Spectronaut 19.7.250203.62635
Computer Name: b3f54014def5
User Domain Name: b3f54014def5
User Name: 
Analysis Mode: cmd
Analysis Type: directDIA
Analysis Date: 09-October-2025 10:43:49 UTC+0


[BEGIN-SETTINGS]
Settings Used: BGS Factory Settings
   ├─ DIA Analysis\Calibration
   │  ├─ MZ Extraction Strategy:	Maximum Intensity
   │  ├─ Allow source specific iRT Calibration:	True
   │  ├─ Precision iRT:	True
   │  │  ├─ Exclude De-amidated Peptides:	True
   │  │  └─ iRT <-> RT Regression Type:	Local (Non-Linear) Regression
   │  ├─ MS1 Mass Tolerance Strategy:	System Default
   │  └─ MS2 Mass Tolerance Strategy:	System Default
   ├─ DIA Analysis\Identification
   │  ├─ Precursor Qvalue Cutoff:	0.01
   │  ├─ Precursor PEP Cutoff:	0.2
   │  ├─ Protein Qvalue Cutoff (Experiment):	0.01
   │  ├─ Protein Qvalue Cutoff (Run):	0.05
   │  ├─ Protein PEP Cutoff:	0.75
   │  ├─ Single Hit Definition:	By Stripped Sequence
   │  ├─ Exclude Single Hit Proteins:	False
   │  ├─ Exclude Duplicate Assays:	True
   │  ├─ Exclude Predicted Fragment Scores:	False
   │  ├─ Generate Decoys:	True
   │  │  ├─ Decoy Generation Method:	Mutated
   │  │  │  └─ Preferred Fragment Source:	NN Predicted Fragments
   │  │  └─ Decoy Limit Strategy:	Dynamic
   │  │     └─ Library Size Fraction:	0.1
   │  └─ Pvalue Estimator:	Kernel Density Estimator
   ├─ DIA Analysis\Pipeline Mode
   │  ├─ Export All XICs:	False
   │  ├─ Generate SNE File:	True
   │  │  └─ Store Ion traces in SNE:	True
   │  ├─ Post Analysis Reports:	
   │  │  ├─ Binned CVs:	False
   │  │  ├─ Binned Identification:	False
   │  │  ├─ CV Density Line Chart:	False
   │  │  ├─ CVs Below X Bar Chart:	False
   │  │  ├─ Data Completeness Bar Chart:	False
   │  │  ├─ Run Identifications Bar Chart:	False
   │  │  └─ Scoring Histograms:	False
   │  ├─ Report Schema:	BGS Factory Report (Normal)
   │  └─ Reporting Unit:	Across Experiment
   ├─ DIA Analysis\Post Analysis
   │  ├─ Differential Abundance Testing:	Unpaired t-test
   │  │  ├─ Assume Equal Variance:	False
   │  │  ├─ Group-Wise Testing Correction:	False
   │  │  ├─ Log2 Ratio Candidate Filter:	0.58
   │  │  └─ Confidence Candidate Filter:	Qvalue
   │  │     └─ Confidence:	0.05
   │  ├─ Differential Abundance Grouping:	Major Group (Quantification Settings)
   │  │  └─ Smallest Quantitative Unit:	Major Group (Quantification Settings)
   │  │     └─ Use All MS-Level Quantities:	True
   │  ├─ Calculate Explained TIC:	None
   │  ├─ Calculate Sample Correlation Matrix:	False
   │  ├─ Gene Ontology:	/home/user/.config/Spectronaut/geneOntology/Ontologies/bgs_default_go-basic.obo
   │  └─ Hierarchical Clustering:	True
   │     ├─ Distance Metric:	Manhattan Distance
   │     ├─ Linkage Strategy:	Ward's Method
   │     ├─ Order Runs by Clustering:	True
   │     └─ Z-score Transformation:	False
   ├─ DIA Analysis\Protein Inference
   │  └─ Protein Inference Workflow:	Automatic
   │     └─ Inference Algorithm:	IDPicker
   ├─ DIA Analysis\PTM Workflow
   │  ├─ Input Normalization Strategy:	None
   │  └─ PTM Localization:	False
   ├─ DIA Analysis\Quantification
   │  ├─ Precursor Filtering:	Identified (Qvalue)
   │  │  ├─ Imputation Strategy:	None
   │  │  └─ Multi Channel Qvalue Filter:	Group Qvalue
   │  ├─ Proteotypicity Filter:	None
   │  ├─ Protein LFQ Method:	Automatic
   │  ├─ Quantity MS Level:	MS2
   │  ├─ Quantity Type:	Area
   │  ├─ Cross-Run Normalization:	True
   │  │  ├─ Normalization Filter Type:	None
   │  │  ├─ Normalization Strategy:	Automatic
   │  │  └─ Row Selection:	Automatic
   │  │     └─ Multi Channel Qvalue Filter:	Group Qvalue
   │  ├─ Quantification window:	Synchronized
   │  ├─ Interference Correction:	True
   │  │  ├─ Only Identified Peptides:	True
   │  │  ├─ Exclude All Multi-Channel Interferences:	True
   │  │  ├─ MS1 Min:	2
   │  │  └─ MS2 Min:	3
   │  ├─ Major (Protein) Grouping:	by Protein Group Id
   │  ├─ Minor (Peptide) Grouping:	by Stripped Sequence
   │  ├─ Major Group Quantity:	Mean peptide quantity
   │  ├─ Major Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Minor Group Quantity:	Mean precursor quantity
   │  ├─ Minor Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ DeepQuant Correction [Beta]:	False
   │  └─ Minimum Log2 Precursor Quantity:	0
   ├─ DIA Analysis\Workflow
   │  ├─ Method Evaluation:	False
   │  ├─ MS2 DeMultiplexing:	Automatic
   │  ├─ Multi-Channel Workflow Definition:	From Library Annotation
   │  │  └─ Fallback Option:	Labeled
   │  ├─ Profiling Strategy:	None
   │  ├─ Run Limit for directDIA Library:	-1
   │  ├─ Hybrid (DDA + DIA) Library:	False
   │  └─ Unify Peptide Peaks Strategy:	None
   ├─ DIA Analysis\XIC Extraction
   │  ├─ XIC IM Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ XIC RT Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ MS1 Mass Tolerance Strategy:	Dynamic
   │  │  └─ Correction Factor:	1
   │  └─ MS2 Mass Tolerance Strategy:	Dynamic
   │     └─ Correction Factor:	1
   ├─ Pulsar Search\Identification
   │  ├─ PSM FDR:	0.01
   │  ├─ Peptide FDR:	0.01
   │  ├─ Protein Group FDR:	0.01
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  │  └─ RT Sampling Reduction:	1
   │  └─ PTM Localization Filter:	False
   ├─ Pulsar Search\Labeling
   │  └─ Channels:	
   │     ├─ Channel 1:	False
   │     ├─ Channel 2:	False
   │     ├─ Channel 3:	False
   │     ├─ Channel 4:	False
   │     └─ Channel 5:	False
   ├─ Pulsar Search\Modifications
   │  ├─ Max Variable Modifications:	5
   │  └─ Select Modifications:	
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications: :	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin
   │  ├─ Digest Type:	Specific
   │  ├─ Decoy Generation Rule:	KR
   │  ├─ Max Peptide Length:	52
   │  ├─ Min Peptide Length:	7
   │  ├─ Missed Cleavages:	2
   │  └─ Toggle N-terminal M:	True
   ├─ Pulsar Search\Result Filters
   │  ├─ Fragment Ions:	
   │  │  ├─ Ion AA Length:	True
   │  │  │  └─ N:	3
   │  │  ├─ Ion Charge:	False
   │  │  ├─ Ion Loss Type:	False
   │  │  ├─ Ion Type:	False
   │  │  ├─ m/z :	True
   │  │  │  ├─ Max:	3000
   │  │  │  └─ Min:	200
   │  │  ├─ Overlapping between Channels:	False
   │  │  └─ Relative Intensity:	True
   │  │     └─ Min:	1
   │  └─ Precursors:	
   │     ├─ Amino Acids:	False
   │     ├─ Best N Fragments per Peptide:	True
   │     │  ├─ Max:	6
   │     │  └─ Min:	3
   │     ├─ Best N Peptides per Protein Group:	False
   │     ├─ Channel Count:	False
   │     ├─ FASTA Matched:	False
   │     ├─ Missed Cleavage:	False
   │     ├─ Modifications:	None
   │     ├─ Peptide Charge:	False
   │     └─ Proteotypicity:	False
   ├─ Pulsar Search\Speed-Up
   │  ├─ MS2 Index:	Automatic
   │  └─ diaPASEF Pre-Processing:	Automatic
   ├─ Pulsar Search\Tolerances
   │  └─ Tolerance Parameters:	
   │     ├─ Thermo IonTrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     ├─ Thermo Orbitrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     └─ TOF:	
   │        ├─ Calibration Search:	Dynamic
   │        │  ├─ MS1 Correction Factor:	1
   │        │  └─ MS2 Correction Factor:	1
   │        └─ Main Search:	Dynamic
   │           ├─ MS1 Correction Factor:	1
   │           └─ MS2 Correction Factor:	1
   └─ Pulsar Search\Workflow
      ├─ Fragment Ion Selection Strategy:	Intensity Based
      ├─ In-Silico Generate Missing Channels:	False
      └─ Use DNN Predicted Ion Mobility:	Auto
[END-SETTINGS]

[BEGIN-SETUP]
Run: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw
   ├─ Vendor: Thermo
   ├─ File: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1
   ├─ Path: "/scratch/A360_Spectronaut19/WU334896/work/input/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw"
   ├─ Condition: 200pg_50pg_H_Y
   ├─ Replicate: 1
   ├─ HTRMS Version: 19.7.250203.62635
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:21:35 UTC+0
   │     ├─ Date Modified: 09-October-2025 10:15:32 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400.4 - 420.4] - CV: -48
      ├─ [420.4 - 440.5] - CV: -48
      ├─ [440.5 - 460.5] - CV: -48
      ├─ [460.5 - 480.5] - CV: -48
      ├─ [480.5 - 500.5] - CV: -48
      ├─ [500.5 - 520.5] - CV: -48
      ├─ [520.5 - 540.5] - CV: -48
      ├─ [540.5 - 560.5] - CV: -48
      ├─ [560.5 - 580.5] - CV: -48
      ├─ [580.5 - 600.5] - CV: -48
      ├─ [600.5 - 620.5] - CV: -48
      ├─ [620.5 - 640.5] - CV: -48
      ├─ [640.5 - 660.6] - CV: -48
      ├─ [660.6 - 680.6] - CV: -48
      ├─ [680.6 - 700.6] - CV: -48
      ├─ [700.6 - 720.6] - CV: -48
      ├─ [720.6 - 740.6] - CV: -48
      ├─ [740.6 - 760.6] - CV: -48
      ├─ [760.6 - 780.6] - CV: -48
      └─ [780.6 - 800.6] - CV: -48

Run: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw
   ├─ Vendor: Thermo
   ├─ File: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2
   ├─ Path: "/scratch/A360_Spectronaut19/WU334896/work/input/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw"
   ├─ Condition: 200pg_50pg_H_Y
   ├─ Replicate: 4
   ├─ HTRMS Version: 19.7.250203.62635
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:21:35 UTC+0
   │     ├─ Date Modified: 09-October-2025 10:15:32 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400.4 - 420.4] - CV: -48
      ├─ [420.4 - 440.5] - CV: -48
      ├─ [440.5 - 460.5] - CV: -48
      ├─ [460.5 - 480.5] - CV: -48
      ├─ [480.5 - 500.5] - CV: -48
      ├─ [500.5 - 520.5] - CV: -48
      ├─ [520.5 - 540.5] - CV: -48
      ├─ [540.5 - 560.5] - CV: -48
      ├─ [560.5 - 580.5] - CV: -48
      ├─ [580.5 - 600.5] - CV: -48
      ├─ [600.5 - 620.5] - CV: -48
      ├─ [620.5 - 640.5] - CV: -48
      ├─ [640.5 - 660.6] - CV: -48
      ├─ [660.6 - 680.6] - CV: -48
      ├─ [680.6 - 700.6] - CV: -48
      ├─ [700.6 - 720.6] - CV: -48
      ├─ [720.6 - 740.6] - CV: -48
      ├─ [740.6 - 760.6] - CV: -48
      ├─ [760.6 - 780.6] - CV: -48
      └─ [780.6 - 800.6] - CV: -48

Run: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw
   ├─ Vendor: Thermo
   ├─ File: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3
   ├─ Path: "/scratch/A360_Spectronaut19/WU334896/work/input/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw"
   ├─ Condition: 200pg_50pg_H_Y
   ├─ Replicate: 3
   ├─ HTRMS Version: 19.7.250203.62635
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:21:35 UTC+0
   │     ├─ Date Modified: 09-October-2025 10:15:32 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400.4 - 420.4] - CV: -48
      ├─ [420.4 - 440.5] - CV: -48
      ├─ [440.5 - 460.5] - CV: -48
      ├─ [460.5 - 480.5] - CV: -48
      ├─ [480.5 - 500.5] - CV: -48
      ├─ [500.5 - 520.5] - CV: -48
      ├─ [520.5 - 540.5] - CV: -48
      ├─ [540.5 - 560.5] - CV: -48
      ├─ [560.5 - 580.5] - CV: -48
      ├─ [580.5 - 600.5] - CV: -48
      ├─ [600.5 - 620.5] - CV: -48
      ├─ [620.5 - 640.5] - CV: -48
      ├─ [640.5 - 660.6] - CV: -48
      ├─ [660.6 - 680.6] - CV: -48
      ├─ [680.6 - 700.6] - CV: -48
      ├─ [700.6 - 720.6] - CV: -48
      ├─ [720.6 - 740.6] - CV: -48
      ├─ [740.6 - 760.6] - CV: -48
      ├─ [760.6 - 780.6] - CV: -48
      └─ [780.6 - 800.6] - CV: -48

Run: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw
   ├─ Vendor: Thermo
   ├─ File: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1
   ├─ Path: "/scratch/A360_Spectronaut19/WU334896/work/input/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw"
   ├─ Condition: 240pg_10pg_H_Y
   ├─ Replicate: 6
   ├─ HTRMS Version: 19.7.250203.62635
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:21:35 UTC+0
   │     ├─ Date Modified: 09-October-2025 10:15:32 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400.4 - 420.4] - CV: -48
      ├─ [420.4 - 440.5] - CV: -48
      ├─ [440.5 - 460.5] - CV: -48
      ├─ [460.5 - 480.5] - CV: -48
      ├─ [480.5 - 500.5] - CV: -48
      ├─ [500.5 - 520.5] - CV: -48
      ├─ [520.5 - 540.5] - CV: -48
      ├─ [540.5 - 560.5] - CV: -48
      ├─ [560.5 - 580.5] - CV: -48
      ├─ [580.5 - 600.5] - CV: -48
      ├─ [600.5 - 620.5] - CV: -48
      ├─ [620.5 - 640.5] - CV: -48
      ├─ [640.5 - 660.6] - CV: -48
      ├─ [660.6 - 680.6] - CV: -48
      ├─ [680.6 - 700.6] - CV: -48
      ├─ [700.6 - 720.6] - CV: -48
      ├─ [720.6 - 740.6] - CV: -48
      ├─ [740.6 - 760.6] - CV: -48
      ├─ [760.6 - 780.6] - CV: -48
      └─ [780.6 - 800.6] - CV: -48

Run: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw
   ├─ Vendor: Thermo
   ├─ File: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2
   ├─ Path: "/scratch/A360_Spectronaut19/WU334896/work/input/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw"
   ├─ Condition: 240pg_10pg_H_Y
   ├─ Replicate: 5
   ├─ HTRMS Version: 19.7.250203.62635
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:21:35 UTC+0
   │     ├─ Date Modified: 09-October-2025 10:15:32 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400.4 - 420.4] - CV: -48
      ├─ [420.4 - 440.5] - CV: -48
      ├─ [440.5 - 460.5] - CV: -48
      ├─ [460.5 - 480.5] - CV: -48
      ├─ [480.5 - 500.5] - CV: -48
      ├─ [500.5 - 520.5] - CV: -48
      ├─ [520.5 - 540.5] - CV: -48
      ├─ [540.5 - 560.5] - CV: -48
      ├─ [560.5 - 580.5] - CV: -48
      ├─ [580.5 - 600.5] - CV: -48
      ├─ [600.5 - 620.5] - CV: -48
      ├─ [620.5 - 640.5] - CV: -48
      ├─ [640.5 - 660.6] - CV: -48
      ├─ [660.6 - 680.6] - CV: -48
      ├─ [680.6 - 700.6] - CV: -48
      ├─ [700.6 - 720.6] - CV: -48
      ├─ [720.6 - 740.6] - CV: -48
      ├─ [740.6 - 760.6] - CV: -48
      ├─ [760.6 - 780.6] - CV: -48
      └─ [780.6 - 800.6] - CV: -48

Run: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw
   ├─ Vendor: Thermo
   ├─ File: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3
   ├─ Path: "/scratch/A360_Spectronaut19/WU334896/work/input/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw"
   ├─ Condition: 240pg_10pg_H_Y
   ├─ Replicate: 2
   ├─ HTRMS Version: 19.7.250203.62635
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:21:35 UTC+0
   │     ├─ Date Modified: 09-October-2025 10:15:32 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400.4 - 420.4] - CV: -48
      ├─ [420.4 - 440.5] - CV: -48
      ├─ [440.5 - 460.5] - CV: -48
      ├─ [460.5 - 480.5] - CV: -48
      ├─ [480.5 - 500.5] - CV: -48
      ├─ [500.5 - 520.5] - CV: -48
      ├─ [520.5 - 540.5] - CV: -48
      ├─ [540.5 - 560.5] - CV: -48
      ├─ [560.5 - 580.5] - CV: -48
      ├─ [580.5 - 600.5] - CV: -48
      ├─ [600.5 - 620.5] - CV: -48
      ├─ [620.5 - 640.5] - CV: -48
      ├─ [640.5 - 660.6] - CV: -48
      ├─ [660.6 - 680.6] - CV: -48
      ├─ [680.6 - 700.6] - CV: -48
      ├─ [700.6 - 720.6] - CV: -48
      ├─ [720.6 - 740.6] - CV: -48
      ├─ [740.6 - 760.6] - CV: -48
      ├─ [760.6 - 780.6] - CV: -48
      └─ [780.6 - 800.6] - CV: -48

[END-SETUP]

[BEGIN-LOG]
INFO:    [09/10/2025 08:21:54] -> Reading report parameter...
INFO:    [09/10/2025 08:21:54] -> 1 valid runs added
INFO:    [09/10/2025 08:21:54] -> 1 valid runs added
INFO:    [09/10/2025 08:21:54] -> 1 valid runs added
INFO:    [09/10/2025 08:21:54] -> 1 valid runs added
INFO:    [09/10/2025 08:21:54] -> 1 valid runs added
INFO:    [09/10/2025 08:21:54] -> 1 valid runs added
INFO:    [09/10/2025 08:22:02] -> Set output destination to: /scratch/A360_Spectronaut19/WU334896/work/spectronaut/output_dir/20251009_082202_WU334896
INFO:    [09/10/2025 08:22:02] -> Selected Analysis Settings: BGS Factory Settings
INFO:    [09/10/2025 08:22:02] -> Initializing Pipeline...
INFO:    [09/10/2025 08:22:02] -> Preprocessing Run #1 of 6...
INFO:    [09/10/2025 08:22:02] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 08:22:02] -> Initialize Pipeline...
INFO:    [09/10/2025 08:22:02] -> Initialize Pipeline
INFO:    [09/10/2025 08:22:06] -> Initialize Pipeline...
INFO:    [09/10/2025 08:22:06] -> Creating Experiment Environment
INFO:    [09/10/2025 08:22:06] -> SuperRun 1/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw)
INFO:    [09/10/2025 08:22:07] -> Run 1/6: Organizing Data from Run
INFO:    [09/10/2025 08:22:07] -> Run 1/6: Creating Calibration Search Space...
INFO:    [09/10/2025 08:22:10] -> Collecting Search Space Parameters...
INFO:    [09/10/2025 08:22:20] -> Creating the Search Space...
INFO:    [09/10/2025 08:22:21] -> Run 1/6: Creating Search Space...
INFO:    [09/10/2025 08:22:21] -> Collecting Search Space Parameters...
INFO:    [09/10/2025 08:23:25] -> Creating the Search Space...
INFO:    [09/10/2025 08:23:25] -> Size of search space [MB]: 0
INFO:    [09/10/2025 08:23:25] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 08:23:25] -> Run 1/6: MS2 Index Generation
INFO:    [09/10/2025 08:27:30] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 08:27:30] -> Initializing...
INFO:    [09/10/2025 08:28:23] -> Finalizing HTRMS File...
INFO:    [09/10/2025 08:28:50] -> Processing Part 1 of 20
INFO:    [09/10/2025 08:28:51] -> Processing Part 2 of 20
INFO:    [09/10/2025 08:28:52] -> Processing Part 3 of 20
INFO:    [09/10/2025 08:28:52] -> Processing Part 4 of 20
INFO:    [09/10/2025 08:28:53] -> Processing Part 5 of 20
INFO:    [09/10/2025 08:28:54] -> Processing Part 6 of 20
INFO:    [09/10/2025 08:28:55] -> Processing Part 7 of 20
INFO:    [09/10/2025 08:28:56] -> Processing Part 8 of 20
INFO:    [09/10/2025 08:28:57] -> Processing Part 9 of 20
INFO:    [09/10/2025 08:28:57] -> Processing Part 10 of 20
INFO:    [09/10/2025 08:28:59] -> Processing Part 11 of 20
INFO:    [09/10/2025 08:29:02] -> Processing Part 12 of 20
INFO:    [09/10/2025 08:29:03] -> Processing Part 13 of 20
INFO:    [09/10/2025 08:29:04] -> Processing Part 14 of 20
INFO:    [09/10/2025 08:29:09] -> Processing Part 15 of 20
INFO:    [09/10/2025 08:29:09] -> Processing Part 16 of 20
INFO:    [09/10/2025 08:29:10] -> Processing Part 17 of 20
INFO:    [09/10/2025 08:29:11] -> Processing Part 18 of 20
INFO:    [09/10/2025 08:29:11] -> Processing Part 19 of 20
INFO:    [09/10/2025 08:29:12] -> Processing Part 20 of 20
INFO:    [09/10/2025 08:29:14] -> Nr of Features Requested: 242286
INFO:    [09/10/2025 08:29:14] -> Size of Featurespace: 242286
INFO:    [09/10/2025 08:29:14] -> Scans/Feature pairs that failed to Match: 40
INFO:    [09/10/2025 08:29:14] -> Maximum Nr of Features for one Scan: 90
INFO:    [09/10/2025 08:29:14] -> Finalizing...
INFO:    [09/10/2025 08:29:21] -> Processed in 31s
INFO:    [09/10/2025 08:29:21] -> Processed in 1.9m
INFO:    [09/10/2025 08:29:22] -> Done
INFO:    [09/10/2025 08:29:22] -> Run 1/6: Process Raw File...
INFO:    [09/10/2025 08:29:38] -> Run 1/6: Preparing Partitions...
INFO:    [09/10/2025 08:29:39] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [09/10/2025 08:29:40] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [09/10/2025 08:30:16] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [09/10/2025 08:31:05] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7340 [48.3s]
INFO:    [09/10/2025 08:31:38] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [09/10/2025 08:31:40] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [09/10/2025 08:31:40] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 08:32:09] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7325 [29.5s]
INFO:    [09/10/2025 08:32:09] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 08:32:31] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3307 [21.9s]
INFO:    [09/10/2025 08:32:31] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 08:32:56] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1336 [25.1s]
INFO:    [09/10/2025 08:32:56] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 08:33:33] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 662 [36.6s]
INFO:    [09/10/2025 08:33:33] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 08:34:02] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 309 [28.8s]
INFO:    [09/10/2025 08:34:02] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 08:34:31] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 138 [29s]
INFO:    [09/10/2025 08:36:18] -> Extracting 96684 MS1 XICs
INFO:    [09/10/2025 08:41:26] -> Run 1/6: Cleaning Up Run..
INFO:    [09/10/2025 08:41:27] -> SuperRun 2/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw)
INFO:    [09/10/2025 08:41:27] -> Run 2/6: Organizing Data from Run
INFO:    [09/10/2025 08:41:27] -> Run 2/6: Creating Calibration Search Space...
INFO:    [09/10/2025 08:41:27] -> Run 2/6: Creating Search Space...
INFO:    [09/10/2025 08:41:27] -> Size of search space [MB]: 0
INFO:    [09/10/2025 08:41:27] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 08:41:27] -> Run 2/6: MS2 Index Generation
INFO:    [09/10/2025 08:41:28] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 08:41:29] -> Initializing...
INFO:    [09/10/2025 08:42:11] -> Finalizing HTRMS File...
INFO:    [09/10/2025 08:42:42] -> Processing Part 1 of 20
INFO:    [09/10/2025 08:42:43] -> Processing Part 2 of 20
INFO:    [09/10/2025 08:42:44] -> Processing Part 3 of 20
INFO:    [09/10/2025 08:42:45] -> Processing Part 4 of 20
INFO:    [09/10/2025 08:42:46] -> Processing Part 5 of 20
INFO:    [09/10/2025 08:42:46] -> Processing Part 6 of 20
INFO:    [09/10/2025 08:42:47] -> Processing Part 7 of 20
INFO:    [09/10/2025 08:42:49] -> Processing Part 8 of 20
INFO:    [09/10/2025 08:42:50] -> Processing Part 9 of 20
INFO:    [09/10/2025 08:42:51] -> Processing Part 10 of 20
INFO:    [09/10/2025 08:42:55] -> Processing Part 11 of 20
INFO:    [09/10/2025 08:42:56] -> Processing Part 12 of 20
INFO:    [09/10/2025 08:42:57] -> Processing Part 13 of 20
INFO:    [09/10/2025 08:42:58] -> Processing Part 14 of 20
INFO:    [09/10/2025 08:42:59] -> Processing Part 15 of 20
INFO:    [09/10/2025 08:43:00] -> Processing Part 16 of 20
INFO:    [09/10/2025 08:43:01] -> Processing Part 17 of 20
INFO:    [09/10/2025 08:43:01] -> Processing Part 18 of 20
INFO:    [09/10/2025 08:43:02] -> Processing Part 19 of 20
INFO:    [09/10/2025 08:43:03] -> Processing Part 20 of 20
INFO:    [09/10/2025 08:43:05] -> Nr of Features Requested: 261706
INFO:    [09/10/2025 08:43:05] -> Size of Featurespace: 261706
INFO:    [09/10/2025 08:43:05] -> Scans/Feature pairs that failed to Match: 34
INFO:    [09/10/2025 08:43:05] -> Maximum Nr of Features for one Scan: 88
INFO:    [09/10/2025 08:43:05] -> Finalizing...
INFO:    [09/10/2025 08:43:16] -> Processed in 33.93s
INFO:    [09/10/2025 08:43:16] -> Processed in 1.8m
INFO:    [09/10/2025 08:43:16] -> Done
INFO:    [09/10/2025 08:43:16] -> Run 2/6: Process Raw File...
INFO:    [09/10/2025 08:43:42] -> Run 2/6: Preparing Partitions...
INFO:    [09/10/2025 08:43:42] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [09/10/2025 08:43:43] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [09/10/2025 08:44:12] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [09/10/2025 08:45:05] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7745 [53.4s]
INFO:    [09/10/2025 08:45:40] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [09/10/2025 08:45:41] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [09/10/2025 08:45:41] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 08:46:35] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7941 [54.1s]
INFO:    [09/10/2025 08:46:35] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 08:46:59] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3956 [24.2s]
INFO:    [09/10/2025 08:46:59] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 08:47:25] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1632 [25.1s]
INFO:    [09/10/2025 08:47:25] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 08:47:55] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 984 [30s]
INFO:    [09/10/2025 08:47:55] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 08:48:17] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 431 [22.3s]
INFO:    [09/10/2025 08:48:17] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 08:48:40] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 123 [23.3s]
INFO:    [09/10/2025 08:50:38] -> Extracting 101281 MS1 XICs
INFO:    [09/10/2025 08:56:12] -> Run 2/6: Cleaning Up Run..
INFO:    [09/10/2025 08:56:13] -> SuperRun 3/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw)
INFO:    [09/10/2025 08:56:13] -> Run 3/6: Organizing Data from Run
INFO:    [09/10/2025 08:56:13] -> Run 3/6: Creating Calibration Search Space...
INFO:    [09/10/2025 08:56:13] -> Run 3/6: Creating Search Space...
INFO:    [09/10/2025 08:56:13] -> Size of search space [MB]: 0
INFO:    [09/10/2025 08:56:13] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 08:56:13] -> Run 3/6: MS2 Index Generation
INFO:    [09/10/2025 08:56:15] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 08:56:15] -> Initializing...
INFO:    [09/10/2025 08:56:50] -> Finalizing HTRMS File...
INFO:    [09/10/2025 08:57:24] -> Processing Part 1 of 20
INFO:    [09/10/2025 08:57:27] -> Processing Part 2 of 20
INFO:    [09/10/2025 08:57:27] -> Processing Part 3 of 20
INFO:    [09/10/2025 08:57:28] -> Processing Part 4 of 20
INFO:    [09/10/2025 08:57:29] -> Processing Part 5 of 20
INFO:    [09/10/2025 08:57:30] -> Processing Part 6 of 20
INFO:    [09/10/2025 08:57:35] -> Processing Part 7 of 20
INFO:    [09/10/2025 08:57:36] -> Processing Part 8 of 20
INFO:    [09/10/2025 08:57:36] -> Processing Part 9 of 20
INFO:    [09/10/2025 08:57:37] -> Processing Part 10 of 20
INFO:    [09/10/2025 08:57:41] -> Processing Part 11 of 20
INFO:    [09/10/2025 08:57:46] -> Processing Part 12 of 20
INFO:    [09/10/2025 08:57:47] -> Processing Part 13 of 20
INFO:    [09/10/2025 08:57:48] -> Processing Part 14 of 20
INFO:    [09/10/2025 08:57:49] -> Processing Part 15 of 20
INFO:    [09/10/2025 08:57:51] -> Processing Part 16 of 20
INFO:    [09/10/2025 08:57:51] -> Processing Part 17 of 20
INFO:    [09/10/2025 08:57:52] -> Processing Part 18 of 20
INFO:    [09/10/2025 08:57:53] -> Processing Part 19 of 20
INFO:    [09/10/2025 08:57:53] -> Processing Part 20 of 20
INFO:    [09/10/2025 08:57:59] -> Nr of Features Requested: 258981
INFO:    [09/10/2025 08:57:59] -> Size of Featurespace: 258981
INFO:    [09/10/2025 08:57:59] -> Scans/Feature pairs that failed to Match: 25
INFO:    [09/10/2025 08:57:59] -> Maximum Nr of Features for one Scan: 89
INFO:    [09/10/2025 08:57:59] -> Finalizing...
INFO:    [09/10/2025 08:58:03] -> Processed in 39.57s
INFO:    [09/10/2025 08:58:03] -> Processed in 1.8m
INFO:    [09/10/2025 08:58:05] -> Done
INFO:    [09/10/2025 08:58:05] -> Run 3/6: Process Raw File...
INFO:    [09/10/2025 08:58:17] -> Run 3/6: Preparing Partitions...
INFO:    [09/10/2025 08:58:17] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [09/10/2025 08:58:18] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [09/10/2025 08:59:01] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [09/10/2025 08:59:54] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7530 [52.8s]
INFO:    [09/10/2025 09:00:27] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [09/10/2025 09:00:30] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [09/10/2025 09:00:30] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:01:18] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7729 [48s]
INFO:    [09/10/2025 09:01:18] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:01:38] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3171 [20.4s]
INFO:    [09/10/2025 09:01:38] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:02:05] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1470 [27s]
INFO:    [09/10/2025 09:02:05] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:02:27] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 813 [22.3s]
INFO:    [09/10/2025 09:02:27] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:02:56] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 410 [28.2s]
INFO:    [09/10/2025 09:02:56] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:03:15] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 47 [19.7s]
INFO:    [09/10/2025 09:04:49] -> Extracting 101841 MS1 XICs
INFO:    [09/10/2025 09:09:30] -> Run 3/6: Cleaning Up Run..
INFO:    [09/10/2025 09:09:34] -> SuperRun 4/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw)
INFO:    [09/10/2025 09:09:34] -> Run 4/6: Organizing Data from Run
INFO:    [09/10/2025 09:09:34] -> Run 4/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:09:34] -> Run 4/6: Creating Search Space...
INFO:    [09/10/2025 09:09:34] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:09:34] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:09:34] -> Run 4/6: MS2 Index Generation
INFO:    [09/10/2025 09:09:35] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:09:35] -> Initializing...
INFO:    [09/10/2025 09:10:05] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:10:25] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:10:28] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:10:28] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:10:29] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:10:29] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:10:30] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:10:31] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:10:31] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:10:33] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:10:33] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:10:34] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:10:34] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:10:37] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:10:38] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:10:38] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:10:39] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:10:40] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:10:41] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:10:41] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:10:42] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:10:44] -> Nr of Features Requested: 235139
INFO:    [09/10/2025 09:10:44] -> Size of Featurespace: 235139
INFO:    [09/10/2025 09:10:44] -> Scans/Feature pairs that failed to Match: 14
INFO:    [09/10/2025 09:10:44] -> Maximum Nr of Features for one Scan: 149
INFO:    [09/10/2025 09:10:44] -> Finalizing...
INFO:    [09/10/2025 09:10:48] -> Processed in 23.04s
INFO:    [09/10/2025 09:10:48] -> Processed in 1.2m
INFO:    [09/10/2025 09:10:49] -> Done
INFO:    [09/10/2025 09:10:49] -> Run 4/6: Process Raw File...
INFO:    [09/10/2025 09:11:00] -> Run 4/6: Preparing Partitions...
INFO:    [09/10/2025 09:11:01] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:11:02] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:11:34] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [09/10/2025 09:12:53] -> The number of PSMs identified during calibration with FDR <= 0.01 is 6952 [1.3m]
INFO:    [09/10/2025 09:13:16] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [09/10/2025 09:13:17] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [09/10/2025 09:13:17] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:13:44] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7011 [26.7s]
INFO:    [09/10/2025 09:13:44] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:14:02] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3421 [18.2s]
INFO:    [09/10/2025 09:14:02] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:14:25] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1319 [22.8s]
INFO:    [09/10/2025 09:14:25] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:14:47] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 620 [22.1s]
INFO:    [09/10/2025 09:14:47] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:15:03] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 319 [16s]
INFO:    [09/10/2025 09:15:03] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:15:20] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 101 [16.9s]
INFO:    [09/10/2025 09:16:42] -> Extracting 92719 MS1 XICs
INFO:    [09/10/2025 09:19:52] -> Run 4/6: Cleaning Up Run..
INFO:    [09/10/2025 09:19:59] -> SuperRun 5/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw)
INFO:    [09/10/2025 09:19:59] -> Run 5/6: Organizing Data from Run
INFO:    [09/10/2025 09:19:59] -> Run 5/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:19:59] -> Run 5/6: Creating Search Space...
INFO:    [09/10/2025 09:19:59] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:19:59] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:19:59] -> Run 5/6: MS2 Index Generation
INFO:    [09/10/2025 09:20:00] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:20:01] -> Initializing...
INFO:    [09/10/2025 09:20:28] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:21:00] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:21:02] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:21:03] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:21:04] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:21:04] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:21:05] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:21:06] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:21:08] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:21:09] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:21:09] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:21:10] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:21:11] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:21:16] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:21:16] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:21:17] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:21:18] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:21:18] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:21:19] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:21:19] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:21:20] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:21:23] -> Nr of Features Requested: 239509
INFO:    [09/10/2025 09:21:23] -> Size of Featurespace: 239509
INFO:    [09/10/2025 09:21:23] -> Scans/Feature pairs that failed to Match: 18
INFO:    [09/10/2025 09:21:23] -> Maximum Nr of Features for one Scan: 161
INFO:    [09/10/2025 09:21:23] -> Finalizing...
INFO:    [09/10/2025 09:21:28] -> Processed in 27.95s
INFO:    [09/10/2025 09:21:28] -> Processed in 1.5m
INFO:    [09/10/2025 09:21:29] -> Done
INFO:    [09/10/2025 09:21:29] -> Run 5/6: Process Raw File...
INFO:    [09/10/2025 09:21:40] -> Run 5/6: Preparing Partitions...
INFO:    [09/10/2025 09:21:40] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:21:41] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:22:15] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [09/10/2025 09:23:19] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7404 [1.1m]
INFO:    [09/10/2025 09:23:53] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [09/10/2025 09:23:54] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [09/10/2025 09:23:54] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:24:19] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7563 [25.3s]
INFO:    [09/10/2025 09:24:19] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:24:37] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3204 [17.3s]
INFO:    [09/10/2025 09:24:37] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:24:52] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1460 [15.1s]
INFO:    [09/10/2025 09:24:52] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:25:16] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 547 [24.6s]
INFO:    [09/10/2025 09:25:16] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:25:33] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 413 [17.2s]
INFO:    [09/10/2025 09:25:33] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:25:51] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 229 [17.8s]
INFO:    [09/10/2025 09:25:51] -> PERFORMING MAIN SEARCH 7
INFO:    [09/10/2025 09:26:10] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 117 [18.6s]
INFO:    [09/10/2025 09:27:28] -> Extracting 105758 MS1 XICs
INFO:    [09/10/2025 09:31:13] -> Run 5/6: Cleaning Up Run..
INFO:    [09/10/2025 09:31:16] -> SuperRun 6/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw)
INFO:    [09/10/2025 09:31:16] -> Run 6/6: Organizing Data from Run
INFO:    [09/10/2025 09:31:16] -> Run 6/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:31:16] -> Run 6/6: Creating Search Space...
INFO:    [09/10/2025 09:31:16] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:31:16] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:31:16] -> Run 6/6: MS2 Index Generation
INFO:    [09/10/2025 09:31:17] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:31:17] -> Initializing...
INFO:    [09/10/2025 09:31:43] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:32:04] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:32:10] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:32:11] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:32:12] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:32:12] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:32:13] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:32:14] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:32:15] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:32:16] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:32:18] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:32:19] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:32:20] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:32:24] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:32:25] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:32:26] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:32:26] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:32:27] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:32:27] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:32:28] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:32:30] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:32:32] -> Nr of Features Requested: 239830
INFO:    [09/10/2025 09:32:32] -> Size of Featurespace: 239848
INFO:    [09/10/2025 09:32:32] -> Scans/Feature pairs that failed to Match: 25
INFO:    [09/10/2025 09:32:32] -> Maximum Nr of Features for one Scan: 134
INFO:    [09/10/2025 09:32:32] -> Finalizing...
INFO:    [09/10/2025 09:32:36] -> Processed in 32.24s
INFO:    [09/10/2025 09:32:36] -> Processed in 1.3m
INFO:    [09/10/2025 09:32:37] -> Done
INFO:    [09/10/2025 09:32:37] -> Run 6/6: Process Raw File...
INFO:    [09/10/2025 09:32:49] -> Run 6/6: Preparing Partitions...
INFO:    [09/10/2025 09:32:49] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:32:50] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:33:34] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [09/10/2025 09:34:09] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7146 [35.4s]
INFO:    [09/10/2025 09:34:34] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [09/10/2025 09:34:36] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [09/10/2025 09:34:36] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:35:06] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7169 [30.2s]
INFO:    [09/10/2025 09:35:06] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:35:25] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3081 [19.2s]
INFO:    [09/10/2025 09:35:25] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:35:54] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1617 [28.4s]
INFO:    [09/10/2025 09:35:54] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:36:11] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 744 [17.6s]
INFO:    [09/10/2025 09:36:11] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:36:25] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 302 [13.6s]
INFO:    [09/10/2025 09:36:25] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:36:50] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 226 [25.2s]
INFO:    [09/10/2025 09:36:50] -> PERFORMING MAIN SEARCH 7
INFO:    [09/10/2025 09:37:15] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 131 [25.4s]
INFO:    [09/10/2025 09:38:32] -> Extracting 105898 MS1 XICs
INFO:    [09/10/2025 09:42:47] -> Run 6/6: Cleaning Up Run..
INFO:    [09/10/2025 09:42:52] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [09/10/2025 09:42:54] -> Score Post-Processing
INFO:    [09/10/2025 09:44:33] -> Score Post-Processing: 1.65m
INFO:    [09/10/2025 09:44:33] -> PSM FDR...
INFO:    [09/10/2025 09:44:46] -> PSM FDR: 13.35s
INFO:    [09/10/2025 09:44:46] -> Converting to non-redundant data structure...
INFO:    [09/10/2025 09:44:56] -> Performing Peptide FDR...
INFO:    [09/10/2025 09:44:59] -> Performing Protein Inference...
INFO:    [09/10/2025 09:45:05] -> Performing Protein FDR...
INFO:    [09/10/2025 09:45:08] -> Calculating Result Values at Run and Experiment Level...
INFO:    [09/10/2025 09:45:17] -> Pulsar identified 127421 PSMs, 29230 stripped sequences, 31077 peptide precursors, 6370 protein groups.
INFO:    [09/10/2025 09:45:17] -> Calculating Summary...
INFO:    [09/10/2025 09:45:18] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 09:45:19] -> iRT Calibration...
INFO:    [09/10/2025 09:45:44] -> Performing directDIA+ search...
INFO:    [09/10/2025 09:48:21] -> Generating directDIA+ search space
INFO:    [09/10/2025 09:50:07] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw
INFO:    [09/10/2025 09:53:03] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw
INFO:    [09/10/2025 09:57:02] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw
INFO:    [09/10/2025 10:00:27] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw
INFO:    [09/10/2025 10:03:00] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw
INFO:    [09/10/2025 10:06:36] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw
INFO:    [09/10/2025 10:09:50] -> Performing directDIA+ Post Processing...
INFO:    [09/10/2025 10:09:57] -> Writing experiment store..
INFO:    [09/10/2025 10:10:17] -> Assigning iRT Source...
INFO:    [09/10/2025 10:10:17] -> Calculating iRT...
INFO:    [09/10/2025 10:10:18] -> Cleaning Up Experiment...
INFO:    [09/10/2025 10:10:18] -> Summarizing Identifications
INFO:    [09/10/2025 10:15:46] -> Pipeline executed...
INFO:    [09/10/2025 10:15:49] -> Pipeline executed...
INFO:    [09/10/2025 10:15:53] -> Initializing Experiment...
INFO:    [09/10/2025 10:15:53] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:16:45] -> Initialize Scoring...
INFO:    [09/10/2025 10:16:45] -> Generating Scan Map...
INFO:    [09/10/2025 10:16:45] -> Initializing Workpackages...
INFO:    [09/10/2025 10:16:45] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:16:45] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:16:45] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:16:50] -> Initializing Pipeline...
INFO:    [09/10/2025 10:16:50] -> Preprocessing Run #1 of 6...
INFO:    [09/10/2025 10:16:50] -> Initialize Scoring...
INFO:    [09/10/2025 10:16:50] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:17:15] -> Machine Learning...
INFO:    [09/10/2025 10:17:17] -> Pipeline executed in 27.64s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:17:21] -> Initializing Pipeline...
INFO:    [09/10/2025 10:17:21] -> Preprocessing Run #1 of 6...
INFO:    [09/10/2025 10:17:21] -> Initialize Scoring...
INFO:    [09/10/2025 10:17:21] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:17:45] -> Machine Learning...
INFO:    [09/10/2025 10:17:57] -> Pipeline executed in 36.3s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:18:03] -> Initialize Scoring...
INFO:    [09/10/2025 10:18:03] -> Preprocessing Run #2 of 6...
INFO:    [09/10/2025 10:18:03] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:18:03] -> Initializing Experiment...
INFO:    [09/10/2025 10:18:03] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:18:03] -> Initialize Scoring...
INFO:    [09/10/2025 10:18:03] -> Generating Scan Map...
INFO:    [09/10/2025 10:18:03] -> Initializing Workpackages...
INFO:    [09/10/2025 10:18:03] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:18:04] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:18:04] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:18:06] -> Initializing Pipeline...
INFO:    [09/10/2025 10:18:06] -> Preprocessing Run #2 of 6...
INFO:    [09/10/2025 10:18:06] -> Initialize Scoring...
INFO:    [09/10/2025 10:18:06] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:18:34] -> Machine Learning...
INFO:    [09/10/2025 10:18:39] -> Pipeline executed in 32.73s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:18:44] -> Initializing Pipeline...
INFO:    [09/10/2025 10:18:44] -> Preprocessing Run #2 of 6...
INFO:    [09/10/2025 10:18:44] -> Initialize Scoring...
INFO:    [09/10/2025 10:18:44] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:19:21] -> Machine Learning...
INFO:    [09/10/2025 10:19:30] -> Pipeline executed in 45.87s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:19:34] -> Initialize Scoring...
INFO:    [09/10/2025 10:19:34] -> Preprocessing Run #3 of 6...
INFO:    [09/10/2025 10:19:34] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:19:34] -> Initializing Experiment...
INFO:    [09/10/2025 10:19:34] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:19:34] -> Initialize Scoring...
INFO:    [09/10/2025 10:19:34] -> Generating Scan Map...
INFO:    [09/10/2025 10:19:34] -> Initializing Workpackages...
INFO:    [09/10/2025 10:19:34] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:19:34] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:19:34] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:19:37] -> Initializing Pipeline...
INFO:    [09/10/2025 10:19:37] -> Preprocessing Run #3 of 6...
INFO:    [09/10/2025 10:19:37] -> Initialize Scoring...
INFO:    [09/10/2025 10:19:37] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:20:04] -> Machine Learning...
INFO:    [09/10/2025 10:20:08] -> Pipeline executed in 31.27s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:20:15] -> Initializing Pipeline...
INFO:    [09/10/2025 10:20:15] -> Preprocessing Run #3 of 6...
INFO:    [09/10/2025 10:20:15] -> Initialize Scoring...
INFO:    [09/10/2025 10:20:15] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:21:01] -> Machine Learning...
INFO:    [09/10/2025 10:21:13] -> Pipeline executed in 57.78s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:21:25] -> Initialize Scoring...
INFO:    [09/10/2025 10:21:25] -> Preprocessing Run #4 of 6...
INFO:    [09/10/2025 10:21:25] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:21:25] -> Initializing Experiment...
INFO:    [09/10/2025 10:21:25] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:21:25] -> Initialize Scoring...
INFO:    [09/10/2025 10:21:25] -> Generating Scan Map...
INFO:    [09/10/2025 10:21:25] -> Initializing Workpackages...
INFO:    [09/10/2025 10:21:25] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:21:25] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:21:25] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:21:27] -> Initializing Pipeline...
INFO:    [09/10/2025 10:21:27] -> Preprocessing Run #4 of 6...
INFO:    [09/10/2025 10:21:27] -> Initialize Scoring...
INFO:    [09/10/2025 10:21:27] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:21:51] -> Machine Learning...
INFO:    [09/10/2025 10:21:55] -> Pipeline executed in 27.93s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:22:02] -> Initializing Pipeline...
INFO:    [09/10/2025 10:22:02] -> Preprocessing Run #4 of 6...
INFO:    [09/10/2025 10:22:02] -> Initialize Scoring...
INFO:    [09/10/2025 10:22:02] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:22:52] -> Machine Learning...
INFO:    [09/10/2025 10:23:05] -> Pipeline executed in 1.05m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:23:17] -> Initialize Scoring...
INFO:    [09/10/2025 10:23:17] -> Preprocessing Run #5 of 6...
INFO:    [09/10/2025 10:23:17] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:23:17] -> Initializing Experiment...
INFO:    [09/10/2025 10:23:17] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:23:17] -> Initialize Scoring...
INFO:    [09/10/2025 10:23:17] -> Generating Scan Map...
INFO:    [09/10/2025 10:23:17] -> Initializing Workpackages...
INFO:    [09/10/2025 10:23:17] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:23:17] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:23:17] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:23:20] -> Initializing Pipeline...
INFO:    [09/10/2025 10:23:20] -> Preprocessing Run #5 of 6...
INFO:    [09/10/2025 10:23:20] -> Initialize Scoring...
INFO:    [09/10/2025 10:23:20] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:23:57] -> Machine Learning...
INFO:    [09/10/2025 10:24:02] -> Pipeline executed in 41.77s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:24:07] -> Initializing Pipeline...
INFO:    [09/10/2025 10:24:07] -> Preprocessing Run #5 of 6...
INFO:    [09/10/2025 10:24:07] -> Initialize Scoring...
INFO:    [09/10/2025 10:24:07] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:24:49] -> Machine Learning...
INFO:    [09/10/2025 10:24:58] -> Pipeline executed in 50.92s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:25:08] -> Initialize Scoring...
INFO:    [09/10/2025 10:25:08] -> Preprocessing Run #6 of 6...
INFO:    [09/10/2025 10:25:08] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:25:08] -> Initializing Experiment...
INFO:    [09/10/2025 10:25:08] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:25:08] -> Initialize Scoring...
INFO:    [09/10/2025 10:25:08] -> Generating Scan Map...
INFO:    [09/10/2025 10:25:08] -> Initializing Workpackages...
INFO:    [09/10/2025 10:25:08] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:25:09] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:25:09] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:25:12] -> Initializing Pipeline...
INFO:    [09/10/2025 10:25:12] -> Preprocessing Run #6 of 6...
INFO:    [09/10/2025 10:25:12] -> Initialize Scoring...
INFO:    [09/10/2025 10:25:12] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:25:45] -> Machine Learning...
INFO:    [09/10/2025 10:25:48] -> Pipeline executed in 36.12s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:25:51] -> Initializing Pipeline...
INFO:    [09/10/2025 10:25:51] -> Preprocessing Run #6 of 6...
INFO:    [09/10/2025 10:25:51] -> Initialize Scoring...
INFO:    [09/10/2025 10:25:51] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:26:15] -> Machine Learning...
INFO:    [09/10/2025 10:26:21] -> Pipeline executed in 29.73s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:26:26] -> Initialize Scoring...
INFO:    [09/10/2025 10:26:26] -> Initializing QC...
INFO:    [09/10/2025 10:26:27] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:26:27] -> Assigning ML Features...
INFO:    [09/10/2025 10:26:27] -> Generating Decoys...
INFO:    [09/10/2025 10:26:39] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:28:10] -> Releasing Raw Files...
INFO:    [09/10/2025 10:28:11] -> Machine Learning...
INFO:    [09/10/2025 10:28:53] -> Initializing HTRMS...
INFO:    [09/10/2025 10:28:53] -> Releasing Run Resources...
INFO:    [09/10/2025 10:28:54] -> Reducing Score Cache...
INFO:    [09/10/2025 10:28:57] -> Calculating Qvalues...
INFO:    [09/10/2025 10:28:58] -> Unique precursors: 47,481 of 50,071 | modified peptides: 46,207 of 48,691 | peptides: 44,467 of 46,344 |  protein groups: 8,391 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw]
INFO:    [09/10/2025 10:28:58] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:28:59] -> Processed in 2.54m
INFO:    [09/10/2025 10:29:00] -> Initializing QC...
INFO:    [09/10/2025 10:29:00] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:29:00] -> Assigning ML Features...
INFO:    [09/10/2025 10:29:00] -> Generating Decoys...
INFO:    [09/10/2025 10:29:01] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:30:36] -> Releasing Raw Files...
INFO:    [09/10/2025 10:30:36] -> Machine Learning...
INFO:    [09/10/2025 10:31:09] -> Initializing HTRMS...
INFO:    [09/10/2025 10:31:09] -> Releasing Run Resources...
INFO:    [09/10/2025 10:31:10] -> Reducing Score Cache...
INFO:    [09/10/2025 10:31:12] -> Calculating Qvalues...
INFO:    [09/10/2025 10:31:12] -> Unique precursors: 48,385 of 50,071 | modified peptides: 47,105 of 48,691 | peptides: 44,830 of 46,344 |  protein groups: 8,440 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw]
INFO:    [09/10/2025 10:31:12] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:31:13] -> Processed in 2.23m
INFO:    [09/10/2025 10:31:19] -> Initializing QC...
INFO:    [09/10/2025 10:31:20] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:31:20] -> Assigning ML Features...
INFO:    [09/10/2025 10:31:20] -> Generating Decoys...
INFO:    [09/10/2025 10:31:20] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:33:10] -> Releasing Raw Files...
INFO:    [09/10/2025 10:33:11] -> Machine Learning...
INFO:    [09/10/2025 10:33:40] -> Initializing HTRMS...
INFO:    [09/10/2025 10:33:41] -> Releasing Run Resources...
INFO:    [09/10/2025 10:33:42] -> Reducing Score Cache...
INFO:    [09/10/2025 10:33:46] -> Calculating Qvalues...
INFO:    [09/10/2025 10:33:47] -> Unique precursors: 48,188 of 50,071 | modified peptides: 46,910 of 48,691 | peptides: 44,627 of 46,344 |  protein groups: 8,408 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw]
INFO:    [09/10/2025 10:33:48] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:33:48] -> Processed in 2.48m
INFO:    [09/10/2025 10:33:49] -> Initializing QC...
INFO:    [09/10/2025 10:33:49] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:33:49] -> Assigning ML Features...
INFO:    [09/10/2025 10:33:49] -> Generating Decoys...
INFO:    [09/10/2025 10:33:50] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:35:21] -> Releasing Raw Files...
INFO:    [09/10/2025 10:35:22] -> Machine Learning...
INFO:    [09/10/2025 10:35:53] -> Initializing HTRMS...
INFO:    [09/10/2025 10:35:54] -> Releasing Run Resources...
INFO:    [09/10/2025 10:35:54] -> Reducing Score Cache...
INFO:    [09/10/2025 10:35:57] -> Calculating Qvalues...
INFO:    [09/10/2025 10:35:57] -> Unique precursors: 45,669 of 50,071 | modified peptides: 44,459 of 48,691 | peptides: 42,850 of 46,344 |  protein groups: 8,056 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw]
INFO:    [09/10/2025 10:35:57] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:35:58] -> Processed in 2.15m
INFO:    [09/10/2025 10:35:58] -> Initializing QC...
INFO:    [09/10/2025 10:35:58] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:35:59] -> Assigning ML Features...
INFO:    [09/10/2025 10:35:59] -> Generating Decoys...
INFO:    [09/10/2025 10:36:00] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:37:35] -> Releasing Raw Files...
INFO:    [09/10/2025 10:37:36] -> Machine Learning...
INFO:    [09/10/2025 10:38:06] -> Initializing HTRMS...
INFO:    [09/10/2025 10:38:06] -> Releasing Run Resources...
INFO:    [09/10/2025 10:38:07] -> Reducing Score Cache...
INFO:    [09/10/2025 10:38:09] -> Calculating Qvalues...
INFO:    [09/10/2025 10:38:10] -> Unique precursors: 45,924 of 50,071 | modified peptides: 44,698 of 48,691 | peptides: 42,968 of 46,344 |  protein groups: 8,105 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw]
INFO:    [09/10/2025 10:38:10] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:38:10] -> Processed in 2.2m
INFO:    [09/10/2025 10:38:11] -> Initializing QC...
INFO:    [09/10/2025 10:38:11] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:38:11] -> Assigning ML Features...
INFO:    [09/10/2025 10:38:11] -> Generating Decoys...
INFO:    [09/10/2025 10:38:11] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:39:49] -> Releasing Raw Files...
INFO:    [09/10/2025 10:39:50] -> Machine Learning...
INFO:    [09/10/2025 10:40:32] -> Initializing HTRMS...
INFO:    [09/10/2025 10:40:33] -> Releasing Run Resources...
INFO:    [09/10/2025 10:40:33] -> Reducing Score Cache...
INFO:    [09/10/2025 10:40:37] -> Calculating Qvalues...
INFO:    [09/10/2025 10:40:37] -> Unique precursors: 45,934 of 50,071 | modified peptides: 44,692 of 48,691 | peptides: 42,961 of 46,344 |  protein groups: 8,085 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw]
INFO:    [09/10/2025 10:40:38] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:40:38] -> Processed in 2.46m
INFO:    [09/10/2025 10:40:40] -> Normalizing Cscores...
INFO:    [09/10/2025 10:40:42] -> Initializing Protein Groups...
INFO:    [09/10/2025 10:41:10] -> Correcting Interferences...
INFO:    [09/10/2025 10:41:36] -> Calculating Global CVs
INFO:    [09/10/2025 10:41:37] -> Calculating Precursor Quantities...
INFO:    [09/10/2025 10:41:39] -> Normalizing Quantification...
INFO:    [09/10/2025 10:41:40] -> Performing Local Normalization...
INFO:    [09/10/2025 10:41:43] -> Calculating Global CVs
INFO:    [09/10/2025 10:41:45] -> Calculating Condition CVs
INFO:    [09/10/2025 10:41:48] -> Excluding Library Duplicates...
INFO:    [09/10/2025 10:41:50] -> Calculating Global CVs
INFO:    [09/10/2025 10:41:52] -> Building Protein Groups...
INFO:    [09/10/2025 10:42:15] -> Calculating Run-Wise Protein Group FDR...
INFO:    [09/10/2025 10:42:18] -> Annotating Protein Single Hits...
INFO:    [09/10/2025 10:42:20] -> Calculating Global CVs
INFO:    [09/10/2025 10:42:21] -> Updating Identification Counts...
INFO:    [09/10/2025 10:42:24] -> Resetting existing imputation...
INFO:    [09/10/2025 10:42:25] -> Calculating Protein Quantities...
INFO:    [09/10/2025 10:42:27] -> Calculating Protein Quantities...
INFO:    [09/10/2025 10:42:27] -> Calculating MaxLFQ Protein Quantities...
INFO:    [09/10/2025 10:42:31] -> Collapsing PTM-Locations...
INFO:    [09/10/2025 10:42:32] -> PTM Stoichiometry calculation...
INFO:    [09/10/2025 10:42:33] -> Creating Protein Map...
INFO:    [09/10/2025 10:42:34] -> Compiling Run Summary Information...
INFO:    [09/10/2025 10:42:35] -> Running Post Analysis Processes...
INFO:    [09/10/2025 10:42:42] -> Saving Qc Data...
INFO:    [09/10/2025 10:42:44] -> No QC Generated for "20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3": Insufficient QC peptides found.
INFO:    [09/10/2025 10:42:44] -> No QC Generated for "20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1": Insufficient QC peptides found.
INFO:    [09/10/2025 10:42:44] -> No QC Generated for "20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2": Insufficient QC peptides found.
INFO:    [09/10/2025 10:42:44] -> No QC Generated for "20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3": Insufficient QC peptides found.
INFO:    [09/10/2025 10:42:46] -> Generating Output
INFO:    [09/10/2025 10:42:47] -> Generating Experiment Report
INFO:    [09/10/2025 10:43:37] -> WU334896_Report_BGS Factory Report (Normal).tsv
INFO:    [09/10/2025 10:43:37] -> Generating RT Recalibration Report
INFO:    [09/10/2025 10:43:38] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw_1_iRTCalibration.tsv
INFO:    [09/10/2025 10:43:38] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw_2_iRTCalibration.tsv
INFO:    [09/10/2025 10:43:38] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw_3_iRTCalibration.tsv
INFO:    [09/10/2025 10:43:38] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw_4_iRTCalibration.tsv
INFO:    [09/10/2025 10:43:38] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw_5_iRTCalibration.tsv
INFO:    [09/10/2025 10:43:38] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw_6_iRTCalibration.tsv
INFO:    [09/10/2025 10:43:38] -> Generating Run Meta Report
INFO:    [09/10/2025 10:43:40] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw_1_RunOverview.tsv
INFO:    [09/10/2025 10:43:40] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw_2_RunOverview.tsv
INFO:    [09/10/2025 10:43:40] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw_3_RunOverview.tsv
INFO:    [09/10/2025 10:43:40] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw_4_RunOverview.tsv
INFO:    [09/10/2025 10:43:40] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw_5_RunOverview.tsv
INFO:    [09/10/2025 10:43:40] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw_6_RunOverview.tsv
INFO:    [09/10/2025 10:43:40] -> Generating Post Analysis Reports
INFO:    [09/10/2025 10:43:48] -> WU334896_AnalysisOverview.txt
INFO:    [09/10/2025 10:43:48] -> Precursor CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:43:48] -> Peptide CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:43:48] -> Protein Group CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:43:48] -> Protein CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:43:48] -> RunIdentifications.tsv
INFO:    [09/10/2025 10:43:48] -> Candidates.tsv
INFO:    [09/10/2025 10:43:48] -> Generating PTM Site Report
INFO:    [09/10/2025 10:43:49] -> Generating Condition Setup Report
INFO:    [09/10/2025 10:43:49] -> WU334896_ConditionSetup.tsv
INFO:    [09/10/2025 10:43:49] -> Generating Experiment Settings Report
[END-LOG]
