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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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MS1 quantitation IonQuant error #1637

Closed Angelwitch closed 1 week ago

Angelwitch commented 1 week ago

- Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

- Describe the issue or question: IonQuant error IonQuant [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx148G -Dlibs.bruker.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.0\ext\bruker" -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.0\ext\thermo" -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\IonQuant-1.10.27.jar" ionquant.IonQuant --threads 42 --ionmobility 0 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\filelist_ionquant.txt --modlist D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\modmasses_ionquant.txt IonQuant version IonQuant-1.10.27 Batmass-IO version 1.28.12 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Windows Server 2012 R2, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 148 GB memory 2024-06-18 17:20:05 [WARNING] - There are only 1 experiments. Will not calculate MaxLFQ intensity. 2024-06-18 17:20:06 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-06-18 17:20:06 [INFO] - Loading and indexing all psm.tsv files... 2024-06-18 17:20:07 [INFO] - Collecting all compensation voltages if applicable... 2024-06-18 17:20:27 [INFO] - B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP does not have FAIMS. If there are any other runs having FAIMS, IonQuant will crash. 2024-06-18 17:20:27 [INFO] - There is no FAIMS in the dataset. java.lang.NoSuchMethodError: 'com.google.protobuf.Internal$ProtobufList N$j.makeMutableCopy(com.google.protobuf.Internal$ProtobufList)' at N$j.a(Unknown Source) at N$j$a.f(Unknown Source) at N$j$a.a(Unknown Source) at aa.a(Unknown Source) at k.a(Unknown Source) at k.b(Unknown Source) at k.a(Unknown Source) at ionquant.IonQuant.a(Unknown Source) at ionquant.IonQuant.main(Unknown Source) Process 'IonQuant' finished, exit code: 1 Process returned non-zero exit code, stopping

log_2024-06-19_09-29-54.txt

fcyu commented 1 week ago

It was due to version incompatibility. Could you upgrade FragPipe, MFragger, and diaTracer to the latest version, and try again?

Thanks,

Fengchao

Angelwitch commented 1 week ago

Dear Fengchao, Thank you very much for the suggestion. Unfortunately, the issue is not solved. I have updated all software listed in the config tab (screenshot attached) After update we had few more errors occurred when analysing the same raw files.

  1. Closed search without ionQuant only run through with “Run MSbooster” unticked.
  2. Open search stopped with a Crystal C error (log attached)
  3. Closed search with ionQunat stopped with an ionQuant error (log attached)

Please let us know what can we do to get the software running. Thank you very much.

Best regards

Zhuo Chen

From: Fengchao @.> Sent: 19 June 2024 15:18 To: Nesvilab/FragPipe @.> Cc: Chen, Zhuo, Dr. @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] MS1 quantitation IonQuant error (Issue #1637)

It was due to version incompatibility. Could you upgrade FragPipe, MFragger, and diaTracer to the latest version, and try again?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1637#issuecomment-2178701966, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEJGI6TZOK5BE3X3J6JPI23ZIGAKDAVCNFSM6AAAAABJRPCYS6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZYG4YDCOJWGY. You are receiving this because you authored the thread.Message ID: @.**@.>>

System OS: Windows Server 2012 R2, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.3.9600

Version info: FragPipe version 20.0 MSFragger version 4.1 IonQuant version 1.10.27 Philosopher version 5.1.0

LCMS files: Experiment/Group:

16 commands to execute: CheckCentroid D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx159G -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw 42 WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\Angel\AppData\Local\Temp\4\f8960d91-df7f-47be-821d-f6662c0d271c MSFragger [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx159G D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\MSFragger-4.1.jar D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\fragger.params D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.raw Crystal-C [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\ext\thermo" -Xmx159G -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\original-crystalc-1.5.2.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\crystalc-0-B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML.params D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML Crystal-C [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\ext\thermo" -Xmx159G -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\original-crystalc-1.5.2.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\crystalc-1-B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pepXML.params D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pepXML Crystal-C: Delete temp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\crystalc-0-B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML.params Crystal-C: Delete temp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\crystalc-1-B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pepXML.params PeptideProphet [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database D:\user\Angel\NativeTrypsin\2022-09-21-decoys-reviewed-contam-UP000005640.fas --combine B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_c.pepXML B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_c.pepXML Rewrite pepxml [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\interact.pep.xml D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_uncalibrated.mzML D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_uncalibrated.mzML ProteinProphet [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe database --annotate D:\user\Angel\NativeTrypsin\2022-09-21-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe filter --sequential --mapmods --prot 0.01 --tag rev --pepxml D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest --protxml D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\combined.prot.xml --razor PhilosopherReport [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report PTMShepherd [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx159G -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\ext\thermo" -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\ptmshepherd-2.0.5.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\commons-math3-3.6.1.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\hipparchus-1.8\hipparchus-core-1.8.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\hipparchus-1.8\hipparchus-stat-1.8.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\shepherd.config" WorkspaceClean [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [CheckCentroid], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [MSFragger], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [Crystal-C], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [PeptideProphet], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [ProteinProphet], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [PhilosopherFilter], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [PhilosopherReport], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [PTMShepherd], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]
    Cmd: [WorkspaceClean], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest]

>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries GN=KRT15 PE=2 SV=1
>rev_sp|O43602|DCX_HUMAN Neuronal migration protein doublecortin OS=Homo sapiens OX=9606 GN=DCX PE=1 SV=4
>rev_sp|P0DMW4|SIL2A_HUMAN Small integral membrane protein 10-like protein 2A OS=Homo sapiens OX=9606 GN=SMIM10L2A PE=4 SV=1
>rev_sp|P49795|RGS19_HUMAN Regulator of G-protein signaling 19 OS=Homo sapiens OX=9606 GN=RGS19 PE=1 SV=1
>rev_sp|Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 OS=Homo sapiens OX=9606 GN=DYNC1H1 PE=1 SV=5
>rev_sp|Q69YW2|STUM_HUMAN Protein stum homolog OS=Homo sapiens OX=9606 GN=STUM PE=1 SV=1
>rev_sp|Q8IWP9|CC28A_HUMAN Coiled-coil domain-containing protein 28A OS=Homo sapiens OX=9606 GN=CCDC28A PE=1 SV=1
>rev_sp|Q8WVS4|DC2I1_HUMAN Cytoplasmic dynein 2 intermediate chain 1 OS=Homo sapiens OX=9606 GN=DYNC2I1 PE=1 SV=3
>rev_sp|Q9BRK3|MXRA8_HUMAN Matrix remodeling-associated protein 8 OS=Homo sapiens OX=9606 GN=MXRA8 PE=1 SV=1
>rev_sp|Q9NUS5|AP5S1_HUMAN AP-5 complex subunit sigma-1 OS=Homo sapiens OX=9606 GN=AP5S1 PE=1 SV=1
>rev_sp|Q9Y6N8|CAD10_HUMAN Cadherin-10 OS=Homo sapiens OX=9606 GN=CDH10 PE=1 SV=2
>sp|O43747|AP1G1_HUMAN AP-1 complex subunit gamma-1 OS=Homo sapiens OX=9606 GN=AP1G1 PE=1 SV=5
>sp|P0DPD7|EFMT4_HUMAN EEF1A lysine methyltransferase 4 OS=Homo sapiens OX=9606 GN=EEF1AKMT4 PE=1 SV=1
>sp|P50402|EMD_HUMAN Emerin OS=Homo sapiens OX=9606 GN=EMD PE=1 SV=1
>sp|Q14451|GRB7_HUMAN Growth factor receptor-bound protein 7 OS=Homo sapiens OX=9606 GN=GRB7 PE=1 SV=2
>sp|Q6DWJ6|GP139_HUMAN Probable G-protein coupled receptor 139 OS=Homo sapiens OX=9606 GN=GPR139 PE=1 SV=1
>sp|Q8IX95|CTGE3_HUMAN Putative cTAGE family member 3 OS=Homo sapiens OX=9606 GN=CTAGE3P PE=5 SV=1
>sp|Q8WWL2|SPIR2_HUMAN Protein spire homolog 2 OS=Homo sapiens OX=9606 GN=SPIRE2 PE=1 SV=3
>sp|Q9BS86|ZPBP1_HUMAN Zona pellucida-binding protein 1 OS=Homo sapiens OX=9606 GN=ZPBP PE=2 SV=1
>sp|Q9NVJ2|ARL8B_HUMAN ADP-ribosylation factor-like protein 8B OS=Homo sapiens OX=9606 GN=ARL8B PE=1 SV=1
>sp|W5XKT8|SACA6_HUMAN Sperm acrosome membrane-associated protein 6 OS=Homo sapiens OX=9606 GN=SPACA6 PE=1 SV=2
# FragPipe v20.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\user\\Angel\\NativeTrypsin\\2022-09-21-decoys-reviewed-contam-UP000005640.fas

crystalc.run-crystalc=true
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
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=true
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
fragpipe-config.bin-ionquant=D\:\\software\\msfragger\\FragPipe-jre-20.0\\fragpipe\\tools\\IonQuant-1.10.27.jar
fragpipe-config.bin-msfragger=D\:\\software\\msfragger\\FragPipe-jre-20.0\\fragpipe\\tools\\MSFragger-4.1\\MSFragger-4.1.jar
fragpipe-config.bin-philosopher=D\:\\software\\msfragger\\FragPipe-jre-20.0\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=D\:\\software\\Python3.9\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
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.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
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=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,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
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
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=0.01
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=500
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=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
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=trypsin
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,2; 6.020129,KR,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=100
msfragger.write_calibrated_mgf=false
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=
opair.max_glycans=4
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 1000.0 --clevel -2
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 --mapmods --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
phi-report.print-decoys=false
phi-report.prot-level-summary=true
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=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.assign_glycans=true
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
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_minIons=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=all
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
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.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=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=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
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.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
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=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
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.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=-1
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=pool
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\user\\Angel\\Ennio\\IP\\2406_DYNC1H1_GFPpulldown\\GFP_OpenMod\\ClosedMS1Q\\IDtest
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=42

CheckCentroid D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx159G -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw 42 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[15:36:59] Executing Workspace v5.1.0
INFO[15:36:59] Removing workspace
INFO[15:36:59] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\Angel\AppData\Local\Temp\4\f8960d91-df7f-47be-821d-f6662c0d271c INFO[15:36:59] Executing Workspace v5.1.0
INFO[15:36:59] Creating workspace
INFO[15:36:59] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx159G D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\MSFragger-4.1.jar D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\fragger.params D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.raw 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 Server 2012 R2, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 159 GB memory Checking database... Parameter 'analyzer_types' was not supplied. Using default value: all Checking spectral files... D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw: Scans = 49210; ITMS: false; FTMS: false; Isolation sizes = [1.4] D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.raw: Scans = 72857; ITMS: false; FTMS: false; Isolation sizes = [1.4] ***FIRST SEARCH**** Parameters: num_threads = 42 database_name = D:\user\Angel\NativeTrypsin\2022-09-21-decoys-reviewed-contam-UP000005640.fas decoyprefix = 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 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 = pepxml_pin 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 = 500.0 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 = 100 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all analyzer_types = all group_variable = 0 require_precursor = 0 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 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 add_topN_complementary = 0 Selected fragment index width 0.10 Da. 318610884 fragments to be searched in 1 slices (4.75 GB total) Operating on slice 1 of 1: Fragment index slice generated in 9.84 s

  1. B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw 105.5 s | deisotoping 1.8 s [progress: 49173/49173 (100%) - 9071 spectra/s] 5.4s | postprocessing 0.5 s
  2. B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.raw 185.1 s | deisotoping 2.6 s [progress: 72842/72842 (100%) - 36403 spectra/s] 2.0s | postprocessing 0.5 s ***FIRST SEARCH DONE IN 5.578 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 3.45 2.72 -0.05 0.73 -0.34 1.77 -0.05 1.76
002 2.57 1.72 -0.04 0.64 -0.45 1.49 -0.06 1.47
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 10452 10489 10314 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 12356 11808 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 12896
------- -------
------- -------
Rm P. 0
------- -------
Count 12747
------- -------

New fragment_mass_tolerance = 7.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 New precursor_true_tolerance = 3.000000 PPM ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 4.605 MIN*****

****MAIN SEARCH**** Checking database... Parameter 'use_detailed_offsets' was not supplied. Using default value: 0 Parameter 'analyzer_types' was not supplied. Using default value: all Parameters: num_threads = 42 database_name = D:\user\Angel\NativeTrypsin\2022-09-21-decoys-reviewed-contam-UP000005640.fas decoyprefix = rev precursor_mass_lower = -150.0 precursor_mass_upper = 500.0 precursor_mass_units = 0 data_type = 0 precursor_true_tolerance = 3.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 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 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = CORRECTED localize_delta_mass = 1 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y 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 = pepxml_pin 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 = 500.0 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 = 0 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 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 add_topN_complementary = 0 Selected fragment index width 0.01 Da. 637221768 fragments to be searched in 1 slices (9.50 GB total) Operating on slice 1 of 1: Fragment index slice generated in 18.59 s

  1. B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.mzBIN_calibrated 5.4 s [progress: 49173/49173 (100%) - 303 spectra/s] 162.1s | remapping alternative proteins and postprocessing 12.7 s
  2. B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.mzBIN_calibrated 5.9 s [progress: 72842/72842 (100%) - 253 spectra/s] 288.3s | remapping alternative proteins and postprocessing 17.2 s MAIN SEARCH DONE IN 8.672 MIN

***TOTAL TIME 18.855 MIN**** Process 'MSFragger' finished, exit code: 0 Crystal-C [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest] D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\ext\thermo" -Xmx159G -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\original-crystalc-1.5.2.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\crystalc-0-B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML.params D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\IDtest\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML 15:56:05.714 [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. 15:56:05.718 [pool-2-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.base/java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:319) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:261) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) 15:56:05.720 [pool-2-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Batmass-IO Thermo stdio (1.4.0.0) By Nesvizhskii Lab, University of Michigan

Usage: BatmassIoThermoServer[.exe] stdinout [options] Options: parseIndex parseRange2 getInstrumentInfo

15:56:11.731 [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. 15:56:11.731 [pool-3-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.base/java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:319) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:261) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) 15:56:11.732 [pool-3-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Batmass-IO Thermo stdio (1.4.0.0) By Nesvizhskii Lab, University of Michigan

Usage: BatmassIoThermoServer[.exe] stdinout [options] Options: parseIndex parseRange2 getInstrumentInfo

15:56:17.743 [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. 15:56:17.743 [pool-4-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.base/java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:319) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:261) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) 15:56:17.744 [pool-4-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Batmass-IO Thermo stdio (1.4.0.0) By Nesvizhskii Lab, University of Michigan

Usage: BatmassIoThermoServer[.exe] stdinout [options] Options: parseIndex parseRange2 getInstrumentInfo

15:56:23.755 [main] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout. 15:56:23.755 [pool-5-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream java.lang.InterruptedException: sleep interrupted at java.base/java.lang.Thread.sleep(Native Method) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:319) at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:261) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) 15:56:23.756 [pool-5-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Batmass-IO Thermo stdio (1.4.0.0) By Nesvizhskii Lab, University of Michigan

Usage: BatmassIoThermoServer[.exe] stdinout [options] Options: parseIndex parseRange2 getInstrumentInfo

Exception in thread "main" umich.ms.fileio.exceptions.FileParsingException: Could not get ThermoIndex at umich.ms.fileio.filetypes.thermo.ThermoRawFile.parseIndex(ThermoRawFile.java:333) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.fetchIndex(ThermoRawFile.java:309) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.parse(ThermoRawFile.java:607) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:807) at umich.ms.datatypes.scancollection.impl.ScanCollectionDefault.loadData(ScanCollectionDefault.java:791) at crystalc.p_ReadData.LoadRawFile(p_ReadData.java:196) at crystalc.Run.ProcessPepXML(Run.java:84) at crystalc.Run.main(Run.java:66) Process 'Crystal-C' finished, exit code: 1 Process returned non-zero exit code, stopping

Cancelling 12 remaining tasks

System OS: Windows Server 2012 R2, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: 6.3.9600

Version info:
FragPipe version 20.0
MSFragger version 4.1
IonQuant version 1.10.27
Philosopher version 5.1.0

LCMS files:
  Experiment/Group: GFP
  - D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw DDA
  - D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.raw  DDA

25 commands to execute:
CheckCentroid
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx160G -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw 42
WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\Angel\AppData\Local\Temp\4\7c91061b-fb68-4211-a4cf-39f0f0a8e32d
WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\Angel\AppData\Local\Temp\4\a5445627-28c2-4698-991c-a6778614cce6
MSFragger [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx160G D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\MSFragger-4.1.jar D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\fragger.params D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.raw D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.raw
MSFragger move pepxml
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/software/msfragger/FragPipe-jre-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pepXML
MSFragger move pin
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/software/msfragger/FragPipe-jre-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pin D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pin
MSFragger move pepxml
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/software/msfragger/FragPipe-jre-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pepXML D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pepXML
MSFragger move pin
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;/D:/software/msfragger/FragPipe-jre-20.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pin D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pin
Percolator [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 42 --results-psms B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_percolator_target_psms.tsv --decoy-results-psms B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pin
Percolator [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 42 --results-psms B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_percolator_target_psms.tsv --decoy-results-psms B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pin
Percolator: Convert to pepxml [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP.pin B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_percolator_target_psms.tsv B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_percolator_decoy_psms.tsv interact-B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP DDA 0.5 D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_uncalibrated.mzML
Percolator: Delete temp
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_percolator_target_psms.tsv
Percolator: Delete temp
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240613_08_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_percolator_decoy_psms.tsv
Percolator: Convert to pepxml [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x.pin B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_percolator_target_psms.tsv B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_percolator_decoy_psms.tsv interact-B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x DDA 0.5 D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_uncalibrated.mzML
Percolator: Delete temp
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_percolator_target_psms.tsv
Percolator: Delete temp
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp D:\software\msfragger\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP\B240614_01_Astral_ZC_QC_47_Ennio_DYNC1H1pulldown-GFP_3x_percolator_decoy_psms.tsv
ProteinProphet [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate D:\user\Angel\NativeTrypsin\2022-09-21-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP --protxml D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\combined.prot.xml --razor
PhilosopherReport [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
WorkspaceClean [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
IonQuant [Work dir: D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
D:\software\msfragger\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx160G -Dlibs.bruker.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\ext\bruker" -Dlibs.thermo.dir="D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\MSFragger-4.1\ext\thermo" -cp "D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\jfreechart-1.5.3.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar;D:\software\msfragger\FragPipe-jre-20.0\fragpipe\tools\IonQuant-1.10.27.jar" ionquant.IonQuant --threads 42 --ionmobility 0 --minexps 1 --mbr 0 --maxlfq 0 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 0 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\filelist_ionquant.txt --modlist D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\modmasses_ionquant.txt

Execution order:

Cmd: [START], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [CheckCentroid], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [WorkspaceCleanInit], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [WorkspaceCleanInit], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
Cmd: [MSFragger], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [Percolator], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [ProteinProphet], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [PhilosopherDbAnnotate], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [PhilosopherFilter], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [PhilosopherReport], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [WorkspaceClean], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]
Cmd: [WorkspaceClean], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q\GFP]
Cmd: [IonQuant], Work dir: [D:\user\Angel\Ennio\IP\2406_DYNC1H1_GFPpulldown\GFP_OpenMod\ClosedMS1Q]

~~~~~~Sample of D:\user\Angel\NativeTrypsin\2022-09-21-decoys-reviewed-contam-UP000005640.fas~~~~~~~
>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries GN=KRT15 PE=2 SV=1
>rev_sp|O43602|DCX_HUMAN Neuronal migration protein doublecortin OS=Homo sapiens OX=9606 GN=DCX PE=1 SV=4
>rev_sp|P0DMW4|SIL2A_HUMAN Small integral membrane protein 10-like protein 2A OS=Homo sapiens OX=9606 GN=SMIM10L2A PE=4 SV=1
>rev_sp|P49795|RGS19_HUMAN Regulator of G-protein signaling 19 OS=Homo sapiens OX=9606 GN=RGS19 PE=1 SV=1
>rev_sp|Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 OS=Homo sapiens OX=9606 GN=DYNC1H1 PE=1 SV=5
>rev_sp|Q69YW2|STUM_HUMAN Protein stum homolog OS=Homo sapiens OX=9606 GN=STUM PE=1 SV=1
>rev_sp|Q8IWP9|CC28A_HUMAN Coiled-coil domain-containing protein 28A OS=Homo sapiens OX=9606 GN=CCDC28A PE=1 SV=1
>rev_sp|Q8WVS4|DC2I1_HUMAN Cytoplasmic dynein 2 intermediate chain 1 OS=Homo sapiens OX=9606 GN=DYNC2I1 PE=1 SV=3
>rev_sp|Q9BRK3|MXRA8_HUMAN Matrix remodeling-associated protein 8 OS=Homo sapiens OX=9606 GN=MXRA8 PE=1 SV=1
>rev_sp|Q9NUS5|AP5S1_HUMAN AP-5 complex subunit sigma-1 OS=Homo sapiens OX=9606 GN=AP5S1 PE=1 SV=1
>rev_sp|Q9Y6N8|CAD10_HUMAN Cadherin-10 OS=Homo sapiens OX=9606 GN=CDH10 PE=1 SV=2
>sp|O43747|AP1G1_HUMAN AP-1 complex subunit gamma-1 OS=Homo sapiens OX=9606 GN=AP1G1 PE=1 SV=5
>sp|P0DPD7|EFMT4_HUMAN EEF1A lysine methyltransferase 4 OS=Homo sapiens OX=9606 GN=EEF1AKMT4 PE=1 SV=1
>sp|P50402|EMD_HUMAN Emerin OS=Homo sapiens OX=9606 GN=EMD PE=1 SV=1
>sp|Q14451|GRB7_HUMAN Growth factor receptor-bound protein 7 OS=Homo sapiens OX=9606 GN=GRB7 PE=1 SV=2
>sp|Q6DWJ6|GP139_HUMAN Probable G-protein coupled receptor 139 OS=Homo sapiens OX=9606 GN=GPR139 PE=1 SV=1
>sp|Q8IX95|CTGE3_HUMAN Putative cTAGE family member 3 OS=Homo sapiens OX=9606 GN=CTAGE3P PE=5 SV=1
>sp|Q8WWL2|SPIR2_HUMAN Protein spire homolog 2 OS=Homo sapiens OX=9606 GN=SPIRE2 PE=1 SV=3
>sp|Q9BS86|ZPBP1_HUMAN Zona pellucida-binding protein 1 OS=Homo sapiens OX=9606 GN=ZPBP PE=2 SV=1
>sp|Q9NVJ2|ARL8B_HUMAN ADP-ribosylation factor-like protein 8B OS=Homo sapiens OX=9606 GN=ARL8B PE=1 SV=1
>sp|W5XKT8|SACA6_HUMAN Sperm acrosome membrane-associated protein 6 OS=Homo sapiens OX=9606 GN=SPACA6 PE=1 SV=2

# FragPipe v20.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=D\:\\user\\Angel\\NativeTrypsin\\2022-09-21-decoys-reviewed-contam-UP000005640.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
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=true
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
fragpipe-config.bin-ionquant=D\:\\software\\msfragger\\FragPipe-jre-20.0\\fragpipe\\tools\\IonQuant-1.10.27.jar
fragpipe-config.bin-msfragger=D\:\\software\\msfragger\\FragPipe-jre-20.0\\fragpipe\\tools\\MSFragger-4.1\\MSFragger-4.1.jar
fragpipe-config.bin-philosopher=D\:\\software\\msfragger\\FragPipe-jre-20.0\\fragpipe\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=D\:\\software\\Python3.9\\python.exe
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=0
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=0
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
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.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
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=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=10
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=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
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=0.01
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=500
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=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
msfragger.override_charge=false
msfragger.precursor_mass_lower=-5
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=5
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_
fcyu commented 1 week ago

The log files were truncated by GitHub. Could you go to https://github.com/Nesvilab/FragPipe/issues/1637 and upload the files there?

Thanks,

Fengchao

fcyu commented 1 week ago

Actually, no need to re-upload the log files. The untruncated one already tells the reason. You were still using the old version of FragPipe. Could you upgrade FragPipe?

Version info:
FragPipe version 20.0
MSFragger version 4.1
IonQuant version 1.10.27
Philosopher version 5.1.0

Also not that when you upgrade FragPipe, remember to put it in a new folder where there is no old version of FragPipe.

Best,

Fengchao