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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Something unexpected happened (TMtannotationValidationExpection) #407

Closed clin888 closed 3 years ago

clin888 commented 3 years ago
fcyu commented 3 years ago

Can you send us your log?

On Fri, Jul 23, 2021 at 1:14 AM clin888 @.***> wrote:

-

Describe the issue or question:

with fragpipe v15, quant label can not be recognized in TMT-integrator No known quant label types match labeling reagent names in given annotations.

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.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/407, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABU27W7BO7VVWW4GZUT6AQ3TZD3BPANCNFSM5A3KA7PA .

-- Dr. Fengchao Yu Research Investigator University of Michigan

clin888 commented 3 years ago

Hi,

Enclosed are three log files. The raw data is download from https://cptac-data-portal.georgetown.edu/study-summary/S060 and converted to mzML format before fragpipe. CPTAC Data Portalhttps://cptac-data-portal.georgetown.edu/study-summary/S060 CPTAC Data Portal cptac-data-portal.georgetown.edu

Thank you so much,

Chenwei

From: Fengchao @.> Sent: Friday, July 23, 2021 5:43 AM To: Nesvilab/FragPipe @.> Cc: Lin PhD, ChenWei @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Something unexpected happened (TMtannotationValidationExpection) (#407)

Can you send us your log?

On Fri, Jul 23, 2021 at 1:14 AM clin888 @.***> wrote:

-

Describe the issue or question:

with fragpipe v15, quant label can not be recognized in TMT-integrator No known quant label types match labeling reagent names in given annotations.

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.)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/407https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_407-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=0-FT85VGHoTJEmQUh3K-WaCVE9aJ3LcM1zrF97pAMNc&s=pKyMEOzgbgNVQ98k6Xi8yIJcrWlLPFrLHDOND-akCOA&e=, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABU27W7BO7VVWW4GZUT6AQ3TZD3BPANCNFSM5A3KA7PAhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABU27W7BO7VVWW4GZUT6AQ3TZD3BPANCNFSM5A3KA7PA-253E&d=DwQFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=0-FT85VGHoTJEmQUh3K-WaCVE9aJ3LcM1zrF97pAMNc&s=AFuDNxFkW44sui7jrrGEkfkFfwaQoEZuBAxNLxG068s&e= .

-- Dr. Fengchao Yu Research Investigator University of Michigan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_407-23issuecomment-2D885611267&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=0-FT85VGHoTJEmQUh3K-WaCVE9aJ3LcM1zrF97pAMNc&s=L2T98G9cPfSCnGmMXokhc8QpjSTHytsMNVpweg5r010&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AK6B7T4OIF6SIZCVPWV2VNTTZFPVPANCNFSM5A3KA7PA&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=0-FT85VGHoTJEmQUh3K-WaCVE9aJ3LcM1zrF97pAMNc&s=2FLNo6AFGUukgBBJbllAKdPCGINVF31IXYySFC6ym5Y&e=.

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 15.0 MSFragger version 3.3 Philosopher version 4.0.0 (build 1626989421)

LCMS files: Experiment/Group: test

31 commands to execute: WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx100G C:\FragPipe\MSFragger-3.3\MSFragger-3.3\MSFragger-3.3.jar C:\frozen_OV_IMAC_data\output5\fragger.params C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML PeptideProphet [Work dir: C:\frozen_OV_IMACdata\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\bluepc\Desktop\2020-05-21-decoys-contam-UP000005640_Human_120119.fasta --combine 01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML Rewrite pepxml [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib/ com.dmtavt.fragpipe.util.RewritePepxml C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML Delay C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib/ com.dmtavt.fragpipe.util.DoNothing 1000 PtmProphet [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe ptmprophet --keepold --static --fragppmtol 15 --em 1 --nions b --mods STY:79.966331,M:15.9949 --minprob 0.5 --maxthreads 6 interact.pep.xml ProteinProphet [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml PhilosopherDbAnnotate [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe database --annotate C:\Users\bluepc\Desktop\2020-05-21-decoys-contam-UP000005640_Human120119.fasta --prefix rev PhilosopherDbAnnotate [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe database --annotate C:\Users\bluepc\Desktop\2020-05-21-decoys-contam-UP000005640_Human120119.fasta --prefix rev PhilosopherFilter [Work dir: C:\frozen_OV_IMACdata\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe filter --sequential --razor --picked --prot 0.01 --mapmods --tag rev --pepxml C:\frozen_OV_IMAC_data\output5\test --protxml C:\frozen_OV_IMAC_data\output5\combined.prot.xml FreeQuant [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\frozen_OV_IMAC_data\test Quant (Isobaric) [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe labelquant --tol 20 --level 2 --plex 10 --annot C:\frozen_OV_IMAC_data\test\annotation.txt --brand tmt --dir C:\frozen_OV_IMAC_data\test PhilosopherReport [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe report TmtIntegrator [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -Xmx100G -cp "C:\FragPipe\FragPipe-15.0\tools\tmt-integrator-2.4.0.jar" TMTIntegrator C:\frozen_OV_IMAC_data\output5\tmt-integrator-conf.yml C:\frozen_OV_IMAC_data\output5\test\psm.tsv WorkspaceClean [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\frozen_OV_IMAC_data\output5\test]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [MSFragger], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [PeptideProphet], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [PtmProphet], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [ProteinProphet], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [PhilosopherFilter], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [FreeQuant], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [Quant (Isobaric)], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [PhilosopherReport], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [TmtIntegrator], Work dir: [C:\frozen_OV_IMAC_data\output5]
    Cmd: [WorkspaceClean], Work dir: [C:\frozen_OV_IMAC_data\output5\test]
    Cmd: [WorkspaceClean], Work dir: [C:\frozen_OV_IMAC_data\output5]

# FragPipe v15.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.2
ExportPrecursorPeak=false
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=true
SE.MassDefectOffset=0.1
SE.NoMissedScan=1
SE.SN=1.1
Table.editor=229.16293
crystalc.correct_isotope_error=false
crystalc.isotope_number=3
crystalc.max-charge=6
crystalc.precursor_isolation_window=0.7
crystalc.precursor_mass=20
crystalc.run-crystalc=false
database.db-path=C\:\\Users\\bluepc\\Desktop\\2020-05-21-decoys-contam-UP000005640_Human_120119.fasta
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\FragPipe\\MSFragger-3.3\\MSFragger-3.3\\MSFragger-3.3.jar
fragpipe-config.bin-philosopher=C\:\\FragPipe\\FragPipe-15.0\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ANACONDA\\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.label=
ionquant.light=
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
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=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deltamass_allowed_residues=ST
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.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
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=10000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=131.5
msfragger.misc.fragger.clear-mz-lo=125.5
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=200
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
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
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=15
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 229.162932,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021460,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 229.162932,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,false,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,false,1; 79.966331,STY,true,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 229.162932,n^,false,1; 229.162930,S,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --picked --prot 0.01 --mapmods
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
phi-report.write-mzid=false
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=--keepold --static --fragppmtol 15 --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
ptmprophet.run-ptmprophet=true
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.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
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=
ptmshepherd.localization_background=4
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.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
run-diaumpire=false
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=10
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=-1
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0.9
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.5
tmtintegrator.min_percent=0.025
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=0.75
tmtintegrator.mod_tag=S[167],T[181],Y[243]
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=true
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=C\:\\frozen_OV_IMAC_data\\output5
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=100
workflow.threads=6

WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[21:57:06] Executing Workspace v4.0.0
INFO[21:57:06] Removing workspace
INFO[21:57:07] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[21:57:09] Executing Workspace v4.0.0
INFO[21:57:09] Creating workspace
INFO[21:57:09] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[21:57:11] Executing Workspace v4.0.0
INFO[21:57:11] Removing workspace
INFO[21:57:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[21:57:13] Executing Workspace v4.0.0
INFO[21:57:13] Creating workspace
INFO[21:57:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx100G C:\FragPipe\MSFragger-3.3\MSFragger-3.3\MSFragger-3.3.jar C:\frozen_OV_IMAC_data\output5\fragger.params C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML MSFragger version MSFragger-3.3 Batmass-IO version 1.23.4 [main] ERROR umich.ms.fileio.filetypes.bruker.Timsdata - JNA could not load native Bruker library [main] ERROR umich.ms.fileio.filetypes.bruker.Timsdata - The ext folder with timsdata-2-8-7-1.dll (Win) or libtimsdata-2-8-7-1.so (Linux) is needed. If you are using an old ext folder, please upgrade. timsdata library version (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 100 GB memory Checking database... Parameter 'use_all_mods_in_first_search' was not supplied. Using default value: 0 Checking spectral files... C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML: Scans = 44190 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML: Scans = 43577 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML: Scans = 44650 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML: Scans = 43938 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML: Scans = 43913 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML: Scans = 45114 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML: Scans = 43594 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML: Scans = 43554 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML: Scans = 43940 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML: Scans = 42745 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML: Scans = 44471 C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML: Scans = 44991 ***FIRST SEARCH**** Parameters: num_threads = 6 database_name = C:\Users\bluepc\Desktop\2020-05-21-decoys-contam-UP000005640_Human_120119.fasta decoyprefix = rev precursor_mass_lower = -15.0 precursor_mass_upper = 15.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 131.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_03 = 79.966331 STY 2 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 229.162932 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 229.16293 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 Selected fragment index width 0.10 Da. 5493990378 fragments to be searched in 2 slices (81.87 GB total) Operating on slice 1 of 2: Fragment index slice generated in 45.13 s

  1. 01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML 3.1 s | deisotoping 1.8 s [progress: 44189/44189 (100%) - 9035 spectra/s] 4.9s
  2. 01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML 2.0 s | deisotoping 0.6 s [progress: 42744/42744 (100%) - 11791 spectra/s] 3.6s
  3. 01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML 2.4 s | deisotoping 0.8 s [progress: 43911/43911 (100%) - 11151 spectra/s] 3.9s
  4. 01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML 2.0 s | deisotoping 0.7 s [progress: 44470/44470 (100%) - 11617 spectra/s] 3.8s
  5. 01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML 2.1 s | deisotoping 0.8 s [progress: 45114/45114 (100%) - 10853 spectra/s] 4.2s
  6. 01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML 2.4 s | deisotoping 0.9 s [progress: 44989/44989 (100%) - 10031 spectra/s] 4.5s
  7. 01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML 2.1 s | deisotoping 0.8 s [progress: 44648/44648 (100%) - 10468 spectra/s] 4.3s
  8. 01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML 2.1 s | deisotoping 0.8 s [progress: 43553/43553 (100%) - 10762 spectra/s] 4.0s
  9. 01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML 2.0 s | deisotoping 0.8 s [progress: 43577/43577 (100%) - 10768 spectra/s] 4.0s
  10. 01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML 2.0 s | deisotoping 0.8 s [progress: 43939/43939 (100%) - 10572 spectra/s] 4.2s
  11. 01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML 2.1 s | deisotoping 0.9 s [progress: 43938/43938 (100%) - 10300 spectra/s] 4.3s
  12. 01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML 2.2 s | deisotoping 0.8 s [progress: 43594/43594 (100%) - 11070 spectra/s] 3.9s Operating on slice 2 of 2: Fragment index slice generated in 39.81 s
  13. 01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML 2.0 s | deisotoping 0.7 s [progress: 44189/44189 (100%) - 21265 spectra/s] 2.1s | postprocessing 0.3 s
  14. 01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML 1.9 s | deisotoping 0.6 s [progress: 42744/42744 (100%) - 22981 spectra/s] 1.9s | postprocessing 0.3 s
  15. 01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML 2.0 s | deisotoping 0.7 s [progress: 43911/43911 (100%) - 20980 spectra/s] 2.1s | postprocessing 0.2 s
  16. 01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML 2.0 s | deisotoping 0.7 s [progress: 44470/44470 (100%) - 21400 spectra/s] 2.1s | postprocessing 0.2 s
  17. 01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML 2.1 s | deisotoping 0.8 s [progress: 45114/45114 (100%) - 19640 spectra/s] 2.3s | postprocessing 0.2 s
  18. 01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML 2.1 s | deisotoping 0.8 s [progress: 44989/44989 (100%) - 18699 spectra/s] 2.4s | postprocessing 0.2 s
  19. 01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML 2.1 s | deisotoping 0.8 s [progress: 44648/44648 (100%) - 19438 spectra/s] 2.3s | postprocessing 0.2 s
  20. 01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML 2.1 s | deisotoping 0.8 s [progress: 43553/43553 (100%) - 19905 spectra/s] 2.2s | postprocessing 0.2 s
  21. 01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML 2.0 s | deisotoping 0.8 s [progress: 43577/43577 (100%) - 19916 spectra/s] 2.2s | postprocessing 0.2 s
  22. 01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML 2.0 s | deisotoping 0.8 s [progress: 43939/43939 (100%) - 21145 spectra/s] 2.1s | postprocessing 0.2 s
  23. 01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML 2.0 s | deisotoping 0.9 s [progress: 43938/43938 (100%) - 19128 spectra/s] 2.3s | postprocessing 0.2 s
  24. 01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML 2.0 s | deisotoping 0.8 s [progress: 43594/43594 (100%) - 22151 spectra/s] 2.0s | postprocessing 0.2 s ***FIRST SEARCH DONE IN 4.376 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 -0.45 1.45 -0.08 0.64 -0.92 0.87 -0.04 0.77
002 -0.32 1.50 -0.06 0.64 -0.88 0.94 -0.02 0.79
003 -0.58 1.45 0.03 0.58 -1.11 0.91 0.01 0.79
004 -0.58 1.59 -0.08 0.63 -1.05 0.94 -0.02 0.82
005 -0.90 1.62 -0.15 0.69 -1.41 0.92 -0.03 0.82
006 -0.91 1.65 -0.06 0.68 -1.41 0.93 -0.05 0.83
007 -0.69 1.60 -0.09 0.68 -1.23 0.92 -0.04 0.82
008 -0.70 1.59 -0.11 0.66 -1.19 0.91 -0.02 0.81
009 -0.36 1.62 -0.14 0.64 -0.86 0.93 -0.02 0.80
010 -0.53 1.52 -0.07 0.63 -1.03 0.91 -0.01 0.81
011 -0.51 1.51 -0.13 0.69 -0.97 0.89 -0.03 0.78
012 -0.60 1.61 -0.12 0.69 -1.06 0.90 -0.05 0.79
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 7560 7519 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 7803 7807 7560 skip rest
------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 7905
------- -------
------- -------
Rm P. 1
------- -------
Count 7900
------- -------

New fragment_mass_tolerance = 7 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 14.682 MIN*****

****MAIN SEARCH**** Checking database... Parameter 'use_all_mods_in_first_search' was not supplied. Using default value: 0 Parameters: num_threads = 6 database_name = C:\Users\bluepc\Desktop\2020-05-21-decoys-contam-UP000005640_Human_120119.fasta decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 15.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mgf = 0 isotope_error = 0/1/2/3 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = false delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 10000 output_format = pepxml output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 200.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 deneutralloss = true track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 add_topN_complementary = 0 minimum_peaks = 15 use_topN_peaks = 200 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 1 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 125.5 clear_mz_range_high = 131.5 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.994900 M 3 variable_mod_03 = 79.966331 STY 3 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.000000 add_E_glutamic_acid = 0.000000 add_F_phenylalanine = 0.000000 add_G_glycine = 0.000000 add_H_histidine = 0.000000 add_I_isoleucine = 0.000000 add_J_user_amino_acid = 0.000000 add_K_lysine = 229.162932 add_L_leucine = 0.000000 add_M_methionine = 0.000000 add_N_asparagine = 0.000000 add_Nterm_peptide = 229.16293 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.000000 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.000000 add_Q_glutamine = 0.000000 add_R_arginine = 0.000000 add_S_serine = 0.000000 add_T_threonine = 0.000000 add_U_user_amino_acid = 0.000000 # U = selenocysteine (150.95363 Da) add_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_X_user_amino_acid = 0.000000 add_Y_tyrosine = 0.000000 Selected fragment index width 0.03 Da. 10200802610 fragments to be searched in 2 slices (152.00 GB total) Operating on slice 1 of 2: Fragment index slice generated in 96.82 s

  1. 01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzBIN_calibrated 1.3 s [progress: 44079/44079 (100%) - 4268 spectra/s] 10.3s
  2. 01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzBIN_calibrated 1.3 s [progress: 42643/42643 (100%) - 4526 spectra/s] 9.4s
  3. 01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzBIN_calibrated 1.3 s [progress: 43813/43813 (100%) - 4451 spectra/s] 9.8s
  4. 01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzBIN_calibrated 1.4 s [progress: 44395/44395 (100%) - 4324 spectra/s] 10.3s
  5. 01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzBIN_calibrated 1.4 s [progress: 45063/45063 (100%) - 3913 spectra/s] 11.5s
  6. 01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzBIN_calibrated 1.4 s [progress: 44919/44919 (100%) - 3758 spectra/s] 12.0s
  7. 01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzBIN_calibrated 1.4 s [progress: 44596/44596 (100%) - 3873 spectra/s] 11.5s
  8. 01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzBIN_calibrated 1.3 s [progress: 43493/43493 (100%) - 4017 spectra/s] 10.8s
  9. 01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzBIN_calibrated 1.4 s [progress: 43506/43506 (100%) - 3944 spectra/s] 11.0s
  10. 01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzBIN_calibrated 1.4 s [progress: 43864/43864 (100%) - 3783 spectra/s] 11.6s
  11. 01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzBIN_calibrated 1.4 s [progress: 43841/43841 (100%) - 4008 spectra/s] 10.9s
  12. 01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzBIN_calibrated 1.4 s [progress: 43486/43486 (100%) - 4005 spectra/s] 10.9s Operating on slice 2 of 2: Fragment index slice generated in 81.38 s
  13. 01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzBIN_calibrated 1.3 s [progress: 44079/44079 (100%) - 8928 spectra/s] 4.9s | postprocessing 4.3 s
  14. 01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzBIN_calibrated 1.3 s [progress: 42643/42643 (100%) - 9747 spectra/s] 4.4s | postprocessing 3.7 s
  15. 01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzBIN_calibrated 1.3 s [progress: 43813/43813 (100%) - 9103 spectra/s] 4.8s | postprocessing 3.4 s
  16. 01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzBIN_calibrated 1.3 s [progress: 44395/44395 (100%) - 8823 spectra/s] 5.0s | postprocessing 3.4 s
  17. 01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzBIN_calibrated 1.4 s [progress: 45063/45063 (100%) - 8384 spectra/s] 5.4s | postprocessing 3.7 s
  18. 01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzBIN_calibrated 1.4 s [progress: 44919/44919 (100%) - 8053 spectra/s] 5.6s | postprocessing 3.8 s
  19. 01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzBIN_calibrated 1.4 s [progress: 44596/44596 (100%) - 7995 spectra/s] 5.6s | postprocessing 3.7 s
  20. 01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzBIN_calibrated 1.3 s [progress: 43493/43493 (100%) - 8838 spectra/s] 4.9s | postprocessing 3.5 s
  21. 01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzBIN_calibrated 1.3 s [progress: 43506/43506 (100%) - 8463 spectra/s] 5.1s | postprocessing 3.5 s
  22. 01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzBIN_calibrated 1.3 s [progress: 43864/43864 (100%) - 8912 spectra/s] 4.9s | postprocessing 3.6 s
  23. 01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzBIN_calibrated 1.4 s [progress: 43841/43841 (100%) - 8902 spectra/s] 4.9s | postprocessing 3.5 s
  24. 01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzBIN_calibrated 1.3 s [progress: 43486/43486 (100%) - 9468 spectra/s] 4.6s | postprocessing 3.5 s MAIN SEARCH DONE IN 7.751 MIN

***TOTAL TIME 26.809 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pepxml C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib\fragpipe-15.0.jar;/C:/FragPipe/FragPipe-15.0/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 PeptideProphet [Work dir: C:\frozen_OV_IMACdata\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\bluepc\Desktop\2020-05-21-decoys-contam-UP000005640_Human_120119.fasta --combine 01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML 01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML INFO[22:24:14] Executing PeptideProphet v4.0.0
file 1: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.pepXML file 2: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.pepXML file 3: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.pepXML file 4: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.pepXML file 5: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.pepXML file 6: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.pepXML file 7: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.pepXML file 8: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.pepXML file 9: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.pepXML file 10: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.pepXML file 11: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.pepXML file 12: C:\frozen_OV_IMAC_data\output5\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.pepXML processed altogether 289766 results INFO: Results written to file: C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml

using Accurate Mass Bins using PPM mass difference Using Decoy Label "rev_". Decoy Probabilities will be reported. Using non-parametric distributions (X! Tandem) (using Tandem's expectation score for modeling) adding ACCMASS mixture distribution using search_offsets in ACCMASS mixture distr: 0 init with X! Tandem stricttrypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 62419 2+, 130363 3+, 68923 4+, 23036 5+, 5025 6+, and 0 7+ spectra. Found 95493 Decoys, and 194273 Non-Decoys 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 (7+). model complete after 28 iterations Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib/ com.dmtavt.fragpipe.util.RewritePepxml C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f12.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f09.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f02.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f08.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f06.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f04.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f07.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f10.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f11.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f01.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f03.mzML C:\frozen_OV_IMAC_data\test\01CPTAC_BCprospective_P_BI_20160927_BL_f05.mzML INFO[22:42:44] Done
Fixing pepxml: C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml Writing output to: C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml7943412345682297468.temp-rewrite Deleting file: C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml Moving rewritten file to original location: [C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml7943412345682297468.temp-rewrite] -> [C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml] Process 'Rewrite pepxml' finished, exit code: 0 Delay C:\FragPipe\FragPipe-15.0\jre\bin\java.exe -cp C:\FragPipe\FragPipe-15.0\lib/ com.dmtavt.fragpipe.util.DoNothing 1000 Sleeping for 1000ms Process 'Delay' finished, exit code: 0 PtmProphet [Work dir: C:\frozen_OV_IMAC_data\output5\test] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe ptmprophet --keepold --static --fragppmtol 15 --em 1 --nions b --mods STY:79.966331,M:15.9949 --minprob 0.5 --maxthreads 6 interact.pep.xml INFO[22:42:51] Executing PTMProphet v4.0.0
INFO: Writing file interact.pep.xml.tmp.a10064 ...

Creating 6 threads Wait for threads to finish ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Using statically set 15 PPM tolerance ... ​ INFO: processed 99000/99030 spectrum_queries
INFO: done ... INFO: Computing EM Models ... Iterating PTM Model: ....5....done INFO: done ... INFO: done ...

Creating 6 threads Wait for threads to finish ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... INFO: Reading file interact.pep.xml ... ​ INFO: written 99000/99030 spectrum_queries
INFO: done ... INFO: Writing file interact.mod.pep.xml ... INFO: done ... INFO[22:58:49] Done
Process 'PtmProphet' finished, exit code: 0 ProteinProphet [Work dir: C:\frozen_OV_IMAC_data\output5] C:\FragPipe\FragPipe-15.0\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\frozen_OV_IMAC_data\output5\test\interact.pep.xml INFO[22:58:51] Executing ProteinProphet v4.0.0
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) (using degen pep info) Reading in C:/frozen_OV_IMAC_data/output5/test/interact.pep.xml... ...read in 0 1+, 21954 2+, 51730 3+, 20208 4+, 4526 5+, 608 6+, 0 7+ spectra with min prob 0.05

Initializing 73078 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database c:/Users/bluepc/Desktop/2020-05-21-decoys-contam-UP000005640_Human_120119.fasta .........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000 .........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000 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fcyu commented 3 years ago

Your log was truncated by github. Can you zip it and send it to us?

Thanks,

Fengchao

clin888 commented 3 years ago

Thank you so much,

Chenwei

From: Fengchao @.> Sent: Friday, July 23, 2021 9:32 AM To: Nesvilab/FragPipe @.> Cc: Lin PhD, ChenWei @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Something unexpected happened (TMtannotationValidationExpection) (#407)

Your log was truncated by github. Can you zip it and send it to us?

Thanks,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_407-23issuecomment-2D885758323&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2Cdo9CbFPBavciYYPU1khCP-CvARxpcIA2m-N5N_N-E&s=MGxwgrh9eyPWFTQMjw7luIte-CN44qdmv4LG2vHyONk&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AK6B7T5CFLG5T7O5PICDARTTZGKQ3ANCNFSM5A3KA7PA&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2Cdo9CbFPBavciYYPU1khCP-CvARxpcIA2m-N5N_N-E&s=c5dGZqaGxtvKhLKwTHEfgdwhngnfZgiFRRAStFC-Xr0&e=.

fcyu commented 3 years ago

Still no log file. OK, can you email it to yufe@umich.edu?

Thanks,

Fengchao

fcyu commented 3 years ago

Hi Chenwei,

Your logs are well received. I put them here as references.

I think upgrading FragPipe to 16.0 should solve your problem.

Best,

Fengchao

log_072321.zip

clin888 commented 3 years ago

Hi

Thank you for your suggestion. I will update fragpipe.

--Chenwei

From: Fengchao @.> Sent: Friday, July 23, 2021 9:50 AM To: Nesvilab/FragPipe @.> Cc: Lin PhD, ChenWei @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Something unexpected happened (TMtannotationValidationExpection) (#407)

Hi Chenwei,

Your logs are well received. I put them here as references.

I think upgrading FragPipe to 16.0 should solve your problem.

Best,

Fengchao

log_072321.ziphttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_files_6870140_log-5F072321.zip&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2o6HlG1SYmA1aR05iLJR7a_QVoSCSXYDIViUFiAGuPI&s=h1_jayZlm3nRX4twrV_wKhUIuBCevoeyn1SJ4n0r6UI&e=

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_407-23issuecomment-2D885768725&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2o6HlG1SYmA1aR05iLJR7a_QVoSCSXYDIViUFiAGuPI&s=udLL1Bq_8b5fJ7378vojoDHfAMzz5TkvvYw_rPQfm0k&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AK6B7T5G5DG6XKE7T5RINETTZGMW5ANCNFSM5A3KA7PA&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2o6HlG1SYmA1aR05iLJR7a_QVoSCSXYDIViUFiAGuPI&s=UJxw37gQgS67yiNu1lM7x7Hz5I-xzU-s2hAZ8kEg8Yw&e=.

clin888 commented 3 years ago

Hi,

I failed to use fragpipe v16 on window 10. It keeps to initial many new fragpipe and force me to kill the process...

Thanks,

Chenwei

From: Fengchao @.> Sent: Friday, July 23, 2021 9:50 AM To: Nesvilab/FragPipe @.> Cc: Lin PhD, ChenWei @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Something unexpected happened (TMtannotationValidationExpection) (#407)

Hi Chenwei,

Your logs are well received. I put them here as references.

I think upgrading FragPipe to 16.0 should solve your problem.

Best,

Fengchao

log_072321.ziphttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_files_6870140_log-5F072321.zip&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2o6HlG1SYmA1aR05iLJR7a_QVoSCSXYDIViUFiAGuPI&s=h1_jayZlm3nRX4twrV_wKhUIuBCevoeyn1SJ4n0r6UI&e=

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Nesvilab_FragPipe_issues_407-23issuecomment-2D885768725&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2o6HlG1SYmA1aR05iLJR7a_QVoSCSXYDIViUFiAGuPI&s=udLL1Bq_8b5fJ7378vojoDHfAMzz5TkvvYw_rPQfm0k&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AK6B7T5G5DG6XKE7T5RINETTZGMW5ANCNFSM5A3KA7PA&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=80c1VYP2YFX8cnwJGnQtrA&m=2o6HlG1SYmA1aR05iLJR7a_QVoSCSXYDIViUFiAGuPI&s=UJxw37gQgS67yiNu1lM7x7Hz5I-xzU-s2hAZ8kEg8Yw&e=.

fcyu commented 3 years ago

I am sorry but it sounds weird. I guess you need to troubleshoot your computer.

Good luck,

Fengchao

fcyu commented 3 years ago

The users create a new issue regarding FragPipe "keeps to initial many new fragpipe and force me to kill the process" (https://github.com/Nesvilab/FragPipe/issues/410). Close this one.