RT is 20.16 seconds, sigma is 0.73
5:03:48.620329 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:03:48.620329 INFO: Starting candidate selection
5:04:36.259161 INFO: Starting candidate scoring
5:04:40.740236 INFO: Finished candidate processing
5:04:40.740236 INFO: Collecting candidate features
5:04:41.406961 INFO: Collecting fragment features
5:04:41.710428 INFO: Finished candidate scoring
5:04:41.892083 PROGRESS: === Extracted 221021 precursors and 2022896 fragments ===
5:04:41.892083 INFO: performing precursor FDR with 47 features
5:04:41.892083 INFO: Decoy channel: -1
5:04:41.892083 INFO: Competetive: True
5:04:46.615846 INFO: Test AUC: 0.580
5:04:46.615846 INFO: Train AUC: 0.604
5:04:46.615846 INFO: AUC difference: 4.07%
5:04:46.804670 INFO: === FDR correction performed with classifier version 8 ===
5:04:46.804670 PROGRESS: ============================= Precursor FDR =============================
5:04:46.804670 PROGRESS: Total precursors accumulated: 1,094
5:04:46.804670 PROGRESS: Target precursors: 1,001 (91.50%)
5:04:46.804670 PROGRESS: Decoy precursors: 93 (8.50%)
5:04:46.804670 PROGRESS: 
5:04:46.804670 PROGRESS: Precursor Summary:
5:04:46.804670 PROGRESS: Channel   0:	 0.05 FDR:   711; 0.01 FDR:   423; 0.001 FDR:   102
5:04:46.804670 PROGRESS: 
5:04:46.804670 PROGRESS: Protein Summary:
5:04:46.804670 PROGRESS: Channel   0:	 0.05 FDR:   676; 0.01 FDR:   395; 0.001 FDR:   101
5:04:46.804670 PROGRESS: =========================================================================
5:04:46.835613 INFO: fragments_df_filtered: 2124
5:04:47.218327 INFO: calibration group: precursor, fitting rt estimator 
5:04:47.346510 INFO: calibration group: fragment, fitting mz estimator 
5:04:48.029680 INFO: calibration group: precursor, predicting mz
5:04:48.029680 WARNING: mz prediction was skipped as it has not been fitted yet
5:04:48.029680 INFO: calibration group: precursor, predicting rt
5:04:48.108471 INFO: calibration group: fragment, predicting mz
5:04:48.433949 INFO: === checking if optimization conditions were reached ===
5:04:48.436044 PROGRESS: ❌ ms2_error      : 11.0692 > 10.0000 or insufficient steps taken.
5:04:48.437042 INFO: ==============================================
5:04:48.437042 INFO: Starting optimization step 10.
5:04:48.438067 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:04:48.438067 PROGRESS: Extracting batch of 110601 precursors
5:04:48.482691 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:04:48.482691 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:04:48.482691 INFO: FWHM in RT is 20.58 seconds, sigma is 0.75
5:04:48.482691 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:04:48.482691 INFO: Starting candidate selection
5:05:36.533197 INFO: Starting candidate scoring
5:05:40.832665 INFO: Finished candidate processing
5:05:40.832665 INFO: Collecting candidate features
5:05:41.419218 WARNING: intensity_correlation has 24 NaNs ( 0.01 % out of 220971)
5:05:41.469177 INFO: Collecting fragment features
5:05:41.737778 INFO: Finished candidate scoring
5:05:41.918758 PROGRESS: === Extracted 220971 precursors and 1727973 fragments ===
5:05:41.918758 INFO: performing precursor FDR with 47 features
5:05:41.918758 INFO: Decoy channel: -1
5:05:41.918758 INFO: Competetive: True
5:05:42.201468 WARNING: dropped 14 target PSMs due to missing features
5:05:42.201468 WARNING: dropped 10 decoy PSMs due to missing features
5:05:46.498267 INFO: Test AUC: 0.579
5:05:46.498267 INFO: Train AUC: 0.605
5:05:46.498267 INFO: AUC difference: 4.26%
5:05:46.707488 INFO: === FDR correction performed with classifier version 9 ===
5:05:46.723060 PROGRESS: ============================= Precursor FDR =============================
5:05:46.723060 PROGRESS: Total precursors accumulated: 1,195
5:05:46.723060 PROGRESS: Target precursors: 1,091 (91.30%)
5:05:46.723060 PROGRESS: Decoy precursors: 104 (8.70%)
5:05:46.723060 PROGRESS: 
5:05:46.723060 PROGRESS: Precursor Summary:
5:05:46.723060 PROGRESS: Channel   0:	 0.05 FDR:   669; 0.01 FDR:    25; 0.001 FDR:    25
5:05:46.723060 PROGRESS: 
5:05:46.723060 PROGRESS: Protein Summary:
5:05:46.723060 PROGRESS: Channel   0:	 0.05 FDR:   625; 0.01 FDR:    25; 0.001 FDR:    25
5:05:46.723060 PROGRESS: =========================================================================
5:05:47.121607 INFO: calibration group: precursor, predicting mz
5:05:47.121607 WARNING: mz prediction was skipped as it has not been fitted yet
5:05:47.121607 INFO: calibration group: precursor, predicting rt
5:05:47.216017 INFO: calibration group: fragment, predicting mz
5:05:47.589236 INFO: === skipping optimization until target number of precursors are found ===
5:05:47.589236 INFO: Starting optimization step 11.
5:05:47.589236 PROGRESS: === Extracting elution groups 56000 to 120000 ===
5:05:47.589236 PROGRESS: Extracting batch of 126403 precursors
5:05:47.636233 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:05:47.636233 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:05:47.636233 INFO: FWHM in RT is 20.58 seconds, sigma is 0.75
5:05:47.636233 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:05:47.636233 INFO: Starting candidate selection
5:06:42.590212 INFO: Starting candidate scoring
5:06:48.328036 INFO: Finished candidate processing
5:06:48.328714 INFO: Collecting candidate features
5:06:48.992639 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 252558)
5:06:49.039604 INFO: Collecting fragment features
5:06:49.350310 INFO: Finished candidate scoring
5:06:49.826465 PROGRESS: === Extracted 473529 precursors and 3702615 fragments ===
5:06:49.914889 INFO: performing precursor FDR with 47 features
5:06:49.914889 INFO: Decoy channel: -1
5:06:49.914889 INFO: Competetive: True
5:06:50.584319 WARNING: dropped 15 target PSMs due to missing features
5:06:50.584319 WARNING: dropped 19 decoy PSMs due to missing features
5:06:59.860958 INFO: Test AUC: 0.581
5:06:59.860958 INFO: Train AUC: 0.597
5:06:59.860958 INFO: AUC difference: 2.66%
5:07:00.149875 INFO: === FDR correction performed with classifier version 9 ===
5:07:00.149875 PROGRESS: ============================= Precursor FDR =============================
5:07:00.149875 PROGRESS: Total precursors accumulated: 2,268
5:07:00.149875 PROGRESS: Target precursors: 2,068 (91.18%)
5:07:00.149875 PROGRESS: Decoy precursors: 200 (8.82%)
5:07:00.149875 PROGRESS: 
5:07:00.149875 PROGRESS: Precursor Summary:
5:07:00.165400 PROGRESS: Channel   0:	 0.05 FDR: 1,472; 0.01 FDR:    16; 0.001 FDR:    16
5:07:00.165400 PROGRESS: 
5:07:00.165400 PROGRESS: Protein Summary:
5:07:00.165400 PROGRESS: Channel   0:	 0.05 FDR: 1,289; 0.01 FDR:    16; 0.001 FDR:    16
5:07:00.165400 PROGRESS: =========================================================================
5:07:00.772092 INFO: calibration group: precursor, predicting mz
5:07:00.772092 WARNING: mz prediction was skipped as it has not been fitted yet
5:07:00.772092 INFO: calibration group: precursor, predicting rt
5:07:00.925964 INFO: calibration group: fragment, predicting mz
5:07:01.669287 INFO: === skipping optimization until target number of precursors are found ===
5:07:01.669287 INFO: Starting optimization step 12.
5:07:01.669287 PROGRESS: === Extracting elution groups 120000 to 248000 ===
5:07:01.669287 PROGRESS: Extracting batch of 252949 precursors
5:07:01.751354 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:07:01.751354 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:07:01.751354 INFO: FWHM in RT is 20.58 seconds, sigma is 0.75
5:07:01.751354 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:07:01.751354 INFO: Starting candidate selection
5:08:50.801695 INFO: Starting candidate scoring
5:09:00.868805 INFO: Finished candidate processing
5:09:00.868805 INFO: Collecting candidate features
5:09:02.163646 WARNING: intensity_correlation has 32 NaNs ( 0.01 % out of 505393)
5:09:02.242186 INFO: Collecting fragment features
5:09:02.858696 INFO: Finished candidate scoring
5:09:03.891350 PROGRESS: === Extracted 978922 precursors and 7648191 fragments ===
5:09:04.083084 INFO: performing precursor FDR with 47 features
5:09:04.083084 INFO: Decoy channel: -1
5:09:04.083084 INFO: Competetive: True
5:09:05.314866 WARNING: dropped 30 target PSMs due to missing features
5:09:05.314866 WARNING: dropped 36 decoy PSMs due to missing features
5:09:25.367485 INFO: Test AUC: 0.580
5:09:25.367485 INFO: Train AUC: 0.592
5:09:25.367485 INFO: AUC difference: 1.91%
5:09:25.778651 INFO: === FDR correction performed with classifier version 9 ===
5:09:25.782782 PROGRESS: ============================= Precursor FDR =============================
5:09:25.782782 PROGRESS: Total precursors accumulated: 4,147
5:09:25.782782 PROGRESS: Target precursors: 3,777 (91.08%)
5:09:25.782782 PROGRESS: Decoy precursors: 370 (8.92%)
5:09:25.782782 PROGRESS: 
5:09:25.782782 PROGRESS: Precursor Summary:
5:09:25.782782 PROGRESS: Channel   0:	 0.05 FDR: 2,968; 0.01 FDR: 2,082; 0.001 FDR:    26
5:09:25.782782 PROGRESS: 
5:09:25.782782 PROGRESS: Protein Summary:
5:09:25.782782 PROGRESS: Channel   0:	 0.05 FDR: 2,284; 0.01 FDR: 1,573; 0.001 FDR:    26
5:09:25.782782 PROGRESS: =========================================================================
5:09:25.917300 INFO: fragments_df_filtered: 5000
5:09:26.315704 INFO: calibration group: precursor, fitting rt estimator 
5:09:27.026527 INFO: calibration group: fragment, fitting mz estimator 
5:09:31.981184 INFO: calibration group: precursor, predicting mz
5:09:31.981184 WARNING: mz prediction was skipped as it has not been fitted yet
5:09:31.981184 INFO: calibration group: precursor, predicting rt
5:09:32.012483 INFO: calibration group: fragment, predicting mz
5:09:32.153787 INFO: === checking if optimization conditions were reached ===
5:09:32.153787 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
5:09:32.153787 INFO: ==============================================
5:09:32.153787 PROGRESS: Optimization finished for ms2_error.
5:09:32.416651 INFO: calibration group: precursor, predicting mz
5:09:32.416651 WARNING: mz prediction was skipped as it has not been fitted yet
5:09:32.416651 INFO: calibration group: precursor, predicting rt
5:09:32.469966 INFO: calibration group: fragment, predicting mz
5:09:32.622745 INFO: Starting optimization step 0.
5:09:32.622745 PROGRESS: === Extracting elution groups 0 to 24000 ===
5:09:32.622745 PROGRESS: Extracting batch of 47395 precursors
5:09:32.653985 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:09:32.653985 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:09:32.653985 INFO: FWHM in RT is 18.60 seconds, sigma is 0.68
5:09:32.653985 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:09:32.653985 INFO: Starting candidate selection
5:09:53.043477 INFO: Starting candidate scoring
5:09:54.839886 INFO: Finished candidate processing
5:09:54.839886 INFO: Collecting candidate features
5:09:55.109200 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 94685)
5:09:55.121811 INFO: Collecting fragment features
5:09:55.253283 INFO: Finished candidate scoring
5:09:55.330939 PROGRESS: === Extracted 94685 precursors and 723840 fragments ===
5:09:55.330939 INFO: performing precursor FDR with 47 features
5:09:55.330939 INFO: Decoy channel: -1
5:09:55.330939 INFO: Competetive: True
5:09:55.445283 WARNING: dropped 4 target PSMs due to missing features
5:09:55.445283 WARNING: dropped 5 decoy PSMs due to missing features
5:09:57.312817 INFO: Test AUC: 0.582
5:09:57.312817 INFO: Train AUC: 0.617
5:09:57.312817 INFO: AUC difference: 5.70%
5:09:57.312817 WARNING: AUC difference > 5%. This may indicate overfitting.
5:09:57.493365 INFO: === FDR correction performed with classifier version 12 ===
5:09:57.493365 PROGRESS: ============================= Precursor FDR =============================
5:09:57.493365 PROGRESS: Total precursors accumulated: 500
5:09:57.493365 PROGRESS: Target precursors: 454 (90.80%)
5:09:57.493365 PROGRESS: Decoy precursors: 46 (9.20%)
5:09:57.493365 PROGRESS: 
5:09:57.493365 PROGRESS: Precursor Summary:
5:09:57.508929 PROGRESS: Channel   0:	 0.05 FDR:   306; 0.01 FDR:     8; 0.001 FDR:     8
5:09:57.508929 PROGRESS: 
5:09:57.508929 PROGRESS: Protein Summary:
5:09:57.513558 PROGRESS: Channel   0:	 0.05 FDR:   299; 0.01 FDR:     8; 0.001 FDR:     8
5:09:57.513558 PROGRESS: =========================================================================
5:09:57.807229 INFO: calibration group: precursor, predicting mz
5:09:57.807229 WARNING: mz prediction was skipped as it has not been fitted yet
5:09:57.807229 INFO: calibration group: precursor, predicting rt
5:09:57.844492 INFO: calibration group: fragment, predicting mz
5:09:58.022489 INFO: === skipping optimization until target number of precursors are found ===
5:09:58.022489 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
5:09:58.022489 INFO: Starting optimization step 1.
5:09:58.022489 PROGRESS: === Extracting elution groups 24000 to 56000 ===
5:09:58.022489 PROGRESS: Extracting batch of 63206 precursors
5:09:58.053749 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:09:58.053749 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:09:58.053749 INFO: FWHM in RT is 18.60 seconds, sigma is 0.68
5:09:58.053749 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:09:58.053749 INFO: Starting candidate selection
5:10:24.708491 INFO: Starting candidate scoring
5:10:27.329509 INFO: Finished candidate processing
5:10:27.329509 INFO: Collecting candidate features
5:10:27.720134 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 126271)
5:10:27.735875 INFO: Collecting fragment features
5:10:27.921354 INFO: Finished candidate scoring
5:10:28.142365 PROGRESS: === Extracted 220956 precursors and 1690081 fragments ===
5:10:28.189902 INFO: performing precursor FDR with 47 features
5:10:28.189902 INFO: Decoy channel: -1
5:10:28.189902 INFO: Competetive: True
5:10:28.503910 WARNING: dropped 8 target PSMs due to missing features
5:10:28.503910 WARNING: dropped 10 decoy PSMs due to missing features
5:10:32.690402 INFO: Test AUC: 0.583
5:10:32.690402 INFO: Train AUC: 0.610
5:10:32.690402 INFO: AUC difference: 4.47%
5:10:32.903702 INFO: === FDR correction performed with classifier version 12 ===
5:10:32.903702 PROGRESS: ============================= Precursor FDR =============================
5:10:32.903702 PROGRESS: Total precursors accumulated: 1,271
5:10:32.903702 PROGRESS: Target precursors: 1,156 (90.95%)
5:10:32.903702 PROGRESS: Decoy precursors: 115 (9.05%)
5:10:32.903702 PROGRESS: 
5:10:32.903702 PROGRESS: Precursor Summary:
5:10:32.919364 PROGRESS: Channel   0:	 0.05 FDR:   694; 0.01 FDR:     0; 0.001 FDR:     0
5:10:32.919364 PROGRESS: 
5:10:33.595497 PROGRESS: Protein Summary:
5:10:33.611886 PROGRESS: Channel   0:	 0.05 FDR:   658; 0.01 FDR:     0; 0.001 FDR:     0
5:10:33.611886 PROGRESS: =========================================================================
5:10:34.013096 INFO: calibration group: precursor, predicting mz
5:10:34.013096 WARNING: mz prediction was skipped as it has not been fitted yet
5:10:34.013096 INFO: calibration group: precursor, predicting rt
5:10:34.107487 INFO: calibration group: fragment, predicting mz
5:10:34.497389 INFO: === skipping optimization until target number of precursors are found ===
5:10:34.497389 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
5:10:34.497389 INFO: Starting optimization step 2.
5:10:34.497389 PROGRESS: === Extracting elution groups 56000 to 120000 ===
5:10:34.497389 PROGRESS: Extracting batch of 126403 precursors
5:10:34.559896 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:10:34.559896 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:10:34.559896 INFO: FWHM in RT is 18.60 seconds, sigma is 0.68
5:10:34.559896 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:10:34.559896 INFO: Starting candidate selection
5:11:27.681057 INFO: Starting candidate scoring
5:11:32.910857 INFO: Finished candidate processing
5:11:32.910857 INFO: Collecting candidate features
5:11:33.581756 WARNING: intensity_correlation has 11 NaNs ( 0.00 % out of 252534)
5:11:33.617320 INFO: Collecting fragment features
5:11:33.923198 INFO: Finished candidate scoring
5:11:34.375980 PROGRESS: === Extracted 473490 precursors and 3620315 fragments ===
5:11:34.472459 INFO: performing precursor FDR with 47 features
5:11:34.484019 INFO: Decoy channel: -1
5:11:34.484019 INFO: Competetive: True
5:11:35.129361 WARNING: dropped 13 target PSMs due to missing features
5:11:35.129361 WARNING: dropped 16 decoy PSMs due to missing features
5:11:44.944175 INFO: Test AUC: 0.583
5:11:44.944175 INFO: Train AUC: 0.600
5:11:44.945076 INFO: AUC difference: 2.93%
5:11:45.235751 INFO: === FDR correction performed with classifier version 12 ===
5:11:45.235751 PROGRESS: ============================= Precursor FDR =============================
5:11:45.235751 PROGRESS: Total precursors accumulated: 2,507
5:11:45.235751 PROGRESS: Target precursors: 2,286 (91.18%)
5:11:45.235751 PROGRESS: Decoy precursors: 221 (8.82%)
5:11:45.235751 PROGRESS: 
5:11:45.235751 PROGRESS: Precursor Summary:
5:11:45.235751 PROGRESS: Channel   0:	 0.05 FDR: 1,615; 0.01 FDR:    14; 0.001 FDR:    14
5:11:45.235751 PROGRESS: 
5:11:45.235751 PROGRESS: Protein Summary:
5:11:45.251312 PROGRESS: Channel   0:	 0.05 FDR: 1,426; 0.01 FDR:    14; 0.001 FDR:    14
5:11:45.251312 PROGRESS: =========================================================================
5:11:45.848536 INFO: calibration group: precursor, predicting mz
5:11:45.848536 WARNING: mz prediction was skipped as it has not been fitted yet
5:11:45.848536 INFO: calibration group: precursor, predicting rt
5:11:46.012591 INFO: calibration group: fragment, predicting mz
5:11:46.780814 INFO: === skipping optimization until target number of precursors are found ===
5:11:46.780814 PROGRESS: === Optimization of rt_error has been skipped 3 time(s); maximum number is 1 ===
5:11:46.780814 INFO: Starting optimization step 3.
5:11:46.780814 PROGRESS: === Extracting elution groups 120000 to 248000 ===
5:11:46.780814 PROGRESS: Extracting batch of 252949 precursors
5:11:46.863863 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:11:46.863863 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:11:46.863863 INFO: FWHM in RT is 18.60 seconds, sigma is 0.68
5:11:46.863863 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:11:46.863863 INFO: Starting candidate selection
5:13:34.600728 INFO: Starting candidate scoring
5:13:44.145182 INFO: Finished candidate processing
5:13:44.145182 INFO: Collecting candidate features
5:13:45.461369 WARNING: intensity_correlation has 38 NaNs ( 0.01 % out of 505314)
5:13:45.522079 INFO: Collecting fragment features
5:13:46.117092 INFO: Finished candidate scoring
5:13:47.206459 PROGRESS: === Extracted 978804 precursors and 7478696 fragments ===
5:13:47.406770 INFO: performing precursor FDR with 47 features
5:13:47.406770 INFO: Decoy channel: -1
5:13:47.406770 INFO: Competetive: True
5:13:48.642700 WARNING: dropped 30 target PSMs due to missing features
5:13:48.642700 WARNING: dropped 37 decoy PSMs due to missing features
5:14:08.186169 INFO: Test AUC: 0.582
5:14:08.186169 INFO: Train AUC: 0.595
5:14:08.186169 INFO: AUC difference: 2.12%
5:14:08.590128 INFO: === FDR correction performed with classifier version 12 ===
5:14:08.621338 PROGRESS: ============================= Precursor FDR =============================
5:14:08.621338 PROGRESS: Total precursors accumulated: 4,512
5:14:08.621338 PROGRESS: Target precursors: 4,127 (91.47%)
5:14:08.621338 PROGRESS: Decoy precursors: 385 (8.53%)
5:14:08.621338 PROGRESS: 
5:14:08.621338 PROGRESS: Precursor Summary:
5:14:08.632861 PROGRESS: Channel   0:	 0.05 FDR: 3,173; 0.01 FDR:    21; 0.001 FDR:    21
5:14:08.632861 PROGRESS: 
5:14:08.632861 PROGRESS: Protein Summary:
5:14:08.637372 PROGRESS: Channel   0:	 0.05 FDR: 2,485; 0.01 FDR:    21; 0.001 FDR:    21
5:14:08.637372 PROGRESS: =========================================================================
5:14:09.697987 INFO: calibration group: precursor, predicting mz
5:14:09.697987 WARNING: mz prediction was skipped as it has not been fitted yet
5:14:09.697987 INFO: calibration group: precursor, predicting rt
5:14:10.045724 INFO: calibration group: fragment, predicting mz
5:14:11.499672 INFO: === skipping optimization until target number of precursors are found ===
5:14:11.499672 PROGRESS: === Optimization of rt_error has been skipped 4 time(s); maximum number is 1 ===
5:14:11.499672 INFO: Starting optimization step 4.
5:14:11.499672 PROGRESS: === Extracting elution groups 248000 to 504000 ===
5:14:11.499672 PROGRESS: Extracting batch of 505702 precursors
5:14:11.664550 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:14:11.664550 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:14:11.664550 INFO: FWHM in RT is 18.60 seconds, sigma is 0.68
5:14:11.664550 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:14:11.664550 INFO: Starting candidate selection
5:17:45.628786 INFO: Starting candidate scoring
5:18:14.832692 INFO: Finished candidate processing
5:18:14.832692 INFO: Collecting candidate features
5:18:17.511494 WARNING: intensity_correlation has 77 NaNs ( 0.01 % out of 1010278)
5:18:17.637102 INFO: Collecting fragment features
5:18:18.826221 INFO: Finished candidate scoring
5:18:21.136510 PROGRESS: === Extracted 1989082 precursors and 15193952 fragments ===
5:18:21.493900 INFO: performing precursor FDR with 47 features
5:18:21.493900 INFO: Decoy channel: -1
5:18:21.493900 INFO: Competetive: True
5:18:23.917124 WARNING: dropped 73 target PSMs due to missing features
5:18:23.917124 WARNING: dropped 71 decoy PSMs due to missing features
5:19:15.454779 INFO: Test AUC: 0.584
5:19:15.454779 INFO: Train AUC: 0.590
5:19:15.454779 INFO: AUC difference: 0.91%
5:19:16.122868 INFO: === FDR correction performed with classifier version 12 ===
5:19:16.138608 PROGRESS: ============================= Precursor FDR =============================
5:19:16.138608 PROGRESS: Total precursors accumulated: 8,488
5:19:16.138608 PROGRESS: Target precursors: 7,799 (91.88%)
5:19:16.138608 PROGRESS: Decoy precursors: 689 (8.12%)
5:19:16.138608 PROGRESS: 
5:19:16.138608 PROGRESS: Precursor Summary:
5:19:16.154135 PROGRESS: Channel   0:	 0.05 FDR: 6,348; 0.01 FDR: 4,259; 0.001 FDR:    18
5:19:16.154135 PROGRESS: 
5:19:16.154135 PROGRESS: Protein Summary:
5:19:16.169761 PROGRESS: Channel   0:	 0.05 FDR: 4,207; 0.01 FDR: 2,665; 0.001 FDR:    18
5:19:16.169761 PROGRESS: =========================================================================
5:19:16.467549 INFO: fragments_df_filtered: 5000
5:19:16.924461 INFO: calibration group: precursor, fitting rt estimator 
5:19:20.430622 INFO: calibration group: fragment, fitting mz estimator 
5:19:25.408916 INFO: calibration group: precursor, predicting mz
5:19:25.408916 WARNING: mz prediction was skipped as it has not been fitted yet
5:19:25.408916 INFO: calibration group: precursor, predicting rt
5:19:25.440573 INFO: calibration group: fragment, predicting mz
5:19:25.566091 INFO: === checking if optimization conditions were reached ===
5:19:25.566091 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
5:19:25.581744 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 831.3454.
5:19:25.581744 INFO: ==============================================
5:19:25.581744 INFO: Starting optimization step 5.
5:19:25.581744 PROGRESS: === Extracting elution groups 0 to 24000 ===
5:19:25.581744 PROGRESS: Extracting batch of 47395 precursors
5:19:25.597336 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:19:25.597336 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:19:25.597336 INFO: FWHM in RT is 18.35 seconds, sigma is 0.67
5:19:25.597336 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:19:25.597336 INFO: Starting candidate selection
5:19:30.425687 INFO: Starting candidate scoring
5:19:32.151570 INFO: Finished candidate processing
5:19:32.151570 INFO: Collecting candidate features
5:19:32.447825 WARNING: intensity_correlation has 113 NaNs ( 0.12 % out of 92640)
5:19:32.465179 INFO: Collecting fragment features
5:19:32.590410 INFO: Finished candidate scoring
5:19:32.653309 PROGRESS: === Extracted 92640 precursors and 612976 fragments ===
5:19:32.653309 INFO: performing precursor FDR with 47 features
5:19:32.653309 INFO: Decoy channel: -1
5:19:32.653309 INFO: Competetive: True
5:19:32.779607 WARNING: dropped 58 target PSMs due to missing features
5:19:32.779607 WARNING: dropped 55 decoy PSMs due to missing features
5:19:34.574569 INFO: Test AUC: 0.567
5:19:34.574569 INFO: Train AUC: 0.599
5:19:34.574569 INFO: AUC difference: 5.29%
5:19:34.574569 WARNING: AUC difference > 5%. This may indicate overfitting.
5:19:35.729481 INFO: === FDR correction performed with classifier version 12 ===
5:19:35.729481 PROGRESS: ============================= Precursor FDR =============================
5:19:35.729481 PROGRESS: Total precursors accumulated: 471
5:19:35.729481 PROGRESS: Target precursors: 428 (90.87%)
5:19:35.729481 PROGRESS: Decoy precursors: 43 (9.13%)
5:19:35.729481 PROGRESS: 
5:19:35.729481 PROGRESS: Precursor Summary:
5:19:35.729481 PROGRESS: Channel   0:	 0.05 FDR:   281; 0.01 FDR:    36; 0.001 FDR:    36
5:19:35.729481 PROGRESS: 
5:19:35.729481 PROGRESS: Protein Summary:
5:19:35.729481 PROGRESS: Channel   0:	 0.05 FDR:   273; 0.01 FDR:    36; 0.001 FDR:    36
5:19:35.729481 PROGRESS: =========================================================================
5:19:36.135617 INFO: calibration group: precursor, predicting mz
5:19:36.135617 WARNING: mz prediction was skipped as it has not been fitted yet
5:19:36.135617 INFO: calibration group: precursor, predicting rt
5:19:36.183235 INFO: calibration group: fragment, predicting mz
5:19:36.377051 INFO: === skipping optimization until target number of precursors are found ===
5:19:36.378115 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
5:19:36.378115 INFO: Starting optimization step 6.
5:19:36.378115 PROGRESS: === Extracting elution groups 24000 to 56000 ===
5:19:36.378115 PROGRESS: Extracting batch of 63206 precursors
5:19:36.408505 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:19:36.408505 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:19:36.409539 INFO: FWHM in RT is 18.35 seconds, sigma is 0.67
5:19:36.409539 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:19:36.409539 INFO: Starting candidate selection
5:19:42.926619 INFO: Starting candidate scoring
5:19:45.289793 INFO: Finished candidate processing
5:19:45.289793 INFO: Collecting candidate features
5:19:45.674495 WARNING: intensity_correlation has 161 NaNs ( 0.13 % out of 123677)
5:19:45.690229 INFO: Collecting fragment features
5:19:45.862260 INFO: Finished candidate scoring
5:19:46.046995 PROGRESS: === Extracted 216317 precursors and 1431982 fragments ===
5:19:46.109727 INFO: performing precursor FDR with 47 features
5:19:46.109727 INFO: Decoy channel: -1
5:19:46.109727 INFO: Competetive: True
5:19:46.451180 WARNING: dropped 147 target PSMs due to missing features
5:19:46.451180 WARNING: dropped 127 decoy PSMs due to missing features
5:19:50.902386 INFO: Test AUC: 0.563
5:19:50.902386 INFO: Train AUC: 0.594
5:19:50.902386 INFO: AUC difference: 5.15%
5:19:50.902386 WARNING: AUC difference > 5%. This may indicate overfitting.
5:19:51.121989 INFO: === FDR correction performed with classifier version 12 ===
5:19:51.121989 PROGRESS: ============================= Precursor FDR =============================
5:19:51.121989 PROGRESS: Total precursors accumulated: 1,037
5:19:51.121989 PROGRESS: Target precursors: 945 (91.13%)
5:19:51.121989 PROGRESS: Decoy precursors: 92 (8.87%)
5:19:51.121989 PROGRESS: 
5:19:51.121989 PROGRESS: Precursor Summary:
5:19:51.137582 PROGRESS: Channel   0:	 0.05 FDR:   724; 0.01 FDR:     8; 0.001 FDR:     8
5:19:51.137582 PROGRESS: 
5:19:51.137582 PROGRESS: Protein Summary:
5:19:51.137582 PROGRESS: Channel   0:	 0.05 FDR:   683; 0.01 FDR:     8; 0.001 FDR:     8
5:19:51.137582 PROGRESS: =========================================================================
5:19:51.545013 INFO: calibration group: precursor, predicting mz
5:19:51.545013 WARNING: mz prediction was skipped as it has not been fitted yet
5:19:51.545013 INFO: calibration group: precursor, predicting rt
5:19:51.644359 INFO: calibration group: fragment, predicting mz
5:19:52.027981 INFO: === skipping optimization until target number of precursors are found ===
5:19:52.027981 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
5:19:52.027981 INFO: Starting optimization step 7.
5:19:52.027981 PROGRESS: === Extracting elution groups 56000 to 120000 ===
5:19:52.027981 PROGRESS: Extracting batch of 126403 precursors
5:19:52.087394 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:19:52.087394 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:19:52.087394 INFO: FWHM in RT is 18.35 seconds, sigma is 0.67
5:19:52.087394 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:19:52.087394 INFO: Starting candidate selection
5:20:04.703814 INFO: Starting candidate scoring
5:20:09.382912 INFO: Finished candidate processing
5:20:09.382912 INFO: Collecting candidate features
5:20:10.049763 WARNING: intensity_correlation has 355 NaNs ( 0.14 % out of 247210)
5:20:10.112943 INFO: Collecting fragment features
5:20:10.376406 INFO: Finished candidate scoring
5:20:10.841048 PROGRESS: === Extracted 463527 precursors and 3069697 fragments ===
5:20:10.924043 INFO: performing precursor FDR with 47 features
5:20:10.939676 INFO: Decoy channel: -1
5:20:10.939676 INFO: Competetive: True
5:20:11.581455 WARNING: dropped 335 target PSMs due to missing features
5:20:11.581455 WARNING: dropped 294 decoy PSMs due to missing features
5:20:21.274991 INFO: Test AUC: 0.569
5:20:21.274991 INFO: Train AUC: 0.588
5:20:21.274991 INFO: AUC difference: 3.26%
5:20:21.554349 INFO: === FDR correction performed with classifier version 12 ===
5:20:21.554349 PROGRESS: ============================= Precursor FDR =============================
5:20:21.554349 PROGRESS: Total precursors accumulated: 2,181
5:20:21.554349 PROGRESS: Target precursors: 1,991 (91.29%)
5:20:21.554349 PROGRESS: Decoy precursors: 190 (8.71%)
5:20:21.554349 PROGRESS: 
5:20:21.554349 PROGRESS: Precursor Summary:
5:20:21.569870 PROGRESS: Channel   0:	 0.05 FDR: 1,463; 0.01 FDR:     8; 0.001 FDR:     8
5:20:21.569870 PROGRESS: 
5:20:21.569870 PROGRESS: Protein Summary:
5:20:21.569870 PROGRESS: Channel   0:	 0.05 FDR: 1,279; 0.01 FDR:     8; 0.001 FDR:     8
5:20:21.569870 PROGRESS: =========================================================================
5:20:22.202354 INFO: calibration group: precursor, predicting mz
5:20:22.202354 WARNING: mz prediction was skipped as it has not been fitted yet
5:20:22.202354 INFO: calibration group: precursor, predicting rt
5:20:22.380136 INFO: calibration group: fragment, predicting mz
5:20:23.103086 INFO: === skipping optimization until target number of precursors are found ===
5:20:23.103086 PROGRESS: === Optimization of rt_error has been skipped 3 time(s); maximum number is 1 ===
5:20:23.103086 INFO: Starting optimization step 8.
5:20:23.103086 PROGRESS: === Extracting elution groups 120000 to 248000 ===
5:20:23.103086 PROGRESS: Extracting batch of 252949 precursors
5:20:23.183908 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:20:23.183908 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:20:23.183908 INFO: FWHM in RT is 18.35 seconds, sigma is 0.67
5:20:23.183908 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:20:23.183908 INFO: Starting candidate selection
5:20:48.170852 INFO: Starting candidate scoring
5:20:57.323518 INFO: Finished candidate processing
5:20:57.323518 INFO: Collecting candidate features
5:20:58.618878 WARNING: intensity_correlation has 676 NaNs ( 0.14 % out of 494029)
5:20:58.665817 INFO: Collecting fragment features
5:20:59.201575 INFO: Finished candidate scoring
5:21:00.220333 PROGRESS: === Extracted 957556 precursors and 6336023 fragments ===
5:21:00.413431 INFO: performing precursor FDR with 47 features
5:21:00.413431 INFO: Decoy channel: -1
5:21:00.413431 INFO: Competetive: True
5:21:01.640274 WARNING: dropped 690 target PSMs due to missing features
5:21:01.640274 WARNING: dropped 615 decoy PSMs due to missing features
5:21:21.595179 INFO: Test AUC: 0.572
5:21:21.595179 INFO: Train AUC: 0.584
5:21:21.595179 INFO: AUC difference: 1.96%
5:21:21.993497 INFO: === FDR correction performed with classifier version 12 ===
5:21:22.009189 PROGRESS: ============================= Precursor FDR =============================
5:21:22.009189 PROGRESS: Total precursors accumulated: 4,368
5:21:22.009189 PROGRESS: Target precursors: 3,985 (91.23%)
5:21:22.009189 PROGRESS: Decoy precursors: 383 (8.77%)
5:21:22.009189 PROGRESS: 
5:21:22.009189 PROGRESS: Precursor Summary:
5:21:22.009189 PROGRESS: Channel   0:	 0.05 FDR: 3,003; 0.01 FDR:    47; 0.001 FDR:    47
5:21:22.009189 PROGRESS: 
5:21:22.009189 PROGRESS: Protein Summary:
5:21:22.009189 PROGRESS: Channel   0:	 0.05 FDR: 2,304; 0.01 FDR:    47; 0.001 FDR:    47
5:21:22.024757 PROGRESS: =========================================================================
5:21:23.087492 INFO: calibration group: precursor, predicting mz
5:21:23.087492 WARNING: mz prediction was skipped as it has not been fitted yet
5:21:23.087492 INFO: calibration group: precursor, predicting rt
5:21:23.411292 INFO: calibration group: fragment, predicting mz
5:21:24.908687 INFO: === skipping optimization until target number of precursors are found ===
5:21:24.908687 PROGRESS: === Optimization of rt_error has been skipped 4 time(s); maximum number is 1 ===
5:21:24.908687 INFO: Starting optimization step 9.
5:21:24.908687 PROGRESS: === Extracting elution groups 248000 to 504000 ===
5:21:24.908687 PROGRESS: Extracting batch of 505702 precursors
5:21:25.068476 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:21:25.068476 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:21:25.068476 INFO: FWHM in RT is 18.35 seconds, sigma is 0.67
5:21:25.068476 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:21:25.068476 INFO: Starting candidate selection
5:22:14.638672 INFO: Starting candidate scoring
5:22:37.840919 INFO: Finished candidate processing
5:22:37.840919 INFO: Collecting candidate features
5:22:40.504138 WARNING: intensity_correlation has 1383 NaNs ( 0.14 % out of 988438)
5:22:40.661772 INFO: Collecting fragment features
5:22:41.757830 INFO: Finished candidate scoring
5:22:43.999486 PROGRESS: === Extracted 1945994 precursors and 12874758 fragments ===
5:22:44.351935 INFO: performing precursor FDR with 47 features
5:22:44.351935 INFO: Decoy channel: -1
5:22:44.351935 INFO: Competetive: True
5:22:46.754414 WARNING: dropped 1404 target PSMs due to missing features
5:22:46.754414 WARNING: dropped 1284 decoy PSMs due to missing features
5:23:28.569701 INFO: Test AUC: 0.572
5:23:28.569701 INFO: Train AUC: 0.580
5:23:28.569701 INFO: AUC difference: 1.30%
5:23:29.209420 INFO: === FDR correction performed with classifier version 12 ===
5:23:29.225330 PROGRESS: ============================= Precursor FDR =============================
5:23:29.225330 PROGRESS: Total precursors accumulated: 8,594
5:23:29.225330 PROGRESS: Target precursors: 7,858 (91.44%)
5:23:29.225330 PROGRESS: Decoy precursors: 736 (8.56%)
5:23:29.225330 PROGRESS: 
5:23:29.225330 PROGRESS: Precursor Summary:
5:23:29.225330 PROGRESS: Channel   0:	 0.05 FDR: 6,261; 0.01 FDR:    74; 0.001 FDR:    74
5:23:29.225330 PROGRESS: 
5:23:29.225330 PROGRESS: Protein Summary:
5:23:29.241070 PROGRESS: Channel   0:	 0.05 FDR: 3,953; 0.01 FDR:    73; 0.001 FDR:    73
5:23:29.241070 PROGRESS: =========================================================================
5:23:31.097596 INFO: calibration group: precursor, predicting mz
5:23:31.097596 WARNING: mz prediction was skipped as it has not been fitted yet
5:23:31.097596 INFO: calibration group: precursor, predicting rt
5:23:31.758279 INFO: calibration group: fragment, predicting mz
5:23:34.762956 INFO: === skipping optimization until target number of precursors are found ===
5:23:34.762956 PROGRESS: === Optimization of rt_error has been skipped 5 time(s); maximum number is 1 ===
5:23:34.762956 INFO: Starting optimization step 10.
5:23:34.762956 PROGRESS: === Extracting elution groups 504000 to 1016000 ===
5:23:34.762956 PROGRESS: Extracting batch of 1011429 precursors
5:23:35.063907 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:23:35.063907 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:23:35.063907 INFO: FWHM in RT is 18.35 seconds, sigma is 0.67
5:23:35.063907 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:23:35.063907 INFO: Starting candidate selection
5:25:14.010413 INFO: Starting candidate scoring
5:25:52.145417 INFO: Finished candidate processing
5:25:52.145417 INFO: Collecting candidate features
5:25:57.319131 WARNING: intensity_correlation has 2803 NaNs ( 0.14 % out of 1976826)
5:25:57.334790 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 1976826)
5:25:57.562784 INFO: Collecting fragment features
5:25:59.666829 INFO: Finished candidate scoring
5:26:05.265240 PROGRESS: === Extracted 3922820 precursors and 25954738 fragments ===
5:26:05.897929 INFO: performing precursor FDR with 47 features
5:26:05.897929 INFO: Decoy channel: -1
5:26:05.897929 INFO: Competetive: True
5:26:10.409690 WARNING: dropped 2910 target PSMs due to missing features
5:26:10.409690 WARNING: dropped 2581 decoy PSMs due to missing features
5:28:34.579372 INFO: Test AUC: 0.572
5:28:34.579372 INFO: Train AUC: 0.578
5:28:34.579372 INFO: AUC difference: 1.13%
5:28:35.646037 INFO: === FDR correction performed with classifier version 12 ===
5:28:35.661555 PROGRESS: ============================= Precursor FDR =============================
5:28:35.661555 PROGRESS: Total precursors accumulated: 16,624
5:28:35.661555 PROGRESS: Target precursors: 15,236 (91.65%)
5:28:35.661555 PROGRESS: Decoy precursors: 1,388 (8.35%)
5:28:35.661555 PROGRESS: 
5:28:35.661555 PROGRESS: Precursor Summary:
5:28:35.682299 PROGRESS: Channel   0:	 0.05 FDR: 12,281; 0.01 FDR: 8,714; 0.001 FDR:    83
5:28:35.682299 PROGRESS: 
5:28:35.682299 PROGRESS: Protein Summary:
5:28:35.693421 PROGRESS: Channel   0:	 0.05 FDR: 6,182; 0.01 FDR: 4,129; 0.001 FDR:    83
5:28:35.693421 PROGRESS: =========================================================================
5:28:36.197160 INFO: fragments_df_filtered: 5000
5:28:36.716710 INFO: calibration group: precursor, fitting rt estimator 
5:28:51.961371 INFO: calibration group: fragment, fitting mz estimator 
5:28:57.146557 INFO: calibration group: precursor, predicting mz
5:28:57.146557 WARNING: mz prediction was skipped as it has not been fitted yet
5:28:57.146557 INFO: calibration group: precursor, predicting rt
5:28:57.177913 INFO: calibration group: fragment, predicting mz
5:28:57.325545 INFO: === checking if optimization conditions were reached ===
5:28:57.325545 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
5:28:57.325545 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 592.8922.
5:28:57.325545 INFO: ==============================================
5:28:57.325545 INFO: Starting optimization step 11.
5:28:57.325545 PROGRESS: === Extracting elution groups 0 to 24000 ===
5:28:57.325545 PROGRESS: Extracting batch of 47395 precursors
5:28:57.359003 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:28:57.359003 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:28:57.359003 INFO: FWHM in RT is 18.30 seconds, sigma is 0.67
5:28:57.359003 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:28:57.359003 INFO: Starting candidate selection
5:29:01.462968 INFO: Starting candidate scoring
5:29:03.197100 INFO: Finished candidate processing
5:29:03.197100 INFO: Collecting candidate features
5:29:03.465390 WARNING: intensity_correlation has 117 NaNs ( 0.13 % out of 89997)
5:29:03.481018 INFO: Collecting fragment features
5:29:03.591472 INFO: Finished candidate scoring
5:29:03.657641 PROGRESS: === Extracted 89997 precursors and 572714 fragments ===
5:29:03.657641 INFO: performing precursor FDR with 47 features
5:29:03.657641 INFO: Decoy channel: -1
5:29:03.657641 INFO: Competetive: True
5:29:03.734920 WARNING: dropped 57 target PSMs due to missing features
5:29:03.734920 WARNING: dropped 60 decoy PSMs due to missing features
5:29:05.397852 INFO: Test AUC: 0.558
5:29:05.397852 INFO: Train AUC: 0.597
5:29:05.397852 INFO: AUC difference: 6.40%
5:29:05.397852 WARNING: AUC difference > 5%. This may indicate overfitting.
5:29:05.574132 INFO: === FDR correction performed with classifier version 12 ===
5:29:05.574132 PROGRESS: ============================= Precursor FDR =============================
5:29:05.574132 PROGRESS: Total precursors accumulated: 419
5:29:05.574132 PROGRESS: Target precursors: 380 (90.69%)
5:29:05.574132 PROGRESS: Decoy precursors: 39 (9.31%)
5:29:05.574132 PROGRESS: 
5:29:05.574132 PROGRESS: Precursor Summary:
5:29:05.574132 PROGRESS: Channel   0:	 0.05 FDR:   280; 0.01 FDR:   136; 0.001 FDR:    39
5:29:05.574132 PROGRESS: 
5:29:05.574132 PROGRESS: Protein Summary:
5:29:05.574132 PROGRESS: Channel   0:	 0.05 FDR:   273; 0.01 FDR:   133; 0.001 FDR:    39
5:29:05.574132 PROGRESS: =========================================================================
5:29:05.845502 INFO: calibration group: precursor, predicting mz
5:29:05.845502 WARNING: mz prediction was skipped as it has not been fitted yet
5:29:05.845502 INFO: calibration group: precursor, predicting rt
5:29:05.901623 INFO: calibration group: fragment, predicting mz
5:29:06.070262 INFO: === skipping optimization until target number of precursors are found ===
5:29:06.070262 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
5:29:06.070262 INFO: Starting optimization step 12.
5:29:06.070262 PROGRESS: === Extracting elution groups 24000 to 56000 ===
5:29:06.070262 PROGRESS: Extracting batch of 63206 precursors
5:29:06.101928 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:29:06.101928 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:29:06.101928 INFO: FWHM in RT is 18.30 seconds, sigma is 0.67
5:29:06.101928 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:29:06.101928 INFO: Starting candidate selection
5:29:11.250499 INFO: Starting candidate scoring
5:29:13.357798 INFO: Finished candidate processing
5:29:13.357798 INFO: Collecting candidate features
5:29:13.754296 WARNING: intensity_correlation has 171 NaNs ( 0.14 % out of 120099)
5:29:13.768377 INFO: Collecting fragment features
5:29:13.934302 INFO: Finished candidate scoring
5:29:14.172390 PROGRESS: === Extracted 210096 precursors and 1336764 fragments ===
5:29:14.219190 INFO: performing precursor FDR with 47 features
5:29:14.219190 INFO: Decoy channel: -1
5:29:14.219190 INFO: Competetive: True
5:29:14.532556 WARNING: dropped 152 target PSMs due to missing features
5:29:14.532556 WARNING: dropped 136 decoy PSMs due to missing features
5:29:18.767510 INFO: Test AUC: 0.564
5:29:18.767510 INFO: Train AUC: 0.589
5:29:18.767510 INFO: AUC difference: 4.26%
5:29:18.985175 INFO: === FDR correction performed with classifier version 12 ===
5:29:18.985175 PROGRESS: ============================= Precursor FDR =============================
5:29:18.985175 PROGRESS: Total precursors accumulated: 971
5:29:18.985175 PROGRESS: Target precursors: 885 (91.14%)
5:29:18.985175 PROGRESS: Decoy precursors: 86 (8.86%)
5:29:18.985175 PROGRESS: 
5:29:18.985175 PROGRESS: Precursor Summary:
5:29:18.985175 PROGRESS: Channel   0:	 0.05 FDR:   674; 0.01 FDR:     8; 0.001 FDR:     8
5:29:18.985175 PROGRESS: 
5:29:18.985175 PROGRESS: Protein Summary:
5:29:19.000822 PROGRESS: Channel   0:	 0.05 FDR:   636; 0.01 FDR:     8; 0.001 FDR:     8
5:29:19.000822 PROGRESS: =========================================================================
5:29:19.418353 INFO: calibration group: precursor, predicting mz
5:29:19.418353 WARNING: mz prediction was skipped as it has not been fitted yet
5:29:19.433981 INFO: calibration group: precursor, predicting rt
5:29:19.515049 INFO: calibration group: fragment, predicting mz
5:29:19.904531 INFO: === skipping optimization until target number of precursors are found ===
5:29:19.904531 PROGRESS: === Optimization of rt_error has been skipped 2 time(s); maximum number is 1 ===
5:29:19.904531 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 831.3454 found after 2 searches.
5:29:19.904531 PROGRESS: Optimization finished for rt_error.
5:29:20.192720 INFO: calibration group: precursor, predicting mz
5:29:20.192720 WARNING: mz prediction was skipped as it has not been fitted yet
5:29:20.192720 INFO: calibration group: precursor, predicting rt
5:29:20.223963 INFO: calibration group: fragment, predicting mz
5:29:20.441742 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:29:20.441742 PROGRESS: ==============================================
5:29:20.442719 PROGRESS: ms2_error      : 10.0000
5:29:20.442719 PROGRESS: rt_error       : 831.3454
5:29:20.442719 PROGRESS: ==============================================
5:29:20.450968 INFO: calibration group: precursor, predicting mz
5:29:20.450968 WARNING: mz prediction was skipped as it has not been fitted yet
5:29:20.450968 INFO: calibration group: precursor, predicting rt
5:29:27.293777 INFO: calibration group: fragment, predicting mz
5:29:58.665564 PROGRESS: Extracting batch of 10640830 precursors
5:30:00.945185 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
5:30:00.945185 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
5:30:00.945185 INFO: FWHM in RT is 18.30 seconds, sigma is 0.67
5:30:00.945185 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
5:30:00.945185 INFO: Starting candidate selection
5:47:09.658822 INFO: Applying score cutoff of 62.71603814315796
5:47:10.600936 INFO: Removed 9540715 precursors with score below cutoff
5:47:13.699888 INFO: Starting candidate scoring
5:52:24.600448 INFO: Finished candidate processing
5:52:24.600448 INFO: Collecting candidate features
5:53:04.877188 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 11644905)
5:53:06.349205 INFO: Collecting fragment features
5:53:21.759337 INFO: Finished candidate scoring
5:53:58.026231 INFO: === FDR correction performed with classifier version 23 ===
5:53:58.041926 INFO: performing precursor FDR with 47 features
5:53:58.041926 INFO: Decoy channel: -1
5:53:58.041926 INFO: Competetive: True
5:54:08.969269 WARNING: dropped 3 target PSMs due to missing features
5:54:08.969269 WARNING: dropped 1 decoy PSMs due to missing features
6:02:55.971916 INFO: Test AUC: 0.578
6:02:55.971916 INFO: Train AUC: 0.580
6:02:55.971916 INFO: AUC difference: 0.29%
6:02:58.082472 INFO: Removing fragments below FDR threshold
6:02:59.698232 PROGRESS: ============================= Precursor FDR =============================
6:03:02.269522 PROGRESS: Total precursors accumulated: 49,191
6:03:02.269522 PROGRESS: Target precursors: 48,704 (99.01%)
6:03:02.281543 PROGRESS: Decoy precursors: 487 (0.99%)
6:03:02.281543 PROGRESS: 
6:03:02.281543 PROGRESS: Precursor Summary:
6:03:02.335317 PROGRESS: Channel   0:	 0.05 FDR: 48,704; 0.01 FDR: 48,704; 0.001 FDR:    55
6:03:02.335317 PROGRESS: 
6:03:02.335317 PROGRESS: Protein Summary:
6:03:02.413697 PROGRESS: Channel   0:	 0.05 FDR: 8,784; 0.01 FDR: 8,784; 0.001 FDR:    53
6:03:02.413697 PROGRESS: =========================================================================
6:03:03.760282 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
6:03:05.553443 PROGRESS: Loading raw file 6/6: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
6:03:05.553443 INFO: Creating workflow folder for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03 at D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
6:03:40.440660 INFO: Determining DIA cycle
6:03:40.457792 WARNING: Failed to determine DIA cycle, will retry without MS1 spectra.
6:03:40.474316 INFO: Determining DIA cycle
6:03:40.489357 INFO: Found cycle with start 0.00 min and length 151.
6:03:40.615749 INFO: ============ Raw file stats ============
6:03:40.615749 INFO: RT (min)            : 0.0 - 150.0
6:03:40.615749 INFO: RT duration (sec)   : 8999.7
6:03:40.615749 INFO: RT duration (min)   : 150.0
6:03:40.615749 INFO: Cycle len (scans)   : 151
6:03:40.615749 INFO: Cycle len (sec)     : 5.84
6:03:40.615749 INFO: Number of cycles    : 1542
6:03:40.615749 INFO: MS2 range (m/z)     : 396.4 - 1004.7
6:03:40.615749 INFO: ========================================
6:03:46.168961 INFO: Initializing CalibrationManager
6:03:46.168961 INFO: Loading calibration config
6:03:46.184594 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)}]}]
6:03:46.184594 INFO: Calibration group :fragment, found 1 estimator(s)
6:03:46.184594 INFO: Calibration group :precursor, found 3 estimator(s)
6:03:46.184594 INFO: Disabling ion mobility calibration
6:03:46.184594 INFO: removed mobility estimator from group precursor
6:03:46.184594 INFO: Initializing OptimizationManager
6:03:46.184594 INFO: initial parameter: ms1_error = 30
6:03:46.184594 INFO: initial parameter: ms2_error = 30
6:03:46.184594 INFO: initial parameter: rt_error = 4499.99853515625
6:03:46.184594 INFO: initial parameter: mobility_error = 0.1
6:03:46.184594 INFO: initial parameter: column_type = library
6:03:46.184594 INFO: initial parameter: num_candidates = 1
6:03:46.184594 INFO: initial parameter: classifier_version = -1
6:03:46.184594 INFO: initial parameter: fwhm_rt = 5
6:03:46.184594 INFO: initial parameter: fwhm_mobility = 0.01
6:03:46.184594 INFO: initial parameter: score_cutoff = 0
6:03:46.184594 INFO: Initializing TimingManager
6:03:46.184594 PROGRESS: Initializing workflow LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
6:03:46.184594 INFO: Initializing FDRManager
6:03:46.184594 INFO: Loading classifier store from C:\Users\robbe\AppData\Local\Programs\AlphaDIA\_internal\alphadia\constants\classifier
6:03:48.802171 PROGRESS: 5,385,906 target precursors potentially observable (0 removed)
6:03:51.953950 PROGRESS: Starting initial search for precursors.
6:03:52.339316 INFO: Starting optimization step 0.
6:03:52.355276 PROGRESS: === Extracting elution groups 0 to 8000 ===
6:03:52.355276 PROGRESS: Extracting batch of 15803 precursors
6:03:52.372485 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:03:52.372485 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:03:52.372485 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
6:03:52.372485 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:03:52.372485 INFO: Starting candidate selection
6:03:58.893583 INFO: Starting candidate scoring
6:03:59.245354 INFO: Finished candidate processing
6:03:59.245354 INFO: Collecting candidate features
6:03:59.303846 INFO: Collecting fragment features
6:03:59.364356 INFO: Finished candidate scoring
6:03:59.375617 PROGRESS: === Extracted 15797 precursors and 131762 fragments ===
6:03:59.375617 INFO: performing precursor FDR with 47 features
6:03:59.375617 INFO: Decoy channel: -1
6:03:59.375617 INFO: Competetive: True
6:03:59.637691 INFO: Test AUC: 0.517
6:03:59.637691 INFO: Train AUC: 0.548
6:03:59.637691 INFO: AUC difference: 5.53%
6:03:59.637691 WARNING: AUC difference > 5%. This may indicate overfitting.
6:03:59.803971 INFO: === FDR correction performed with classifier version -1 ===
6:03:59.803971 PROGRESS: ============================= Precursor FDR =============================
6:03:59.803971 PROGRESS: Total precursors accumulated: 1
6:03:59.803971 PROGRESS: Target precursors: 1 (100.00%)
6:03:59.803971 PROGRESS: Decoy precursors: 0 (0.00%)
6:03:59.803971 PROGRESS: 
6:03:59.803971 PROGRESS: Precursor Summary:
6:03:59.803971 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:03:59.803971 PROGRESS: 
6:03:59.803971 PROGRESS: Protein Summary:
6:03:59.803971 PROGRESS: Channel   0:	 0.05 FDR:     1; 0.01 FDR:     1; 0.001 FDR:     1
6:03:59.803971 PROGRESS: =========================================================================
6:04:00.022362 INFO: Starting optimization step 1.
6:04:00.022362 PROGRESS: === Extracting elution groups 8000 to 24000 ===
6:04:00.022362 PROGRESS: Extracting batch of 31592 precursors
6:04:00.035567 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:04:00.035567 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:04:00.035567 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
6:04:00.035567 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:04:00.035567 INFO: Starting candidate selection
6:04:13.105521 INFO: Starting candidate scoring
6:04:13.775301 INFO: Finished candidate processing
6:04:13.775301 INFO: Collecting candidate features
6:04:13.914030 INFO: Collecting fragment features
6:04:13.962944 INFO: Finished candidate scoring
6:04:14.057296 PROGRESS: === Extracted 47348 precursors and 395362 fragments ===
6:04:14.088593 INFO: performing precursor FDR with 47 features
6:04:14.088593 INFO: Decoy channel: -1
6:04:14.088593 INFO: Competetive: True
6:04:15.410699 INFO: Test AUC: 0.549
6:04:15.410699 INFO: Train AUC: 0.569
6:04:15.410699 INFO: AUC difference: 3.59%
6:04:15.586068 INFO: === FDR correction performed with classifier version -1 ===
6:04:15.617460 PROGRESS: ============================= Precursor FDR =============================
6:04:15.617460 PROGRESS: Total precursors accumulated: 23,968
6:04:15.617460 PROGRESS: Target precursors: 14,177 (59.15%)
6:04:15.617460 PROGRESS: Decoy precursors: 9,791 (40.85%)
6:04:15.617460 PROGRESS: 
6:04:15.617460 PROGRESS: Precursor Summary:
6:04:15.617460 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:04:15.617460 PROGRESS: 
6:04:15.617460 PROGRESS: Protein Summary:
6:04:15.617460 PROGRESS: Channel   0:	 0.05 FDR:     0; 0.01 FDR:     0; 0.001 FDR:     0
6:04:15.617460 PROGRESS: =========================================================================
6:04:15.925059 INFO: Starting optimization step 2.
6:04:15.925059 PROGRESS: === Extracting elution groups 24000 to 56000 ===
6:04:15.926060 PROGRESS: Extracting batch of 63206 precursors
6:04:15.949449 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:04:15.949449 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:04:15.960002 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
6:04:15.960002 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:04:15.960002 INFO: Starting candidate selection
6:04:42.122726 INFO: Starting candidate scoring
6:04:43.839917 INFO: Finished candidate processing
6:04:43.839917 INFO: Collecting candidate features
6:04:44.140521 INFO: Collecting fragment features
6:04:44.280912 INFO: Finished candidate scoring
6:04:44.447150 PROGRESS: === Extracted 110506 precursors and 923664 fragments ===
6:04:44.494759 INFO: performing precursor FDR with 47 features
6:04:44.494759 INFO: Decoy channel: -1
6:04:44.494759 INFO: Competetive: True
6:04:46.910146 INFO: Test AUC: 0.568
6:04:46.910146 INFO: Train AUC: 0.577
6:04:46.911168 INFO: AUC difference: 1.50%
6:04:47.091885 INFO: === FDR correction performed with classifier version -1 ===
6:04:47.091885 PROGRESS: ============================= Precursor FDR =============================
6:04:47.091885 PROGRESS: Total precursors accumulated: 338
6:04:47.091885 PROGRESS: Target precursors: 308 (91.12%)
6:04:47.091885 PROGRESS: Decoy precursors: 30 (8.88%)
6:04:47.091885 PROGRESS: 
6:04:47.091885 PROGRESS: Precursor Summary:
6:04:47.091885 PROGRESS: Channel   0:	 0.05 FDR:   205; 0.01 FDR:    12; 0.001 FDR:    12
6:04:47.091885 PROGRESS: 
6:04:47.091885 PROGRESS: Protein Summary:
6:04:47.107499 PROGRESS: Channel   0:	 0.05 FDR:   199; 0.01 FDR:    12; 0.001 FDR:    12
6:04:47.107499 PROGRESS: =========================================================================
6:04:47.526386 INFO: Starting optimization step 3.
6:04:47.526386 PROGRESS: === Extracting elution groups 56000 to 120000 ===
6:04:47.526386 PROGRESS: Extracting batch of 126403 precursors
6:04:47.604860 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:04:47.604860 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:04:47.604860 INFO: FWHM in RT is 5.00 seconds, sigma is 0.18
6:04:47.604860 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 1.00
6:04:47.604860 INFO: Starting candidate selection
6:05:40.147319 INFO: Starting candidate scoring
6:05:42.477194 INFO: Finished candidate processing
6:05:42.477194 INFO: Collecting candidate features
6:05:43.059862 INFO: Collecting fragment features
6:05:43.264160 INFO: Finished candidate scoring
6:05:43.575288 PROGRESS: === Extracted 236806 precursors and 1979263 fragments ===
6:05:43.637854 INFO: performing precursor FDR with 47 features
6:05:43.637854 INFO: Decoy channel: -1
6:05:43.637854 INFO: Competetive: True
6:05:48.661651 INFO: Test AUC: 0.569
6:05:48.661651 INFO: Train AUC: 0.586
6:05:48.661651 INFO: AUC difference: 2.91%
6:05:48.934031 INFO: === FDR correction performed with classifier version -1 ===
6:05:48.935968 PROGRESS: ============================= Precursor FDR =============================
6:05:48.936969 PROGRESS: Total precursors accumulated: 1,021
6:05:48.936969 PROGRESS: Target precursors: 929 (90.99%)
6:05:48.936969 PROGRESS: Decoy precursors: 92 (9.01%)
6:05:48.936969 PROGRESS: 
6:05:48.937973 PROGRESS: Precursor Summary:
6:05:48.941120 PROGRESS: Channel   0:	 0.05 FDR:   796; 0.01 FDR:   518; 0.001 FDR:   337
6:05:48.941120 PROGRESS: 
6:05:48.941120 PROGRESS: Protein Summary:
6:05:48.941120 PROGRESS: Channel   0:	 0.05 FDR:   707; 0.01 FDR:   471; 0.001 FDR:   315
6:05:48.941120 PROGRESS: =========================================================================
6:05:48.979928 INFO: fragments_df_filtered: 3314
6:05:49.414136 INFO: calibration group: precursor, fitting rt estimator 
6:05:49.554625 INFO: calibration group: fragment, fitting mz estimator 
6:05:51.724300 INFO: calibration group: precursor, predicting mz
6:05:51.724300 WARNING: mz prediction was skipped as it has not been fitted yet
6:05:51.724300 INFO: calibration group: precursor, predicting rt
6:05:51.837432 INFO: calibration group: fragment, predicting mz
6:05:52.157013 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:05:52.157013 INFO: Starting optimization step 4.
6:05:52.157013 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:05:52.157013 PROGRESS: Extracting batch of 110601 precursors
6:05:52.219926 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:05:52.219926 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:05:52.219926 INFO: FWHM in RT is 18.53 seconds, sigma is 0.67
6:05:52.219926 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:05:52.219926 INFO: Starting candidate selection
6:06:39.626678 INFO: Starting candidate scoring
6:06:44.590856 INFO: Finished candidate processing
6:06:44.590856 INFO: Collecting candidate features
6:06:45.253582 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 221023)
6:06:45.285192 INFO: Collecting fragment features
6:06:45.590472 INFO: Finished candidate scoring
6:06:45.833505 PROGRESS: === Extracted 221023 precursors and 1905918 fragments ===
6:06:45.833505 INFO: performing precursor FDR with 47 features
6:06:45.833505 INFO: Decoy channel: -1
6:06:45.833505 INFO: Competetive: True
6:06:46.124074 WARNING: dropped 2 target PSMs due to missing features
6:06:46.124074 WARNING: dropped 2 decoy PSMs due to missing features
6:06:50.539864 INFO: Test AUC: 0.572
6:06:50.539864 INFO: Train AUC: 0.587
6:06:50.539864 INFO: AUC difference: 2.51%
6:06:50.759634 INFO: === FDR correction performed with classifier version 3 ===
6:06:50.759634 PROGRESS: ============================= Precursor FDR =============================
6:06:50.759634 PROGRESS: Total precursors accumulated: 479
6:06:50.759634 PROGRESS: Target precursors: 438 (91.44%)
6:06:50.759634 PROGRESS: Decoy precursors: 41 (8.56%)
6:06:50.759634 PROGRESS: 
6:06:50.759634 PROGRESS: Precursor Summary:
6:06:50.759634 PROGRESS: Channel   0:	 0.05 FDR:   395; 0.01 FDR:   302; 0.001 FDR:   200
6:06:50.759634 PROGRESS: 
6:06:50.775255 PROGRESS: Protein Summary:
6:06:50.775255 PROGRESS: Channel   0:	 0.05 FDR:   378; 0.01 FDR:   289; 0.001 FDR:   198
6:06:50.775255 PROGRESS: =========================================================================
6:06:50.795744 INFO: fragments_df_filtered: 1825
6:06:51.190380 INFO: calibration group: precursor, fitting rt estimator 
6:06:53.136372 INFO: calibration group: fragment, fitting mz estimator 
6:06:53.912438 INFO: calibration group: precursor, predicting mz
6:06:53.912438 WARNING: mz prediction was skipped as it has not been fitted yet
6:06:53.912438 INFO: calibration group: precursor, predicting rt
6:06:54.006837 INFO: calibration group: fragment, predicting mz
6:06:54.328450 INFO: === checking if optimization conditions were reached ===
6:06:54.328450 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:06:54.328450 INFO: ==============================================
6:06:54.344595 INFO: Starting optimization step 5.
6:06:54.344934 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:06:54.344934 PROGRESS: Extracting batch of 110601 precursors
6:06:54.398365 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:06:54.398365 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:06:54.398365 INFO: FWHM in RT is 18.69 seconds, sigma is 0.68
6:06:54.398365 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:06:54.398365 INFO: Starting candidate selection
6:07:42.479287 INFO: Starting candidate scoring
6:07:46.946560 INFO: Finished candidate processing
6:07:46.946560 INFO: Collecting candidate features
6:07:47.555733 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 220908)
6:07:47.620382 INFO: Collecting fragment features
6:07:47.877331 INFO: Finished candidate scoring
6:07:48.098821 PROGRESS: === Extracted 220908 precursors and 1561544 fragments ===
6:07:48.098821 INFO: performing precursor FDR with 47 features
6:07:48.098821 INFO: Decoy channel: -1
6:07:48.098821 INFO: Competetive: True
6:07:48.424935 WARNING: dropped 7 target PSMs due to missing features
6:07:48.424935 WARNING: dropped 10 decoy PSMs due to missing features
6:07:52.986879 INFO: Test AUC: 0.567
6:07:52.986879 INFO: Train AUC: 0.589
6:07:52.986879 INFO: AUC difference: 3.88%
6:07:53.160366 INFO: === FDR correction performed with classifier version 4 ===
6:07:53.175984 PROGRESS: ============================= Precursor FDR =============================
6:07:53.175984 PROGRESS: Total precursors accumulated: 590
6:07:53.175984 PROGRESS: Target precursors: 537 (91.02%)
6:07:53.175984 PROGRESS: Decoy precursors: 53 (8.98%)
6:07:53.175984 PROGRESS: 
6:07:53.175984 PROGRESS: Precursor Summary:
6:07:53.175984 PROGRESS: Channel   0:	 0.05 FDR:   404; 0.01 FDR:   206; 0.001 FDR:   184
6:07:53.175984 PROGRESS: 
6:07:53.175984 PROGRESS: Protein Summary:
6:07:53.175984 PROGRESS: Channel   0:	 0.05 FDR:   379; 0.01 FDR:   199; 0.001 FDR:   179
6:07:53.175984 PROGRESS: =========================================================================
6:07:53.191615 INFO: fragments_df_filtered: 1249
6:07:53.593959 INFO: calibration group: precursor, fitting rt estimator 
6:07:53.688275 INFO: calibration group: fragment, fitting mz estimator 
6:07:54.077376 INFO: calibration group: precursor, predicting mz
6:07:54.077376 WARNING: mz prediction was skipped as it has not been fitted yet
6:07:54.077376 INFO: calibration group: precursor, predicting rt
6:07:54.171788 INFO: calibration group: fragment, predicting mz
6:07:54.495727 INFO: === checking if optimization conditions were reached ===
6:07:54.495727 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:07:54.495727 INFO: ==============================================
6:07:54.495727 PROGRESS: Optimization finished for ms2_error.
6:07:54.893153 INFO: calibration group: precursor, predicting mz
6:07:54.894158 WARNING: mz prediction was skipped as it has not been fitted yet
6:07:54.894158 INFO: calibration group: precursor, predicting rt
6:07:54.996093 INFO: calibration group: fragment, predicting mz
6:07:55.299105 INFO: Starting optimization step 0.
6:07:55.299105 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:07:55.299105 PROGRESS: Extracting batch of 110601 precursors
6:07:55.350828 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:07:55.350828 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:07:55.350828 INFO: FWHM in RT is 17.57 seconds, sigma is 0.64
6:07:55.350828 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:07:55.350828 INFO: Starting candidate selection
6:08:43.447427 INFO: Starting candidate scoring
6:08:47.604084 INFO: Finished candidate processing
6:08:47.604084 INFO: Collecting candidate features
6:08:48.232014 WARNING: intensity_correlation has 17 NaNs ( 0.01 % out of 220914)
6:08:48.294632 INFO: Collecting fragment features
6:08:48.575806 INFO: Finished candidate scoring
6:08:48.797277 PROGRESS: === Extracted 220914 precursors and 1556449 fragments ===
6:08:48.797277 INFO: performing precursor FDR with 47 features
6:08:48.797277 INFO: Decoy channel: -1
6:08:48.797277 INFO: Competetive: True
6:08:49.107722 WARNING: dropped 7 target PSMs due to missing features
6:08:49.107722 WARNING: dropped 10 decoy PSMs due to missing features
6:08:53.543315 INFO: Test AUC: 0.576
6:08:53.543315 INFO: Train AUC: 0.597
6:08:53.543315 INFO: AUC difference: 3.50%
6:08:53.748325 INFO: === FDR correction performed with classifier version 5 ===
6:08:53.763945 PROGRESS: ============================= Precursor FDR =============================
6:08:53.763945 PROGRESS: Total precursors accumulated: 605
6:08:53.763945 PROGRESS: Target precursors: 551 (91.07%)
6:08:53.763945 PROGRESS: Decoy precursors: 54 (8.93%)
6:08:53.763945 PROGRESS: 
6:08:53.763945 PROGRESS: Precursor Summary:
6:08:53.763945 PROGRESS: Channel   0:	 0.05 FDR:   423; 0.01 FDR:   251; 0.001 FDR:   169
6:08:53.763945 PROGRESS: 
6:08:53.763945 PROGRESS: Protein Summary:
6:08:53.763945 PROGRESS: Channel   0:	 0.05 FDR:   397; 0.01 FDR:   243; 0.001 FDR:   164
6:08:53.763945 PROGRESS: =========================================================================
6:08:53.779574 INFO: fragments_df_filtered: 1330
6:08:54.196469 INFO: calibration group: precursor, fitting rt estimator 
6:08:54.306338 INFO: calibration group: fragment, fitting mz estimator 
6:08:54.742112 INFO: calibration group: precursor, predicting mz
6:08:54.757827 WARNING: mz prediction was skipped as it has not been fitted yet
6:08:54.757827 INFO: calibration group: precursor, predicting rt
6:08:54.844088 INFO: calibration group: fragment, predicting mz
6:08:55.148118 INFO: === checking if optimization conditions were reached ===
6:08:55.148118 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
6:08:55.163749 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 681.7986.
6:08:55.163749 INFO: ==============================================
6:08:55.163749 INFO: Starting optimization step 1.
6:08:55.163749 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:08:55.163749 PROGRESS: Extracting batch of 110601 precursors
6:08:55.215188 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:08:55.215188 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:08:55.215188 INFO: FWHM in RT is 17.13 seconds, sigma is 0.62
6:08:55.215188 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:08:55.215188 INFO: Starting candidate selection
6:09:05.097035 INFO: Starting candidate scoring
6:09:08.836720 INFO: Finished candidate processing
6:09:08.836720 INFO: Collecting candidate features
6:09:09.479712 WARNING: intensity_correlation has 362 NaNs ( 0.17 % out of 210454)
6:09:09.526664 INFO: Collecting fragment features
6:09:09.760682 INFO: Finished candidate scoring
6:09:09.976820 PROGRESS: === Extracted 210454 precursors and 1215463 fragments ===
6:09:09.992445 INFO: performing precursor FDR with 47 features
6:09:09.992445 INFO: Decoy channel: -1
6:09:09.992445 INFO: Competetive: True
6:09:10.296402 WARNING: dropped 197 target PSMs due to missing features
6:09:10.296402 WARNING: dropped 165 decoy PSMs due to missing features
6:09:14.629209 INFO: Test AUC: 0.558
6:09:14.629209 INFO: Train AUC: 0.580
6:09:14.629209 INFO: AUC difference: 3.90%
6:09:14.796441 INFO: === FDR correction performed with classifier version 5 ===
6:09:14.796441 PROGRESS: ============================= Precursor FDR =============================
6:09:14.796441 PROGRESS: Total precursors accumulated: 707
6:09:14.796441 PROGRESS: Target precursors: 644 (91.09%)
6:09:14.796441 PROGRESS: Decoy precursors: 63 (8.91%)
6:09:14.796441 PROGRESS: 
6:09:14.796441 PROGRESS: Precursor Summary:
6:09:14.796441 PROGRESS: Channel   0:	 0.05 FDR:   531; 0.01 FDR:   357; 0.001 FDR:   334
6:09:14.796441 PROGRESS: 
6:09:14.796441 PROGRESS: Protein Summary:
6:09:14.812916 PROGRESS: Channel   0:	 0.05 FDR:   501; 0.01 FDR:   335; 0.001 FDR:   315
6:09:14.815082 PROGRESS: =========================================================================
6:09:14.827163 INFO: fragments_df_filtered: 1396
6:09:15.217166 INFO: calibration group: precursor, fitting rt estimator 
6:09:15.327648 INFO: calibration group: fragment, fitting mz estimator 
6:09:15.824043 INFO: calibration group: precursor, predicting mz
6:09:15.824043 WARNING: mz prediction was skipped as it has not been fitted yet
6:09:15.824043 INFO: calibration group: precursor, predicting rt
6:09:15.939422 INFO: calibration group: fragment, predicting mz
6:09:16.259086 INFO: === checking if optimization conditions were reached ===
6:09:16.259086 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
6:09:16.259086 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 551.5347.
6:09:16.273685 INFO: ==============================================
6:09:16.273685 INFO: Starting optimization step 2.
6:09:16.275197 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:09:16.275197 PROGRESS: Extracting batch of 110601 precursors
6:09:16.327278 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:09:16.327278 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:09:16.327278 INFO: FWHM in RT is 16.89 seconds, sigma is 0.61
6:09:16.327278 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:09:16.327278 INFO: Starting candidate selection
6:09:24.750372 INFO: Starting candidate scoring
6:09:28.256261 INFO: Finished candidate processing
6:09:28.256261 INFO: Collecting candidate features
6:09:28.866284 WARNING: intensity_correlation has 367 NaNs ( 0.18 % out of 208077)
6:09:28.908178 INFO: Collecting fragment features
6:09:29.143555 INFO: Finished candidate scoring
6:09:29.322371 PROGRESS: === Extracted 208077 precursors and 1168017 fragments ===
6:09:29.322371 INFO: performing precursor FDR with 47 features
6:09:29.322371 INFO: Decoy channel: -1
6:09:29.322371 INFO: Competetive: True
6:09:29.605422 WARNING: dropped 199 target PSMs due to missing features
6:09:29.605422 WARNING: dropped 168 decoy PSMs due to missing features
6:09:33.651655 INFO: Test AUC: 0.557
6:09:33.651655 INFO: Train AUC: 0.578
6:09:33.651655 INFO: AUC difference: 3.66%
6:09:33.866217 INFO: === FDR correction performed with classifier version 5 ===
6:09:33.884350 PROGRESS: ============================= Precursor FDR =============================
6:09:33.884350 PROGRESS: Total precursors accumulated: 722
6:09:33.884350 PROGRESS: Target precursors: 656 (90.86%)
6:09:33.884350 PROGRESS: Decoy precursors: 66 (9.14%)
6:09:33.884350 PROGRESS: 
6:09:33.884350 PROGRESS: Precursor Summary:
6:09:33.884350 PROGRESS: Channel   0:	 0.05 FDR:   544; 0.01 FDR:   408; 0.001 FDR:   282
6:09:33.884350 PROGRESS: 
6:09:33.884350 PROGRESS: Protein Summary:
6:09:33.884350 PROGRESS: Channel   0:	 0.05 FDR:   515; 0.01 FDR:   381; 0.001 FDR:   269
6:09:33.884350 PROGRESS: =========================================================================
6:09:33.903565 INFO: fragments_df_filtered: 1461
6:09:34.304639 INFO: calibration group: precursor, fitting rt estimator 
6:09:34.425087 INFO: calibration group: fragment, fitting mz estimator 
6:09:34.955021 INFO: calibration group: precursor, predicting mz
6:09:34.956023 WARNING: mz prediction was skipped as it has not been fitted yet
6:09:34.956023 INFO: calibration group: precursor, predicting rt
6:09:35.057515 INFO: calibration group: fragment, predicting mz
6:09:35.381448 INFO: === checking if optimization conditions were reached ===
6:09:35.381448 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
6:09:35.384923 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 516.2129.
6:09:35.384923 INFO: ==============================================
6:09:35.384923 INFO: Starting optimization step 3.
6:09:35.384923 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:09:35.384923 PROGRESS: Extracting batch of 110601 precursors
6:09:35.450452 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:09:35.450452 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:09:35.450452 INFO: FWHM in RT is 16.92 seconds, sigma is 0.62
6:09:35.450452 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:09:35.450452 INFO: Starting candidate selection
6:09:43.222904 INFO: Starting candidate scoring
6:09:46.676458 INFO: Finished candidate processing
6:09:46.676458 INFO: Collecting candidate features
6:09:47.321835 WARNING: intensity_correlation has 367 NaNs ( 0.18 % out of 208915)
6:09:47.355365 INFO: Collecting fragment features
6:09:47.596940 INFO: Finished candidate scoring
6:09:47.829582 PROGRESS: === Extracted 208915 precursors and 1172495 fragments ===
6:09:47.829582 INFO: performing precursor FDR with 47 features
6:09:47.829582 INFO: Decoy channel: -1
6:09:47.829582 INFO: Competetive: True
6:09:48.110505 WARNING: dropped 191 target PSMs due to missing features
6:09:48.110505 WARNING: dropped 176 decoy PSMs due to missing features
6:09:52.229960 INFO: Test AUC: 0.558
6:09:52.229960 INFO: Train AUC: 0.579
6:09:52.229960 INFO: AUC difference: 3.69%
6:09:52.448972 INFO: === FDR correction performed with classifier version 5 ===
6:09:52.449972 PROGRESS: ============================= Precursor FDR =============================
6:09:52.450972 PROGRESS: Total precursors accumulated: 796
6:09:52.452127 PROGRESS: Target precursors: 723 (90.83%)
6:09:52.452127 PROGRESS: Decoy precursors: 73 (9.17%)
6:09:52.452127 PROGRESS: 
6:09:52.452127 PROGRESS: Precursor Summary:
6:09:52.455038 PROGRESS: Channel   0:	 0.05 FDR:   537; 0.01 FDR:   418; 0.001 FDR:   327
6:09:52.455038 PROGRESS: 
6:09:52.455038 PROGRESS: Protein Summary:
6:09:52.457979 PROGRESS: Channel   0:	 0.05 FDR:   506; 0.01 FDR:   394; 0.001 FDR:   309
6:09:52.457979 PROGRESS: =========================================================================
6:09:52.463159 INFO: fragments_df_filtered: 1494
6:09:52.862360 INFO: calibration group: precursor, fitting rt estimator 
6:09:52.976779 INFO: calibration group: fragment, fitting mz estimator 
6:09:53.413876 INFO: calibration group: precursor, predicting mz
6:09:53.413876 WARNING: mz prediction was skipped as it has not been fitted yet
6:09:53.413876 INFO: calibration group: precursor, predicting rt
6:09:53.509306 INFO: calibration group: fragment, predicting mz
6:09:53.829011 INFO: === checking if optimization conditions were reached ===
6:09:53.829011 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
6:09:53.843831 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 503.6492.
6:09:53.843831 INFO: ==============================================
6:09:53.844777 INFO: Starting optimization step 4.
6:09:53.844777 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:09:53.844777 PROGRESS: Extracting batch of 110601 precursors
6:09:53.893236 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:09:53.893236 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:09:53.893236 INFO: FWHM in RT is 16.87 seconds, sigma is 0.61
6:09:53.893236 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:09:53.893236 INFO: Starting candidate selection
6:10:01.526086 INFO: Starting candidate scoring
6:10:06.401258 INFO: Finished candidate processing
6:10:06.401258 INFO: Collecting candidate features
6:10:07.022817 WARNING: intensity_correlation has 361 NaNs ( 0.17 % out of 208115)
6:10:07.070214 INFO: Collecting fragment features
6:10:07.342750 INFO: Finished candidate scoring
6:10:07.552766 PROGRESS: === Extracted 208115 precursors and 1156755 fragments ===
6:10:07.564355 INFO: performing precursor FDR with 47 features
6:10:07.564355 INFO: Decoy channel: -1
6:10:07.564355 INFO: Competetive: True
6:10:07.826268 WARNING: dropped 190 target PSMs due to missing features
6:10:07.826268 WARNING: dropped 171 decoy PSMs due to missing features
6:10:11.873484 INFO: Test AUC: 0.556
6:10:11.873484 INFO: Train AUC: 0.579
6:10:11.873484 INFO: AUC difference: 4.00%
6:10:12.080799 INFO: === FDR correction performed with classifier version 5 ===
6:10:12.080799 PROGRESS: ============================= Precursor FDR =============================
6:10:12.080799 PROGRESS: Total precursors accumulated: 764
6:10:12.080799 PROGRESS: Target precursors: 696 (91.10%)
6:10:12.080799 PROGRESS: Decoy precursors: 68 (8.90%)
6:10:12.080799 PROGRESS: 
6:10:12.080799 PROGRESS: Precursor Summary:
6:10:12.080799 PROGRESS: Channel   0:	 0.05 FDR:   536; 0.01 FDR:   384; 0.001 FDR:   283
6:10:12.080799 PROGRESS: 
6:10:12.080799 PROGRESS: Protein Summary:
6:10:12.097315 PROGRESS: Channel   0:	 0.05 FDR:   505; 0.01 FDR:   361; 0.001 FDR:   272
6:10:12.097315 PROGRESS: =========================================================================
6:10:12.112421 INFO: fragments_df_filtered: 1453
6:10:12.499072 INFO: calibration group: precursor, fitting rt estimator 
6:10:12.609090 INFO: calibration group: fragment, fitting mz estimator 
6:10:13.109979 INFO: calibration group: precursor, predicting mz
6:10:13.109979 WARNING: mz prediction was skipped as it has not been fitted yet
6:10:13.109979 INFO: calibration group: precursor, predicting rt
6:10:13.219839 INFO: calibration group: fragment, predicting mz
6:10:13.562840 INFO: === checking if optimization conditions were reached ===
6:10:13.562840 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
6:10:13.562840 PROGRESS: ✅ rt_error       : optimization complete. Optimal parameter 503.6492 found after 5 searches.
6:10:13.562840 INFO: ==============================================
6:10:13.562840 PROGRESS: Optimization finished for rt_error.
6:10:13.950093 INFO: calibration group: precursor, predicting mz
6:10:13.965715 WARNING: mz prediction was skipped as it has not been fitted yet
6:10:13.965715 INFO: calibration group: precursor, predicting rt
6:10:14.060189 INFO: calibration group: fragment, predicting mz
6:10:14.421587 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:10:14.421587 PROGRESS: ==============================================
6:10:14.421587 PROGRESS: ms2_error      : 10.0000
6:10:14.437320 PROGRESS: rt_error       : 503.6492
6:10:14.437320 PROGRESS: ==============================================
6:10:14.452956 INFO: calibration group: precursor, predicting mz
6:10:14.452956 WARNING: mz prediction was skipped as it has not been fitted yet
6:10:14.452956 INFO: calibration group: precursor, predicting rt
6:10:21.508094 INFO: calibration group: fragment, predicting mz
6:10:53.071732 PROGRESS: Extracting batch of 10640830 precursors
6:10:55.338878 INFO: Duty cycle consists of 151 frames, 5.84 seconds cycle time
6:10:55.339877 INFO: Duty cycle consists of 1 scans, 0.00000 1/K_0 resolution
6:10:55.339877 INFO: FWHM in RT is 17.08 seconds, sigma is 0.62
6:10:55.339877 INFO: FWHM in mobility is 0.000 1/K_0, sigma is 1.00
6:10:55.340779 INFO: Starting candidate selection
6:23:15.570025 INFO: Applying score cutoff of 73.89944689941406
6:23:15.910513 INFO: Removed 17622736 precursors with score below cutoff
6:23:19.074142 INFO: Starting candidate scoring
6:24:53.058325 INFO: Finished candidate processing
6:24:53.058325 INFO: Collecting candidate features
6:25:04.297717 INFO: Collecting fragment features
6:25:09.200423 INFO: Finished candidate scoring
6:25:18.646334 INFO: === FDR correction performed with classifier version 10 ===
6:25:18.646334 INFO: performing precursor FDR with 47 features
6:25:18.646334 INFO: Decoy channel: -1
6:25:18.646334 INFO: Competetive: True
6:26:30.320276 INFO: Test AUC: 0.581
6:26:30.320276 INFO: Train AUC: 0.586
6:26:30.320276 INFO: AUC difference: 0.76%
6:26:31.187881 INFO: Removing fragments below FDR threshold
6:26:31.709750 PROGRESS: ============================= Precursor FDR =============================
6:26:31.709750 PROGRESS: Total precursors accumulated: 45,856
6:26:31.709750 PROGRESS: Target precursors: 45,402 (99.01%)
6:26:31.709750 PROGRESS: Decoy precursors: 454 (0.99%)
6:26:31.713878 PROGRESS: 
6:26:31.713878 PROGRESS: Precursor Summary:
6:26:31.757930 PROGRESS: Channel   0:	 0.05 FDR: 45,402; 0.01 FDR: 45,402; 0.001 FDR: 30,770
6:26:31.757930 PROGRESS: 
6:26:31.757930 PROGRESS: Protein Summary:
6:26:31.854405 PROGRESS: Channel   0:	 0.05 FDR: 8,388; 0.01 FDR: 8,388; 0.001 FDR: 6,287
6:26:31.854405 PROGRESS: =========================================================================
6:26:32.948514 INFO: Finished workflow for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
6:27:32.822479 PROGRESS: Processing search outputs
6:27:32.823387 PROGRESS: Performing protein grouping and FDR
6:27:32.825544 INFO: Building output for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
6:27:33.036536 INFO: Building output for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
6:27:33.241478 INFO: Building output for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
6:27:33.430547 INFO: Building output for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
6:27:33.567894 INFO: Building output for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
6:27:33.646609 INFO: Building output for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
6:27:33.724824 INFO: Building combined output
6:27:34.403400 INFO: Performing protein inference
6:27:34.954644 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
6:27:59.217823 INFO: Performing protein FDR
6:28:08.899220 INFO: Normalizing q-values using 11,510 targets and 2,069 decoys
6:28:08.907227 INFO: Test AUC: 0.880
6:28:08.907227 INFO: Train AUC: 0.878
6:28:08.907227 INFO: AUC difference: 0.20%
6:28:09.770810 PROGRESS: ================ Protein FDR =================
6:28:09.770810 PROGRESS: Unique protein groups in output
6:28:09.770810 PROGRESS:   1% protein FDR: 6,889
6:28:09.770810 PROGRESS: 
6:28:09.770810 PROGRESS: Unique precursor in output
6:28:09.770810 PROGRESS:   1% protein FDR: 72,235
6:28:09.770810 PROGRESS: ================================================
6:28:09.770810 PROGRESS: Building search statistics
6:28:10.051996 INFO: Loaded OptimizationManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01\optimization_manager.pkl
6:28:10.067511 INFO: Initializing OptimizationManager
6:28:10.184156 INFO: Loaded OptimizationManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02\optimization_manager.pkl
6:28:10.200778 INFO: Initializing OptimizationManager
6:28:10.309502 INFO: Loaded OptimizationManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03\optimization_manager.pkl
6:28:10.333662 INFO: Initializing OptimizationManager
6:28:10.439774 INFO: Loaded OptimizationManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01\optimization_manager.pkl
6:28:10.439774 INFO: Initializing OptimizationManager
6:28:10.549386 INFO: Loaded OptimizationManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02\optimization_manager.pkl
6:28:10.549386 INFO: Initializing OptimizationManager
6:28:10.643693 INFO: Loaded OptimizationManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03\optimization_manager.pkl
6:28:10.659265 INFO: Initializing OptimizationManager
6:28:10.659265 INFO: Writing stat output to disk
6:28:10.659265 INFO: Saving D:\Proteobench_manuscript_data\run_output\alphadia_default\stat.tsv to disk
6:28:10.701496 PROGRESS: Building internal statistics
6:28:10.706506 INFO: Loaded TimingManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01\timing_manager.pkl
6:28:10.706506 INFO: Initializing TimingManager
6:28:10.706506 INFO: Loaded TimingManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02\timing_manager.pkl
6:28:10.706506 INFO: Initializing TimingManager
6:28:10.706506 INFO: Loaded TimingManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03\timing_manager.pkl
6:28:10.706506 INFO: Initializing TimingManager
6:28:10.706506 INFO: Loaded TimingManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01\timing_manager.pkl
6:28:10.706506 INFO: Initializing TimingManager
6:28:10.706506 INFO: Loaded TimingManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02\timing_manager.pkl
6:28:10.706506 INFO: Initializing TimingManager
6:28:10.706506 INFO: Loaded TimingManager from D:\Proteobench_manuscript_data\run_output\alphadia_default\.progress\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03\timing_manager.pkl
6:28:10.706506 INFO: Initializing TimingManager
6:28:10.706506 INFO: Writing internal output to disk
6:28:10.706506 INFO: Saving D:\Proteobench_manuscript_data\run_output\alphadia_default\internal.tsv to disk
6:28:10.722258 PROGRESS: Performing label free quantification
6:28:10.823793 INFO: Accumulating fragment data
6:28:10.839535 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
6:28:11.579931 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
6:28:12.854958 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
6:28:14.007851 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
6:28:15.269397 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
6:28:16.450445 INFO: reading frag file for LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
6:28:17.942302 PROGRESS: Performing label free quantification on the pg level
6:28:17.942302 INFO: Filtering fragments by quality
6:28:18.368423 INFO: Performing label-free quantification using directLFQ
6:28:20.603886 INFO: 6889 lfq-groups total
6:28:22.698249 INFO: using 10 processes
6:28:32.412211 INFO: Writing pg output to disk
6:28:32.412211 INFO: Saving D:\Proteobench_manuscript_data\run_output\alphadia_default\pg.matrix.tsv to disk
6:28:32.714729 INFO: Writing psm output to disk
6:28:32.714729 INFO: Saving D:\Proteobench_manuscript_data\run_output\alphadia_default\precursors.tsv to disk
6:29:02.175754 PROGRESS: Building spectral library
6:29:02.270160 INFO: Building MBR spectral library
6:29:02.270160 INFO: Running MbrLibraryBuilder
6:29:04.623568 INFO: MBR spectral library contains 72,235 precursors, 6,889 proteins
6:29:04.623568 INFO: Writing MBR spectral library to disk
6:29:05.908718 PROGRESS: =================== Search Finished ===================
6:29:44.511014 WARNING: WARNING: Temp mmap arrays were written to C:\Users\robbe\AppData\Local\Temp\temp_mmap_8v_pxnr2. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 53,300,146,176
