System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium .NET Core Info: N/A Version info: FragPipe version 22.0 MSFragger version 4.1 IonQuant version 1.10.27 diaTracer version 1.1.3 Philosopher version 5.1.1 LCMS files: Experiment/Group: June (if "spectral library generation" is enabled, all files will be analyzed together) - D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML DDA - D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML DDA Experiment/Group: May (if "spectral library generation" is enabled, all files will be analyzed together) - D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML DDA - D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML DDA 30 commands to execute: CheckCentroid C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx111G -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML 63 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\jparedes\AppData\Local\Temp\ab0ea830-43de-4b5d-b128-f5cb84b7c53c WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\jparedes\AppData\Local\Temp\43b9937e-db68-4e52-8be8-04cf722542e2 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\jparedes\AppData\Local\Temp\17c29ee1-090c-4e19-bdae-9bf78e0dfb39 MSFragger [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx111G C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\fragger.params D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.tsv MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.tsv MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.tsv MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.tsv PeptideProphet [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc --decoy rev_ --database D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas --combine ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML PeptideProphet [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc --decoy rev_ --database D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas --combine ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML Rewrite pepxml [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML Rewrite pepxml [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML ProteinProphet [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe database --annotate D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June --protxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\combined.prot.xml --razor PhilosopherFilter [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May --dbbin D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June --protxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\combined.prot.xml --probin D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June --razor PhilosopherReport [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report PhilosopherReport [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe report PTMShepherd [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx111G -Dlibs.thermo.dir=C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\ext\thermo -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\ptmshepherd-3.0.0.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\commons-math3-3.6.1.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\commons-lang3-3.14.0.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar edu.umich.andykong.ptmshepherd.PTMShepherd "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\shepherd.config" WorkspaceClean [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [CheckCentroid], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [WorkspaceCleanInit], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] Cmd: [WorkspaceCleanInit], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [WorkspaceCleanInit], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] Cmd: [MSFragger], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [PeptideProphet], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [ProteinProphet], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [PhilosopherDbAnnotate], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [PhilosopherFilter], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [PhilosopherReport], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [PTMShepherd], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [WorkspaceClean], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] Cmd: [WorkspaceClean], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] Cmd: [WorkspaceClean], Work dir: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas~~~~~~~ >rev_sp|A0A024R1R8|TMA7B_HUMAN Translation machinery-associated protein 7B OS=Homo sapiens OX=9606 GN=TMA7B PE=3 SV=1 >rev_sp|O43900|PRIC3_HUMAN Prickle planar cell polarity protein 3 OS=Homo sapiens OX=9606 GN=PRICKLE3 PE=1 SV=2 >rev_sp|P0DUB6|AMY1A_HUMAN Alpha-amylase 1A OS=Homo sapiens OX=9606 GN=AMY1A PE=1 SV=1 >rev_sp|P51159|RB27A_HUMAN Ras-related protein Rab-27A OS=Homo sapiens OX=9606 GN=RAB27A PE=1 SV=3 >rev_sp|Q14767|LTBP2_HUMAN Latent-transforming growth factor beta-binding protein 2 OS=Homo sapiens OX=9606 GN=LTBP2 PE=1 SV=3 >rev_sp|Q6L8G8|KRA57_HUMAN Keratin-associated protein 5-7 OS=Homo sapiens OX=9606 GN=KRTAP5-7 PE=1 SV=1 >rev_sp|Q8IZ13|F200C_HUMAN Protein FAM200C OS=Homo sapiens OX=9606 GN=FAM200C PE=1 SV=1 >rev_sp|Q92536|YLAT2_HUMAN Y+L amino acid transporter 2 OS=Homo sapiens OX=9606 GN=SLC7A6 PE=1 SV=3 >rev_sp|Q9BVM4|GGACT_HUMAN Gamma-glutamylaminecyclotransferase OS=Homo sapiens OX=9606 GN=GGACT PE=1 SV=2 >rev_sp|Q9NYM4|GPR83_HUMAN G-protein coupled receptor 83 OS=Homo sapiens OX=9606 GN=GPR83 PE=1 SV=2 >rev_tr|Q6JHZ5|Q6JHZ5_HUMAN NS5ATP13TP1 OS=Homo sapiens OX=9606 PE=2 SV=1 >sp|O43865|SAHH2_HUMAN S-adenosylhomocysteine hydrolase-like protein 1 OS=Homo sapiens OX=9606 GN=AHCYL1 PE=1 SV=2 >sp|P0DTF9|PTIP2_HUMAN PTTG1IP family member 2 OS=Homo sapiens OX=9606 GN=PTTG1IP2 PE=3 SV=1 >sp|P51114|FXR1_HUMAN RNA-binding protein FXR1 OS=Homo sapiens OX=9606 GN=FXR1 PE=1 SV=3 >sp|Q14738|2A5D_HUMAN Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform OS=Homo sapiens OX=9606 GN=PPP2R5D PE=1 SV=1 >sp|Q6JVE9|LCN8_HUMAN Epididymal-specific lipocalin-8 OS=Homo sapiens OX=9606 GN=LCN8 PE=2 SV=1 >sp|Q8IYX3|CC116_HUMAN Coiled-coil domain-containing protein 116 OS=Homo sapiens OX=9606 GN=CCDC116 PE=1 SV=3 >sp|Q92521|PIGB_HUMAN GPI mannosyltransferase 3 OS=Homo sapiens OX=9606 GN=PIGB PE=1 SV=1 >sp|Q9BVJ6|UT14A_HUMAN U3 small nucleolar RNA-associated protein 14 homolog A OS=Homo sapiens OX=9606 GN=UTP14A PE=1 SV=1 >sp|Q9NYJ8|TAB2_HUMAN TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 OS=Homo sapiens OX=9606 GN=TAB2 PE=1 SV=1 >tr|A0N4Z8|A0N4Z8_HUMAN HCG2039779 (Fragment) OS=Homo sapiens OX=9606 GN=TRAJ9 PE=4 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v22.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=D\:\\Databases\\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=false diatracer.corr-threshold=0.3 diatracer.delta-apex-im=0.01 diatracer.delta-apex-rt=3 diatracer.mass-defect-filter=true diatracer.mass-defect-offset=0.1 diatracer.rf-max=500 diatracer.run-diatracer=false diatracer.write-intermediate-files=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=C\:\\Users\\jparedes\\FragPipe-jre-22.0\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe fragpipe-config.bin-python=C\:\\Users\\jparedes\\python.exe fragpipe-config.tools-folder=C\:\\Users\\jparedes\\FragPipe-jre-22.0\\fragpipe\\lib\\..\\tools freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=0 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=10 ionquant.medium= ionquant.minfreq=0 ionquant.minions=1 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.find-best-rt-model=false msbooster.find-best-spectra-model=false msbooster.koina-url= msbooster.predict-rt=false msbooster.predict-spectra=false msbooster.rt-model=DIA-NN msbooster.run-msbooster=false msbooster.spectra-model=DIA-NN msfragger.Y_type_masses=0 203.07937 406.15874 568.21156 730.26438 892.3172 349.137279 msfragger.activation_types=all msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.analyzer_types=all msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments=204.086646 186.076086 168.065526 366.139466 144.0656 138.055 512.197375 292.1026925 274.0921325 657.2349 243.026426 405.079246 485.045576 308.09761 msfragger.diagnostic_intensity_filter=0.03 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y,c,z,Y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=nglycan msfragger.localize_delta_mass=true msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 203.0793762 568.2115783 892.3172301 1038.3751372 1054.370056 1095.3966063 1200.4279631 1216.4228819 1241.4545134 1257.4494322 1298.4759825 1362.480789 1378.4757078 1387.5124205 1403.5073393 1419.5022581 1444.5338896 1460.5288084 1501.5553587 1524.5336149 1533.5703276 1540.5285337 1548.5448607 1549.5652464 1565.5601652 1581.555084 1589.571411 1606.5867155 1622.5816343 1647.6132658 1663.6081846 1686.5864408 1694.6027678 1695.6231535 1702.5813596 1704.6347349 1710.5976866 1711.6180723 1727.6129911 1735.6293181 1736.6497038 1751.6242369 1752.6446226 1768.6395414 1784.6344602 1793.6711729 1809.6660917 1825.6610105 1848.6392667 1850.692642 1856.6555937 1857.6759794 1864.6341855 1866.6875608 1872.6505125 1873.6708982 1880.6668395 1889.665817 1897.682144 1898.7025297 1907.7141111 1913.6770628 1914.6974485 1930.6923673 1938.7086943 1946.6872861 1954.7036131 1955.7239988 1971.7189176 1987.7138364 1996.7505491 2010.6920926 2012.7454679 2018.7084196 2019.7288053 2026.6870114 2028.7403867 2042.7196654 2043.7400511 2053.7720182 2059.7349699 2060.7553556 2069.766937 2075.7298887 2076.7502744 2092.7451932 2100.7615202 2101.7819059 2108.740112 2110.7934873 2116.756439 2117.7768247 2133.7717435 2141.7880705 2142.8084562 2157.7829893 2158.803375 2172.7449185 2174.7982938 2188.7398373 2190.7932126 2204.7724913 2205.792877 2206.8132627 2215.8248441 2221.7877958 2222.8081815 2231.8197629 2237.7827146 2245.7990416 2246.8194273 2254.7980191 2256.8513944 2262.8143461 2263.8347318 2270.7929379 2278.8092649 2279.8296506 2287.8459776 2313.8728635 2320.8562009 2334.7977444 2336.8511197 2350.7926632 2350.8303984 2352.8460385 2352.8711698 2366.8253172 2391.8569487 2393.8725888 2407.8518675 2408.8722532 2424.867172 2425.8875577 2432.883499 2434.8991391 2448.8784178 2457.8773953 2459.9307706 2463.840347 2465.8937223 2475.9256894 2481.8886411 2498.9039456 2528.8781431 2539.9304959 2545.8934476 2553.9097746 2555.9254147 2569.9046934 2570.9250791 2571.9454648 2580.9570462 2586.9199979 2621.9835965 2627.9465482 2643.941467 2644.9618527 2674.9360502 2701.9833218 2715.9626005 2716.9829862 2717.9782406 2772.9840696 2775.024841 2786.9633483 2789.9993741 2791.0197598 2798.0157011 2814.0106199 2823.0095974 2861.0001219 2864.0361477 2871.0572203 2878.0154264 2880.0310665 2896.0511166 2919.0419767 2935.0368955 2937.0776669 2966.0314787 2968.0471188 3007.058029 3009.0736691 3010.1191861 3048.0845793 3064.0794981 3081.0948026 3083.1104427 3083.135574 3138.1162717 3140.1570431 3147.1152492 3153.1159361 3155.1315762 3156.1519619 3210.1374052 3226.132324 3228.1730954 3229.1683498 3234.148651 3284.1741788 3300.1690976 3302.209869 3372.1902311 3374.2058712 3405.2004544 3407.2412258 3447.2473904 3448.2426448 3448.2677761 3503.2484738 3517.2277525 3519.2685239 3520.2637783 3521.284164 3589.248886 3591.2645261 3594.3005519 3663.2856596 3665.3012997 3665.326431 3704.3122099 3720.3071287 3738.3428189 3809.3435667 3812.3795925 3827.3541256 3866.3650358 3882.3599546 3886.4163661 3959.432754 4028.4178617 4101.4593809 4103.475021 4118.4495541 4176.4914089 4247.517288 4272.5237882 4307.5496516 4393.5500638 4409.5449826 4412.5810084 4412.6061397 4412.6187436 4468.6072231 4475.6031644 4483.5817562 4833.7394252 5563.008575 6441.3465264 6586.3840478 6732.4419549 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.00 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=400 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=2 msfragger.output_format=tsv_pepXML msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=corrected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=2 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=N msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,3; 6.020129,R,false,3 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=300 msfragger.write_calibrated_mzml=false msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db=HexNAc(1),HexNAc(2)Hex(1),HexNAc(2)Hex(3),HexNAc(2)Hex(3)Fuc(1),HexNAc(2)Hex(4),HexNAc(3)Hex(3),HexNAc(2)Hex(4)Fuc(1),HexNAc(2)Hex(5),HexNAc(3)Hex(3)Fuc(1),HexNAc(3)Hex(4),HexNAc(4)Hex(3),HexNAc(2)Hex(5)Fuc(1),HexNAc(2)Hex(6),HexNAc(3)Hex(3)Fuc(2),HexNAc(3)Hex(4)Fuc(1),HexNAc(3)Hex(5),HexNAc(4)Hex(3)Fuc(1),HexNAc(4)Hex(4),HexNAc(5)Hex(3),HexNAc(2)Hex(6)Fuc(1),HexNAc(3)Hex(3)Fuc(3),HexNAc(2)Hex(7),HexNAc(3)Hex(4)NeuAc(1),HexNAc(3)Hex(4)Fuc(2),HexNAc(3)Hex(5)Fuc(1),HexNAc(3)Hex(6),HexNAc(4)Hex(3)NeuAc(1),HexNAc(4)Hex(4)Fuc(1),HexNAc(4)Hex(5),HexNAc(5)Hex(3)Fuc(1),HexNAc(5)Hex(4),HexNAc(2)Hex(7)Fuc(1),HexNAc(3)Hex(4)Fuc(1)NeuAc(1),HexNAc(3)Hex(4)Fuc(3),HexNAc(2)Hex(8),HexNAc(6)Hex(3),HexNAc(3)Hex(5)NeuAc(1),HexNAc(3)Hex(5)Fuc(2),HexNAc(3)Hex(6)Fuc(1),HexNAc(4)Hex(3)Fuc(1)NeuAc(1),HexNAc(4)Hex(3)Fuc(3),HexNAc(4)Hex(4)NeuAc(1),HexNAc(4)Hex(4)Fuc(2),HexNAc(4)Hex(5)Fuc(1),HexNAc(4)Hex(6),HexNAc(5)Hex(3)Fuc(2),HexNAc(5)Hex(4)Fuc(1),HexNAc(5)Hex(5),HexNAc(2)Hex(8)Fuc(1),HexNAc(6)Hex(3)Fuc(1),HexNAc(3)Hex(5)Fuc(1)NeuAc(1),HexNAc(3)Hex(5)Fuc(3),HexNAc(2)Hex(9),HexNAc(6)Hex(4),HexNAc(3)Hex(6)NeuAc(1),HexNAc(3)Hex(6)Fuc(2),HexNAc(4)Hex(3)NeuAc(2),HexNAc(3)Hex(7)Fuc(1),HexNAc(4)Hex(4)Fuc(1)NeuAc(1),HexNAc(4)Hex(4)Fuc(3),HexNAc(7)Hex(3),HexNAc(4)Hex(5)NeuAc(1),HexNAc(4)Hex(5)Fuc(2),HexNAc(4)Hex(6)Fuc(1),HexNAc(5)Hex(3)Fuc(1)NeuAc(1),HexNAc(4)Hex(7),HexNAc(5)Hex(4)NeuAc(1),HexNAc(5)Hex(4)Fuc(2),HexNAc(5)Hex(5)Fuc(1),HexNAc(5)Hex(6),HexNAc(6)Hex(3)Fuc(2),HexNAc(2)Hex(9)Fuc(1),HexNAc(6)Hex(4)Fuc(1),HexNAc(3)Hex(6)Fuc(1)NeuAc(1),HexNAc(3)Hex(6)Fuc(3),HexNAc(2)Hex(10),HexNAc(6)Hex(5),HexNAc(4)Hex(4)NeuAc(2),HexNAc(4)Hex(4)Fuc(2)NeuAc(1),HexNAc(7)Hex(3)Fuc(1),HexNAc(4)Hex(5)Fuc(1)NeuAc(1),HexNAc(4)Hex(5)Fuc(3),HexNAc(7)Hex(4),HexNAc(4)Hex(6)NeuAc(1),HexNAc(4)Hex(6)Fuc(2),HexNAc(4)Hex(7)Fuc(1),HexNAc(5)Hex(4)Fuc(1)NeuAc(1),HexNAc(5)Hex(4)Fuc(3),HexNAc(4)Hex(8),HexNAc(8)Hex(3),HexNAc(5)Hex(5)NeuAc(1),HexNAc(5)Hex(5)Fuc(2),HexNAc(5)Hex(6)Fuc(1),HexNAc(6)Hex(3)Fuc(1)NeuAc(1),HexNAc(6)Hex(3)Fuc(3),HexNAc(6)Hex(4)NeuAc(1),HexNAc(6)Hex(4)Fuc(2),HexNAc(2)Hex(10)Fuc(1),HexNAc(6)Hex(5)Fuc(1),HexNAc(2)Hex(11),HexNAc(6)Hex(6),HexNAc(4)Hex(5)NeuAc(2),HexNAc(4)Hex(5)Fuc(2)NeuAc(1),HexNAc(4)Hex(5)Fuc(4),HexNAc(7)Hex(4)Fuc(1),HexNAc(4)Hex(6)Fuc(1)NeuAc(1),HexNAc(4)Hex(6)Fuc(3),HexNAc(7)Hex(5),HexNAc(4)Hex(7)NeuAc(1),HexNAc(5)Hex(4)NeuAc(2),HexNAc(5)Hex(4)Fuc(2)NeuAc(1),HexNAc(4)Hex(8)Fuc(1),HexNAc(8)Hex(3)Fuc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(1),HexNAc(5)Hex(5)Fuc(3),HexNAc(4)Hex(9),HexNAc(5)Hex(6)NeuAc(1),HexNAc(5)Hex(6)Fuc(2),HexNAc(6)Hex(3)Fuc(2)NeuAc(1),HexNAc(9)Hex(3),HexNAc(6)Hex(5)Fuc(2),HexNAc(2)Hex(11)Fuc(1),HexNAc(6)Hex(6)Fuc(1),HexNAc(2)Hex(12),HexNAc(4)Hex(5)Fuc(1)NeuAc(2),HexNAc(6)Hex(7),HexNAc(4)Hex(5)Fuc(5),HexNAc(4)Hex(6)NeuAc(2),HexNAc(5)Hex(4)Fuc(1)NeuAc(2),HexNAc(7)Hex(6),HexNAc(5)Hex(5)NeuAc(2),HexNAc(5)Hex(5)Fuc(2)NeuAc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(1),HexNAc(5)Hex(6)Fuc(3),HexNAc(6)Hex(3)Fuc(1)NeuAc(2),HexNAc(8)Hex(5),HexNAc(6)Hex(4)NeuAc(2),HexNAc(5)Hex(8)Fuc(1),HexNAc(9)Hex(3)Fuc(1),HexNAc(2)Hex(10)Fuc(1)NeuAc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(1),HexNAc(9)Hex(4),HexNAc(6)Hex(6)NeuAc(1),HexNAc(6)Hex(7)Fuc(1),HexNAc(4)Hex(7)NeuAc(2),HexNAc(7)Hex(6)Fuc(1),HexNAc(4)Hex(8)Fuc(1)NeuAc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(2),HexNAc(7)Hex(7),HexNAc(5)Hex(6)NeuAc(2),HexNAc(5)Hex(6)Fuc(2)NeuAc(1),HexNAc(5)Hex(6)Fuc(4),HexNAc(8)Hex(5)Fuc(1),HexNAc(5)Hex(7)Fuc(1)NeuAc(1),HexNAc(9)Hex(4)Fuc(1),HexNAc(6)Hex(6)Fuc(1)NeuAc(1),HexNAc(6)Hex(7)NeuAc(1),HexNAc(6)Hex(7)Fuc(2),HexNAc(4)Hex(7)Fuc(1)NeuAc(2),HexNAc(7)Hex(7)Fuc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(2),HexNAc(5)Hex(6)Fuc(3)NeuAc(1),HexNAc(7)Hex(8),HexNAc(6)Hex(6)NeuAc(2),HexNAc(6)Hex(6)Fuc(4),HexNAc(4)Hex(5)NeuAc(4),HexNAc(6)Hex(7)Fuc(1)NeuAc(1),HexNAc(6)Hex(7)Fuc(3),HexNAc(7)Hex(4)Fuc(1)NeuAc(2),HexNAc(7)Hex(5)NeuAc(2),HexNAc(6)Hex(9)Fuc(1),HexNAc(5)Hex(6)NeuAc(3),HexNAc(7)Hex(8)Fuc(1),HexNAc(6)Hex(3)Fuc(4)NeuAc(2),HexNAc(5)Hex(7)Fuc(1)NeuAc(2),HexNAc(7)Hex(9),HexNAc(5)Hex(8)Fuc(4),HexNAc(6)Hex(6)Fuc(1)NeuAc(2),HexNAc(6)Hex(7)NeuAc(2),HexNAc(6)Hex(7)Fuc(4),HexNAc(4)Hex(7)Fuc(1)NeuAc(3),HexNAc(6)Hex(9)NeuAc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(3),HexNAc(7)Hex(8)NeuAc(1),HexNAc(5)Hex(6)Fuc(7),HexNAc(6)Hex(5)Fuc(1)NeuAc(3),HexNAc(6)Hex(6)NeuAc(3),HexNAc(6)Hex(7)Fuc(1)NeuAc(2),HexNAc(8)Hex(9),HexNAc(6)Hex(7)Fuc(5),HexNAc(7)Hex(7)NeuAc(2),HexNAc(7)Hex(7)Fuc(4),HexNAc(6)Hex(11)Fuc(1),HexNAc(5)Hex(6)Fuc(2)NeuAc(3),HexNAc(7)Hex(8)Fuc(1)NeuAc(1),HexNAc(7)Hex(8)Fuc(3),HexNAc(6)Hex(6)Fuc(1)NeuAc(3),HexNAc(6)Hex(7)NeuAc(3),HexNAc(6)Hex(7)Fuc(4)NeuAc(1),HexNAc(8)Hex(9)Fuc(1),HexNAc(7)Hex(4)NeuAc(4),HexNAc(7)Hex(7)Fuc(1)NeuAc(2),HexNAc(7)Hex(8)NeuAc(2),HexNAc(7)Hex(8)Fuc(4),HexNAc(6)Hex(7)Fuc(1)NeuAc(3),HexNAc(8)Hex(9)NeuAc(1),HexNAc(6)Hex(9)Fuc(1)NeuAc(2),HexNAc(6)Hex(9)Fuc(5),HexNAc(7)Hex(8)Fuc(3)NeuAc(1),HexNAc(9)Hex(10),HexNAc(7)Hex(8)Fuc(5),HexNAc(8)Hex(8)NeuAc(2),HexNAc(6)Hex(7)NeuAc(4),HexNAc(6)Hex(7)Fuc(4)NeuAc(2),HexNAc(8)Hex(9)Fuc(1)NeuAc(1),HexNAc(8)Hex(9)Fuc(3),HexNAc(5)Hex(6)Fuc(1)NeuAc(5),HexNAc(7)Hex(8)NeuAc(3),HexNAc(9)Hex(10)Fuc(1),HexNAc(6)Hex(7)Fuc(1)NeuAc(4),HexNAc(8)Hex(9)NeuAc(2),HexNAc(6)Hex(7)Fuc(5)NeuAc(2),HexNAc(7)Hex(6)Fuc(1)NeuAc(4),HexNAc(7)Hex(7)NeuAc(4),HexNAc(7)Hex(8)Fuc(3)NeuAc(2),HexNAc(6)Hex(7)Fuc(2)NeuAc(4),HexNAc(8)Hex(9)Fuc(3)NeuAc(1),HexNAc(8)Hex(10)NeuAc(2),HexNAc(7)Hex(7)Fuc(1)NeuAc(4),HexNAc(7)Hex(8)NeuAc(4),HexNAc(9)Hex(10)Fuc(3),HexNAc(10)Hex(11)Fuc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(4),HexNAc(6)Hex(7)Fuc(4)NeuAc(4),HexNAc(8)Hex(9)Fuc(3)NeuAc(2),HexNAc(8)Hex(10)NeuAc(3),HexNAc(9)Hex(10)Fuc(1)NeuAc(2),HexNAc(6)Hex(7)Fuc(5)NeuAc(4),HexNAc(9)Hex(7)Fuc(1)NeuAc(4),HexNAc(11)Hex(11)NeuAc(1),HexNAc(8)Hex(9)Fuc(1)NeuAc(4),HexNAc(8)Hex(10)NeuAc(4),HexNAc(10)Hex(12)Fuc(1)NeuAc(1),HexNAc(8)Hex(10)Fuc(6)NeuAc(1),HexNAc(12)Hex(5)Fuc(2)NeuAc(3),HexNAc(9)Hex(10)Fuc(3)NeuAc(2),HexNAc(10)Hex(7)Fuc(1)NeuAc(4),HexNAc(9)Hex(11)NeuAc(3),HexNAc(10)Hex(11)Fuc(3)NeuAc(2),HexNAc(10)Hex(11)Fuc(6)NeuAc(3),HexNAc(14)Hex(15)Fuc(6)NeuAc(1),HexNAc(14)Hex(15)Fuc(5)NeuAc(2),HexNAc(14)Hex(15)Fuc(6)NeuAc(2) opair.max_glycans=1 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc peptide-prophet.combine-pepxml=true peptide-prophet.run-peptide-prophet=true percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=false phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --prot 0.01 phi-report.pep-level-summary=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline= ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=true ptmshepherd.annotation-unimod=false ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions=0,203.07937,406.15874,568.21156,730.26438,892.3172,349.137279 ptmshepherd.decoy_type=1 ptmshepherd.diag_ions=204.086646,186.076086,168.065526,366.139466,144.0656,138.055,512.197375,292.1026925,274.0921325,657.2349,243.026426,405.079246,485.045576,308.09761 ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=25 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=12.5 ptmshepherd.diagmine_fragMinSpecDiff=25 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=25 ptmshepherd.glyco_fdr=0.01 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase=HexNAc(1),HexNAc(2)Hex(1),HexNAc(2)Hex(3),HexNAc(2)Hex(3)Fuc(1),HexNAc(2)Hex(4),HexNAc(3)Hex(3),HexNAc(2)Hex(4)Fuc(1),HexNAc(2)Hex(5),HexNAc(3)Hex(3)Fuc(1),HexNAc(3)Hex(4),HexNAc(4)Hex(3),HexNAc(2)Hex(5)Fuc(1),HexNAc(2)Hex(6),HexNAc(3)Hex(3)Fuc(2),HexNAc(3)Hex(4)Fuc(1),HexNAc(3)Hex(5),HexNAc(4)Hex(3)Fuc(1),HexNAc(4)Hex(4),HexNAc(5)Hex(3),HexNAc(2)Hex(6)Fuc(1),HexNAc(3)Hex(3)Fuc(3),HexNAc(2)Hex(7),HexNAc(3)Hex(4)NeuAc(1),HexNAc(3)Hex(4)Fuc(2),HexNAc(3)Hex(5)Fuc(1),HexNAc(3)Hex(6),HexNAc(4)Hex(3)NeuAc(1),HexNAc(4)Hex(4)Fuc(1),HexNAc(4)Hex(5),HexNAc(5)Hex(3)Fuc(1),HexNAc(5)Hex(4),HexNAc(2)Hex(7)Fuc(1),HexNAc(3)Hex(4)Fuc(1)NeuAc(1),HexNAc(3)Hex(4)Fuc(3),HexNAc(2)Hex(8),HexNAc(6)Hex(3),HexNAc(3)Hex(5)NeuAc(1),HexNAc(3)Hex(5)Fuc(2),HexNAc(3)Hex(6)Fuc(1),HexNAc(4)Hex(3)Fuc(1)NeuAc(1),HexNAc(4)Hex(3)Fuc(3),HexNAc(4)Hex(4)NeuAc(1),HexNAc(4)Hex(4)Fuc(2),HexNAc(4)Hex(5)Fuc(1),HexNAc(4)Hex(6),HexNAc(5)Hex(3)Fuc(2),HexNAc(5)Hex(4)Fuc(1),HexNAc(5)Hex(5),HexNAc(2)Hex(8)Fuc(1),HexNAc(6)Hex(3)Fuc(1),HexNAc(3)Hex(5)Fuc(1)NeuAc(1),HexNAc(3)Hex(5)Fuc(3),HexNAc(2)Hex(9),HexNAc(6)Hex(4),HexNAc(3)Hex(6)NeuAc(1),HexNAc(3)Hex(6)Fuc(2),HexNAc(4)Hex(3)NeuAc(2),HexNAc(3)Hex(7)Fuc(1),HexNAc(4)Hex(4)Fuc(1)NeuAc(1),HexNAc(4)Hex(4)Fuc(3),HexNAc(7)Hex(3),HexNAc(4)Hex(5)NeuAc(1),HexNAc(4)Hex(5)Fuc(2),HexNAc(4)Hex(6)Fuc(1),HexNAc(5)Hex(3)Fuc(1)NeuAc(1),HexNAc(4)Hex(7),HexNAc(5)Hex(4)NeuAc(1),HexNAc(5)Hex(4)Fuc(2),HexNAc(5)Hex(5)Fuc(1),HexNAc(5)Hex(6),HexNAc(6)Hex(3)Fuc(2),HexNAc(2)Hex(9)Fuc(1),HexNAc(6)Hex(4)Fuc(1),HexNAc(3)Hex(6)Fuc(1)NeuAc(1),HexNAc(3)Hex(6)Fuc(3),HexNAc(2)Hex(10),HexNAc(6)Hex(5),HexNAc(4)Hex(4)NeuAc(2),HexNAc(4)Hex(4)Fuc(2)NeuAc(1),HexNAc(7)Hex(3)Fuc(1),HexNAc(4)Hex(5)Fuc(1)NeuAc(1),HexNAc(4)Hex(5)Fuc(3),HexNAc(7)Hex(4),HexNAc(4)Hex(6)NeuAc(1),HexNAc(4)Hex(6)Fuc(2),HexNAc(4)Hex(7)Fuc(1),HexNAc(5)Hex(4)Fuc(1)NeuAc(1),HexNAc(5)Hex(4)Fuc(3),HexNAc(4)Hex(8),HexNAc(8)Hex(3),HexNAc(5)Hex(5)NeuAc(1),HexNAc(5)Hex(5)Fuc(2),HexNAc(5)Hex(6)Fuc(1),HexNAc(6)Hex(3)Fuc(1)NeuAc(1),HexNAc(6)Hex(3)Fuc(3),HexNAc(6)Hex(4)NeuAc(1),HexNAc(6)Hex(4)Fuc(2),HexNAc(2)Hex(10)Fuc(1),HexNAc(6)Hex(5)Fuc(1),HexNAc(2)Hex(11),HexNAc(6)Hex(6),HexNAc(4)Hex(5)NeuAc(2),HexNAc(4)Hex(5)Fuc(2)NeuAc(1),HexNAc(4)Hex(5)Fuc(4),HexNAc(7)Hex(4)Fuc(1),HexNAc(4)Hex(6)Fuc(1)NeuAc(1),HexNAc(4)Hex(6)Fuc(3),HexNAc(7)Hex(5),HexNAc(4)Hex(7)NeuAc(1),HexNAc(5)Hex(4)NeuAc(2),HexNAc(5)Hex(4)Fuc(2)NeuAc(1),HexNAc(4)Hex(8)Fuc(1),HexNAc(8)Hex(3)Fuc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(1),HexNAc(5)Hex(5)Fuc(3),HexNAc(4)Hex(9),HexNAc(5)Hex(6)NeuAc(1),HexNAc(5)Hex(6)Fuc(2),HexNAc(6)Hex(3)Fuc(2)NeuAc(1),HexNAc(9)Hex(3),HexNAc(6)Hex(5)Fuc(2),HexNAc(2)Hex(11)Fuc(1),HexNAc(6)Hex(6)Fuc(1),HexNAc(2)Hex(12),HexNAc(4)Hex(5)Fuc(1)NeuAc(2),HexNAc(6)Hex(7),HexNAc(4)Hex(5)Fuc(5),HexNAc(4)Hex(6)NeuAc(2),HexNAc(5)Hex(4)Fuc(1)NeuAc(2),HexNAc(7)Hex(6),HexNAc(5)Hex(5)NeuAc(2),HexNAc(5)Hex(5)Fuc(2)NeuAc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(1),HexNAc(5)Hex(6)Fuc(3),HexNAc(6)Hex(3)Fuc(1)NeuAc(2),HexNAc(8)Hex(5),HexNAc(6)Hex(4)NeuAc(2),HexNAc(5)Hex(8)Fuc(1),HexNAc(9)Hex(3)Fuc(1),HexNAc(2)Hex(10)Fuc(1)NeuAc(1),HexNAc(6)Hex(5)Fuc(1)NeuAc(1),HexNAc(9)Hex(4),HexNAc(6)Hex(6)NeuAc(1),HexNAc(6)Hex(7)Fuc(1),HexNAc(4)Hex(7)NeuAc(2),HexNAc(7)Hex(6)Fuc(1),HexNAc(4)Hex(8)Fuc(1)NeuAc(1),HexNAc(5)Hex(5)Fuc(1)NeuAc(2),HexNAc(7)Hex(7),HexNAc(5)Hex(6)NeuAc(2),HexNAc(5)Hex(6)Fuc(2)NeuAc(1),HexNAc(5)Hex(6)Fuc(4),HexNAc(8)Hex(5)Fuc(1),HexNAc(5)Hex(7)Fuc(1)NeuAc(1),HexNAc(9)Hex(4)Fuc(1),HexNAc(6)Hex(6)Fuc(1)NeuAc(1),HexNAc(6)Hex(7)NeuAc(1),HexNAc(6)Hex(7)Fuc(2),HexNAc(4)Hex(7)Fuc(1)NeuAc(2),HexNAc(7)Hex(7)Fuc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(2),HexNAc(5)Hex(6)Fuc(3)NeuAc(1),HexNAc(7)Hex(8),HexNAc(6)Hex(6)NeuAc(2),HexNAc(6)Hex(6)Fuc(4),HexNAc(4)Hex(5)NeuAc(4),HexNAc(6)Hex(7)Fuc(1)NeuAc(1),HexNAc(6)Hex(7)Fuc(3),HexNAc(7)Hex(4)Fuc(1)NeuAc(2),HexNAc(7)Hex(5)NeuAc(2),HexNAc(6)Hex(9)Fuc(1),HexNAc(5)Hex(6)NeuAc(3),HexNAc(7)Hex(8)Fuc(1),HexNAc(6)Hex(3)Fuc(4)NeuAc(2),HexNAc(5)Hex(7)Fuc(1)NeuAc(2),HexNAc(7)Hex(9),HexNAc(5)Hex(8)Fuc(4),HexNAc(6)Hex(6)Fuc(1)NeuAc(2),HexNAc(6)Hex(7)NeuAc(2),HexNAc(6)Hex(7)Fuc(4),HexNAc(4)Hex(7)Fuc(1)NeuAc(3),HexNAc(6)Hex(9)NeuAc(1),HexNAc(5)Hex(6)Fuc(1)NeuAc(3),HexNAc(7)Hex(8)NeuAc(1),HexNAc(5)Hex(6)Fuc(7),HexNAc(6)Hex(5)Fuc(1)NeuAc(3),HexNAc(6)Hex(6)NeuAc(3),HexNAc(6)Hex(7)Fuc(1)NeuAc(2),HexNAc(8)Hex(9),HexNAc(6)Hex(7)Fuc(5),HexNAc(7)Hex(7)NeuAc(2),HexNAc(7)Hex(7)Fuc(4),HexNAc(6)Hex(11)Fuc(1),HexNAc(5)Hex(6)Fuc(2)NeuAc(3),HexNAc(7)Hex(8)Fuc(1)NeuAc(1),HexNAc(7)Hex(8)Fuc(3),HexNAc(6)Hex(6)Fuc(1)NeuAc(3),HexNAc(6)Hex(7)NeuAc(3),HexNAc(6)Hex(7)Fuc(4)NeuAc(1),HexNAc(8)Hex(9)Fuc(1),HexNAc(7)Hex(4)NeuAc(4),HexNAc(7)Hex(7)Fuc(1)NeuAc(2),HexNAc(7)Hex(8)NeuAc(2),HexNAc(7)Hex(8)Fuc(4),HexNAc(6)Hex(7)Fuc(1)NeuAc(3),HexNAc(8)Hex(9)NeuAc(1),HexNAc(6)Hex(9)Fuc(1)NeuAc(2),HexNAc(6)Hex(9)Fuc(5),HexNAc(7)Hex(8)Fuc(3)NeuAc(1),HexNAc(9)Hex(10),HexNAc(7)Hex(8)Fuc(5),HexNAc(8)Hex(8)NeuAc(2),HexNAc(6)Hex(7)NeuAc(4),HexNAc(6)Hex(7)Fuc(4)NeuAc(2),HexNAc(8)Hex(9)Fuc(1)NeuAc(1),HexNAc(8)Hex(9)Fuc(3),HexNAc(5)Hex(6)Fuc(1)NeuAc(5),HexNAc(7)Hex(8)NeuAc(3),HexNAc(9)Hex(10)Fuc(1),HexNAc(6)Hex(7)Fuc(1)NeuAc(4),HexNAc(8)Hex(9)NeuAc(2),HexNAc(6)Hex(7)Fuc(5)NeuAc(2),HexNAc(7)Hex(6)Fuc(1)NeuAc(4),HexNAc(7)Hex(7)NeuAc(4),HexNAc(7)Hex(8)Fuc(3)NeuAc(2),HexNAc(6)Hex(7)Fuc(2)NeuAc(4),HexNAc(8)Hex(9)Fuc(3)NeuAc(1),HexNAc(8)Hex(10)NeuAc(2),HexNAc(7)Hex(7)Fuc(1)NeuAc(4),HexNAc(7)Hex(8)NeuAc(4),HexNAc(9)Hex(10)Fuc(3),HexNAc(10)Hex(11)Fuc(1),HexNAc(7)Hex(8)Fuc(1)NeuAc(4),HexNAc(6)Hex(7)Fuc(4)NeuAc(4),HexNAc(8)Hex(9)Fuc(3)NeuAc(2),HexNAc(8)Hex(10)NeuAc(3),HexNAc(9)Hex(10)Fuc(1)NeuAc(2),HexNAc(6)Hex(7)Fuc(5)NeuAc(4),HexNAc(9)Hex(7)Fuc(1)NeuAc(4),HexNAc(11)Hex(11)NeuAc(1),HexNAc(8)Hex(9)Fuc(1)NeuAc(4),HexNAc(8)Hex(10)NeuAc(4),HexNAc(10)Hex(12)Fuc(1)NeuAc(1),HexNAc(8)Hex(10)Fuc(6)NeuAc(1),HexNAc(12)Hex(5)Fuc(2)NeuAc(3),HexNAc(9)Hex(10)Fuc(3)NeuAc(2),HexNAc(10)Hex(7)Fuc(1)NeuAc(4),HexNAc(9)Hex(11)NeuAc(3),HexNAc(10)Hex(11)Fuc(3)NeuAc(2),HexNAc(10)Hex(11)Fuc(6)NeuAc(3),HexNAc(14)Hex(15)Fuc(6)NeuAc(1),HexNAc(14)Hex(15)Fuc(5)NeuAc(2),HexNAc(14)Hex(15)Fuc(6)NeuAc(2) ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=true ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=true ptmshepherd.iterloc_maxEpoch=100 ptmshepherd.iterloc_mode=false ptmshepherd.localization_allowed_res=N ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.print_full_glyco_params=true ptmshepherd.prob_mass=1.0 ptmshepherd.remainder_masses=203.07937 ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=true ptmshepherd.run_diagextract_mode=true ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=true ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=false run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=3 saintexpress.run-saint-express=true saintexpress.virtual-controls=100 skyline.run-skyline=false skyline.skyline=true skyline.skyline-custom=false skyline.skyline-custom-path= skyline.skyline-daily=false skyline.skyline-mode=0 skyline.skyline-mods-mode=Default speclibgen.convert-pepxml=false speclibgen.convert-psm=true speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.max_glycan_qval=1 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.ignore_unannotated=true speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.labile_mode=N-glyco+HexNAc speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=0.01 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.philosopher-msstats=false tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=true workdir=D\:\\ICAM3_testing\\ICAM3Celcius\\MSfraggerTesting workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -Xmx111G -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\batmass-io-1.33.4.jar com.dmtavt.fragpipe.util.CheckCentroid D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML 63 Done in 2.5 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="12:05:35" level=info msg="Executing Workspace v5.1.1" time="12:05:35" level=info msg="Removing workspace" time="12:05:35" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\jparedes\AppData\Local\Temp\ab0ea830-43de-4b5d-b128-f5cb84b7c53c time="12:05:36" level=info msg="Executing Workspace v5.1.1" time="12:05:36" level=info msg="Creating workspace" time="12:05:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="12:05:36" level=info msg="Executing Workspace v5.1.1" time="12:05:36" level=info msg="Removing workspace" time="12:05:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\jparedes\AppData\Local\Temp\43b9937e-db68-4e52-8be8-04cf722542e2 time="12:05:37" level=info msg="Executing Workspace v5.1.1" time="12:05:37" level=info msg="Creating workspace" time="12:05:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --clean --nocheck time="12:05:37" level=info msg="Executing Workspace v5.1.1" time="12:05:37" level=info msg="Removing workspace" time="12:05:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe workspace --init --nocheck --temp C:\Users\jparedes\AppData\Local\Temp\17c29ee1-090c-4e19-bdae-9bf78e0dfb39 time="12:05:37" level=info msg="Executing Workspace v5.1.1" time="12:05:37" level=info msg="Creating workspace" time="12:05:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx111G C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\..\tools\MSFragger-4.1\MSFragger-4.1.jar D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\fragger.params D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML MSFragger version MSFragger-4.1 Batmass-IO version 1.33.4 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Windows 11, Architecture: AMD64 Java Info: 17.0.10, OpenJDK 64-Bit Server VM, Eclipse Adoptium JVM started with 111 GB memory Checking database... Checking spectral files... D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML: Scans = 85; ITMS: false; FTMS: false; Isolation sizes = [] D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML: Scans = 2277; ITMS: false; FTMS: false; Isolation sizes = [] D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML: Scans = 2794; ITMS: false; FTMS: false; Isolation sizes = [] D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML: Scans = 2326; ITMS: false; FTMS: false; Isolation sizes = [] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 63 database_name = D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = CORRECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y,c,z, ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 400.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 2 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 647614620 fragments to be searched in 1 slices (9.65 GB total) Operating on slice 1 of 1: Fragment index slice generated in 31.54 s 001. ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML 1.3 s | deisotoping 0.3 s [progress: 85/85 (100%) - 403 spectra/s] 0.2s | postprocessing 0.0 s 002. ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML 3.4 s | deisotoping 0.2 s [progress: 2277/2277 (100%) - 3383 spectra/s] 0.7s | postprocessing 0.0 s 003. ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML 2.6 s | deisotoping 0.1 s [progress: 2326/2326 (100%) - 10670 spectra/s] 0.2s | postprocessing 0.0 s 004. ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML 2.2 s | deisotoping 0.1 s [progress: 2794/2794 (100%) - 12418 spectra/s] 0.2s | postprocessing 0.1 s ***************************FIRST SEARCH DONE IN 0.927 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | Not enough data to perform mass calibration. Using the uncalibrated data. 002 | Not enough data to perform mass calibration. Using the uncalibrated data. 003 | -0.05 2.13 | 0.43 1.00 | -3.03 5.12 | -0.47 5.15 004 | Not enough data to perform mass calibration. Using the uncalibrated data. -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|-------|-------|------- MS2 | 5 | 7 | 10 | 15 | 20 | 25 | 30 | 50 -------|-------|-------|-------|-------|-------|-------|-------|------- Count | skip | skip | skip | 171| 179| 203| 183| skip rest -------|-------|-------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 -------|-------|-------|-------|-------|-------|------- Count | 203| 166| skip rest -------|-------|-------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 235 -------|------- New fragment_mass_tolerance = 25.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 2 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.150 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 63 database_name = D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 25.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0/1038.3751/1054.37/1095.3966/1200.428/1216.4229/1241.4545/1257.4495/1298.476/1362.4808/1378.4757/1387.5125/1403.5073/1419.5022/1444.5339/1460.5288/1501.5553/1524.5336/1533.5703/1540.5286/1548.5448/1549.5652/1565.5602/1581.555/1589.5714/1606.5867/1622.5817/1647.6133/1663.6082/1686.5864/1694.6028/1695.6232/1702.5813/1704.6348/1710.5977/1711.618/1727.613/1735.6293/1736.6497/1751.6243/1752.6447/1768.6395/1784.6344/1793.6711/1809.6661/1825.661/1848.6393/1850.6926/1856.6556/1857.676/1864.6342/1866.6875/1872.6505/1873.6709/1880.6669/1889.6658/1897.6821/1898.7025/1907.7141/1913.677/1914.6974/1930.6924/1938.7087/1946.6873/1954.7036/1955.724/1971.7189/1987.7139/1996.7505/2010.6921/2012.7455/2018.7084/2019.7288/2026.687/2028.7404/203.07938/2042.7196/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.73/2076.7502/2092.745/2100.7615/2101.782/2108.74/2110.7935/2116.7563/2117.7769/2133.7717/2141.788/2142.8083/2157.783/2158.8035/2172.7449/2174.7983/2188.7397/2190.7932/2204.7725/2205.793/2206.8132/2215.825/2221.7878/2222.808/2231.8198/2237.7827/2245.799/2246.8193/2254.798/2256.8513/2262.8145/2263.8347/2270.793/2278.8093/2279.8296/2287.846/2313.8728/2320.8562/2334.7979/2336.851/2350.7927/2350.8303/2352.846/2352.871/2366.8252/2391.857/2393.8726/2407.8518/2408.8723/2424.8672/2425.8875/2432.8835/2434.8992/2448.8784/2457.8774/2459.9307/2463.8403/2465.8938/2475.9258/2481.8887/2498.904/2528.8782/2539.9304/2545.8936/2553.9097/2555.9253/2569.9048/2570.925/2571.9456/2580.957/2586.92/2621.9836/2627.9465/2643.9414/2644.962/2674.936/2701.9834/2715.9626/2716.983/2717.9783/2772.9841/2775.025/2786.9634/2789.9993/2791.0198/2798.0156/2814.0105/2823.0095/2861.0/2864.0361/2871.0571/2878.0154/2880.031/2896.051/2919.042/2935.0369/2937.0776/2966.0315/2968.047/3007.058/3009.0737/3010.1191/3048.0845/3064.0796/3081.0947/3083.1104/3083.1355/3138.1162/3140.157/3147.1152/3153.116/3155.1316/3156.1519/3210.1375/3226.1323/3228.173/3229.1685/3234.1487/3284.174/3300.1692/3302.21/3372.1902/3374.2058/3405.2004/3407.2412/3447.2473/3448.2427/3448.2678/3503.2485/3517.2278/3519.2686/3520.2637/3521.2842/3589.2488/3591.2644/3594.3005/3663.2856/3665.3013/3665.3264/3704.3123/3720.3071/3738.3428/3809.3435/3812.3796/3827.354/3866.365/3882.3599/3886.4163/3959.4329/4028.418/4101.4595/4103.475/4118.4497/4176.491/4247.517/4272.524/4307.55/4393.5503/4409.545/4412.581/4412.606/4412.6187/4468.6074/4475.603/4483.5815/4833.7393/5563.009/568.21155/6441.3467/6586.3843/6732.442/892.3172 labile_search_mode = NGLYCAN restrict_deltamass_to = N precursor_mass_mode = CORRECTED localize_delta_mass = 1 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y,c,z, ion_series_definitions = diagnostic_intensity_filter = 0.03 Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279 diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761 search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = tsv_pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 400.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 2 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.13 Da. 1295229240 fragments to be searched in 1 slices (19.30 GB total) Operating on slice 1 of 1: Fragment index slice generated in 2.83 s 001. ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML 0.2 s | deisotoping 0.0 s [progress: 85/85 (100%) - 252 spectra/s] 0.3s | remapping alternative proteins and postprocessing 0.9 s 002. ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML 0.5 s | deisotoping 0.0 s [progress: 2277/2277 (100%) - 410 spectra/s] 5.6s | remapping alternative proteins and postprocessing 1.0 s 003. ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzBIN_calibrated 0.1 s [progress: 2326/2326 (100%) - 537 spectra/s] 4.3s | remapping alternative proteins and postprocessing 1.1 s 004. ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML 3.5 s | deisotoping 0.0 s [progress: 2794/2794 (100%) - 354 spectra/s] 7.9s | remapping alternative proteins and postprocessing 0.5 s ***************************MAIN SEARCH DONE IN 0.516 MIN*************************** *******************************TOTAL TIME 2.592 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.tsv Process 'MSFragger move tsv' finished, exit code: 0 MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.tsv Process 'MSFragger move tsv' finished, exit code: 0 MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.tsv Process 'MSFragger move tsv' finished, exit code: 0 MSFragger move pepxml C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move tsv C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib\fragpipe-22.0.jar;/C:/Users/jparedes/FragPipe-jre-22.0/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.tsv D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.tsv Process 'MSFragger move tsv' finished, exit code: 0 PeptideProphet [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc --decoy rev_ --database D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas --combine ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML PeptideProphet [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 4000.0 --glyc --decoy rev_ --database D:\Databases\2024-06-21-decoys-contam-Hsapiens_UP000005640_9606_2024_06_21.fasta.fas --combine ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. time="12:08:15" level=info msg="Executing PeptideProphet v5.1.1" file 1: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.pepXML file 2: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.pepXML processed altogether 1239 results INFO: Results written to file: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml - D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 964 2+, 228 3+, 47 4+, 0 5+, 0 6+, and 0 7+ spectra. Found 583 Decoys, and 656 Non-Decoys using N-glyc info Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) using search_offsets in mass mixture distr: 0.0/1038.3751/1054.37/1095.3966/1200.428/1216.4229/1241.4545/1257.4495/1298.476/1362.4808/1378.4757/1387.5125/1403.5073/1419.5022/1444.5339/1460.5288/1501.5553/1524.5336/1533.5703/1540.5286/1548.5448/1549.5652/1565.5602/1581.555/1589.5714/1606.5867/1622.5817/1647.6133/1663.6082/1686.5864/1694.6028/1695.6232/1702.5813/1704.6348/1710.5977/1711.618/1727.613/1735.6293/1736.6497/1751.6243/1752.6447/1768.6395/1784.6344/1793.6711/1809.6661/1825.661/1848.6393/1850.6926/1856.6556/1857.676/1864.6342/1866.6875/1872.6505/1873.6709/1880.6669/1889.6658/1897.6821/1898.7025/1907.7141/1913.677/1914.6974/1930.6924/1938.7087/1946.6873/1954.7036/1955.724/1971.7189/1987.7139/1996.7505/2010.6921/2012.7455/2018.7084/2019.7288/2026.687/2028.7404/203.07938/2042.7196/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.73/2076.7502/2092.745/2100.7615/2101.782/2108.74/2110.7935/2116.7563/2117.7769/2133.7717/2141.788/2142.8083/2157.783/2158.8035/2172.7449/2174.7983/2188.7397/2190.7932/2204.7725/2205.793/2206.8132/2215.825/2221.7878/2222.808/2231.8198/2237.7827/2245.799/2246.8193/2254.798/2256.8513/2262.8145/2263.8347/2270.793/2278.8093/2279.8296/2287.846/2313.8728/2320.8562/2334.7979/2336.851/2350.7927/2350.8303/2352.846/2352.871/2366.8252/2391.857/2393.8726/2407.8518/2408.8723/2424.8672/2425.8875/2432.8835/2434.8992/2448.8784/2457.8774/2459.9307/2463.8403/2465.8938/2475.9258/2481.8887/2498.904/2528.8782/2539.9304/2545.8936/2553.9097/2555.9253/2569.9048/2570.925/2571.9456/2580.957/2586.92/2621.9836/2627.9465/2643.9414/2644.962/2674.936/2701.9834/2715.9626/2716.983/2717.9783/2772.9841/2775.025/2786.9634/2789.9993/2791.0198/2798.0156/2814.0105/2823.0095/2861.0/2864.0361/2871.0571/2878.0154/2880.031/2896.051/2919.042/2935.0369/2937.0776/2966.0315/2968.047/3007.058/3009.0737/3010.1191/3048.0845/3064.0796/3081.0947/3083.1104/3083.1355/3138.1162/3140.157/3147.1152/3153.116/3155.1316/3156.1519/3210.1375/3226.1323/3228.173/3229.1685/3234.1487/3284.174/3300.1692/3302.21/3372.1902/3374.2058/3405.2004/3407.2412/3447.2473/3448.2427/3448.2678/3503.2485/3517.2278/3519.2686/3520.2637/3521.2842/3589.2488/3591.2644/3594.3005/3663.2856/3665.3013/3665.3264/3704.3123/3720.3071/3738.3428/3809.3435/3812.3796/3827.354/3866.365/3882.3599/3886.4163/3959.4329/4028.418/4101.4595/4103.475/4118.4497/4176.491/4247.517/4272.524/4307.55/4393.5503/4409.545/4412.581/4412.606/4412.6187/4468.6074/4475.603/4483.5815/4833.7393/5563.009/568.21155/6441.3467/6586.3843/6732.442/892.3172 init with X! Tandem stricttrypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10........WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). .20..... model complete after 26 iterations 'mv' is not recognized as an internal or external command, operable program or batch file. command "mv -f "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml.tmp.a23140" "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml"" failed: Operation not permitted failed to update D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml from temp file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml.tmp.a23140, error 2 "No such file or directory"'mv' is not recognized as an internal or external command, operable program or batch file. command "mv -f "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml.tmp.a23140" "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml"" failed: Operation not permitted failed to update D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml from temp file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml.tmp.a23140, error 2 "No such file or directory"'mv' is not recognized as an internal or external command, operable program or batch file. error: no peptideprophet data written to file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml command "mv -f "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml.tmp.a23140" "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml"" failed: Operation not permitted failed to update D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml from temp file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml.tmp.a23140, error 2 "No such file or directory"time="12:08:40" level=info msg=Done Process 'PeptideProphet' finished, exit code: 0 time="12:08:15" level=info msg="Executing PeptideProphet v5.1.1" file 1: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.pepXML file 2: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.pepXML processed altogether 3180 results INFO: Results written to file: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml - D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... using N-glyc info Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) using search_offsets in mass mixture distr: 0.0/1038.3751/1054.37/1095.3966/1200.428/1216.4229/1241.4545/1257.4495/1298.476/1362.4808/1378.4757/1387.5125/1403.5073/1419.5022/1444.5339/1460.5288/1501.5553/1524.5336/1533.5703/1540.5286/1548.5448/1549.5652/1565.5602/1581.555/1589.5714/1606.5867/1622.5817/1647.6133/1663.6082/1686.5864/1694.6028/1695.6232/1702.5813/1704.6348/1710.5977/1711.618/1727.613/1735.6293/1736.6497/1751.6243/1752.6447/1768.6395/1784.6344/1793.6711/1809.6661/1825.661/1848.6393/1850.6926/1856.6556/1857.676/1864.6342/1866.6875/1872.6505/1873.6709/1880.6669/1889.6658/1897.6821/1898.7025/1907.7141/1913.677/1914.6974/1930.6924/1938.7087/1946.6873/1954.7036/1955.724/1971.7189/1987.7139/1996.7505/2010.6921/2012.7455/2018.7084/2019.7288/2026.687/2028.7404/203.07938/2042.7196/2043.74/2053.772/2059.7349/2060.7554/2069.7668/2075.73/2076.7502/2092.745/2100.7615/2101.782/2108.74/2110.7935/2116.7563/2117.7769/2133.7717/2141.788/2142.8083/2157.783/2158.8035/2172.7449/2174.7983/2188.7397/2190.7932/2204.7725/2205.793/2206.8132/2215.825/2221.7878/2222.808/2231.8198/2237.7827/2245.799/2246.8193/2254.798/2256.8513/2262.8145/2263.8347/2270.793/2278.8093/2279.8296/2287.846/2313.8728/2320.8562/2334.7979/2336.851/2350.7927/2350.8303/2352.846/2352.871/2366.8252/2391.857/2393.8726/2407.8518/2408.8723/2424.8672/2425.8875/2432.8835/2434.8992/2448.8784/2457.8774/2459.9307/2463.8403/2465.8938/2475.9258/2481.8887/2498.904/2528.8782/2539.9304/2545.8936/2553.9097/2555.9253/2569.9048/2570.925/2571.9456/2580.957/2586.92/2621.9836/2627.9465/2643.9414/2644.962/2674.936/2701.9834/2715.9626/2716.983/2717.9783/2772.9841/2775.025/2786.9634/2789.9993/2791.0198/2798.0156/2814.0105/2823.0095/2861.0/2864.0361/2871.0571/2878.0154/2880.031/2896.051/2919.042/2935.0369/2937.0776/2966.0315/2968.047/3007.058/3009.0737/3010.1191/3048.0845/3064.0796/3081.0947/3083.1104/3083.1355/3138.1162/3140.157/3147.1152/3153.116/3155.1316/3156.1519/3210.1375/3226.1323/3228.173/3229.1685/3234.1487/3284.174/3300.1692/3302.21/3372.1902/3374.2058/3405.2004/3407.2412/3447.2473/3448.2427/3448.2678/3503.2485/3517.2278/3519.2686/3520.2637/3521.2842/3589.2488/3591.2644/3594.3005/3663.2856/3665.3013/3665.3264/3704.3123/3720.3071/3738.3428/3809.3435/3812.3796/3827.354/3866.365/3882.3599/3886.4163/3959.4329/4028.418/4101.4595/4103.475/4118.4497/4176.491/4247.517/4272.524/4307.55/4393.5503/4409.545/4412.581/4412.606/4412.6187/4468.6074/4475.603/4483.5815/4833.7393/5563.009/568.21155/6441.3467/6586.3843/6732.442/892.3172 PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 2424 2+, 565 3+, 185 4+, 6 5+, 0 6+, and 0 7+ spectra. Found 1323 Decoys, and 1857 Non-Decoys init with X! Tandem stricttrypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... Initialising statistical models ... Iterations: .........10.........20.......WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). . model complete after 29 iterations 'mv' is not recognized as an internal or external command, operable program or batch file. command "mv -f "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml.tmp.a31516" "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml"" failed: Operation not permitted failed to update D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml from temp file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml.tmp.a31516, error 2 "No such file or directory"'mv' is not recognized as an internal or external command, operable program or batch file. command "mv -f "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml.tmp.a31516" "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml"" failed: Operation not permitted failed to update D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml from temp file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml.tmp.a31516, error 2 "No such file or directory"'mv' is not recognized as an internal or external command, operable program or batch file. error: no peptideprophet data written to file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml command "mv -f "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml.tmp.a31516" "D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml"" failed: Operation not permitted failed to update D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml from temp file D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml.tmp.a31516, error 2 "No such file or directory"time="12:08:45" level=info msg=Done Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml D:\ICAM3_testing\ICAM3Celcius\ICAM3_Elute-D3_EAD1_12Jun2024-1-ICAM3_Elute_D3_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_Org_EAD5_11Jun2024-3-ICAM3_organic_wiff2.mzML Fixing pepxml: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml Writing output to: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml5075529308960425241.temp-rewrite Deleting file: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml Moving rewritten file to original location: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml5075529308960425241.temp-rewrite] -> [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Rewrite pepxml [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -cp C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_wash_EAD_23May2024-1-ICAM3_digest_Wash_BB_wiff2.mzML D:\ICAM3_testing\ICAM3Celcius\ICAM3_digest_elute_EAD_23May2024-1-ICAM3_digest_Elute_BB_wiff2.mzML Fixing pepxml: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml Writing output to: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml13396200034032274353.temp-rewrite Deleting file: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml Moving rewritten file to original location: [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml13396200034032274353.temp-rewrite] -> [D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 ProteinProphet [Work dir: D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting] C:\Users\jparedes\FragPipe-jre-22.0\fragpipe\tools\Philosopher\philosopher-v5.1.1.exe proteinprophet --maxppmdiff 2000000 --output combined D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\filelist_proteinprophet.txt time="12:08:46" level=info msg="Executing ProteinProphet v5.1.1" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\June\interact.pep.xml... did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? ...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in D:\ICAM3_testing\ICAM3Celcius\MSfraggerTesting\May\interact.pep.xml... did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? ...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 WARNING: no data - output file will be empty time="12:08:48" level=error msg="Cannot execute program. there was an error with ProteinProphet, please check your parameters and input files" Process 'ProteinProphet' finished, exit code: 1 Process returned non-zero exit code, stopping ~~~~~~~~~~~~~~~~~~~~ Cancelling 10 remaining tasks