Spectronaut 20.1.250624.92449
Computer Name: 5250a1ae9606
User Domain Name: 5250a1ae9606
User Name: 
Analysis Mode: cmd
Analysis Type: directDIA
Analysis Date: 09-October-2025 10:49:38 UTC +00:00 


[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 Qvalue Cutoff (Experiment):	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
   │  ├─ Single Hit Protein Rule:	Keep Single Hit Proteins
   │  ├─ Run-Level Protein Scoring:	All Observations
   │  ├─ 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
   │  ├─ Export report in Parquet format:	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
   │  │  ├─ Modification Enrichment:	False
   │  │  ├─ Run Identifications Bar Chart:	False
   │  │  ├─ Scoring Histograms:	False
   │  │  └─ TIC Overlay:	False
   │  ├─ PTM Report Schema:	
   │  ├─ 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:	False
   │  ├─ 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
   │  ├─ Perform background noise removal:	True
   │  ├─ Quantification window:	Synchronized
   │  ├─ Interference Correction:	True
   │  │  ├─ Only Identified Peptides:	True
   │  │  ├─ Exclude All Multi-Channel Interferences:	True
   │  │  ├─ MS1 Min:	2
   │  │  └─ MS2 Min:	3
   │  ├─ Major Group Quantity:	Mean peptide quantity
   │  ├─ Minor (Peptide) Grouping:	by Stripped Sequence
   │  ├─ Major (Protein) Grouping:	by Protein Group Id
   │  ├─ Major Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Minor Group Quantity:	Mean precursor quantity
   │  ├─ Minor Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Use Log2 Quantity Filter:	True
   │  │  └─ Minimum Log2 Precursor Quantity:	0
   │  └─ Perform IM Peak Picking for Quantification:	True
   ├─ 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
   │  ├─ Grouped Peptide FDR:	None
   │  ├─ PSM FDR:	0.01
   │  ├─ Peptide FDR:	0.01
   │  ├─ Protein Group FDR:	0.01
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  │  ├─ IM Sampling Reduction:	7
   │  │  └─ RT Sampling Reduction:	1
   │  └─ PTM Localization Filter:	False
   ├─ Pulsar Search\iRT Calibration
   │  ├─ Calibrate from Empirical RT:	False
   │  ├─ Auto-assign iRT source:	True
   │  ├─ iRT Reference Strategy:	Deep Learning Assisted iRT Regression
   │  ├─ Use Source Specific iRT:	Auto
   │  └─ Minimum Rsquare:	0.8
   ├─ Pulsar Search\Labeling
   │  └─ Channels:	
   │     ├─ Channel 1:	False
   │     ├─ Channel 2:	False
   │     ├─ Channel 3:	False
   │     ├─ Channel 4:	False
   │     └─ Channel 5:	False
   ├─ Pulsar Search\Modifications
   │  └─ Search Mode:	Closed Search
   │     ├─ Max Variable Modifications:	5
   │     ├─ 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/A382_Spectronaut20/WU334900/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: 20.1.250624.92449
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:36:05 UTC +00:00 
   │     ├─ Date Modified: 09-October-2025 10:23:39 UTC +00:00 
   │     └─ 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/A382_Spectronaut20/WU334900/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: 20.1.250624.92449
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:36:05 UTC +00:00 
   │     ├─ Date Modified: 09-October-2025 10:23:39 UTC +00:00 
   │     └─ 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/A382_Spectronaut20/WU334900/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: 20.1.250624.92449
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:36:05 UTC +00:00 
   │     ├─ Date Modified: 09-October-2025 10:23:39 UTC +00:00 
   │     └─ 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/A382_Spectronaut20/WU334900/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: 20.1.250624.92449
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:36:05 UTC +00:00 
   │     ├─ Date Modified: 09-October-2025 10:23:39 UTC +00:00 
   │     └─ 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/A382_Spectronaut20/WU334900/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: 20.1.250624.92449
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:36:05 UTC +00:00 
   │     ├─ Date Modified: 09-October-2025 10:23:39 UTC +00:00 
   │     └─ 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/A382_Spectronaut20/WU334900/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: 20.1.250624.92449
   ├─ Protein Databases Used
   │  └─ p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Protein Entries: 27,488
   │     ├─ Original File: p34486_ProteoBenchFASTA_DDAQuantification_noecoli.fasta
   │     ├─ Date Created: 09-October-2025 08:36:05 UTC +00:00 
   │     ├─ Date Modified: 09-October-2025 10:23:39 UTC +00:00 
   │     └─ 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 08:36:19] -> Reading report parameter...
INFO:    [09/10/2025 08:36:19] -> 1 valid runs added
INFO:    [09/10/2025 08:36:19] -> 1 valid runs added
INFO:    [09/10/2025 08:36:19] -> 1 valid runs added
INFO:    [09/10/2025 08:36:19] -> 1 valid runs added
INFO:    [09/10/2025 08:36:19] -> 1 valid runs added
INFO:    [09/10/2025 08:36:19] -> 1 valid runs added
INFO:    [09/10/2025 08:36:30] -> Set output destination to: /scratch/A382_Spectronaut20/WU334900/work/spectronaut/output_dir/20251009_083630_WU334900
INFO:    [09/10/2025 08:36:30] -> Selected Analysis Settings: BGS Factory Settings
INFO:    [09/10/2025 08:36:31] -> Initializing Pipeline...
INFO:    [09/10/2025 08:36:31] -> Preprocessing Run #1 of 6...
INFO:    [09/10/2025 08:36:31] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 08:36:31] -> Initialize Pipeline...
INFO:    [09/10/2025 08:36:31] -> Initialize Pipeline
INFO:    [09/10/2025 08:36:37] -> Initialize Pipeline...
INFO:    [09/10/2025 08:36:37] -> Creating Experiment Environment
INFO:    [09/10/2025 08:36:39] -> SuperRun 1/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw)
INFO:    [09/10/2025 08:36:39] -> Run 1/6: Organizing Data from Run
INFO:    [09/10/2025 08:36:39] -> Run 1/6: Creating Calibration Search Space...
INFO:    [09/10/2025 08:36:43] -> Collecting Search Space Parameters...
INFO:    [09/10/2025 08:37:02] -> Creating the Search Space...
INFO:    [09/10/2025 08:37:04] -> Run 1/6: Creating Search Space...
INFO:    [09/10/2025 08:37:04] -> Collecting Search Space Parameters...
INFO:    [09/10/2025 08:39:15] -> Creating the Search Space...
INFO:    [09/10/2025 08:39:17] -> Size of search space [MB]: 0
INFO:    [09/10/2025 08:39:17] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 08:39:17] -> Run 1/6: MS2 Index Generation
INFO:    [09/10/2025 08:44:46] -> MS2 Index Generation Time: 5.5m
INFO:    [09/10/2025 08:44:46] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 08:44:47] -> Initializing...
INFO:    [09/10/2025 08:45:21] -> Finalizing HTRMS File...
INFO:    [09/10/2025 08:46:11] -> Processing Part 1 of 20
INFO:    [09/10/2025 08:46:12] -> Processing Part 2 of 20
INFO:    [09/10/2025 08:46:13] -> Processing Part 3 of 20
INFO:    [09/10/2025 08:46:14] -> Processing Part 4 of 20
INFO:    [09/10/2025 08:46:15] -> Processing Part 5 of 20
INFO:    [09/10/2025 08:46:16] -> Processing Part 6 of 20
INFO:    [09/10/2025 08:46:17] -> Processing Part 7 of 20
INFO:    [09/10/2025 08:46:18] -> Processing Part 8 of 20
INFO:    [09/10/2025 08:46:19] -> Processing Part 9 of 20
INFO:    [09/10/2025 08:46:19] -> Processing Part 10 of 20
INFO:    [09/10/2025 08:46:20] -> Processing Part 11 of 20
INFO:    [09/10/2025 08:46:28] -> Processing Part 12 of 20
INFO:    [09/10/2025 08:46:29] -> Processing Part 13 of 20
INFO:    [09/10/2025 08:46:30] -> Processing Part 14 of 20
INFO:    [09/10/2025 08:46:32] -> Processing Part 15 of 20
INFO:    [09/10/2025 08:46:33] -> Processing Part 16 of 20
INFO:    [09/10/2025 08:46:33] -> Processing Part 17 of 20
INFO:    [09/10/2025 08:46:34] -> Processing Part 18 of 20
INFO:    [09/10/2025 08:46:40] -> Processing Part 19 of 20
INFO:    [09/10/2025 08:46:41] -> Processing Part 20 of 20
INFO:    [09/10/2025 08:46:42] -> Nr of Features Requested: 242271
INFO:    [09/10/2025 08:46:42] -> Size of Featurespace: 242271
INFO:    [09/10/2025 08:46:42] -> Scans/Feature pairs that failed to Match: 40
INFO:    [09/10/2025 08:46:42] -> Maximum Nr of Features for one Scan: 90
INFO:    [09/10/2025 08:46:42] -> Finalizing...
INFO:    [09/10/2025 08:46:50] -> Processed in 38.78s
INFO:    [09/10/2025 08:46:50] -> Processed in 2m
INFO:    [09/10/2025 08:46:50] -> Done
INFO:    [09/10/2025 08:46:50] -> Run 1/6: Process Raw File...
INFO:    [09/10/2025 08:47:07] -> Run 1/6: Preparing Partitions...
INFO:    [09/10/2025 08:47:08] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [09/10/2025 08:47:09] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [09/10/2025 08:48:00] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [09/10/2025 08:48:47] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7316 [47s]
INFO:    [09/10/2025 08:50:24] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [09/10/2025 08:50:26] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [09/10/2025 08:50:26] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 08:50:53] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7317 [27.1s]
INFO:    [09/10/2025 08:50:53] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 08:51:26] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3339 [33.5s]
INFO:    [09/10/2025 08:51:26] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 08:51:55] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1341 [28.9s]
INFO:    [09/10/2025 08:51:55] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 08:52:38] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 660 [42.7s]
INFO:    [09/10/2025 08:52:38] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 08:53:02] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 305 [24.2s]
INFO:    [09/10/2025 08:53:02] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 08:53:32] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 137 [29.5s]
INFO:    [09/10/2025 08:56:52] -> Extracting 96673 MS1 XICs
INFO:    [09/10/2025 08:59:34] -> Run 1/6: Cleaning Up Run...
INFO:    [09/10/2025 08:59:35] -> SuperRun 2/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw)
INFO:    [09/10/2025 08:59:35] -> Run 2/6: Organizing Data from Run
INFO:    [09/10/2025 08:59:35] -> Run 2/6: Creating Calibration Search Space...
INFO:    [09/10/2025 08:59:35] -> Run 2/6: Creating Search Space...
INFO:    [09/10/2025 08:59:35] -> Size of search space [MB]: 0
INFO:    [09/10/2025 08:59:35] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 08:59:35] -> Run 2/6: MS2 Index Generation
INFO:    [09/10/2025 08:59:36] -> MS2 Index Generation Time: 927.93ms
INFO:    [09/10/2025 08:59:36] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 08:59:36] -> Initializing...
INFO:    [09/10/2025 08:59:57] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:00:42] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:00:43] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:00:44] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:00:45] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:00:47] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:00:48] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:00:49] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:00:50] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:00:51] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:00:52] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:00:57] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:00:58] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:00:58] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:00:59] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:01:00] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:01:01] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:01:01] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:01:02] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:01:03] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:01:06] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:01:09] -> Nr of Features Requested: 261700
INFO:    [09/10/2025 09:01:09] -> Size of Featurespace: 261700
INFO:    [09/10/2025 09:01:09] -> Scans/Feature pairs that failed to Match: 34
INFO:    [09/10/2025 09:01:09] -> Maximum Nr of Features for one Scan: 86
INFO:    [09/10/2025 09:01:09] -> Finalizing...
INFO:    [09/10/2025 09:01:19] -> Processed in 37s
INFO:    [09/10/2025 09:01:19] -> Processed in 1.7m
INFO:    [09/10/2025 09:01:20] -> Done
INFO:    [09/10/2025 09:01:20] -> Run 2/6: Process Raw File...
INFO:    [09/10/2025 09:01:43] -> Run 2/6: Preparing Partitions...
INFO:    [09/10/2025 09:01:43] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:01:44] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:02:17] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [09/10/2025 09:03:01] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7746 [43.7s]
INFO:    [09/10/2025 09:04:13] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [09/10/2025 09:04:15] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [09/10/2025 09:04:15] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:04:41] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7878 [26s]
INFO:    [09/10/2025 09:04:41] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:05:01] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3921 [20.2s]
INFO:    [09/10/2025 09:05:01] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:05:46] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1723 [44.9s]
INFO:    [09/10/2025 09:05:46] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:06:04] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 981 [17.3s]
INFO:    [09/10/2025 09:06:04] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:06:30] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 504 [26.3s]
INFO:    [09/10/2025 09:06:30] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:06:57] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 126 [27.3s]
INFO:    [09/10/2025 09:10:04] -> Extracting 101284 MS1 XICs
INFO:    [09/10/2025 09:12:48] -> Run 2/6: Cleaning Up Run...
INFO:    [09/10/2025 09:12:49] -> SuperRun 3/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw)
INFO:    [09/10/2025 09:12:49] -> Run 3/6: Organizing Data from Run
INFO:    [09/10/2025 09:12:49] -> Run 3/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:12:49] -> Run 3/6: Creating Search Space...
INFO:    [09/10/2025 09:12:49] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:12:49] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:12:49] -> Run 3/6: MS2 Index Generation
INFO:    [09/10/2025 09:12:50] -> MS2 Index Generation Time: 1.06s
INFO:    [09/10/2025 09:12:50] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:12:50] -> Initializing...
INFO:    [09/10/2025 09:13:10] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:13:45] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:13:47] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:13:48] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:13:49] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:13:50] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:13:51] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:13:52] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:13:53] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:13:53] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:13:55] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:13:57] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:13:58] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:13:59] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:14:00] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:14:01] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:14:01] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:14:03] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:14:04] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:14:04] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:14:05] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:14:07] -> Nr of Features Requested: 258970
INFO:    [09/10/2025 09:14:07] -> Size of Featurespace: 258970
INFO:    [09/10/2025 09:14:07] -> Scans/Feature pairs that failed to Match: 25
INFO:    [09/10/2025 09:14:07] -> Maximum Nr of Features for one Scan: 92
INFO:    [09/10/2025 09:14:07] -> Finalizing...
INFO:    [09/10/2025 09:14:10] -> Processed in 24.75s
INFO:    [09/10/2025 09:14:10] -> Processed in 1.3m
INFO:    [09/10/2025 09:14:11] -> Done
INFO:    [09/10/2025 09:14:11] -> Run 3/6: Process Raw File...
INFO:    [09/10/2025 09:14:23] -> Run 3/6: Preparing Partitions...
INFO:    [09/10/2025 09:14:23] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:14:24] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:14:53] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [09/10/2025 09:15:13] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7518 [20.7s]
INFO:    [09/10/2025 09:16:20] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [09/10/2025 09:16:21] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [09/10/2025 09:16:21] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:16:34] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7719 [12.9s]
INFO:    [09/10/2025 09:16:34] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:17:13] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3159 [38.7s]
INFO:    [09/10/2025 09:17:13] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:17:33] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1471 [20.6s]
INFO:    [09/10/2025 09:17:33] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:18:12] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 673 [38.8s]
INFO:    [09/10/2025 09:18:12] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:18:45] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 410 [33.5s]
INFO:    [09/10/2025 09:18:45] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:19:02] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 46 [16s]
INFO:    [09/10/2025 09:21:09] -> Extracting 101809 MS1 XICs
INFO:    [09/10/2025 09:23:35] -> Run 3/6: Cleaning Up Run...
INFO:    [09/10/2025 09:23:39] -> SuperRun 4/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw)
INFO:    [09/10/2025 09:23:39] -> Run 4/6: Organizing Data from Run
INFO:    [09/10/2025 09:23:39] -> Run 4/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:23:39] -> Run 4/6: Creating Search Space...
INFO:    [09/10/2025 09:23:39] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:23:39] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:23:39] -> Run 4/6: MS2 Index Generation
INFO:    [09/10/2025 09:23:40] -> MS2 Index Generation Time: 1.11s
INFO:    [09/10/2025 09:23:40] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:23:40] -> Initializing...
INFO:    [09/10/2025 09:23:55] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:24:26] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:24:28] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:24:29] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:24:29] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:24:30] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:24:31] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:24:32] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:24:32] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:24:33] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:24:34] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:24:35] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:24:36] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:24:40] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:24:40] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:24:41] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:24:42] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:24:43] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:24:44] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:24:44] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:24:45] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:24:47] -> Nr of Features Requested: 235117
INFO:    [09/10/2025 09:24:47] -> Size of Featurespace: 235117
INFO:    [09/10/2025 09:24:47] -> Scans/Feature pairs that failed to Match: 14
INFO:    [09/10/2025 09:24:47] -> Maximum Nr of Features for one Scan: 149
INFO:    [09/10/2025 09:24:47] -> Finalizing...
INFO:    [09/10/2025 09:24:51] -> Processed in 25.4s
INFO:    [09/10/2025 09:24:51] -> Processed in 1.2m
INFO:    [09/10/2025 09:24:52] -> Done
INFO:    [09/10/2025 09:24:52] -> Run 4/6: Process Raw File...
INFO:    [09/10/2025 09:25:07] -> Run 4/6: Preparing Partitions...
INFO:    [09/10/2025 09:25:07] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:25:08] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:25:35] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [09/10/2025 09:25:56] -> The number of PSMs identified during calibration with FDR <= 0.01 is 6940 [20.6s]
INFO:    [09/10/2025 09:26:27] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [09/10/2025 09:26:29] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [09/10/2025 09:26:29] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:27:17] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7029 [47.8s]
INFO:    [09/10/2025 09:27:17] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:27:34] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3503 [17.5s]
INFO:    [09/10/2025 09:27:34] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:28:10] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1223 [35.8s]
INFO:    [09/10/2025 09:28:10] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:28:24] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 613 [14.2s]
INFO:    [09/10/2025 09:28:24] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:28:41] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 320 [17s]
INFO:    [09/10/2025 09:28:41] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:29:03] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 70 [21.8s]
INFO:    [09/10/2025 09:31:41] -> Extracting 92710 MS1 XICs
INFO:    [09/10/2025 09:33:59] -> Run 4/6: Cleaning Up Run...
INFO:    [09/10/2025 09:34:01] -> SuperRun 5/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw)
INFO:    [09/10/2025 09:34:01] -> Run 5/6: Organizing Data from Run
INFO:    [09/10/2025 09:34:01] -> Run 5/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:34:01] -> Run 5/6: Creating Search Space...
INFO:    [09/10/2025 09:34:01] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:34:01] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:34:01] -> Run 5/6: MS2 Index Generation
INFO:    [09/10/2025 09:34:02] -> MS2 Index Generation Time: 966.15ms
INFO:    [09/10/2025 09:34:02] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:34:02] -> Initializing...
INFO:    [09/10/2025 09:34:21] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:34:50] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:34:52] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:34:52] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:34:53] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:34:53] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:34:54] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:34:55] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:34:55] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:34:57] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:34:57] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:34:58] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:34:58] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:35:02] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:35:02] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:35:03] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:35:04] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:35:05] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:35:05] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:35:06] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:35:06] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:35:08] -> Nr of Features Requested: 239511
INFO:    [09/10/2025 09:35:08] -> Size of Featurespace: 239511
INFO:    [09/10/2025 09:35:08] -> Scans/Feature pairs that failed to Match: 18
INFO:    [09/10/2025 09:35:08] -> Maximum Nr of Features for one Scan: 161
INFO:    [09/10/2025 09:35:08] -> Finalizing...
INFO:    [09/10/2025 09:35:15] -> Processed in 25.22s
INFO:    [09/10/2025 09:35:15] -> Processed in 1.2m
INFO:    [09/10/2025 09:35:16] -> Done
INFO:    [09/10/2025 09:35:16] -> Run 5/6: Process Raw File...
INFO:    [09/10/2025 09:35:29] -> Run 5/6: Preparing Partitions...
INFO:    [09/10/2025 09:35:29] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:35:30] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:35:58] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [09/10/2025 09:36:20] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7421 [22.6s]
INFO:    [09/10/2025 09:36:43] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [09/10/2025 09:36:44] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [09/10/2025 09:36:44] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:37:09] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7558 [25.2s]
INFO:    [09/10/2025 09:37:09] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:37:29] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3227 [19.7s]
INFO:    [09/10/2025 09:37:29] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:38:04] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1460 [34.6s]
INFO:    [09/10/2025 09:38:04] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:38:26] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 541 [22.4s]
INFO:    [09/10/2025 09:38:26] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:38:41] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 415 [14.8s]
INFO:    [09/10/2025 09:38:41] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:38:54] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 231 [13.5s]
INFO:    [09/10/2025 09:38:54] -> PERFORMING MAIN SEARCH 7
INFO:    [09/10/2025 09:39:05] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 119 [10.7s]
INFO:    [09/10/2025 09:42:39] -> Extracting 105760 MS1 XICs
INFO:    [09/10/2025 09:45:05] -> Run 5/6: Cleaning Up Run...
INFO:    [09/10/2025 09:45:06] -> SuperRun 6/6: Initializing (20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw)
INFO:    [09/10/2025 09:45:06] -> Run 6/6: Organizing Data from Run
INFO:    [09/10/2025 09:45:06] -> Run 6/6: Creating Calibration Search Space...
INFO:    [09/10/2025 09:45:06] -> Run 6/6: Creating Search Space...
INFO:    [09/10/2025 09:45:06] -> Size of search space [MB]: 0
INFO:    [09/10/2025 09:45:06] -> Number of IMPGs in search space: 0
INFO:    [09/10/2025 09:45:06] -> Run 6/6: MS2 Index Generation
INFO:    [09/10/2025 09:45:07] -> MS2 Index Generation Time: 1.02s
INFO:    [09/10/2025 09:45:07] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [09/10/2025 09:45:07] -> Initializing...
INFO:    [09/10/2025 09:45:21] -> Finalizing HTRMS File...
INFO:    [09/10/2025 09:46:01] -> Processing Part 1 of 20
INFO:    [09/10/2025 09:46:03] -> Processing Part 2 of 20
INFO:    [09/10/2025 09:46:03] -> Processing Part 3 of 20
INFO:    [09/10/2025 09:46:04] -> Processing Part 4 of 20
INFO:    [09/10/2025 09:46:05] -> Processing Part 5 of 20
INFO:    [09/10/2025 09:46:05] -> Processing Part 6 of 20
INFO:    [09/10/2025 09:46:06] -> Processing Part 7 of 20
INFO:    [09/10/2025 09:46:07] -> Processing Part 8 of 20
INFO:    [09/10/2025 09:46:08] -> Processing Part 9 of 20
INFO:    [09/10/2025 09:46:08] -> Processing Part 10 of 20
INFO:    [09/10/2025 09:46:09] -> Processing Part 11 of 20
INFO:    [09/10/2025 09:46:10] -> Processing Part 12 of 20
INFO:    [09/10/2025 09:46:13] -> Processing Part 13 of 20
INFO:    [09/10/2025 09:46:14] -> Processing Part 14 of 20
INFO:    [09/10/2025 09:46:15] -> Processing Part 15 of 20
INFO:    [09/10/2025 09:46:15] -> Processing Part 16 of 20
INFO:    [09/10/2025 09:46:16] -> Processing Part 17 of 20
INFO:    [09/10/2025 09:46:16] -> Processing Part 18 of 20
INFO:    [09/10/2025 09:46:17] -> Processing Part 19 of 20
INFO:    [09/10/2025 09:46:17] -> Processing Part 20 of 20
INFO:    [09/10/2025 09:46:19] -> Nr of Features Requested: 239834
INFO:    [09/10/2025 09:46:19] -> Size of Featurespace: 239852
INFO:    [09/10/2025 09:46:19] -> Scans/Feature pairs that failed to Match: 25
INFO:    [09/10/2025 09:46:19] -> Maximum Nr of Features for one Scan: 135
INFO:    [09/10/2025 09:46:19] -> Finalizing...
INFO:    [09/10/2025 09:46:23] -> Processed in 22.14s
INFO:    [09/10/2025 09:46:23] -> Processed in 1.3m
INFO:    [09/10/2025 09:46:24] -> Done
INFO:    [09/10/2025 09:46:24] -> Run 6/6: Process Raw File...
INFO:    [09/10/2025 09:46:37] -> Run 6/6: Preparing Partitions...
INFO:    [09/10/2025 09:46:37] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [09/10/2025 09:46:38] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [09/10/2025 09:47:06] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [09/10/2025 09:47:28] -> The number of PSMs identified during calibration with FDR <= 0.01 is 7218 [21.9s]
INFO:    [09/10/2025 09:48:07] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [09/10/2025 09:48:08] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [09/10/2025 09:48:08] -> PERFORMING MAIN SEARCH 1
INFO:    [09/10/2025 09:48:45] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7188 [36.6s]
INFO:    [09/10/2025 09:48:45] -> PERFORMING MAIN SEARCH 2
INFO:    [09/10/2025 09:49:08] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 3130 [23.2s]
INFO:    [09/10/2025 09:49:08] -> PERFORMING MAIN SEARCH 3
INFO:    [09/10/2025 09:49:39] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1626 [31.5s]
INFO:    [09/10/2025 09:49:39] -> PERFORMING MAIN SEARCH 4
INFO:    [09/10/2025 09:50:07] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 748 [27.4s]
INFO:    [09/10/2025 09:50:07] -> PERFORMING MAIN SEARCH 5
INFO:    [09/10/2025 09:50:23] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 306 [16.4s]
INFO:    [09/10/2025 09:50:23] -> PERFORMING MAIN SEARCH 6
INFO:    [09/10/2025 09:50:45] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 226 [22.3s]
INFO:    [09/10/2025 09:50:45] -> PERFORMING MAIN SEARCH 7
INFO:    [09/10/2025 09:50:56] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 131 [10.2s]
INFO:    [09/10/2025 09:52:34] -> Extracting 105925 MS1 XICs
INFO:    [09/10/2025 09:55:21] -> Run 6/6: Cleaning Up Run...
INFO:    [09/10/2025 09:55:27] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [09/10/2025 09:55:27] -> Score Post-Processing
INFO:    [09/10/2025 09:56:54] -> Score Post-Processing: 1.44m
INFO:    [09/10/2025 09:56:54] -> PSM FDR...
INFO:    [09/10/2025 09:57:14] -> PSM FDR: 19.94s
INFO:    [09/10/2025 09:57:14] -> Converting to non-redundant data structure...
INFO:    [09/10/2025 09:57:26] -> Performing Peptide FDR...
INFO:    [09/10/2025 09:57:28] -> Performing Protein Inference...
INFO:    [09/10/2025 09:57:29] -> Performing Protein FDR...
INFO:    [09/10/2025 09:57:30] -> Calculating Result Values at Run and Experiment Level...
INFO:    [09/10/2025 09:57:39] -> Pulsar identified 129749 PSMs, 30037 stripped sequences, 31923 peptide precursors, 6488 protein groups.
INFO:    [09/10/2025 09:57:39] -> Calculating Summary...
INFO:    [09/10/2025 09:57:41] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 09:57:42] -> iRT Calibration...
INFO:    [09/10/2025 09:58:06] -> Performing directDIA+ search...
INFO:    [09/10/2025 10:02:30] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw
INFO:    [09/10/2025 10:06:22] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw
INFO:    [09/10/2025 10:08:58] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw
INFO:    [09/10/2025 10:10:52] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw
INFO:    [09/10/2025 10:12:50] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw
INFO:    [09/10/2025 10:14:52] -> directDIA+ search: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw
INFO:    [09/10/2025 10:16:58] -> Total nr of Searched Peptides: 978,284 of 1,350,043
INFO:    [09/10/2025 10:16:58] -> Performing directDIA+ Post Processing...
INFO:    [09/10/2025 10:17:05] -> Writing experiment store..
INFO:    [09/10/2025 10:17:11] -> Assigning iRT Source...
INFO:    [09/10/2025 10:17:12] -> Calculating iRT...
INFO:    [09/10/2025 10:17:12] -> Cleaning Up Experiment...
INFO:    [09/10/2025 10:17:12] -> Summarizing Identifications
INFO:    [09/10/2025 10:23:52] -> Pipeline executed...
INFO:    [09/10/2025 10:23:54] -> Pipeline executed...
INFO:    [09/10/2025 10:24:00] -> Initializing Experiment...
INFO:    [09/10/2025 10:24:00] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:25:21] -> Initialize Scoring...
INFO:    [09/10/2025 10:25:22] -> Generating Scan Map...
INFO:    [09/10/2025 10:25:22] -> Initializing Workpackages...
INFO:    [09/10/2025 10:25:22] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:25:22] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:25:22] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:25:26] -> Initializing Pipeline...
INFO:    [09/10/2025 10:25:26] -> Preprocessing Run #1 of 6...
INFO:    [09/10/2025 10:25:26] -> Initialize Scoring...
INFO:    [09/10/2025 10:25:26] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:26:10] -> Machine Learning...
INFO:    [09/10/2025 10:26:14] -> Pipeline executed in 48.32s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:26:17] -> Initializing Pipeline...
INFO:    [09/10/2025 10:26:17] -> Preprocessing Run #1 of 6...
INFO:    [09/10/2025 10:26:17] -> Initialize Scoring...
INFO:    [09/10/2025 10:26:17] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:26:54] -> Machine Learning...
INFO:    [09/10/2025 10:27:00] -> Pipeline executed in 42.62s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:27:06] -> Initialize Scoring...
INFO:    [09/10/2025 10:27:06] -> Preprocessing Run #2 of 6...
INFO:    [09/10/2025 10:27:06] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:27:06] -> Initializing Experiment...
INFO:    [09/10/2025 10:27:06] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:27:06] -> Initialize Scoring...
INFO:    [09/10/2025 10:27:06] -> Generating Scan Map...
INFO:    [09/10/2025 10:27:06] -> Initializing Workpackages...
INFO:    [09/10/2025 10:27:06] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:27:06] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:27:06] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:27:07] -> Initializing Pipeline...
INFO:    [09/10/2025 10:27:07] -> Preprocessing Run #2 of 6...
INFO:    [09/10/2025 10:27:07] -> Initialize Scoring...
INFO:    [09/10/2025 10:27:08] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:27:18] -> Machine Learning...
INFO:    [09/10/2025 10:27:20] -> Pipeline executed in 12.6s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:27:22] -> Initializing Pipeline...
INFO:    [09/10/2025 10:27:22] -> Preprocessing Run #2 of 6...
INFO:    [09/10/2025 10:27:22] -> Initialize Scoring...
INFO:    [09/10/2025 10:27:22] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:27:47] -> Machine Learning...
INFO:    [09/10/2025 10:27:53] -> Pipeline executed in 31.47s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:27:59] -> Initialize Scoring...
INFO:    [09/10/2025 10:27:59] -> Preprocessing Run #3 of 6...
INFO:    [09/10/2025 10:27:59] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:27:59] -> Initializing Experiment...
INFO:    [09/10/2025 10:27:59] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:27:59] -> Initialize Scoring...
INFO:    [09/10/2025 10:27:59] -> Generating Scan Map...
INFO:    [09/10/2025 10:27:59] -> Initializing Workpackages...
INFO:    [09/10/2025 10:27:59] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:27:59] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:27:59] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:28:01] -> Initializing Pipeline...
INFO:    [09/10/2025 10:28:01] -> Preprocessing Run #3 of 6...
INFO:    [09/10/2025 10:28:01] -> Initialize Scoring...
INFO:    [09/10/2025 10:28:01] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:28:20] -> Machine Learning...
INFO:    [09/10/2025 10:28:22] -> Pipeline executed in 21.13s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:28:26] -> Initializing Pipeline...
INFO:    [09/10/2025 10:28:26] -> Preprocessing Run #3 of 6...
INFO:    [09/10/2025 10:28:26] -> Initialize Scoring...
INFO:    [09/10/2025 10:28:26] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:28:59] -> Machine Learning...
INFO:    [09/10/2025 10:29:07] -> Pipeline executed in 41.47s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:29:15] -> Initialize Scoring...
INFO:    [09/10/2025 10:29:15] -> Preprocessing Run #4 of 6...
INFO:    [09/10/2025 10:29:15] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:29:15] -> Initializing Experiment...
INFO:    [09/10/2025 10:29:15] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:29:15] -> Initialize Scoring...
INFO:    [09/10/2025 10:29:15] -> Generating Scan Map...
INFO:    [09/10/2025 10:29:15] -> Initializing Workpackages...
INFO:    [09/10/2025 10:29:15] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:29:15] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:29:15] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:29:18] -> Initializing Pipeline...
INFO:    [09/10/2025 10:29:18] -> Preprocessing Run #4 of 6...
INFO:    [09/10/2025 10:29:18] -> Initialize Scoring...
INFO:    [09/10/2025 10:29:18] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:29:56] -> Machine Learning...
INFO:    [09/10/2025 10:29:59] -> Pipeline executed in 40.81s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:30:02] -> Initializing Pipeline...
INFO:    [09/10/2025 10:30:02] -> Preprocessing Run #4 of 6...
INFO:    [09/10/2025 10:30:02] -> Initialize Scoring...
INFO:    [09/10/2025 10:30:02] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:30:41] -> Machine Learning...
INFO:    [09/10/2025 10:30:47] -> Pipeline executed in 44.66s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:30:55] -> Initialize Scoring...
INFO:    [09/10/2025 10:30:55] -> Preprocessing Run #5 of 6...
INFO:    [09/10/2025 10:30:55] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:30:55] -> Initializing Experiment...
INFO:    [09/10/2025 10:30:55] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:30:55] -> Initialize Scoring...
INFO:    [09/10/2025 10:30:55] -> Generating Scan Map...
INFO:    [09/10/2025 10:30:55] -> Initializing Workpackages...
INFO:    [09/10/2025 10:30:55] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:30:55] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:30:55] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:30:57] -> Initializing Pipeline...
INFO:    [09/10/2025 10:30:57] -> Preprocessing Run #5 of 6...
INFO:    [09/10/2025 10:30:57] -> Initialize Scoring...
INFO:    [09/10/2025 10:30:57] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:31:09] -> Machine Learning...
INFO:    [09/10/2025 10:31:11] -> Pipeline executed in 13.79s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:31:14] -> Initializing Pipeline...
INFO:    [09/10/2025 10:31:14] -> Preprocessing Run #5 of 6...
INFO:    [09/10/2025 10:31:14] -> Initialize Scoring...
INFO:    [09/10/2025 10:31:14] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:31:45] -> Machine Learning...
INFO:    [09/10/2025 10:31:52] -> Pipeline executed in 37.45s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:31:56] -> Initialize Scoring...
INFO:    [09/10/2025 10:31:56] -> Preprocessing Run #6 of 6...
INFO:    [09/10/2025 10:31:56] -> Searching DIA with Pulsar...
INFO:    [09/10/2025 10:31:56] -> Initializing Experiment...
INFO:    [09/10/2025 10:31:56] -> Loading Spectral Libraries...
INFO:    [09/10/2025 10:31:56] -> Initialize Scoring...
INFO:    [09/10/2025 10:31:56] -> Generating Scan Map...
INFO:    [09/10/2025 10:31:56] -> Initializing Workpackages...
INFO:    [09/10/2025 10:31:56] -> Performing Basic Calibration...
INFO:    [09/10/2025 10:31:57] -> Identifying Calibration Peptides...
INFO:    [09/10/2025 10:31:57] -> Correcting Gradient Fine Structure...
INFO:    [09/10/2025 10:31:58] -> Initializing Pipeline...
INFO:    [09/10/2025 10:31:58] -> Preprocessing Run #6 of 6...
INFO:    [09/10/2025 10:31:58] -> Initialize Scoring...
INFO:    [09/10/2025 10:31:58] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:32:18] -> Machine Learning...
INFO:    [09/10/2025 10:32:21] -> Pipeline executed in 22.88s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:32:25] -> Initializing Pipeline...
INFO:    [09/10/2025 10:32:25] -> Preprocessing Run #6 of 6...
INFO:    [09/10/2025 10:32:25] -> Initialize Scoring...
INFO:    [09/10/2025 10:32:25] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:32:59] -> Machine Learning...
INFO:    [09/10/2025 10:33:04] -> Pipeline executed in 38.88s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/10/2025 10:33:10] -> Initialize Scoring...
INFO:    [09/10/2025 10:33:10] -> Initializing QC...
INFO:    [09/10/2025 10:33:10] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:33:10] -> Assigning ML Features...
INFO:    [09/10/2025 10:33:10] -> Generating Decoys...
INFO:    [09/10/2025 10:33:26] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:34:35] -> Releasing Raw Files...
INFO:    [09/10/2025 10:34:36] -> Machine Learning...
INFO:    [09/10/2025 10:35:36] -> Initializing HTRMS...
INFO:    [09/10/2025 10:35:36] -> Releasing Run Resources...
INFO:    [09/10/2025 10:35:36] -> Reducing Score Cache...
INFO:    [09/10/2025 10:35:38] -> Calculating Qvalues...
INFO:    [09/10/2025 10:35:39] -> Unique precursors: 47,500 of 50,999 | modified peptides: 46,242 of 49,582 | peptides: 44,603 of 47,189 |  protein groups: 8,468 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw]
INFO:    [09/10/2025 10:35:39] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:35:40] -> Processed in 2.5m
INFO:    [09/10/2025 10:35:40] -> Initializing QC...
INFO:    [09/10/2025 10:35:40] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:35:41] -> Assigning ML Features...
INFO:    [09/10/2025 10:35:41] -> Generating Decoys...
INFO:    [09/10/2025 10:35:41] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:36:54] -> Releasing Raw Files...
INFO:    [09/10/2025 10:36:54] -> Machine Learning...
INFO:    [09/10/2025 10:37:44] -> Initializing HTRMS...
INFO:    [09/10/2025 10:37:44] -> Releasing Run Resources...
INFO:    [09/10/2025 10:37:45] -> Reducing Score Cache...
INFO:    [09/10/2025 10:37:49] -> Calculating Qvalues...
INFO:    [09/10/2025 10:37:50] -> Unique precursors: 49,368 of 50,999 | modified peptides: 48,040 of 49,582 | peptides: 45,707 of 47,189 |  protein groups: 8,565 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw]
INFO:    [09/10/2025 10:37:50] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:37:50] -> Processed in 2.17m
INFO:    [09/10/2025 10:37:51] -> Initializing QC...
INFO:    [09/10/2025 10:37:51] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:37:51] -> Assigning ML Features...
INFO:    [09/10/2025 10:37:51] -> Generating Decoys...
INFO:    [09/10/2025 10:37:51] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:39:01] -> Releasing Raw Files...
INFO:    [09/10/2025 10:39:02] -> Machine Learning...
INFO:    [09/10/2025 10:39:49] -> Initializing HTRMS...
INFO:    [09/10/2025 10:39:50] -> Releasing Run Resources...
INFO:    [09/10/2025 10:39:50] -> Reducing Score Cache...
INFO:    [09/10/2025 10:39:52] -> Calculating Qvalues...
INFO:    [09/10/2025 10:39:53] -> Unique precursors: 49,211 of 50,999 | modified peptides: 47,896 of 49,582 | peptides: 45,563 of 47,189 |  protein groups: 8,569 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw]
INFO:    [09/10/2025 10:39:53] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:39:53] -> Processed in 2.05m
INFO:    [09/10/2025 10:39:54] -> Initializing QC...
INFO:    [09/10/2025 10:39:54] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:39:54] -> Assigning ML Features...
INFO:    [09/10/2025 10:39:54] -> Generating Decoys...
INFO:    [09/10/2025 10:39:54] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:40:56] -> Releasing Raw Files...
INFO:    [09/10/2025 10:40:56] -> Machine Learning...
INFO:    [09/10/2025 10:41:45] -> Initializing HTRMS...
INFO:    [09/10/2025 10:41:45] -> Releasing Run Resources...
INFO:    [09/10/2025 10:41:46] -> Reducing Score Cache...
INFO:    [09/10/2025 10:41:50] -> Calculating Qvalues...
INFO:    [09/10/2025 10:41:51] -> Unique precursors: 46,859 of 50,999 | modified peptides: 45,607 of 49,582 | peptides: 43,910 of 47,189 |  protein groups: 8,261 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw]
INFO:    [09/10/2025 10:41:51] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:41:52] -> Processed in 1.97m
INFO:    [09/10/2025 10:41:53] -> Initializing QC...
INFO:    [09/10/2025 10:41:53] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:41:53] -> Assigning ML Features...
INFO:    [09/10/2025 10:41:53] -> Generating Decoys...
INFO:    [09/10/2025 10:41:53] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:42:52] -> Releasing Raw Files...
INFO:    [09/10/2025 10:42:53] -> Machine Learning...
INFO:    [09/10/2025 10:43:38] -> Initializing HTRMS...
INFO:    [09/10/2025 10:43:38] -> Releasing Run Resources...
INFO:    [09/10/2025 10:43:39] -> Reducing Score Cache...
INFO:    [09/10/2025 10:43:43] -> Calculating Qvalues...
INFO:    [09/10/2025 10:43:45] -> Unique precursors: 46,095 of 50,999 | modified peptides: 44,855 of 49,582 | peptides: 43,152 of 47,189 |  protein groups: 8,133 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw]
INFO:    [09/10/2025 10:43:45] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:43:46] -> Processed in 1.89m
INFO:    [09/10/2025 10:43:46] -> Initializing QC...
INFO:    [09/10/2025 10:43:46] -> Determining Calibration Parameter...
INFO:    [09/10/2025 10:43:47] -> Assigning ML Features...
INFO:    [09/10/2025 10:43:47] -> Generating Decoys...
INFO:    [09/10/2025 10:43:47] -> Extracting Ion Currents...
INFO:    [09/10/2025 10:44:48] -> Releasing Raw Files...
INFO:    [09/10/2025 10:44:48] -> Machine Learning...
INFO:    [09/10/2025 10:45:42] -> Initializing HTRMS...
INFO:    [09/10/2025 10:45:42] -> Releasing Run Resources...
INFO:    [09/10/2025 10:45:43] -> Reducing Score Cache...
INFO:    [09/10/2025 10:45:47] -> Calculating Qvalues...
INFO:    [09/10/2025 10:45:50] -> Unique precursors: 47,103 of 50,999 | modified peptides: 45,832 of 49,582 | peptides: 43,992 of 47,189 |  protein groups: 8,302 (Qvalue <= 0.01) [20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw]
INFO:    [09/10/2025 10:45:50] -> Collapsing Search Tree...
INFO:    [09/10/2025 10:45:50] -> Processed in 2.07m
INFO:    [09/10/2025 10:45:52] -> Normalizing Cscores...
INFO:    [09/10/2025 10:45:53] -> Calculating Global CVs
INFO:    [09/10/2025 10:45:56] -> Calculating Profile Qvalues...
INFO:    [09/10/2025 10:45:59] -> Initializing Protein Groups...
INFO:    [09/10/2025 10:46:27] -> Correcting Interferences...
INFO:    [09/10/2025 10:46:55] -> Calculating Global CVs
INFO:    [09/10/2025 10:46:59] -> Calculating Precursor Quantities...
INFO:    [09/10/2025 10:47:00] -> Normalizing Quantification...
INFO:    [09/10/2025 10:47:02] -> Performing Local Normalization...
INFO:    [09/10/2025 10:47:06] -> Calculating Global CVs
INFO:    [09/10/2025 10:47:08] -> Calculating Condition CVs
INFO:    [09/10/2025 10:47:15] -> Excluding Library Duplicates...
INFO:    [09/10/2025 10:47:18] -> Calculating Global CVs
INFO:    [09/10/2025 10:47:20] -> Building Protein Groups...
INFO:    [09/10/2025 10:47:45] -> Calculating Run-Wise Protein Group FDR...
INFO:    [09/10/2025 10:47:50] -> Annotating Protein Single Hits...
INFO:    [09/10/2025 10:47:52] -> Calculating Global CVs
INFO:    [09/10/2025 10:47:55] -> Updating Identification Counts...
INFO:    [09/10/2025 10:48:00] -> Subtracting background noise...
INFO:    [09/10/2025 10:48:01] -> Resetting existing imputation...
INFO:    [09/10/2025 10:48:02] -> Calculating Protein Quantities...
INFO:    [09/10/2025 10:48:06] -> Calculating Protein Quantities...
INFO:    [09/10/2025 10:48:06] -> Calculating MaxLFQ Protein Quantities...
INFO:    [09/10/2025 10:48:17] -> Collapsing PTM-Locations...
INFO:    [09/10/2025 10:48:18] -> PTM Stoichiometry calculation...
INFO:    [09/10/2025 10:48:19] -> Creating Protein Map...
INFO:    [09/10/2025 10:48:19] -> Compiling Run Summary Information...
INFO:    [09/10/2025 10:48:21] -> Running Post Analysis Processes...
INFO:    [09/10/2025 10:48:30] -> Saving Qc Data...
INFO:    [09/10/2025 10:48:31] -> No QC Generated for "20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1": Insufficient QC peptides found.
INFO:    [09/10/2025 10:48:32] -> 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 10:48:32] -> 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 10:48:33] -> 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 10:48:33] -> 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 10:48:33] -> Generating Output
INFO:    [09/10/2025 10:48:34] -> Generating Experiment Report
INFO:    [09/10/2025 10:49:27] -> WU334900_Report_BGS Factory Report (Normal).tsv
INFO:    [09/10/2025 10:49:27] -> Generating RT Recalibration Report
INFO:    [09/10/2025 10:49:28] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw_1_iRTCalibration.tsv
INFO:    [09/10/2025 10:49:28] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw_2_iRTCalibration.tsv
INFO:    [09/10/2025 10:49:28] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw_3_iRTCalibration.tsv
INFO:    [09/10/2025 10:49:28] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw_4_iRTCalibration.tsv
INFO:    [09/10/2025 10:49:28] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw_5_iRTCalibration.tsv
INFO:    [09/10/2025 10:49:28] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw_6_iRTCalibration.tsv
INFO:    [09/10/2025 10:49:28] -> Generating Run Meta Report
INFO:    [09/10/2025 10:49:29] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw_1_RunOverview.tsv
INFO:    [09/10/2025 10:49:29] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw_2_RunOverview.tsv
INFO:    [09/10/2025 10:49:29] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw_3_RunOverview.tsv
INFO:    [09/10/2025 10:49:29] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw_4_RunOverview.tsv
INFO:    [09/10/2025 10:49:29] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw_5_RunOverview.tsv
INFO:    [09/10/2025 10:49:29] -> 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw_6_RunOverview.tsv
INFO:    [09/10/2025 10:49:29] -> Generating Post Analysis Reports
INFO:    [09/10/2025 10:49:37] -> WU334900_AnalysisOverview.txt
INFO:    [09/10/2025 10:49:37] -> Precursor CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:49:37] -> Peptide CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:49:37] -> Protein Group CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:49:37] -> Protein CVs_CVsBelowX.tsv
INFO:    [09/10/2025 10:49:37] -> RunIdentifications.tsv
INFO:    [09/10/2025 10:49:37] -> Candidates.tsv
INFO:    [09/10/2025 10:49:37] -> Generating PTM Site Report
INFO:    [09/10/2025 10:49:38] -> Generating Condition Setup Report
INFO:    [09/10/2025 10:49:38] -> WU334900_ConditionSetup.tsv
INFO:    [09/10/2025 10:49:38] -> Generating Experiment Settings Report
[END-LOG]
