Spectronaut 19.0.240606.62635
Computer Name: fgcz-spectronaut
User Domain Name: fgcz-spectronaut
User Name: root
Analysis Mode: cmd
Analysis Type: directDIA
Analysis Date: 14-November-2024 11:24:27 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
   │  └─ 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
   │  ├─ [Beta] 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
   ├─ 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
   ├─ 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/P
   │  ├─ Digest Type:	Specific
   │  ├─ 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:	Fast (Spectronaut 19)
   ├─ 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: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
   ├─ Path: "/scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw"
   ├─ Condition: Not Defined
   ├─ Replicate: 1
   ├─ HTRMS Version: 19.0.240606.62635
   ├─ Protein Databases Used
   │  └─ p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Protein Entries: 31,890
   │     ├─ Original File: p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Date Created: 14-November-2024 09:10:33 UTC+0
   │     ├─ Date Modified: 14-November-2024 10:48:00 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
   ├─ Path: "/scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw"
   ├─ Condition: Not Defined
   ├─ Replicate: 2
   ├─ HTRMS Version: 19.0.240606.62635
   ├─ Protein Databases Used
   │  └─ p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Protein Entries: 31,890
   │     ├─ Original File: p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Date Created: 14-November-2024 09:10:33 UTC+0
   │     ├─ Date Modified: 14-November-2024 10:48:00 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
   ├─ Path: "/scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw"
   ├─ Condition: Not Defined
   ├─ Replicate: 3
   ├─ HTRMS Version: 19.0.240606.62635
   ├─ Protein Databases Used
   │  └─ p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Protein Entries: 31,890
   │     ├─ Original File: p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Date Created: 14-November-2024 09:10:33 UTC+0
   │     ├─ Date Modified: 14-November-2024 10:48:00 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
   ├─ Path: "/scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw"
   ├─ Condition: Not Defined
   ├─ Replicate: 4
   ├─ HTRMS Version: 19.0.240606.62635
   ├─ Protein Databases Used
   │  └─ p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Protein Entries: 31,890
   │     ├─ Original File: p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Date Created: 14-November-2024 09:10:33 UTC+0
   │     ├─ Date Modified: 14-November-2024 10:48:00 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
   ├─ Path: "/scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw"
   ├─ Condition: Not Defined
   ├─ Replicate: 5
   ├─ HTRMS Version: 19.0.240606.62635
   ├─ Protein Databases Used
   │  └─ p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Protein Entries: 31,890
   │     ├─ Original File: p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Date Created: 14-November-2024 09:10:33 UTC+0
   │     ├─ Date Modified: 14-November-2024 10:48:00 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
   ├─ Path: "/scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw"
   ├─ Condition: Not Defined
   ├─ Replicate: 6
   ├─ HTRMS Version: 19.0.240606.62635
   ├─ Protein Databases Used
   │  └─ p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Protein Entries: 31,890
   │     ├─ Original File: p34486_Proteobench_TripleProteome_20240614.fasta
   │     ├─ Date Created: 14-November-2024 09:10:33 UTC+0
   │     ├─ Date Modified: 14-November-2024 10:48:00 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

[END-SETUP]

[BEGIN-LOG]
INFO:    [14/11/2024 09:10:33] -> Update available: https://files.biognosys.com/058_Spectronaut/Installer/SN19/Spectronaut_19.4.241104.62635.tgz
INFO:    [14/11/2024 09:10:33] -> Update available: https://files.biognosys.com/058_Spectronaut/Installer/SN19/Spectronaut_19.4.241104.62635.deb
INFO:    [14/11/2024 09:10:33] -> Running /usr/share/dotnet/dotnet /usr/lib/spectronaut/SpectronautCMD.dll directdia -fasta /scratch/cpanse/Spectronaut//p34486_Proteobench_TripleProteome_20240614.fasta -r /scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw -r /scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw -r /scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw -r /scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw -r /scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw -r /scratch/cpanse/Spectronaut//wolski_20240614_proteobench_DIA_data/LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw -o /scratch/cpanse/Spectronaut//output/SanityCheck/
INFO:    [14/11/2024 09:10:33] -> Reading report parameter...
INFO:    [14/11/2024 09:10:33] -> 1 valid runs added
INFO:    [14/11/2024 09:10:33] -> 1 valid runs added
INFO:    [14/11/2024 09:10:33] -> 1 valid runs added
INFO:    [14/11/2024 09:10:33] -> 1 valid runs added
INFO:    [14/11/2024 09:10:33] -> 1 valid runs added
INFO:    [14/11/2024 09:10:33] -> 1 valid runs added
INFO:    [14/11/2024 09:10:33] -> Importing FASTA file...
INFO:    [14/11/2024 09:11:04] -> Set output destination to: /scratch/cpanse/Spectronaut//output/SanityCheck/20241114_091104_Experiment1
INFO:    [14/11/2024 09:11:04] -> Selected Analysis Settings: BGS Factory Settings
INFO:    [14/11/2024 09:11:04] -> Initializing Pipeline...
INFO:    [14/11/2024 09:11:04] -> Preprocessing Run #1 of 6...
INFO:    [14/11/2024 09:11:04] -> Searching DIA with Pulsar...
INFO:    [14/11/2024 09:11:04] -> Initialize Pipeline...
INFO:    [14/11/2024 09:11:04] -> Initialize Pipeline
INFO:    [14/11/2024 09:11:20] -> Initialize Pipeline...
INFO:    [14/11/2024 09:11:20] -> Creating Experiment Environment
INFO:    [14/11/2024 09:11:21] -> SuperRun 1/6: Initializing (LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw)
INFO:    [14/11/2024 09:11:21] -> Run 1/6: Organizing Data from Run
INFO:    [14/11/2024 09:11:21] -> Run 1/6: Creating Calibration Search Space...
INFO:    [14/11/2024 09:11:25] -> Collecting Search Space Parameters...
INFO:    [14/11/2024 09:11:29] -> Creating the Search Space...
INFO:    [14/11/2024 09:11:29] -> Run 1/6: Creating Search Space...
INFO:    [14/11/2024 09:11:29] -> Collecting Search Space Parameters...
INFO:    [14/11/2024 09:11:57] -> Creating the Search Space...
INFO:    [14/11/2024 09:11:58] -> Size of search space [MB]: 0
INFO:    [14/11/2024 09:11:58] -> Number of IMPGs in search space: 0
INFO:    [14/11/2024 09:11:58] -> Run 1/6: MS2 Index Generation
INFO:    [14/11/2024 09:14:49] -> MS2 Index Generation Time: 2.86m
INFO:    [14/11/2024 09:14:49] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [14/11/2024 09:14:53] -> Initializing...
INFO:    [14/11/2024 09:15:31] -> Finalizing HTRMS File...
INFO:    [14/11/2024 09:15:51] -> Processing Part 1 of 152
INFO:    [14/11/2024 09:15:53] -> Processing Part 2 of 152
INFO:    [14/11/2024 09:15:54] -> Processing Part 3 of 152
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INFO:    [14/11/2024 09:17:07] -> Processing Part 136 of 152
INFO:    [14/11/2024 09:17:08] -> Processing Part 137 of 152
INFO:    [14/11/2024 09:17:08] -> Processing Part 138 of 152
INFO:    [14/11/2024 09:17:08] -> Processing Part 139 of 152
INFO:    [14/11/2024 09:17:08] -> Processing Part 140 of 152
INFO:    [14/11/2024 09:17:09] -> Processing Part 141 of 152
INFO:    [14/11/2024 09:17:09] -> Processing Part 142 of 152
INFO:    [14/11/2024 09:17:09] -> Processing Part 143 of 152
INFO:    [14/11/2024 09:17:09] -> Processing Part 144 of 152
INFO:    [14/11/2024 09:17:10] -> Processing Part 145 of 152
INFO:    [14/11/2024 09:17:10] -> Processing Part 146 of 152
INFO:    [14/11/2024 09:17:10] -> Processing Part 147 of 152
INFO:    [14/11/2024 09:17:10] -> Processing Part 148 of 152
INFO:    [14/11/2024 09:17:10] -> Processing Part 149 of 152
INFO:    [14/11/2024 09:17:10] -> Processing Part 150 of 152
INFO:    [14/11/2024 09:17:11] -> Processing Part 151 of 152
INFO:    [14/11/2024 09:17:11] -> Processing Part 152 of 152
INFO:    [14/11/2024 09:17:13] -> Nr of Features Requested: 253516
INFO:    [14/11/2024 09:17:13] -> Size of Featurespace: 253527
INFO:    [14/11/2024 09:17:13] -> Scans/Feature pairs that failed to Match: 1420
INFO:    [14/11/2024 09:17:13] -> Maximum Nr of Features for one Scan: 11
INFO:    [14/11/2024 09:17:13] -> Finalizing...
INFO:    [14/11/2024 09:17:15] -> Processed in 1.4m
INFO:    [14/11/2024 09:17:15] -> Processed in 2.4m
INFO:    [14/11/2024 09:17:16] -> Done
INFO:    [14/11/2024 09:17:16] -> Run 1/6: Process Raw File...
INFO:    [14/11/2024 09:17:25] -> Run 1/6: Preparing Partitions...
INFO:    [14/11/2024 09:17:26] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [14/11/2024 09:17:27] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [14/11/2024 09:17:33] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [14/11/2024 09:17:43] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5345 [10.1s]
INFO:    [14/11/2024 09:17:53] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [14/11/2024 09:17:54] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [14/11/2024 09:17:54] -> PERFORMING MAIN SEARCH 1
INFO:    [14/11/2024 09:18:50] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 43542 [56.1s]
INFO:    [14/11/2024 09:18:50] -> PERFORMING MAIN SEARCH 2
INFO:    [14/11/2024 09:19:13] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7985 [23s]
INFO:    [14/11/2024 09:19:13] -> PERFORMING MAIN SEARCH 3
INFO:    [14/11/2024 09:19:25] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1200 [11.6s]
INFO:    [14/11/2024 09:19:25] -> PERFORMING MAIN SEARCH 4
INFO:    [14/11/2024 09:19:35] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 157 [9.7s]
INFO:    [14/11/2024 09:20:44] -> Extracting 162025 MS1 XICs
INFO:    [14/11/2024 09:24:55] -> Run 1/6: Cleaning Up Run..
INFO:    [14/11/2024 09:24:56] -> SuperRun 2/6: Initializing (LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw)
INFO:    [14/11/2024 09:24:56] -> Run 2/6: Organizing Data from Run
INFO:    [14/11/2024 09:24:56] -> Run 2/6: Creating Calibration Search Space...
INFO:    [14/11/2024 09:24:56] -> Run 2/6: Creating Search Space...
INFO:    [14/11/2024 09:24:56] -> Size of search space [MB]: 0
INFO:    [14/11/2024 09:24:56] -> Number of IMPGs in search space: 0
INFO:    [14/11/2024 09:24:56] -> Run 2/6: MS2 Index Generation
INFO:    [14/11/2024 09:24:57] -> MS2 Index Generation Time: 940.21ms
INFO:    [14/11/2024 09:24:57] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [14/11/2024 09:24:59] -> Initializing...
INFO:    [14/11/2024 09:25:31] -> Finalizing HTRMS File...
INFO:    [14/11/2024 09:26:00] -> Processing Part 1 of 152
INFO:    [14/11/2024 09:26:03] -> Processing Part 2 of 152
INFO:    [14/11/2024 09:26:03] -> Processing Part 3 of 152
INFO:    [14/11/2024 09:26:04] -> Processing Part 4 of 152
INFO:    [14/11/2024 09:26:05] -> Processing Part 5 of 152
INFO:    [14/11/2024 09:26:06] -> Processing Part 6 of 152
INFO:    [14/11/2024 09:26:06] -> Processing Part 7 of 152
INFO:    [14/11/2024 09:26:07] -> Processing Part 8 of 152
INFO:    [14/11/2024 09:26:08] -> Processing Part 9 of 152
INFO:    [14/11/2024 09:26:08] -> Processing Part 10 of 152
INFO:    [14/11/2024 09:26:10] -> Processing Part 11 of 152
INFO:    [14/11/2024 09:26:10] -> Processing Part 12 of 152
INFO:    [14/11/2024 09:26:12] -> Processing Part 13 of 152
INFO:    [14/11/2024 09:26:12] -> Processing Part 14 of 152
INFO:    [14/11/2024 09:26:13] -> Processing Part 15 of 152
INFO:    [14/11/2024 09:26:14] -> Processing Part 16 of 152
INFO:    [14/11/2024 09:26:14] -> Processing Part 17 of 152
INFO:    [14/11/2024 09:26:15] -> Processing Part 18 of 152
INFO:    [14/11/2024 09:26:16] -> Processing Part 19 of 152
INFO:    [14/11/2024 09:26:16] -> Processing Part 20 of 152
INFO:    [14/11/2024 09:26:17] -> Processing Part 21 of 152
INFO:    [14/11/2024 09:26:17] -> Processing Part 22 of 152
INFO:    [14/11/2024 09:26:19] -> Processing Part 23 of 152
INFO:    [14/11/2024 09:26:19] -> Processing Part 24 of 152
INFO:    [14/11/2024 09:26:20] -> Processing Part 25 of 152
INFO:    [14/11/2024 09:26:20] -> Processing Part 26 of 152
INFO:    [14/11/2024 09:26:22] -> Processing Part 27 of 152
INFO:    [14/11/2024 09:26:23] -> Processing Part 28 of 152
INFO:    [14/11/2024 09:26:23] -> Processing Part 29 of 152
INFO:    [14/11/2024 09:26:24] -> Processing Part 30 of 152
INFO:    [14/11/2024 09:26:25] -> Processing Part 31 of 152
INFO:    [14/11/2024 09:26:25] -> Processing Part 32 of 152
INFO:    [14/11/2024 09:26:27] -> Processing Part 33 of 152
INFO:    [14/11/2024 09:26:27] -> Processing Part 34 of 152
INFO:    [14/11/2024 09:26:27] -> Processing Part 35 of 152
INFO:    [14/11/2024 09:26:28] -> Processing Part 36 of 152
INFO:    [14/11/2024 09:26:28] -> Processing Part 37 of 152
INFO:    [14/11/2024 09:26:30] -> Processing Part 38 of 152
INFO:    [14/11/2024 09:26:30] -> Processing Part 39 of 152
INFO:    [14/11/2024 09:26:31] -> Processing Part 40 of 152
INFO:    [14/11/2024 09:26:31] -> Processing Part 41 of 152
INFO:    [14/11/2024 09:26:33] -> Processing Part 42 of 152
INFO:    [14/11/2024 09:26:33] -> Processing Part 43 of 152
INFO:    [14/11/2024 09:26:33] -> Processing Part 44 of 152
INFO:    [14/11/2024 09:26:34] -> Processing Part 45 of 152
INFO:    [14/11/2024 09:26:34] -> Processing Part 46 of 152
INFO:    [14/11/2024 09:26:35] -> Processing Part 47 of 152
INFO:    [14/11/2024 09:26:36] -> Processing Part 48 of 152
INFO:    [14/11/2024 09:26:37] -> Processing Part 49 of 152
INFO:    [14/11/2024 09:26:38] -> Processing Part 50 of 152
INFO:    [14/11/2024 09:26:38] -> Processing Part 51 of 152
INFO:    [14/11/2024 09:26:40] -> Processing Part 52 of 152
INFO:    [14/11/2024 09:26:41] -> Processing Part 53 of 152
INFO:    [14/11/2024 09:26:42] -> Processing Part 54 of 152
INFO:    [14/11/2024 09:26:43] -> Processing Part 55 of 152
INFO:    [14/11/2024 09:26:43] -> Processing Part 56 of 152
INFO:    [14/11/2024 09:26:44] -> Processing Part 57 of 152
INFO:    [14/11/2024 09:26:45] -> Processing Part 58 of 152
INFO:    [14/11/2024 09:26:46] -> Processing Part 59 of 152
INFO:    [14/11/2024 09:26:46] -> Processing Part 60 of 152
INFO:    [14/11/2024 09:26:47] -> Processing Part 61 of 152
INFO:    [14/11/2024 09:26:47] -> Processing Part 62 of 152
INFO:    [14/11/2024 09:26:47] -> Processing Part 63 of 152
INFO:    [14/11/2024 09:26:49] -> Processing Part 64 of 152
INFO:    [14/11/2024 09:26:50] -> Processing Part 65 of 152
INFO:    [14/11/2024 09:26:51] -> Processing Part 66 of 152
INFO:    [14/11/2024 09:26:51] -> Processing Part 67 of 152
INFO:    [14/11/2024 09:26:51] -> Processing Part 68 of 152
INFO:    [14/11/2024 09:26:53] -> Processing Part 69 of 152
INFO:    [14/11/2024 09:26:54] -> Processing Part 70 of 152
INFO:    [14/11/2024 09:26:54] -> Processing Part 71 of 152
INFO:    [14/11/2024 09:26:55] -> Processing Part 72 of 152
INFO:    [14/11/2024 09:26:55] -> Processing Part 73 of 152
INFO:    [14/11/2024 09:26:57] -> Processing Part 74 of 152
INFO:    [14/11/2024 09:26:58] -> Processing Part 75 of 152
INFO:    [14/11/2024 09:26:58] -> Processing Part 76 of 152
INFO:    [14/11/2024 09:26:58] -> Processing Part 77 of 152
INFO:    [14/11/2024 09:26:59] -> Processing Part 78 of 152
INFO:    [14/11/2024 09:26:59] -> Processing Part 79 of 152
INFO:    [14/11/2024 09:26:59] -> Processing Part 80 of 152
INFO:    [14/11/2024 09:27:00] -> Processing Part 81 of 152
INFO:    [14/11/2024 09:27:00] -> Processing Part 82 of 152
INFO:    [14/11/2024 09:27:00] -> Processing Part 83 of 152
INFO:    [14/11/2024 09:27:03] -> Processing Part 84 of 152
INFO:    [14/11/2024 09:27:03] -> Processing Part 85 of 152
INFO:    [14/11/2024 09:27:04] -> Processing Part 86 of 152
INFO:    [14/11/2024 09:27:04] -> Processing Part 87 of 152
INFO:    [14/11/2024 09:27:05] -> Processing Part 88 of 152
INFO:    [14/11/2024 09:27:06] -> Processing Part 89 of 152
INFO:    [14/11/2024 09:27:06] -> Processing Part 90 of 152
INFO:    [14/11/2024 09:27:07] -> Processing Part 91 of 152
INFO:    [14/11/2024 09:27:07] -> Processing Part 92 of 152
INFO:    [14/11/2024 09:27:09] -> Processing Part 93 of 152
INFO:    [14/11/2024 09:27:09] -> Processing Part 94 of 152
INFO:    [14/11/2024 09:27:10] -> Processing Part 95 of 152
INFO:    [14/11/2024 09:27:10] -> Processing Part 96 of 152
INFO:    [14/11/2024 09:27:10] -> Processing Part 97 of 152
INFO:    [14/11/2024 09:27:11] -> Processing Part 98 of 152
INFO:    [14/11/2024 09:27:11] -> Processing Part 99 of 152
INFO:    [14/11/2024 09:27:11] -> Processing Part 100 of 152
INFO:    [14/11/2024 09:27:12] -> Processing Part 101 of 152
INFO:    [14/11/2024 09:27:12] -> Processing Part 102 of 152
INFO:    [14/11/2024 09:27:13] -> Processing Part 103 of 152
INFO:    [14/11/2024 09:27:13] -> Processing Part 104 of 152
INFO:    [14/11/2024 09:27:14] -> Processing Part 105 of 152
INFO:    [14/11/2024 09:27:14] -> Processing Part 106 of 152
INFO:    [14/11/2024 09:27:14] -> Processing Part 107 of 152
INFO:    [14/11/2024 09:27:15] -> Processing Part 108 of 152
INFO:    [14/11/2024 09:27:15] -> Processing Part 109 of 152
INFO:    [14/11/2024 09:27:16] -> Processing Part 110 of 152
INFO:    [14/11/2024 09:27:17] -> Processing Part 111 of 152
INFO:    [14/11/2024 09:27:17] -> Processing Part 112 of 152
INFO:    [14/11/2024 09:27:17] -> Processing Part 113 of 152
INFO:    [14/11/2024 09:27:17] -> Processing Part 114 of 152
INFO:    [14/11/2024 09:27:18] -> Processing Part 115 of 152
INFO:    [14/11/2024 09:27:18] -> Processing Part 116 of 152
INFO:    [14/11/2024 09:27:18] -> Processing Part 117 of 152
INFO:    [14/11/2024 09:27:19] -> Processing Part 118 of 152
INFO:    [14/11/2024 09:27:19] -> Processing Part 119 of 152
INFO:    [14/11/2024 09:27:20] -> Processing Part 120 of 152
INFO:    [14/11/2024 09:27:20] -> Processing Part 121 of 152
INFO:    [14/11/2024 09:27:21] -> Processing Part 122 of 152
INFO:    [14/11/2024 09:27:21] -> Processing Part 123 of 152
INFO:    [14/11/2024 09:27:21] -> Processing Part 124 of 152
INFO:    [14/11/2024 09:27:22] -> Processing Part 125 of 152
INFO:    [14/11/2024 09:27:22] -> Processing Part 126 of 152
INFO:    [14/11/2024 09:27:23] -> Processing Part 127 of 152
INFO:    [14/11/2024 09:27:23] -> Processing Part 128 of 152
INFO:    [14/11/2024 09:27:23] -> Processing Part 129 of 152
INFO:    [14/11/2024 09:27:24] -> Processing Part 130 of 152
INFO:    [14/11/2024 09:27:24] -> Processing Part 131 of 152
INFO:    [14/11/2024 09:27:24] -> Processing Part 132 of 152
INFO:    [14/11/2024 09:27:24] -> Processing Part 133 of 152
INFO:    [14/11/2024 09:27:25] -> Processing Part 134 of 152
INFO:    [14/11/2024 09:27:25] -> Processing Part 135 of 152
INFO:    [14/11/2024 09:27:26] -> Processing Part 136 of 152
INFO:    [14/11/2024 09:27:26] -> Processing Part 137 of 152
INFO:    [14/11/2024 09:27:26] -> Processing Part 138 of 152
INFO:    [14/11/2024 09:27:27] -> Processing Part 139 of 152
INFO:    [14/11/2024 09:27:27] -> Processing Part 140 of 152
INFO:    [14/11/2024 09:27:27] -> Processing Part 141 of 152
INFO:    [14/11/2024 09:27:27] -> Processing Part 142 of 152
INFO:    [14/11/2024 09:27:27] -> Processing Part 143 of 152
INFO:    [14/11/2024 09:27:27] -> Processing Part 144 of 152
INFO:    [14/11/2024 09:27:28] -> Processing Part 145 of 152
INFO:    [14/11/2024 09:27:28] -> Processing Part 146 of 152
INFO:    [14/11/2024 09:27:28] -> Processing Part 147 of 152
INFO:    [14/11/2024 09:27:31] -> Processing Part 148 of 152
INFO:    [14/11/2024 09:27:31] -> Processing Part 149 of 152
INFO:    [14/11/2024 09:27:31] -> Processing Part 150 of 152
INFO:    [14/11/2024 09:27:32] -> Processing Part 151 of 152
INFO:    [14/11/2024 09:27:33] -> Processing Part 152 of 152
INFO:    [14/11/2024 09:27:34] -> Nr of Features Requested: 239407
INFO:    [14/11/2024 09:27:34] -> Size of Featurespace: 239407
INFO:    [14/11/2024 09:27:34] -> Scans/Feature pairs that failed to Match: 1573
INFO:    [14/11/2024 09:27:34] -> Maximum Nr of Features for one Scan: 11
INFO:    [14/11/2024 09:27:35] -> Finalizing...
INFO:    [14/11/2024 09:27:36] -> Processed in 1.6m
INFO:    [14/11/2024 09:27:36] -> Processed in 2.6m
INFO:    [14/11/2024 09:27:37] -> Done
INFO:    [14/11/2024 09:27:37] -> Run 2/6: Process Raw File...
INFO:    [14/11/2024 09:27:45] -> Run 2/6: Preparing Partitions...
INFO:    [14/11/2024 09:27:45] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [14/11/2024 09:27:47] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [14/11/2024 09:27:53] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [14/11/2024 09:28:05] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5001 [11.7s]
INFO:    [14/11/2024 09:28:12] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [14/11/2024 09:28:14] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [14/11/2024 09:28:14] -> PERFORMING MAIN SEARCH 1
INFO:    [14/11/2024 09:28:59] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 42877 [45.2s]
INFO:    [14/11/2024 09:28:59] -> PERFORMING MAIN SEARCH 2
INFO:    [14/11/2024 09:29:15] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7479 [15.9s]
INFO:    [14/11/2024 09:29:15] -> PERFORMING MAIN SEARCH 3
INFO:    [14/11/2024 09:29:23] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1015 [7.7s]
INFO:    [14/11/2024 09:29:23] -> PERFORMING MAIN SEARCH 4
INFO:    [14/11/2024 09:29:28] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 230 [5.8s]
INFO:    [14/11/2024 09:30:12] -> Extracting 154843 MS1 XICs
INFO:    [14/11/2024 09:32:24] -> Run 2/6: Cleaning Up Run..
INFO:    [14/11/2024 09:32:25] -> SuperRun 3/6: Initializing (LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw)
INFO:    [14/11/2024 09:32:25] -> Run 3/6: Organizing Data from Run
INFO:    [14/11/2024 09:32:25] -> Run 3/6: Creating Calibration Search Space...
INFO:    [14/11/2024 09:32:25] -> Run 3/6: Creating Search Space...
INFO:    [14/11/2024 09:32:25] -> Size of search space [MB]: 0
INFO:    [14/11/2024 09:32:25] -> Number of IMPGs in search space: 0
INFO:    [14/11/2024 09:32:25] -> Run 3/6: MS2 Index Generation
INFO:    [14/11/2024 09:32:25] -> MS2 Index Generation Time: 677.31ms
INFO:    [14/11/2024 09:32:25] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [14/11/2024 09:32:27] -> Initializing...
INFO:    [14/11/2024 09:32:45] -> Finalizing HTRMS File...
INFO:    [14/11/2024 09:32:58] -> Processing Part 1 of 152
INFO:    [14/11/2024 09:32:59] -> Processing Part 2 of 152
INFO:    [14/11/2024 09:33:00] -> Processing Part 3 of 152
INFO:    [14/11/2024 09:33:00] -> Processing Part 4 of 152
INFO:    [14/11/2024 09:33:00] -> Processing Part 5 of 152
INFO:    [14/11/2024 09:33:01] -> Processing Part 6 of 152
INFO:    [14/11/2024 09:33:01] -> Processing Part 7 of 152
INFO:    [14/11/2024 09:33:02] -> Processing Part 8 of 152
INFO:    [14/11/2024 09:33:03] -> Processing Part 9 of 152
INFO:    [14/11/2024 09:33:04] -> Processing Part 10 of 152
INFO:    [14/11/2024 09:33:04] -> Processing Part 11 of 152
INFO:    [14/11/2024 09:33:05] -> Processing Part 12 of 152
INFO:    [14/11/2024 09:33:05] -> Processing Part 13 of 152
INFO:    [14/11/2024 09:33:05] -> Processing Part 14 of 152
INFO:    [14/11/2024 09:33:06] -> Processing Part 15 of 152
INFO:    [14/11/2024 09:33:07] -> Processing Part 16 of 152
INFO:    [14/11/2024 09:33:07] -> Processing Part 17 of 152
INFO:    [14/11/2024 09:33:07] -> Processing Part 18 of 152
INFO:    [14/11/2024 09:33:08] -> Processing Part 19 of 152
INFO:    [14/11/2024 09:33:08] -> Processing Part 20 of 152
INFO:    [14/11/2024 09:33:09] -> Processing Part 21 of 152
INFO:    [14/11/2024 09:33:09] -> Processing Part 22 of 152
INFO:    [14/11/2024 09:33:09] -> Processing Part 23 of 152
INFO:    [14/11/2024 09:33:10] -> Processing Part 24 of 152
INFO:    [14/11/2024 09:33:10] -> Processing Part 25 of 152
INFO:    [14/11/2024 09:33:10] -> Processing Part 26 of 152
INFO:    [14/11/2024 09:33:11] -> Processing Part 27 of 152
INFO:    [14/11/2024 09:33:11] -> Processing Part 28 of 152
INFO:    [14/11/2024 09:33:12] -> Processing Part 29 of 152
INFO:    [14/11/2024 09:33:12] -> Processing Part 30 of 152
INFO:    [14/11/2024 09:33:12] -> Processing Part 31 of 152
INFO:    [14/11/2024 09:33:12] -> Processing Part 32 of 152
INFO:    [14/11/2024 09:33:12] -> Processing Part 33 of 152
INFO:    [14/11/2024 09:33:13] -> Processing Part 34 of 152
INFO:    [14/11/2024 09:33:14] -> Processing Part 35 of 152
INFO:    [14/11/2024 09:33:14] -> Processing Part 36 of 152
INFO:    [14/11/2024 09:33:14] -> Processing Part 37 of 152
INFO:    [14/11/2024 09:33:14] -> Processing Part 38 of 152
INFO:    [14/11/2024 09:33:15] -> Processing Part 39 of 152
INFO:    [14/11/2024 09:33:15] -> Processing Part 40 of 152
INFO:    [14/11/2024 09:33:16] -> Processing Part 41 of 152
INFO:    [14/11/2024 09:33:16] -> Processing Part 42 of 152
INFO:    [14/11/2024 09:33:16] -> Processing Part 43 of 152
INFO:    [14/11/2024 09:33:17] -> Processing Part 44 of 152
INFO:    [14/11/2024 09:33:17] -> Processing Part 45 of 152
INFO:    [14/11/2024 09:33:17] -> Processing Part 46 of 152
INFO:    [14/11/2024 09:33:18] -> Processing Part 47 of 152
INFO:    [14/11/2024 09:33:18] -> Processing Part 48 of 152
INFO:    [14/11/2024 09:33:19] -> Processing Part 49 of 152
INFO:    [14/11/2024 09:33:19] -> Processing Part 50 of 152
INFO:    [14/11/2024 09:33:20] -> Processing Part 51 of 152
INFO:    [14/11/2024 09:33:20] -> Processing Part 52 of 152
INFO:    [14/11/2024 09:33:20] -> Processing Part 53 of 152
INFO:    [14/11/2024 09:33:20] -> Processing Part 54 of 152
INFO:    [14/11/2024 09:33:21] -> Processing Part 55 of 152
INFO:    [14/11/2024 09:33:21] -> Processing Part 56 of 152
INFO:    [14/11/2024 09:33:22] -> Processing Part 57 of 152
INFO:    [14/11/2024 09:33:22] -> Processing Part 58 of 152
INFO:    [14/11/2024 09:33:22] -> Processing Part 59 of 152
INFO:    [14/11/2024 09:33:22] -> Processing Part 60 of 152
INFO:    [14/11/2024 09:33:22] -> Processing Part 61 of 152
INFO:    [14/11/2024 09:33:23] -> Processing Part 62 of 152
INFO:    [14/11/2024 09:33:23] -> Processing Part 63 of 152
INFO:    [14/11/2024 09:33:23] -> Processing Part 64 of 152
INFO:    [14/11/2024 09:33:23] -> Processing Part 65 of 152
INFO:    [14/11/2024 09:33:24] -> Processing Part 66 of 152
INFO:    [14/11/2024 09:33:24] -> Processing Part 67 of 152
INFO:    [14/11/2024 09:33:24] -> Processing Part 68 of 152
INFO:    [14/11/2024 09:33:24] -> Processing Part 69 of 152
INFO:    [14/11/2024 09:33:25] -> Processing Part 70 of 152
INFO:    [14/11/2024 09:33:25] -> Processing Part 71 of 152
INFO:    [14/11/2024 09:33:25] -> Processing Part 72 of 152
INFO:    [14/11/2024 09:33:25] -> Processing Part 73 of 152
INFO:    [14/11/2024 09:33:26] -> Processing Part 74 of 152
INFO:    [14/11/2024 09:33:26] -> Processing Part 75 of 152
INFO:    [14/11/2024 09:33:26] -> Processing Part 76 of 152
INFO:    [14/11/2024 09:33:27] -> Processing Part 77 of 152
INFO:    [14/11/2024 09:33:28] -> Processing Part 78 of 152
INFO:    [14/11/2024 09:33:28] -> Processing Part 79 of 152
INFO:    [14/11/2024 09:33:28] -> Processing Part 80 of 152
INFO:    [14/11/2024 09:33:28] -> Processing Part 81 of 152
INFO:    [14/11/2024 09:33:29] -> Processing Part 82 of 152
INFO:    [14/11/2024 09:33:29] -> Processing Part 83 of 152
INFO:    [14/11/2024 09:33:29] -> Processing Part 84 of 152
INFO:    [14/11/2024 09:33:29] -> Processing Part 85 of 152
INFO:    [14/11/2024 09:33:30] -> Processing Part 86 of 152
INFO:    [14/11/2024 09:33:30] -> Processing Part 87 of 152
INFO:    [14/11/2024 09:33:30] -> Processing Part 88 of 152
INFO:    [14/11/2024 09:33:31] -> Processing Part 89 of 152
INFO:    [14/11/2024 09:33:31] -> Processing Part 90 of 152
INFO:    [14/11/2024 09:33:31] -> Processing Part 91 of 152
INFO:    [14/11/2024 09:33:31] -> Processing Part 92 of 152
INFO:    [14/11/2024 09:33:31] -> Processing Part 93 of 152
INFO:    [14/11/2024 09:33:32] -> Processing Part 94 of 152
INFO:    [14/11/2024 09:33:32] -> Processing Part 95 of 152
INFO:    [14/11/2024 09:33:32] -> Processing Part 96 of 152
INFO:    [14/11/2024 09:33:33] -> Processing Part 97 of 152
INFO:    [14/11/2024 09:33:33] -> Processing Part 98 of 152
INFO:    [14/11/2024 09:33:33] -> Processing Part 99 of 152
INFO:    [14/11/2024 09:33:33] -> Processing Part 100 of 152
INFO:    [14/11/2024 09:33:33] -> Processing Part 101 of 152
INFO:    [14/11/2024 09:33:34] -> Processing Part 102 of 152
INFO:    [14/11/2024 09:33:34] -> Processing Part 103 of 152
INFO:    [14/11/2024 09:33:34] -> Processing Part 104 of 152
INFO:    [14/11/2024 09:33:34] -> Processing Part 105 of 152
INFO:    [14/11/2024 09:33:34] -> Processing Part 106 of 152
INFO:    [14/11/2024 09:33:35] -> Processing Part 107 of 152
INFO:    [14/11/2024 09:33:35] -> Processing Part 108 of 152
INFO:    [14/11/2024 09:33:35] -> Processing Part 109 of 152
INFO:    [14/11/2024 09:33:35] -> Processing Part 110 of 152
INFO:    [14/11/2024 09:33:35] -> Processing Part 111 of 152
INFO:    [14/11/2024 09:33:36] -> Processing Part 112 of 152
INFO:    [14/11/2024 09:33:36] -> Processing Part 113 of 152
INFO:    [14/11/2024 09:33:36] -> Processing Part 114 of 152
INFO:    [14/11/2024 09:33:36] -> Processing Part 115 of 152
INFO:    [14/11/2024 09:33:36] -> Processing Part 116 of 152
INFO:    [14/11/2024 09:33:36] -> Processing Part 117 of 152
INFO:    [14/11/2024 09:33:37] -> Processing Part 118 of 152
INFO:    [14/11/2024 09:33:37] -> Processing Part 119 of 152
INFO:    [14/11/2024 09:33:37] -> Processing Part 120 of 152
INFO:    [14/11/2024 09:33:37] -> Processing Part 121 of 152
INFO:    [14/11/2024 09:33:37] -> Processing Part 122 of 152
INFO:    [14/11/2024 09:33:38] -> Processing Part 123 of 152
INFO:    [14/11/2024 09:33:38] -> Processing Part 124 of 152
INFO:    [14/11/2024 09:33:38] -> Processing Part 125 of 152
INFO:    [14/11/2024 09:33:38] -> Processing Part 126 of 152
INFO:    [14/11/2024 09:33:38] -> Processing Part 127 of 152
INFO:    [14/11/2024 09:33:38] -> Processing Part 128 of 152
INFO:    [14/11/2024 09:33:39] -> Processing Part 129 of 152
INFO:    [14/11/2024 09:33:39] -> Processing Part 130 of 152
INFO:    [14/11/2024 09:33:39] -> Processing Part 131 of 152
INFO:    [14/11/2024 09:33:39] -> Processing Part 132 of 152
INFO:    [14/11/2024 09:33:39] -> Processing Part 133 of 152
INFO:    [14/11/2024 09:33:39] -> Processing Part 134 of 152
INFO:    [14/11/2024 09:33:40] -> Processing Part 135 of 152
INFO:    [14/11/2024 09:33:40] -> Processing Part 136 of 152
INFO:    [14/11/2024 09:33:40] -> Processing Part 137 of 152
INFO:    [14/11/2024 09:33:40] -> Processing Part 138 of 152
INFO:    [14/11/2024 09:33:40] -> Processing Part 139 of 152
INFO:    [14/11/2024 09:33:41] -> Processing Part 140 of 152
INFO:    [14/11/2024 09:33:41] -> Processing Part 141 of 152
INFO:    [14/11/2024 09:33:41] -> Processing Part 142 of 152
INFO:    [14/11/2024 09:33:41] -> Processing Part 143 of 152
INFO:    [14/11/2024 09:33:41] -> Processing Part 144 of 152
INFO:    [14/11/2024 09:33:41] -> Processing Part 145 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 146 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 147 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 148 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 149 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 150 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 151 of 152
INFO:    [14/11/2024 09:33:42] -> Processing Part 152 of 152
INFO:    [14/11/2024 09:33:43] -> Nr of Features Requested: 249277
INFO:    [14/11/2024 09:33:43] -> Size of Featurespace: 249277
INFO:    [14/11/2024 09:33:43] -> Scans/Feature pairs that failed to Match: 2144
INFO:    [14/11/2024 09:33:43] -> Maximum Nr of Features for one Scan: 14
INFO:    [14/11/2024 09:33:43] -> Finalizing...
INFO:    [14/11/2024 09:33:45] -> Processed in 46.48s
INFO:    [14/11/2024 09:33:45] -> Processed in 1.3m
INFO:    [14/11/2024 09:33:45] -> Done
INFO:    [14/11/2024 09:33:45] -> Run 3/6: Process Raw File...
INFO:    [14/11/2024 09:33:51] -> Run 3/6: Preparing Partitions...
INFO:    [14/11/2024 09:33:51] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [14/11/2024 09:33:51] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [14/11/2024 09:33:56] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [14/11/2024 09:34:00] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4856 [4.5s]
INFO:    [14/11/2024 09:34:03] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [14/11/2024 09:34:04] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [14/11/2024 09:34:04] -> PERFORMING MAIN SEARCH 1
INFO:    [14/11/2024 09:34:40] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 40263 [35.9s]
INFO:    [14/11/2024 09:34:40] -> PERFORMING MAIN SEARCH 2
INFO:    [14/11/2024 09:34:52] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 6749 [11.9s]
INFO:    [14/11/2024 09:34:52] -> PERFORMING MAIN SEARCH 3
INFO:    [14/11/2024 09:34:58] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 879 [6.4s]
INFO:    [14/11/2024 09:34:58] -> PERFORMING MAIN SEARCH 4
INFO:    [14/11/2024 09:35:04] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 56 [5.6s]
INFO:    [14/11/2024 09:35:46] -> Extracting 158553 MS1 XICs
INFO:    [14/11/2024 09:38:25] -> Run 3/6: Cleaning Up Run..
INFO:    [14/11/2024 09:38:26] -> SuperRun 4/6: Initializing (LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw)
INFO:    [14/11/2024 09:38:26] -> Run 4/6: Organizing Data from Run
INFO:    [14/11/2024 09:38:26] -> Run 4/6: Creating Calibration Search Space...
INFO:    [14/11/2024 09:38:26] -> Run 4/6: Creating Search Space...
INFO:    [14/11/2024 09:38:26] -> Size of search space [MB]: 0
INFO:    [14/11/2024 09:38:26] -> Number of IMPGs in search space: 0
INFO:    [14/11/2024 09:38:26] -> Run 4/6: MS2 Index Generation
INFO:    [14/11/2024 09:38:26] -> MS2 Index Generation Time: 690.25ms
INFO:    [14/11/2024 09:38:26] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [14/11/2024 09:38:28] -> Initializing...
INFO:    [14/11/2024 09:38:46] -> Finalizing HTRMS File...
INFO:    [14/11/2024 09:38:59] -> Processing Part 1 of 152
INFO:    [14/11/2024 09:39:00] -> Processing Part 2 of 152
INFO:    [14/11/2024 09:39:00] -> Processing Part 3 of 152
INFO:    [14/11/2024 09:39:01] -> Processing Part 4 of 152
INFO:    [14/11/2024 09:39:01] -> Processing Part 5 of 152
INFO:    [14/11/2024 09:39:01] -> Processing Part 6 of 152
INFO:    [14/11/2024 09:39:01] -> Processing Part 7 of 152
INFO:    [14/11/2024 09:39:01] -> Processing Part 8 of 152
INFO:    [14/11/2024 09:39:02] -> Processing Part 9 of 152
INFO:    [14/11/2024 09:39:03] -> Processing Part 10 of 152
INFO:    [14/11/2024 09:39:03] -> Processing Part 11 of 152
INFO:    [14/11/2024 09:39:04] -> Processing Part 12 of 152
INFO:    [14/11/2024 09:39:07] -> Processing Part 13 of 152
INFO:    [14/11/2024 09:39:08] -> Processing Part 14 of 152
INFO:    [14/11/2024 09:39:08] -> Processing Part 15 of 152
INFO:    [14/11/2024 09:39:08] -> Processing Part 16 of 152
INFO:    [14/11/2024 09:39:09] -> Processing Part 17 of 152
INFO:    [14/11/2024 09:39:09] -> Processing Part 18 of 152
INFO:    [14/11/2024 09:39:10] -> Processing Part 19 of 152
INFO:    [14/11/2024 09:39:10] -> Processing Part 20 of 152
INFO:    [14/11/2024 09:39:10] -> Processing Part 21 of 152
INFO:    [14/11/2024 09:39:11] -> Processing Part 22 of 152
INFO:    [14/11/2024 09:39:11] -> Processing Part 23 of 152
INFO:    [14/11/2024 09:39:12] -> Processing Part 24 of 152
INFO:    [14/11/2024 09:39:12] -> Processing Part 25 of 152
INFO:    [14/11/2024 09:39:12] -> Processing Part 26 of 152
INFO:    [14/11/2024 09:39:12] -> Processing Part 27 of 152
INFO:    [14/11/2024 09:39:12] -> Processing Part 28 of 152
INFO:    [14/11/2024 09:39:14] -> Processing Part 29 of 152
INFO:    [14/11/2024 09:39:14] -> Processing Part 30 of 152
INFO:    [14/11/2024 09:39:14] -> Processing Part 31 of 152
INFO:    [14/11/2024 09:39:14] -> Processing Part 32 of 152
INFO:    [14/11/2024 09:39:15] -> Processing Part 33 of 152
INFO:    [14/11/2024 09:39:15] -> Processing Part 34 of 152
INFO:    [14/11/2024 09:39:16] -> Processing Part 35 of 152
INFO:    [14/11/2024 09:39:16] -> Processing Part 36 of 152
INFO:    [14/11/2024 09:39:16] -> Processing Part 37 of 152
INFO:    [14/11/2024 09:39:17] -> Processing Part 38 of 152
INFO:    [14/11/2024 09:39:17] -> Processing Part 39 of 152
INFO:    [14/11/2024 09:39:17] -> Processing Part 40 of 152
INFO:    [14/11/2024 09:39:17] -> Processing Part 41 of 152
INFO:    [14/11/2024 09:39:18] -> Processing Part 42 of 152
INFO:    [14/11/2024 09:39:19] -> Processing Part 43 of 152
INFO:    [14/11/2024 09:39:19] -> Processing Part 44 of 152
INFO:    [14/11/2024 09:39:19] -> Processing Part 45 of 152
INFO:    [14/11/2024 09:39:19] -> Processing Part 46 of 152
INFO:    [14/11/2024 09:39:20] -> Processing Part 47 of 152
INFO:    [14/11/2024 09:39:21] -> Processing Part 48 of 152
INFO:    [14/11/2024 09:39:21] -> Processing Part 49 of 152
INFO:    [14/11/2024 09:39:21] -> Processing Part 50 of 152
INFO:    [14/11/2024 09:39:22] -> Processing Part 51 of 152
INFO:    [14/11/2024 09:39:22] -> Processing Part 52 of 152
INFO:    [14/11/2024 09:39:22] -> Processing Part 53 of 152
INFO:    [14/11/2024 09:39:26] -> Processing Part 54 of 152
INFO:    [14/11/2024 09:39:26] -> Processing Part 55 of 152
INFO:    [14/11/2024 09:39:27] -> Processing Part 56 of 152
INFO:    [14/11/2024 09:39:27] -> Processing Part 57 of 152
INFO:    [14/11/2024 09:39:27] -> Processing Part 58 of 152
INFO:    [14/11/2024 09:39:28] -> Processing Part 59 of 152
INFO:    [14/11/2024 09:39:28] -> Processing Part 60 of 152
INFO:    [14/11/2024 09:39:28] -> Processing Part 61 of 152
INFO:    [14/11/2024 09:39:29] -> Processing Part 62 of 152
INFO:    [14/11/2024 09:39:29] -> Processing Part 63 of 152
INFO:    [14/11/2024 09:39:29] -> Processing Part 64 of 152
INFO:    [14/11/2024 09:39:30] -> Processing Part 65 of 152
INFO:    [14/11/2024 09:39:31] -> Processing Part 66 of 152
INFO:    [14/11/2024 09:39:31] -> Processing Part 67 of 152
INFO:    [14/11/2024 09:39:31] -> Processing Part 68 of 152
INFO:    [14/11/2024 09:39:31] -> Processing Part 69 of 152
INFO:    [14/11/2024 09:39:32] -> Processing Part 70 of 152
INFO:    [14/11/2024 09:39:32] -> Processing Part 71 of 152
INFO:    [14/11/2024 09:39:32] -> Processing Part 72 of 152
INFO:    [14/11/2024 09:39:32] -> Processing Part 73 of 152
INFO:    [14/11/2024 09:39:32] -> Processing Part 74 of 152
INFO:    [14/11/2024 09:39:34] -> Processing Part 75 of 152
INFO:    [14/11/2024 09:39:34] -> Processing Part 76 of 152
INFO:    [14/11/2024 09:39:34] -> Processing Part 77 of 152
INFO:    [14/11/2024 09:39:34] -> Processing Part 78 of 152
INFO:    [14/11/2024 09:39:35] -> Processing Part 79 of 152
INFO:    [14/11/2024 09:39:35] -> Processing Part 80 of 152
INFO:    [14/11/2024 09:39:35] -> Processing Part 81 of 152
INFO:    [14/11/2024 09:39:35] -> Processing Part 82 of 152
INFO:    [14/11/2024 09:39:36] -> Processing Part 83 of 152
INFO:    [14/11/2024 09:39:36] -> Processing Part 84 of 152
INFO:    [14/11/2024 09:39:36] -> Processing Part 85 of 152
INFO:    [14/11/2024 09:39:36] -> Processing Part 86 of 152
INFO:    [14/11/2024 09:39:37] -> Processing Part 87 of 152
INFO:    [14/11/2024 09:39:37] -> Processing Part 88 of 152
INFO:    [14/11/2024 09:39:37] -> Processing Part 89 of 152
INFO:    [14/11/2024 09:39:38] -> Processing Part 90 of 152
INFO:    [14/11/2024 09:39:38] -> Processing Part 91 of 152
INFO:    [14/11/2024 09:39:38] -> Processing Part 92 of 152
INFO:    [14/11/2024 09:39:38] -> Processing Part 93 of 152
INFO:    [14/11/2024 09:39:38] -> Processing Part 94 of 152
INFO:    [14/11/2024 09:39:39] -> Processing Part 95 of 152
INFO:    [14/11/2024 09:39:39] -> Processing Part 96 of 152
INFO:    [14/11/2024 09:39:39] -> Processing Part 97 of 152
INFO:    [14/11/2024 09:39:40] -> Processing Part 98 of 152
INFO:    [14/11/2024 09:39:40] -> Processing Part 99 of 152
INFO:    [14/11/2024 09:39:40] -> Processing Part 100 of 152
INFO:    [14/11/2024 09:39:41] -> Processing Part 101 of 152
INFO:    [14/11/2024 09:39:41] -> Processing Part 102 of 152
INFO:    [14/11/2024 09:39:41] -> Processing Part 103 of 152
INFO:    [14/11/2024 09:39:42] -> Processing Part 104 of 152
INFO:    [14/11/2024 09:39:42] -> Processing Part 105 of 152
INFO:    [14/11/2024 09:39:42] -> Processing Part 106 of 152
INFO:    [14/11/2024 09:39:42] -> Processing Part 107 of 152
INFO:    [14/11/2024 09:39:43] -> Processing Part 108 of 152
INFO:    [14/11/2024 09:39:43] -> Processing Part 109 of 152
INFO:    [14/11/2024 09:39:43] -> Processing Part 110 of 152
INFO:    [14/11/2024 09:39:43] -> Processing Part 111 of 152
INFO:    [14/11/2024 09:39:43] -> Processing Part 112 of 152
INFO:    [14/11/2024 09:39:43] -> Processing Part 113 of 152
INFO:    [14/11/2024 09:39:44] -> Processing Part 114 of 152
INFO:    [14/11/2024 09:39:45] -> Processing Part 115 of 152
INFO:    [14/11/2024 09:39:46] -> Processing Part 116 of 152
INFO:    [14/11/2024 09:39:46] -> Processing Part 117 of 152
INFO:    [14/11/2024 09:39:47] -> Processing Part 118 of 152
INFO:    [14/11/2024 09:39:48] -> Processing Part 119 of 152
INFO:    [14/11/2024 09:39:48] -> Processing Part 120 of 152
INFO:    [14/11/2024 09:39:48] -> Processing Part 121 of 152
INFO:    [14/11/2024 09:39:49] -> Processing Part 122 of 152
INFO:    [14/11/2024 09:39:49] -> Processing Part 123 of 152
INFO:    [14/11/2024 09:39:49] -> Processing Part 124 of 152
INFO:    [14/11/2024 09:39:49] -> Processing Part 125 of 152
INFO:    [14/11/2024 09:39:50] -> Processing Part 126 of 152
INFO:    [14/11/2024 09:39:50] -> Processing Part 127 of 152
INFO:    [14/11/2024 09:39:50] -> Processing Part 128 of 152
INFO:    [14/11/2024 09:39:50] -> Processing Part 129 of 152
INFO:    [14/11/2024 09:39:50] -> Processing Part 130 of 152
INFO:    [14/11/2024 09:39:50] -> Processing Part 131 of 152
INFO:    [14/11/2024 09:39:51] -> Processing Part 132 of 152
INFO:    [14/11/2024 09:39:51] -> Processing Part 133 of 152
INFO:    [14/11/2024 09:39:51] -> Processing Part 134 of 152
INFO:    [14/11/2024 09:39:51] -> Processing Part 135 of 152
INFO:    [14/11/2024 09:39:51] -> Processing Part 136 of 152
INFO:    [14/11/2024 09:39:51] -> Processing Part 137 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 138 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 139 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 140 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 141 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 142 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 143 of 152
INFO:    [14/11/2024 09:39:52] -> Processing Part 144 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 145 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 146 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 147 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 148 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 149 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 150 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 151 of 152
INFO:    [14/11/2024 09:39:53] -> Processing Part 152 of 152
INFO:    [14/11/2024 09:39:54] -> Nr of Features Requested: 254721
INFO:    [14/11/2024 09:39:54] -> Size of Featurespace: 254731
INFO:    [14/11/2024 09:39:54] -> Scans/Feature pairs that failed to Match: 1488
INFO:    [14/11/2024 09:39:54] -> Maximum Nr of Features for one Scan: 13
INFO:    [14/11/2024 09:39:54] -> Finalizing...
INFO:    [14/11/2024 09:39:56] -> Processed in 56.47s
INFO:    [14/11/2024 09:39:56] -> Processed in 1.5m
INFO:    [14/11/2024 09:39:56] -> Done
INFO:    [14/11/2024 09:39:56] -> Run 4/6: Process Raw File...
INFO:    [14/11/2024 09:40:01] -> Run 4/6: Preparing Partitions...
INFO:    [14/11/2024 09:40:01] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [14/11/2024 09:40:01] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [14/11/2024 09:40:10] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [14/11/2024 09:40:14] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3793 [3.8s]
INFO:    [14/11/2024 09:40:17] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [14/11/2024 09:40:17] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [14/11/2024 09:40:18] -> PERFORMING MAIN SEARCH 1
INFO:    [14/11/2024 09:40:50] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 40822 [32.9s]
INFO:    [14/11/2024 09:40:50] -> PERFORMING MAIN SEARCH 2
INFO:    [14/11/2024 09:41:07] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 6954 [16.8s]
INFO:    [14/11/2024 09:41:07] -> PERFORMING MAIN SEARCH 3
INFO:    [14/11/2024 09:41:14] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 1014 [6.4s]
INFO:    [14/11/2024 09:41:14] -> PERFORMING MAIN SEARCH 4
INFO:    [14/11/2024 09:41:20] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 136 [6s]
INFO:    [14/11/2024 09:42:10] -> Extracting 161203 MS1 XICs
INFO:    [14/11/2024 09:45:02] -> Run 4/6: Cleaning Up Run..
INFO:    [14/11/2024 09:45:03] -> SuperRun 5/6: Initializing (LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw)
INFO:    [14/11/2024 09:45:03] -> Run 5/6: Organizing Data from Run
INFO:    [14/11/2024 09:45:03] -> Run 5/6: Creating Calibration Search Space...
INFO:    [14/11/2024 09:45:03] -> Run 5/6: Creating Search Space...
INFO:    [14/11/2024 09:45:03] -> Size of search space [MB]: 0
INFO:    [14/11/2024 09:45:03] -> Number of IMPGs in search space: 0
INFO:    [14/11/2024 09:45:03] -> Run 5/6: MS2 Index Generation
INFO:    [14/11/2024 09:45:04] -> MS2 Index Generation Time: 778.33ms
INFO:    [14/11/2024 09:45:04] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [14/11/2024 09:45:05] -> Initializing...
INFO:    [14/11/2024 09:45:25] -> Finalizing HTRMS File...
INFO:    [14/11/2024 09:45:37] -> Processing Part 1 of 152
INFO:    [14/11/2024 09:45:38] -> Processing Part 2 of 152
INFO:    [14/11/2024 09:45:38] -> Processing Part 3 of 152
INFO:    [14/11/2024 09:45:38] -> Processing Part 4 of 152
INFO:    [14/11/2024 09:45:38] -> Processing Part 5 of 152
INFO:    [14/11/2024 09:45:39] -> Processing Part 6 of 152
INFO:    [14/11/2024 09:45:40] -> Processing Part 7 of 152
INFO:    [14/11/2024 09:45:40] -> Processing Part 8 of 152
INFO:    [14/11/2024 09:45:41] -> Processing Part 9 of 152
INFO:    [14/11/2024 09:45:41] -> Processing Part 10 of 152
INFO:    [14/11/2024 09:45:41] -> Processing Part 11 of 152
INFO:    [14/11/2024 09:45:41] -> Processing Part 12 of 152
INFO:    [14/11/2024 09:45:41] -> Processing Part 13 of 152
INFO:    [14/11/2024 09:45:42] -> Processing Part 14 of 152
INFO:    [14/11/2024 09:45:43] -> Processing Part 15 of 152
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INFO:    [14/11/2024 09:45:50] -> Processing Part 27 of 152
INFO:    [14/11/2024 09:45:51] -> Processing Part 28 of 152
INFO:    [14/11/2024 09:45:51] -> Processing Part 29 of 152
INFO:    [14/11/2024 09:45:51] -> Processing Part 30 of 152
INFO:    [14/11/2024 09:45:52] -> Processing Part 31 of 152
INFO:    [14/11/2024 09:45:52] -> Processing Part 32 of 152
INFO:    [14/11/2024 09:45:53] -> Processing Part 33 of 152
INFO:    [14/11/2024 09:45:53] -> Processing Part 34 of 152
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INFO:    [14/11/2024 09:45:54] -> Processing Part 36 of 152
INFO:    [14/11/2024 09:45:55] -> Processing Part 37 of 152
INFO:    [14/11/2024 09:45:55] -> Processing Part 38 of 152
INFO:    [14/11/2024 09:45:55] -> Processing Part 39 of 152
INFO:    [14/11/2024 09:45:56] -> Processing Part 40 of 152
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INFO:    [14/11/2024 09:45:56] -> Processing Part 42 of 152
INFO:    [14/11/2024 09:45:57] -> Processing Part 43 of 152
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INFO:    [14/11/2024 09:45:59] -> Processing Part 48 of 152
INFO:    [14/11/2024 09:45:59] -> Processing Part 49 of 152
INFO:    [14/11/2024 09:45:59] -> Processing Part 50 of 152
INFO:    [14/11/2024 09:46:00] -> Processing Part 51 of 152
INFO:    [14/11/2024 09:46:00] -> Processing Part 52 of 152
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INFO:    [14/11/2024 09:46:02] -> Processing Part 58 of 152
INFO:    [14/11/2024 09:46:03] -> Processing Part 59 of 152
INFO:    [14/11/2024 09:46:03] -> Processing Part 60 of 152
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INFO:    [14/11/2024 09:46:04] -> Processing Part 63 of 152
INFO:    [14/11/2024 09:46:04] -> Processing Part 64 of 152
INFO:    [14/11/2024 09:46:05] -> Processing Part 65 of 152
INFO:    [14/11/2024 09:46:05] -> Processing Part 66 of 152
INFO:    [14/11/2024 09:46:05] -> Processing Part 67 of 152
INFO:    [14/11/2024 09:46:06] -> Processing Part 68 of 152
INFO:    [14/11/2024 09:46:06] -> Processing Part 69 of 152
INFO:    [14/11/2024 09:46:06] -> Processing Part 70 of 152
INFO:    [14/11/2024 09:46:07] -> Processing Part 71 of 152
INFO:    [14/11/2024 09:46:07] -> Processing Part 72 of 152
INFO:    [14/11/2024 09:46:07] -> Processing Part 73 of 152
INFO:    [14/11/2024 09:46:08] -> Processing Part 74 of 152
INFO:    [14/11/2024 09:46:08] -> Processing Part 75 of 152
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INFO:    [14/11/2024 09:46:11] -> Processing Part 78 of 152
INFO:    [14/11/2024 09:46:12] -> Processing Part 79 of 152
INFO:    [14/11/2024 09:46:13] -> Processing Part 80 of 152
INFO:    [14/11/2024 09:46:14] -> Processing Part 81 of 152
INFO:    [14/11/2024 09:46:14] -> Processing Part 82 of 152
INFO:    [14/11/2024 09:46:14] -> Processing Part 83 of 152
INFO:    [14/11/2024 09:46:14] -> Processing Part 84 of 152
INFO:    [14/11/2024 09:46:15] -> Processing Part 85 of 152
INFO:    [14/11/2024 09:46:15] -> Processing Part 86 of 152
INFO:    [14/11/2024 09:46:15] -> Processing Part 87 of 152
INFO:    [14/11/2024 09:46:16] -> Processing Part 88 of 152
INFO:    [14/11/2024 09:46:16] -> Processing Part 89 of 152
INFO:    [14/11/2024 09:46:16] -> Processing Part 90 of 152
INFO:    [14/11/2024 09:46:17] -> Processing Part 91 of 152
INFO:    [14/11/2024 09:46:17] -> Processing Part 92 of 152
INFO:    [14/11/2024 09:46:17] -> Processing Part 93 of 152
INFO:    [14/11/2024 09:46:17] -> Processing Part 94 of 152
INFO:    [14/11/2024 09:46:18] -> Processing Part 95 of 152
INFO:    [14/11/2024 09:46:18] -> Processing Part 96 of 152
INFO:    [14/11/2024 09:46:18] -> Processing Part 97 of 152
INFO:    [14/11/2024 09:46:18] -> Processing Part 98 of 152
INFO:    [14/11/2024 09:46:19] -> Processing Part 99 of 152
INFO:    [14/11/2024 09:46:19] -> Processing Part 100 of 152
INFO:    [14/11/2024 09:46:20] -> Processing Part 101 of 152
INFO:    [14/11/2024 09:46:20] -> Processing Part 102 of 152
INFO:    [14/11/2024 09:46:20] -> Processing Part 103 of 152
INFO:    [14/11/2024 09:46:20] -> Processing Part 104 of 152
INFO:    [14/11/2024 09:46:20] -> Processing Part 105 of 152
INFO:    [14/11/2024 09:46:21] -> Processing Part 106 of 152
INFO:    [14/11/2024 09:46:21] -> Processing Part 107 of 152
INFO:    [14/11/2024 09:46:21] -> Processing Part 108 of 152
INFO:    [14/11/2024 09:46:21] -> Processing Part 109 of 152
INFO:    [14/11/2024 09:46:22] -> Processing Part 110 of 152
INFO:    [14/11/2024 09:46:22] -> Processing Part 111 of 152
INFO:    [14/11/2024 09:46:22] -> Processing Part 112 of 152
INFO:    [14/11/2024 09:46:23] -> Processing Part 113 of 152
INFO:    [14/11/2024 09:46:23] -> Processing Part 114 of 152
INFO:    [14/11/2024 09:46:23] -> Processing Part 115 of 152
INFO:    [14/11/2024 09:46:24] -> Processing Part 116 of 152
INFO:    [14/11/2024 09:46:24] -> Processing Part 117 of 152
INFO:    [14/11/2024 09:46:24] -> Processing Part 118 of 152
INFO:    [14/11/2024 09:46:24] -> Processing Part 119 of 152
INFO:    [14/11/2024 09:46:24] -> Processing Part 120 of 152
INFO:    [14/11/2024 09:46:25] -> Processing Part 121 of 152
INFO:    [14/11/2024 09:46:25] -> Processing Part 122 of 152
INFO:    [14/11/2024 09:46:25] -> Processing Part 123 of 152
INFO:    [14/11/2024 09:46:26] -> Processing Part 124 of 152
INFO:    [14/11/2024 09:46:26] -> Processing Part 125 of 152
INFO:    [14/11/2024 09:46:26] -> Processing Part 126 of 152
INFO:    [14/11/2024 09:46:26] -> Processing Part 127 of 152
INFO:    [14/11/2024 09:46:26] -> Processing Part 128 of 152
INFO:    [14/11/2024 09:46:27] -> Processing Part 129 of 152
INFO:    [14/11/2024 09:46:27] -> Processing Part 130 of 152
INFO:    [14/11/2024 09:46:27] -> Processing Part 131 of 152
INFO:    [14/11/2024 09:46:27] -> Processing Part 132 of 152
INFO:    [14/11/2024 09:46:27] -> Processing Part 133 of 152
INFO:    [14/11/2024 09:46:28] -> Processing Part 134 of 152
INFO:    [14/11/2024 09:46:28] -> Processing Part 135 of 152
INFO:    [14/11/2024 09:46:28] -> Processing Part 136 of 152
INFO:    [14/11/2024 09:46:28] -> Processing Part 137 of 152
INFO:    [14/11/2024 09:46:28] -> Processing Part 138 of 152
INFO:    [14/11/2024 09:46:29] -> Processing Part 139 of 152
INFO:    [14/11/2024 09:46:29] -> Processing Part 140 of 152
INFO:    [14/11/2024 09:46:29] -> Processing Part 141 of 152
INFO:    [14/11/2024 09:46:29] -> Processing Part 142 of 152
INFO:    [14/11/2024 09:46:29] -> Processing Part 143 of 152
INFO:    [14/11/2024 09:46:29] -> Processing Part 144 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 145 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 146 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 147 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 148 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 149 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 150 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 151 of 152
INFO:    [14/11/2024 09:46:30] -> Processing Part 152 of 152
INFO:    [14/11/2024 09:46:31] -> Nr of Features Requested: 243107
INFO:    [14/11/2024 09:46:31] -> Size of Featurespace: 243129
INFO:    [14/11/2024 09:46:31] -> Scans/Feature pairs that failed to Match: 1802
INFO:    [14/11/2024 09:46:31] -> Maximum Nr of Features for one Scan: 13
INFO:    [14/11/2024 09:46:32] -> Finalizing...
INFO:    [14/11/2024 09:46:35] -> Processed in 58.55s
INFO:    [14/11/2024 09:46:35] -> Processed in 1.5m
INFO:    [14/11/2024 09:46:36] -> Done
INFO:    [14/11/2024 09:46:36] -> Run 5/6: Process Raw File...
INFO:    [14/11/2024 09:46:41] -> Run 5/6: Preparing Partitions...
INFO:    [14/11/2024 09:46:41] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [14/11/2024 09:46:41] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [14/11/2024 09:46:46] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [14/11/2024 09:46:54] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4039 [7.7s]
INFO:    [14/11/2024 09:46:57] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [14/11/2024 09:46:58] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [14/11/2024 09:46:58] -> PERFORMING MAIN SEARCH 1
INFO:    [14/11/2024 09:47:39] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 40499 [41.2s]
INFO:    [14/11/2024 09:47:39] -> PERFORMING MAIN SEARCH 2
INFO:    [14/11/2024 09:47:53] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 7106 [13.9s]
INFO:    [14/11/2024 09:47:53] -> PERFORMING MAIN SEARCH 3
INFO:    [14/11/2024 09:48:03] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 747 [9.9s]
INFO:    [14/11/2024 09:48:46] -> Extracting 151679 MS1 XICs
INFO:    [14/11/2024 09:51:18] -> Run 5/6: Cleaning Up Run..
INFO:    [14/11/2024 09:51:19] -> SuperRun 6/6: Initializing (LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw)
INFO:    [14/11/2024 09:51:19] -> Run 6/6: Organizing Data from Run
INFO:    [14/11/2024 09:51:19] -> Run 6/6: Creating Calibration Search Space...
INFO:    [14/11/2024 09:51:19] -> Run 6/6: Creating Search Space...
INFO:    [14/11/2024 09:51:19] -> Size of search space [MB]: 0
INFO:    [14/11/2024 09:51:19] -> Number of IMPGs in search space: 0
INFO:    [14/11/2024 09:51:19] -> Run 6/6: MS2 Index Generation
INFO:    [14/11/2024 09:51:20] -> MS2 Index Generation Time: 748.87ms
INFO:    [14/11/2024 09:51:20] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [14/11/2024 09:51:21] -> Initializing...
INFO:    [14/11/2024 09:51:36] -> Finalizing HTRMS File...
INFO:    [14/11/2024 09:51:53] -> Processing Part 1 of 152
INFO:    [14/11/2024 09:51:54] -> Processing Part 2 of 152
INFO:    [14/11/2024 09:51:55] -> Processing Part 3 of 152
INFO:    [14/11/2024 09:51:55] -> Processing Part 4 of 152
INFO:    [14/11/2024 09:51:56] -> Processing Part 5 of 152
INFO:    [14/11/2024 09:51:56] -> Processing Part 6 of 152
INFO:    [14/11/2024 09:51:56] -> Processing Part 7 of 152
INFO:    [14/11/2024 09:51:56] -> Processing Part 8 of 152
INFO:    [14/11/2024 09:51:57] -> Processing Part 9 of 152
INFO:    [14/11/2024 09:51:57] -> Processing Part 10 of 152
INFO:    [14/11/2024 09:51:58] -> Processing Part 11 of 152
INFO:    [14/11/2024 09:51:58] -> Processing Part 12 of 152
INFO:    [14/11/2024 09:51:58] -> Processing Part 13 of 152
INFO:    [14/11/2024 09:51:59] -> Processing Part 14 of 152
INFO:    [14/11/2024 09:51:59] -> Processing Part 15 of 152
INFO:    [14/11/2024 09:52:00] -> Processing Part 16 of 152
INFO:    [14/11/2024 09:52:00] -> Processing Part 17 of 152
INFO:    [14/11/2024 09:52:00] -> Processing Part 18 of 152
INFO:    [14/11/2024 09:52:00] -> Processing Part 19 of 152
INFO:    [14/11/2024 09:52:01] -> Processing Part 20 of 152
INFO:    [14/11/2024 09:52:01] -> Processing Part 21 of 152
INFO:    [14/11/2024 09:52:01] -> Processing Part 22 of 152
INFO:    [14/11/2024 09:52:02] -> Processing Part 23 of 152
INFO:    [14/11/2024 09:52:03] -> Processing Part 24 of 152
INFO:    [14/11/2024 09:52:03] -> Processing Part 25 of 152
INFO:    [14/11/2024 09:52:03] -> Processing Part 26 of 152
INFO:    [14/11/2024 09:52:03] -> Processing Part 27 of 152
INFO:    [14/11/2024 09:52:03] -> Processing Part 28 of 152
INFO:    [14/11/2024 09:52:04] -> Processing Part 29 of 152
INFO:    [14/11/2024 09:52:05] -> Processing Part 30 of 152
INFO:    [14/11/2024 09:52:05] -> Processing Part 31 of 152
INFO:    [14/11/2024 09:52:05] -> Processing Part 32 of 152
INFO:    [14/11/2024 09:52:05] -> Processing Part 33 of 152
INFO:    [14/11/2024 09:52:05] -> Processing Part 34 of 152
INFO:    [14/11/2024 09:52:05] -> Processing Part 35 of 152
INFO:    [14/11/2024 09:52:06] -> Processing Part 36 of 152
INFO:    [14/11/2024 09:52:07] -> Processing Part 37 of 152
INFO:    [14/11/2024 09:52:07] -> Processing Part 38 of 152
INFO:    [14/11/2024 09:52:08] -> Processing Part 39 of 152
INFO:    [14/11/2024 09:52:08] -> Processing Part 40 of 152
INFO:    [14/11/2024 09:52:08] -> Processing Part 41 of 152
INFO:    [14/11/2024 09:52:09] -> Processing Part 42 of 152
INFO:    [14/11/2024 09:52:10] -> Processing Part 43 of 152
INFO:    [14/11/2024 09:52:10] -> Processing Part 44 of 152
INFO:    [14/11/2024 09:52:11] -> Processing Part 45 of 152
INFO:    [14/11/2024 09:52:11] -> Processing Part 46 of 152
INFO:    [14/11/2024 09:52:11] -> Processing Part 47 of 152
INFO:    [14/11/2024 09:52:13] -> Processing Part 48 of 152
INFO:    [14/11/2024 09:52:14] -> Processing Part 49 of 152
INFO:    [14/11/2024 09:52:15] -> Processing Part 50 of 152
INFO:    [14/11/2024 09:52:15] -> Processing Part 51 of 152
INFO:    [14/11/2024 09:52:15] -> Processing Part 52 of 152
INFO:    [14/11/2024 09:52:16] -> Processing Part 53 of 152
INFO:    [14/11/2024 09:52:16] -> Processing Part 54 of 152
INFO:    [14/11/2024 09:52:17] -> Processing Part 55 of 152
INFO:    [14/11/2024 09:52:18] -> Processing Part 56 of 152
INFO:    [14/11/2024 09:52:18] -> Processing Part 57 of 152
INFO:    [14/11/2024 09:52:18] -> Processing Part 58 of 152
INFO:    [14/11/2024 09:52:19] -> Processing Part 59 of 152
INFO:    [14/11/2024 09:52:19] -> Processing Part 60 of 152
INFO:    [14/11/2024 09:52:19] -> Processing Part 61 of 152
INFO:    [14/11/2024 09:52:19] -> Processing Part 62 of 152
INFO:    [14/11/2024 09:52:20] -> Processing Part 63 of 152
INFO:    [14/11/2024 09:52:20] -> Processing Part 64 of 152
INFO:    [14/11/2024 09:52:20] -> Processing Part 65 of 152
INFO:    [14/11/2024 09:52:21] -> Processing Part 66 of 152
INFO:    [14/11/2024 09:52:21] -> Processing Part 67 of 152
INFO:    [14/11/2024 09:52:21] -> Processing Part 68 of 152
INFO:    [14/11/2024 09:52:22] -> Processing Part 69 of 152
INFO:    [14/11/2024 09:52:22] -> Processing Part 70 of 152
INFO:    [14/11/2024 09:52:22] -> Processing Part 71 of 152
INFO:    [14/11/2024 09:52:23] -> Processing Part 72 of 152
INFO:    [14/11/2024 09:52:23] -> Processing Part 73 of 152
INFO:    [14/11/2024 09:52:23] -> Processing Part 74 of 152
INFO:    [14/11/2024 09:52:23] -> Processing Part 75 of 152
INFO:    [14/11/2024 09:52:23] -> Processing Part 76 of 152
INFO:    [14/11/2024 09:52:24] -> Processing Part 77 of 152
INFO:    [14/11/2024 09:52:25] -> Processing Part 78 of 152
INFO:    [14/11/2024 09:52:25] -> Processing Part 79 of 152
INFO:    [14/11/2024 09:52:25] -> Processing Part 80 of 152
INFO:    [14/11/2024 09:52:25] -> Processing Part 81 of 152
INFO:    [14/11/2024 09:52:25] -> Processing Part 82 of 152
INFO:    [14/11/2024 09:52:26] -> Processing Part 83 of 152
INFO:    [14/11/2024 09:52:26] -> Processing Part 84 of 152
INFO:    [14/11/2024 09:52:26] -> Processing Part 85 of 152
INFO:    [14/11/2024 09:52:26] -> Processing Part 86 of 152
INFO:    [14/11/2024 09:52:27] -> Processing Part 87 of 152
INFO:    [14/11/2024 09:52:28] -> Processing Part 88 of 152
INFO:    [14/11/2024 09:52:28] -> Processing Part 89 of 152
INFO:    [14/11/2024 09:52:28] -> Processing Part 90 of 152
INFO:    [14/11/2024 09:52:28] -> Processing Part 91 of 152
INFO:    [14/11/2024 09:52:28] -> Processing Part 92 of 152
INFO:    [14/11/2024 09:52:29] -> Processing Part 93 of 152
INFO:    [14/11/2024 09:52:29] -> Processing Part 94 of 152
INFO:    [14/11/2024 09:52:29] -> Processing Part 95 of 152
INFO:    [14/11/2024 09:52:29] -> Processing Part 96 of 152
INFO:    [14/11/2024 09:52:30] -> Processing Part 97 of 152
INFO:    [14/11/2024 09:52:30] -> Processing Part 98 of 152
INFO:    [14/11/2024 09:52:30] -> Processing Part 99 of 152
INFO:    [14/11/2024 09:52:31] -> Processing Part 100 of 152
INFO:    [14/11/2024 09:52:31] -> Processing Part 101 of 152
INFO:    [14/11/2024 09:52:31] -> Processing Part 102 of 152
INFO:    [14/11/2024 09:52:31] -> Processing Part 103 of 152
INFO:    [14/11/2024 09:52:31] -> Processing Part 104 of 152
INFO:    [14/11/2024 09:52:31] -> Processing Part 105 of 152
INFO:    [14/11/2024 09:52:32] -> Processing Part 106 of 152
INFO:    [14/11/2024 09:52:32] -> Processing Part 107 of 152
INFO:    [14/11/2024 09:52:34] -> Processing Part 108 of 152
INFO:    [14/11/2024 09:52:35] -> Processing Part 109 of 152
INFO:    [14/11/2024 09:52:35] -> Processing Part 110 of 152
INFO:    [14/11/2024 09:52:35] -> Processing Part 111 of 152
INFO:    [14/11/2024 09:52:36] -> Processing Part 112 of 152
INFO:    [14/11/2024 09:52:36] -> Processing Part 113 of 152
INFO:    [14/11/2024 09:52:37] -> Processing Part 114 of 152
INFO:    [14/11/2024 09:52:37] -> Processing Part 115 of 152
INFO:    [14/11/2024 09:52:38] -> Processing Part 116 of 152
INFO:    [14/11/2024 09:52:38] -> Processing Part 117 of 152
INFO:    [14/11/2024 09:52:38] -> Processing Part 118 of 152
INFO:    [14/11/2024 09:52:39] -> Processing Part 119 of 152
INFO:    [14/11/2024 09:52:39] -> Processing Part 120 of 152
INFO:    [14/11/2024 09:52:40] -> Processing Part 121 of 152
INFO:    [14/11/2024 09:52:40] -> Processing Part 122 of 152
INFO:    [14/11/2024 09:52:41] -> Processing Part 123 of 152
INFO:    [14/11/2024 09:52:41] -> Processing Part 124 of 152
INFO:    [14/11/2024 09:52:42] -> Processing Part 125 of 152
INFO:    [14/11/2024 09:52:42] -> Processing Part 126 of 152
INFO:    [14/11/2024 09:52:42] -> Processing Part 127 of 152
INFO:    [14/11/2024 09:52:43] -> Processing Part 128 of 152
INFO:    [14/11/2024 09:52:43] -> Processing Part 129 of 152
INFO:    [14/11/2024 09:52:43] -> Processing Part 130 of 152
INFO:    [14/11/2024 09:52:43] -> Processing Part 131 of 152
INFO:    [14/11/2024 09:52:44] -> Processing Part 132 of 152
INFO:    [14/11/2024 09:52:44] -> Processing Part 133 of 152
INFO:    [14/11/2024 09:52:45] -> Processing Part 134 of 152
INFO:    [14/11/2024 09:52:45] -> Processing Part 135 of 152
INFO:    [14/11/2024 09:52:45] -> Processing Part 136 of 152
INFO:    [14/11/2024 09:52:45] -> Processing Part 137 of 152
INFO:    [14/11/2024 09:52:45] -> Processing Part 138 of 152
INFO:    [14/11/2024 09:52:45] -> Processing Part 139 of 152
INFO:    [14/11/2024 09:52:46] -> Processing Part 140 of 152
INFO:    [14/11/2024 09:52:46] -> Processing Part 141 of 152
INFO:    [14/11/2024 09:52:46] -> Processing Part 142 of 152
INFO:    [14/11/2024 09:52:46] -> Processing Part 143 of 152
INFO:    [14/11/2024 09:52:46] -> Processing Part 144 of 152
INFO:    [14/11/2024 09:52:46] -> Processing Part 145 of 152
INFO:    [14/11/2024 09:52:47] -> Processing Part 146 of 152
INFO:    [14/11/2024 09:52:47] -> Processing Part 147 of 152
INFO:    [14/11/2024 09:52:47] -> Processing Part 148 of 152
INFO:    [14/11/2024 09:52:47] -> Processing Part 149 of 152
INFO:    [14/11/2024 09:52:48] -> Processing Part 150 of 152
INFO:    [14/11/2024 09:52:48] -> Processing Part 151 of 152
INFO:    [14/11/2024 09:52:48] -> Processing Part 152 of 152
INFO:    [14/11/2024 09:52:48] -> Nr of Features Requested: 249692
INFO:    [14/11/2024 09:52:48] -> Size of Featurespace: 249692
INFO:    [14/11/2024 09:52:48] -> Scans/Feature pairs that failed to Match: 1899
INFO:    [14/11/2024 09:52:48] -> Maximum Nr of Features for one Scan: 13
INFO:    [14/11/2024 09:52:48] -> Finalizing...
INFO:    [14/11/2024 09:52:50] -> Processed in 56.09s
INFO:    [14/11/2024 09:52:50] -> Processed in 1.5m
INFO:    [14/11/2024 09:52:50] -> Done
INFO:    [14/11/2024 09:52:50] -> Run 6/6: Process Raw File...
INFO:    [14/11/2024 09:52:55] -> Run 6/6: Preparing Partitions...
INFO:    [14/11/2024 09:52:55] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [14/11/2024 09:52:55] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [14/11/2024 09:53:00] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [14/11/2024 09:53:09] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3838 [9s]
INFO:    [14/11/2024 09:53:15] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [14/11/2024 09:53:16] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [14/11/2024 09:53:16] -> PERFORMING MAIN SEARCH 1
INFO:    [14/11/2024 09:53:56] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 38810 [40.5s]
INFO:    [14/11/2024 09:53:56] -> PERFORMING MAIN SEARCH 2
INFO:    [14/11/2024 09:54:08] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 5857 [11.9s]
INFO:    [14/11/2024 09:54:08] -> PERFORMING MAIN SEARCH 3
INFO:    [14/11/2024 09:54:21] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 748 [12.6s]
INFO:    [14/11/2024 09:54:21] -> PERFORMING MAIN SEARCH 4
INFO:    [14/11/2024 09:54:28] -> The number of PSMs identified with FDR (for subtraction) <= 0.01 is 45 [7.6s]
INFO:    [14/11/2024 09:55:17] -> Extracting 158180 MS1 XICs
INFO:    [14/11/2024 09:58:25] -> Run 6/6: Cleaning Up Run..
INFO:    [14/11/2024 09:58:33] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [14/11/2024 09:58:34] -> Score Post-Processing
INFO:    [14/11/2024 10:00:04] -> Score Post-Processing: 1.51m
INFO:    [14/11/2024 10:00:04] -> PSM FDR...
INFO:    [14/11/2024 10:00:27] -> PSM FDR: 22.93s
INFO:    [14/11/2024 10:00:27] -> Converting to non-redundant data structure...
INFO:    [14/11/2024 10:00:48] -> Performing Peptide FDR...
INFO:    [14/11/2024 10:00:52] -> Performing Protein Inference...
INFO:    [14/11/2024 10:00:55] -> Performing Protein FDR...
INFO:    [14/11/2024 10:00:56] -> Calculating Result Values at Run and Experiment Level...
INFO:    [14/11/2024 10:01:10] -> Pulsar identified 221249 PSMs, 50373 stripped sequences, 62317 peptide precursors, 6544 protein groups.
INFO:    [14/11/2024 10:01:10] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:01:11] -> iRT Calibration...
INFO:    [14/11/2024 10:01:21] -> Performing directDIA+ search...
INFO:    [14/11/2024 10:01:47] -> Generating directDIA+ search space
INFO:    [14/11/2024 10:05:34] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw
INFO:    [14/11/2024 10:11:37] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw
INFO:    [14/11/2024 10:16:42] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw
INFO:    [14/11/2024 10:21:03] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw
INFO:    [14/11/2024 10:24:59] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw
INFO:    [14/11/2024 10:30:02] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw
INFO:    [14/11/2024 10:34:39] -> Performing directDIA+ Post Processing...
INFO:    [14/11/2024 10:34:58] -> Writing experiment store..
INFO:    [14/11/2024 10:35:13] -> Assigning iRT Source...
INFO:    [14/11/2024 10:35:13] -> Calculating iRT...
INFO:    [14/11/2024 10:35:14] -> Cleaning Up Experiment...
INFO:    [14/11/2024 10:35:14] -> Summarizing Identifications
INFO:    [14/11/2024 10:48:29] -> Pipeline executed...
INFO:    [14/11/2024 10:48:30] -> Pipeline executed...
INFO:    [14/11/2024 10:49:01] -> Initializing Experiment...
INFO:    [14/11/2024 10:49:01] -> Loading Spectral Libraries...
INFO:    [14/11/2024 10:50:18] -> Initialize Scoring...
INFO:    [14/11/2024 10:50:18] -> Generating Scan Map...
INFO:    [14/11/2024 10:50:18] -> Initializing Workpackages...
INFO:    [14/11/2024 10:50:18] -> Performing Basic Calibration...
INFO:    [14/11/2024 10:50:18] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:50:18] -> Correcting Gradient Fine Structure...
INFO:    [14/11/2024 10:50:23] -> Initializing Pipeline...
INFO:    [14/11/2024 10:50:23] -> Preprocessing Run #1 of 6...
INFO:    [14/11/2024 10:50:23] -> Initialize Scoring...
INFO:    [14/11/2024 10:50:23] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:50:50] -> Machine Learning...
INFO:    [14/11/2024 10:50:52] -> Pipeline executed in 29.25s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:50:57] -> Initializing Pipeline...
INFO:    [14/11/2024 10:50:57] -> Preprocessing Run #1 of 6...
INFO:    [14/11/2024 10:50:57] -> Initialize Scoring...
INFO:    [14/11/2024 10:50:57] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:51:45] -> Machine Learning...
INFO:    [14/11/2024 10:51:51] -> Pipeline executed in 54.1s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:52:03] -> Initialize Scoring...
INFO:    [14/11/2024 10:52:03] -> Preprocessing Run #2 of 6...
INFO:    [14/11/2024 10:52:03] -> Searching DIA with Pulsar...
INFO:    [14/11/2024 10:52:03] -> Initializing Experiment...
INFO:    [14/11/2024 10:52:03] -> Loading Spectral Libraries...
INFO:    [14/11/2024 10:52:03] -> Initialize Scoring...
INFO:    [14/11/2024 10:52:03] -> Generating Scan Map...
INFO:    [14/11/2024 10:52:03] -> Initializing Workpackages...
INFO:    [14/11/2024 10:52:03] -> Performing Basic Calibration...
INFO:    [14/11/2024 10:52:03] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:52:03] -> Correcting Gradient Fine Structure...
INFO:    [14/11/2024 10:52:06] -> Initializing Pipeline...
INFO:    [14/11/2024 10:52:06] -> Preprocessing Run #2 of 6...
INFO:    [14/11/2024 10:52:06] -> Initialize Scoring...
INFO:    [14/11/2024 10:52:06] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:52:34] -> Machine Learning...
INFO:    [14/11/2024 10:52:36] -> Pipeline executed in 30.21s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:52:41] -> Initializing Pipeline...
INFO:    [14/11/2024 10:52:41] -> Preprocessing Run #2 of 6...
INFO:    [14/11/2024 10:52:41] -> Initialize Scoring...
INFO:    [14/11/2024 10:52:41] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:53:24] -> Machine Learning...
INFO:    [14/11/2024 10:53:30] -> Pipeline executed in 48.08s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:53:39] -> Initialize Scoring...
INFO:    [14/11/2024 10:53:39] -> Preprocessing Run #3 of 6...
INFO:    [14/11/2024 10:53:39] -> Searching DIA with Pulsar...
INFO:    [14/11/2024 10:53:39] -> Initializing Experiment...
INFO:    [14/11/2024 10:53:39] -> Loading Spectral Libraries...
INFO:    [14/11/2024 10:53:39] -> Initialize Scoring...
INFO:    [14/11/2024 10:53:39] -> Generating Scan Map...
INFO:    [14/11/2024 10:53:39] -> Initializing Workpackages...
INFO:    [14/11/2024 10:53:39] -> Performing Basic Calibration...
INFO:    [14/11/2024 10:53:39] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:53:39] -> Correcting Gradient Fine Structure...
INFO:    [14/11/2024 10:53:42] -> Initializing Pipeline...
INFO:    [14/11/2024 10:53:42] -> Preprocessing Run #3 of 6...
INFO:    [14/11/2024 10:53:42] -> Initialize Scoring...
INFO:    [14/11/2024 10:53:42] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:54:07] -> Machine Learning...
INFO:    [14/11/2024 10:54:09] -> Pipeline executed in 26.2s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:54:12] -> Initializing Pipeline...
INFO:    [14/11/2024 10:54:12] -> Preprocessing Run #3 of 6...
INFO:    [14/11/2024 10:54:12] -> Initialize Scoring...
INFO:    [14/11/2024 10:54:12] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:54:41] -> Machine Learning...
INFO:    [14/11/2024 10:54:46] -> Pipeline executed in 33.91s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:54:54] -> Initialize Scoring...
INFO:    [14/11/2024 10:54:54] -> Preprocessing Run #4 of 6...
INFO:    [14/11/2024 10:54:54] -> Searching DIA with Pulsar...
INFO:    [14/11/2024 10:54:54] -> Initializing Experiment...
INFO:    [14/11/2024 10:54:54] -> Loading Spectral Libraries...
INFO:    [14/11/2024 10:54:54] -> Initialize Scoring...
INFO:    [14/11/2024 10:54:54] -> Generating Scan Map...
INFO:    [14/11/2024 10:54:54] -> Initializing Workpackages...
INFO:    [14/11/2024 10:54:54] -> Performing Basic Calibration...
INFO:    [14/11/2024 10:54:54] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:54:54] -> Correcting Gradient Fine Structure...
INFO:    [14/11/2024 10:54:57] -> Initializing Pipeline...
INFO:    [14/11/2024 10:54:57] -> Preprocessing Run #4 of 6...
INFO:    [14/11/2024 10:54:57] -> Initialize Scoring...
INFO:    [14/11/2024 10:54:57] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:55:12] -> Machine Learning...
INFO:    [14/11/2024 10:55:14] -> Pipeline executed in 16.5s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:55:17] -> Initializing Pipeline...
INFO:    [14/11/2024 10:55:17] -> Preprocessing Run #4 of 6...
INFO:    [14/11/2024 10:55:17] -> Initialize Scoring...
INFO:    [14/11/2024 10:55:17] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:55:47] -> Machine Learning...
INFO:    [14/11/2024 10:55:52] -> Pipeline executed in 34.85s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:56:00] -> Initialize Scoring...
INFO:    [14/11/2024 10:56:00] -> Preprocessing Run #5 of 6...
INFO:    [14/11/2024 10:56:00] -> Searching DIA with Pulsar...
INFO:    [14/11/2024 10:56:00] -> Initializing Experiment...
INFO:    [14/11/2024 10:56:00] -> Loading Spectral Libraries...
INFO:    [14/11/2024 10:56:00] -> Initialize Scoring...
INFO:    [14/11/2024 10:56:00] -> Generating Scan Map...
INFO:    [14/11/2024 10:56:00] -> Initializing Workpackages...
INFO:    [14/11/2024 10:56:00] -> Performing Basic Calibration...
INFO:    [14/11/2024 10:56:00] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:56:00] -> Correcting Gradient Fine Structure...
INFO:    [14/11/2024 10:56:02] -> Initializing Pipeline...
INFO:    [14/11/2024 10:56:02] -> Preprocessing Run #5 of 6...
INFO:    [14/11/2024 10:56:02] -> Initialize Scoring...
INFO:    [14/11/2024 10:56:02] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:56:19] -> Machine Learning...
INFO:    [14/11/2024 10:56:20] -> Pipeline executed in 17.94s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:56:24] -> Initializing Pipeline...
INFO:    [14/11/2024 10:56:24] -> Preprocessing Run #5 of 6...
INFO:    [14/11/2024 10:56:24] -> Initialize Scoring...
INFO:    [14/11/2024 10:56:24] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:56:55] -> Machine Learning...
INFO:    [14/11/2024 10:57:00] -> Pipeline executed in 35.26s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:57:07] -> Initialize Scoring...
INFO:    [14/11/2024 10:57:07] -> Preprocessing Run #6 of 6...
INFO:    [14/11/2024 10:57:07] -> Searching DIA with Pulsar...
INFO:    [14/11/2024 10:57:07] -> Initializing Experiment...
INFO:    [14/11/2024 10:57:07] -> Loading Spectral Libraries...
INFO:    [14/11/2024 10:57:07] -> Initialize Scoring...
INFO:    [14/11/2024 10:57:07] -> Generating Scan Map...
INFO:    [14/11/2024 10:57:07] -> Initializing Workpackages...
INFO:    [14/11/2024 10:57:07] -> Performing Basic Calibration...
INFO:    [14/11/2024 10:57:07] -> Identifying Calibration Peptides...
INFO:    [14/11/2024 10:57:07] -> Correcting Gradient Fine Structure...
INFO:    [14/11/2024 10:57:10] -> Initializing Pipeline...
INFO:    [14/11/2024 10:57:10] -> Preprocessing Run #6 of 6...
INFO:    [14/11/2024 10:57:10] -> Initialize Scoring...
INFO:    [14/11/2024 10:57:10] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:57:26] -> Machine Learning...
INFO:    [14/11/2024 10:57:28] -> Pipeline executed in 17.96s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:57:32] -> Initializing Pipeline...
INFO:    [14/11/2024 10:57:32] -> Preprocessing Run #6 of 6...
INFO:    [14/11/2024 10:57:32] -> Initialize Scoring...
INFO:    [14/11/2024 10:57:32] -> Extracting Ion Currents...
INFO:    [14/11/2024 10:58:06] -> Machine Learning...
INFO:    [14/11/2024 10:58:11] -> Pipeline executed in 38.75s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/11/2024 10:58:18] -> Initialize Scoring...
INFO:    [14/11/2024 10:58:18] -> Initializing QC...
INFO:    [14/11/2024 10:58:18] -> Determining Calibration Parameter...
INFO:    [14/11/2024 10:58:18] -> Assigning ML Features...
INFO:    [14/11/2024 10:58:19] -> Generating Decoys...
INFO:    [14/11/2024 10:58:34] -> Extracting Ion Currents...
INFO:    [14/11/2024 11:01:06] -> Releasing Raw Files...
INFO:    [14/11/2024 11:01:06] -> Machine Learning...
INFO:    [14/11/2024 11:01:50] -> Initializing HTRMS...
INFO:    [14/11/2024 11:01:50] -> Releasing Run Resources...
INFO:    [14/11/2024 11:01:50] -> Reducing Score Cache...
INFO:    [14/11/2024 11:01:53] -> Calculating Qvalues...
INFO:    [14/11/2024 11:01:54] -> Unique precursors: 98,398 of 105,535 | modified peptides: 86,470 of 92,142 | peptides: 78,347 of 82,943 |  protein groups: 8,765 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw]
INFO:    [14/11/2024 11:01:54] -> Collapsing Search Tree...
INFO:    [14/11/2024 11:01:54] -> Processed in 3.6m
INFO:    [14/11/2024 11:01:55] -> Initializing QC...
INFO:    [14/11/2024 11:01:55] -> Determining Calibration Parameter...
INFO:    [14/11/2024 11:01:55] -> Assigning ML Features...
INFO:    [14/11/2024 11:01:55] -> Generating Decoys...
INFO:    [14/11/2024 11:01:55] -> Extracting Ion Currents...
INFO:    [14/11/2024 11:04:38] -> Releasing Raw Files...
INFO:    [14/11/2024 11:04:39] -> Machine Learning...
INFO:    [14/11/2024 11:05:30] -> Initializing HTRMS...
INFO:    [14/11/2024 11:05:30] -> Releasing Run Resources...
INFO:    [14/11/2024 11:05:30] -> Reducing Score Cache...
INFO:    [14/11/2024 11:05:33] -> Calculating Qvalues...
INFO:    [14/11/2024 11:05:34] -> Unique precursors: 99,007 of 105,535 | modified peptides: 86,576 of 92,142 | peptides: 78,426 of 82,943 |  protein groups: 8,770 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw]
INFO:    [14/11/2024 11:05:34] -> Collapsing Search Tree...
INFO:    [14/11/2024 11:05:34] -> Processed in 3.66m
INFO:    [14/11/2024 11:05:35] -> Initializing QC...
INFO:    [14/11/2024 11:05:35] -> Determining Calibration Parameter...
INFO:    [14/11/2024 11:05:35] -> Assigning ML Features...
INFO:    [14/11/2024 11:05:35] -> Generating Decoys...
INFO:    [14/11/2024 11:05:35] -> Extracting Ion Currents...
INFO:    [14/11/2024 11:08:15] -> Releasing Raw Files...
INFO:    [14/11/2024 11:08:15] -> Machine Learning...
INFO:    [14/11/2024 11:08:52] -> Initializing HTRMS...
INFO:    [14/11/2024 11:08:52] -> Releasing Run Resources...
INFO:    [14/11/2024 11:08:53] -> Reducing Score Cache...
INFO:    [14/11/2024 11:08:57] -> Calculating Qvalues...
INFO:    [14/11/2024 11:08:58] -> Unique precursors: 96,681 of 105,535 | modified peptides: 85,125 of 92,142 | peptides: 77,338 of 82,943 |  protein groups: 8,686 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw]
INFO:    [14/11/2024 11:08:58] -> Collapsing Search Tree...
INFO:    [14/11/2024 11:08:59] -> Processed in 3.4m
INFO:    [14/11/2024 11:09:00] -> Initializing QC...
INFO:    [14/11/2024 11:09:00] -> Determining Calibration Parameter...
INFO:    [14/11/2024 11:09:00] -> Assigning ML Features...
INFO:    [14/11/2024 11:09:00] -> Generating Decoys...
INFO:    [14/11/2024 11:09:00] -> Extracting Ion Currents...
INFO:    [14/11/2024 11:11:52] -> Releasing Raw Files...
INFO:    [14/11/2024 11:11:52] -> Machine Learning...
INFO:    [14/11/2024 11:12:46] -> Initializing HTRMS...
INFO:    [14/11/2024 11:12:46] -> Releasing Run Resources...
INFO:    [14/11/2024 11:12:47] -> Reducing Score Cache...
INFO:    [14/11/2024 11:12:53] -> Calculating Qvalues...
INFO:    [14/11/2024 11:12:56] -> Unique precursors: 83,359 of 105,535 | modified peptides: 73,042 of 92,142 | peptides: 71,248 of 82,943 |  protein groups: 8,558 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw]
INFO:    [14/11/2024 11:12:56] -> Collapsing Search Tree...
INFO:    [14/11/2024 11:12:56] -> Processed in 3.94m
INFO:    [14/11/2024 11:12:57] -> Initializing QC...
INFO:    [14/11/2024 11:12:57] -> Determining Calibration Parameter...
INFO:    [14/11/2024 11:12:57] -> Assigning ML Features...
INFO:    [14/11/2024 11:12:57] -> Generating Decoys...
INFO:    [14/11/2024 11:12:58] -> Extracting Ion Currents...
INFO:    [14/11/2024 11:15:38] -> Releasing Raw Files...
INFO:    [14/11/2024 11:15:38] -> Machine Learning...
INFO:    [14/11/2024 11:16:27] -> Initializing HTRMS...
INFO:    [14/11/2024 11:16:27] -> Releasing Run Resources...
INFO:    [14/11/2024 11:16:27] -> Reducing Score Cache...
INFO:    [14/11/2024 11:16:30] -> Calculating Qvalues...
INFO:    [14/11/2024 11:16:31] -> Unique precursors: 86,943 of 105,535 | modified peptides: 75,694 of 92,142 | peptides: 72,459 of 82,943 |  protein groups: 8,644 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw]
INFO:    [14/11/2024 11:16:31] -> Collapsing Search Tree...
INFO:    [14/11/2024 11:16:31] -> Processed in 3.57m
INFO:    [14/11/2024 11:16:31] -> Initializing QC...
INFO:    [14/11/2024 11:16:31] -> Determining Calibration Parameter...
INFO:    [14/11/2024 11:16:31] -> Assigning ML Features...
INFO:    [14/11/2024 11:16:31] -> Generating Decoys...
INFO:    [14/11/2024 11:16:32] -> Extracting Ion Currents...
INFO:    [14/11/2024 11:19:11] -> Releasing Raw Files...
INFO:    [14/11/2024 11:19:11] -> Machine Learning...
INFO:    [14/11/2024 11:19:53] -> Initializing HTRMS...
INFO:    [14/11/2024 11:19:53] -> Releasing Run Resources...
INFO:    [14/11/2024 11:19:54] -> Reducing Score Cache...
INFO:    [14/11/2024 11:19:56] -> Calculating Qvalues...
INFO:    [14/11/2024 11:19:57] -> Unique precursors: 83,475 of 105,535 | modified peptides: 73,246 of 92,142 | peptides: 70,699 of 82,943 |  protein groups: 8,482 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw]
INFO:    [14/11/2024 11:19:57] -> Collapsing Search Tree...
INFO:    [14/11/2024 11:19:57] -> Processed in 3.44m
INFO:    [14/11/2024 11:19:58] -> Normalizing Cscores...
INFO:    [14/11/2024 11:19:59] -> Initializing Protein Groups...
INFO:    [14/11/2024 11:20:58] -> Correcting Interferences...
INFO:    [14/11/2024 11:21:24] -> Calculating Global CVs
INFO:    [14/11/2024 11:21:25] -> Calculating Precursor Quantities...
INFO:    [14/11/2024 11:21:26] -> Normalizing Quantification...
INFO:    [14/11/2024 11:21:27] -> Performing Local Normalization...
INFO:    [14/11/2024 11:21:33] -> Calculating Global CVs
INFO:    [14/11/2024 11:21:35] -> Calculating Condition CVs
INFO:    [14/11/2024 11:21:40] -> Excluding Library Duplicates...
INFO:    [14/11/2024 11:21:42] -> Calculating Global CVs
INFO:    [14/11/2024 11:21:44] -> Building Protein Groups...
INFO:    [14/11/2024 11:22:42] -> Calculating Run-Wise Protein Group FDR...
INFO:    [14/11/2024 11:22:47] -> Annotating Protein Single Hits...
INFO:    [14/11/2024 11:22:48] -> Calculating Global CVs
INFO:    [14/11/2024 11:22:50] -> Updating Identification Counts...
INFO:    [14/11/2024 11:22:53] -> Resetting existing imputation...
INFO:    [14/11/2024 11:22:53] -> Calculating Protein Quantities...
INFO:    [14/11/2024 11:22:55] -> Calculating Protein Quantities...
INFO:    [14/11/2024 11:22:55] -> Calculating MaxLFQ Protein Quantities...
INFO:    [14/11/2024 11:23:03] -> Collapsing PTM-Locations...
INFO:    [14/11/2024 11:23:03] -> PTM Stoichiometry calculation...
INFO:    [14/11/2024 11:23:04] -> Creating Protein Map...
INFO:    [14/11/2024 11:23:04] -> Compiling Run Summary Information...
INFO:    [14/11/2024 11:23:05] -> Running Post Analysis Processes...
INFO:    [14/11/2024 11:23:12] -> Saving Qc Data...
INFO:    [14/11/2024 11:23:18] -> Generating Output
INFO:    [14/11/2024 11:23:18] -> Generating Experiment Report
INFO:    [14/11/2024 11:24:20] -> Experiment1_Report_BGS Factory Report (Normal).tsv
INFO:    [14/11/2024 11:24:20] -> Generating RT Recalibration Report
INFO:    [14/11/2024 11:24:21] -> LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw_1_iRTCalibration.tsv
INFO:    [14/11/2024 11:24:21] -> LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw_2_iRTCalibration.tsv
INFO:    [14/11/2024 11:24:21] -> LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw_3_iRTCalibration.tsv
INFO:    [14/11/2024 11:24:21] -> LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw_4_iRTCalibration.tsv
INFO:    [14/11/2024 11:24:21] -> LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw_5_iRTCalibration.tsv
INFO:    [14/11/2024 11:24:21] -> LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw_6_iRTCalibration.tsv
INFO:    [14/11/2024 11:24:21] -> Generating Run Meta Report
INFO:    [14/11/2024 11:24:22] -> LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw_1_RunOverview.tsv
INFO:    [14/11/2024 11:24:22] -> LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw_2_RunOverview.tsv
INFO:    [14/11/2024 11:24:22] -> LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw_3_RunOverview.tsv
INFO:    [14/11/2024 11:24:22] -> LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw_4_RunOverview.tsv
INFO:    [14/11/2024 11:24:22] -> LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw_5_RunOverview.tsv
INFO:    [14/11/2024 11:24:22] -> LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw_6_RunOverview.tsv
INFO:    [14/11/2024 11:24:22] -> Generating Post Analysis Reports
INFO:    [14/11/2024 11:24:27] -> Experiment1_AnalysisOverview.txt
INFO:    [14/11/2024 11:24:27] -> Precursor CVs_CVsBelowX.tsv
INFO:    [14/11/2024 11:24:27] -> Peptide CVs_CVsBelowX.tsv
INFO:    [14/11/2024 11:24:27] -> Protein Group CVs_CVsBelowX.tsv
INFO:    [14/11/2024 11:24:27] -> Protein CVs_CVsBelowX.tsv
INFO:    [14/11/2024 11:24:27] -> RunIdentifications.tsv
INFO:    [14/11/2024 11:24:27] -> Generating PTM Site Report
INFO:    [14/11/2024 11:24:27] -> Generating Condition Setup Report
INFO:    [14/11/2024 11:24:27] -> Experiment1_ConditionSetup.tsv
INFO:    [14/11/2024 11:24:27] -> Generating Experiment Settings Report
[END-LOG]
