Messed up files broke FragPipe

ProteomicsPSG commented 10 months ago

Describe the issue or question: I recently updated the whole FragPipe workflow ( all tools updated for V21.0, 8jan 2024). Standaard DDA search runs repeatedly into error message after PeptideProphet. I tried several datasets.. same error. No idea how to solve this..

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: N/A Version info: FragPipe version 21.0 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0

... INFO[16:14:28] Done
Process 'PeptideProphet' finished, exit code: 0 Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5] ..... ...... Fixing pepxml: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\interact.pep.xml Didn't find correct mapping for raw file path in pepxml: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5/G4Gr_SDS_D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5/G4Gr_SDS_A101_5xWriting output to: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\interact.pep.xml1389634936862962355.temp-rewriteA101_5xWriting output to: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\interact.pep.xml1389634936862962355.temp-rewrite Process 'Rewrite pepxml' finished, exit code: 1 Process returned non-zero exit code, stopping

NB please note inconsistency in forward and backward slashes in folder path of output .xml path as generated by the script !!

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.) log_2024-01-08_16-14-31.txt

fcyu commented 10 months ago

Can you uncheck single combined pepxml file per experiment/group and try again?

Best,

Fengchao

ProteomicsPSG commented 10 months ago

Hi Fengchao, I have unchecked it now, ( thought I had it unchecked already before...however, apparently not). Running the validation again, with the existing Db search results... ... results into the same error. New log file attached..

... Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_5.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 PeptideProphet: Delete temp C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_6.pepXML-temp Process 'PeptideProphet: Delete temp' finished, exit code: 0 Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3] C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\interact-G4Gr_SDS_A100_03.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_03_uncalibrated.mzML 16:47:24,445 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] 16:47:24,445 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy] 16:47:24,445 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/MyPrograms/FragPipe21/lib/fragpipe-15.0.jar!/logback.xml] 16:47:24,445 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath. 16:47:24,445 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/MyPrograms/FragPipe21/lib/fragpipe-17.1.jar!/logback.xml] 16:47:24,445 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/MyPrograms/FragPipe21/lib/fragpipe-15.0.jar!/logback.xml] 16:47:24,445 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/MyPrograms/FragPipe21/lib/fragpipe-16.0.jar!/logback.xml] 16:47:24,445 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:/C:/MyPrograms/FragPipe21/lib/fragpipe-21.0.jar!/logback.xml] 16:47:24,460 |-INFO in @.**@.> - URL [jar:file:/C:/MyPrograms/FragPipe21/lib/fragpipe-15.0.jar!/logback.xml] is not of type file 16:47:24,570 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set 16:47:24,570 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] 16:47:24,585 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [STDOUT] 16:47:24,585 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property 16:47:24,632 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [com.dmtavt.fragpipe.FragpipeLoader] to INFO 16:47:24,632 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [com.dmtavt.fragpipe.api.Bus] to INFO 16:47:24,632 |-INFO in ch.qos.logback.classic.joran.action.LoggerAction - Setting level of logger [com.dmtavt.fragpipe.FragpipeUpdater] to INFO 16:47:24,632 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO 16:47:24,632 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [STDOUT] to Logger[ROOT] 16:47:24,648 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration. 16:47:24,648 |-INFO in @.**@.> - Registering current configuration as safe fallback point

Fixing pepxml: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\interact-G4Gr_SDS_A100_03.pep.xml Writing output to: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\interact-G4Gr_SDS_A100_03.pep.xml14532116914673556305.temp-rewrite Didn't find correct mapping for raw file path in pepxml: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3/G4Gr_SDS_A100_03Process 'Rewrite pepxml' finished, exit code: 1 Process returned non-zero exit code, stopping

Cancelling 35 remaining tasks

With best regards,
Twan America
Proteomics facility, BU Bioscience
Wageningen Plant Research
Wageningen University & Research
[WUR_RGB_standard]
BU Bioscience (bode 53), Po box 16, 6700AA Wageningen, the Netherlands
Tel.  0317 480891 (desk) or 0317 483050 (mobile)
http://www.pri.wur.nl/UK/
http://www.wur.nl/en/Expertise-Services/Research-Institutes/plant-research/Bioscience.htm
Analyzing proteins in biological materials<http://www.dutchfoodinnovations.com/innovation/analyzing-proteins-in-biological-materials>

From: Fengchao ***@***.***>
Sent: 08 January 2024 16:43
To: Nesvilab/FragPipe ***@***.***>
Cc: America, Twan ***@***.***>; Author ***@***.***>
Subject: Re: [Nesvilab/FragPipe] Rewrite pepXML after PeptideProphet not working. logback.xml issue? (Issue #1401)

Can you uncheck single combined pepxml file per experiment/group and try again?

image.png (view on web)<https://github.com/Nesvilab/FragPipe/assets/6926299/c791301e-0395-4f88-8b82-a94f865250b5>

Best,

Fengchao

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System OS: Windows 10, Architecture: AMD64
Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK
.NET Core Info: N/A

Version info:
FragPipe version 21.0
MSFragger version 4.0
IonQuant version 1.10.12
Philosopher version 5.1.0

LCMS files:
  Experiment/Group: A100_1
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_01.raw DDA
  Experiment/Group: A100_2
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_02.raw DDA
  Experiment/Group: A100_3
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_03.raw DDA
  Experiment/Group: A101_1
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A101_01.raw DDA
  Experiment/Group: A101_3
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A101_03.raw DDA
  Experiment/Group: A101_5
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A101_5x.raw DDA
  Experiment/Group: Amix5_5
  (if "spectral library generation" is enabled, all files will be analyzed together)
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_Amix5_5.raw DDA
  - D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_Amix5_6.raw DDA

76 commands to execute:
CheckCentroid
C:\MyPrograms\FragPipe21\jre\bin\java.exe -Xmx117G -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar;C:\MyPrograms\FragPipe21\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_01.raw 55
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\e42db50b-a67b-4646-a68e-817dd5416825
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\f18943b0-596f-48e7-896c-040b2db43f4c
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\29886699-bdfc-4281-9176-ce1834c35879
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\8ae7af7b-d63c-4146-884e-5fbef1f3219a
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\e7f295f3-bc29-4056-b6e7-b1828b17d7a4
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\9a447ff3-9ede-46c7-accd-bd4775bdca0d
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\05ffd3de-42ee-4a3e-9a31-70d148a39ff0
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\b587a705-9574-40e4-89bd-918f56c138bf
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1\fragpipe-G4Gr_SDS_A100_01.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\39bc6f53-c445-4831-b95f-08f71800c028
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\fragpipe-G4Gr_SDS_A100_02.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\faeb94f2-a6bd-416e-ab97-4cd546f302cf
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\fragpipe-G4Gr_SDS_A100_03.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\163b13f6-d374-4b3d-bba7-219571fcde3d
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1\fragpipe-G4Gr_SDS_A101_01.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\2663bebe-7cfb-466f-900d-795cc8cc4c6c
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3\fragpipe-G4Gr_SDS_A101_03.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\93cd70d9-06a6-457e-896f-2f1015c3cadf
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\fragpipe-G4Gr_SDS_A101_5x.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\70d7c78e-8f6b-43d0-bd0e-e4ef81484253
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_5.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\cfb30a49-9afc-4a26-a340-0b1fe964171e
PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_6.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\f03c9df8-ee93-435d-9568-208177f2dd95
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1\fragpipe-G4Gr_SDS_A100_01.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A100_01.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\fragpipe-G4Gr_SDS_A100_02.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A100_02.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\fragpipe-G4Gr_SDS_A100_03.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A100_03.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1\fragpipe-G4Gr_SDS_A101_01.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A101_01.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3\fragpipe-G4Gr_SDS_A101_03.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A101_03.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\fragpipe-G4Gr_SDS_A101_5x.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A101_5x.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_5.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_Amix5_5.pepXML
PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_6.pepXML-temp]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_Amix5_6.pepXML
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1\fragpipe-G4Gr_SDS_A100_01.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\fragpipe-G4Gr_SDS_A100_02.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\fragpipe-G4Gr_SDS_A100_03.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1\fragpipe-G4Gr_SDS_A101_01.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3\fragpipe-G4Gr_SDS_A101_03.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\fragpipe-G4Gr_SDS_A101_5x.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_5.pepXML-temp
PeptideProphet: Delete temp
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar com.github.chhh.utils.FileDelete D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_6.pepXML-temp
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\interact-G4Gr_SDS_A100_03.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_03_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\interact-G4Gr_SDS_A101_5x.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A101_5x_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1\interact-G4Gr_SDS_A101_01.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A101_01_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\interact-G4Gr_SDS_A100_02.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_02_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\interact-G4Gr_SDS_Amix5_6.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_Amix5_6_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1\interact-G4Gr_SDS_A100_01.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_01_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3\interact-G4Gr_SDS_A101_03.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A101_03_uncalibrated.mzML
Rewrite pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.RewritePepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\interact-G4Gr_SDS_Amix5_5.pep.xml D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_Amix5_5_uncalibrated.mzML
ProteinProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 20 --output combined D:\Fragger_output\G4Gr_SDS_Mix-101_tst\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe database --annotate T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas --prefix rev_
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --razor
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2 --dbbin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --probin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --razor
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3 --dbbin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --probin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --razor
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1 --dbbin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --probin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --razor
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3 --dbbin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --probin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --razor
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5 --dbbin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --probin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --razor
PhilosopherFilter [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5 --dbbin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --protxml D:\Fragger_output\G4Gr_SDS_Mix-101_tst\combined.prot.xml --probin D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1 --razor
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PhilosopherReport [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe report
PTMShepherd [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -Xmx117G -Dlibs.thermo.dir=C:\MyPrograms\FragPipe21\tools\MSFragger-4.0\ext\thermo -cp C:\MyPrograms\FragPipe21\tools\ptmshepherd-2.0.6.jar;C:\MyPrograms\FragPipe21\tools\batmass-io-1.30.0.jar;C:\MyPrograms\FragPipe21\tools\commons-math3-3.6.1.jar;C:\MyPrograms\FragPipe21\tools\hipparchus-1.8\hipparchus-core-1.8.jar;C:\MyPrograms\FragPipe21\tools\hipparchus-1.8\hipparchus-stat-1.8.jar edu.umich.andykong.ptmshepherd.PTMShepherd "D:\Fragger_output\G4Gr_SDS_Mix-101_tst\shepherd.config"
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
WorkspaceClean [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck
AppendFile
C:\MyPrograms\FragPipe21\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21\lib/* com.dmtavt.fragpipe.util.AppendToFile D:\Fragger_output\G4Gr_SDS_Mix-101_tst\modmasses_ionquant.txt D:\Fragger_output\G4Gr_SDS_Mix-101_tst\ptm-shepherd-output\glyco_masses_list.txt
IonQuant [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
C:\MyPrograms\FragPipe21\jre\bin\java.exe -Xmx117G -Dlibs.bruker.dir=C:\MyPrograms\FragPipe21\tools\MSFragger-4.0\ext\bruker -Dlibs.thermo.dir=C:\MyPrograms\FragPipe21\tools\MSFragger-4.0\ext\thermo -cp C:\MyPrograms\FragPipe21\tools\jfreechart-1.5.3.jar;C:\MyPrograms\FragPipe21\tools\batmass-io-1.30.0.jar;C:\MyPrograms\FragPipe21\tools\IonQuant-1.10.12.jar ionquant.IonQuant --threads 55 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.5 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100000 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 4 --writeindex 1 --tp 5 --minfreq 0.5 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\Fragger_output\G4Gr_SDS_Mix-101_tst\filelist_ionquant.txt --modlist D:\Fragger_output\G4Gr_SDS_Mix-101_tst\modmasses_ionquant.txt

Execution order:

Cmd: [START], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [CheckCentroid], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [WorkspaceCleanInit], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
Cmd: [PeptideProphet], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [ProteinProphet], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [PhilosopherDbAnnotate], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [PhilosopherFilter], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [PhilosopherReport], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [PTMShepherd], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [WorkspaceClean], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5]
Cmd: [AppendFile], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]
Cmd: [IonQuant], Work dir: [D:\Fragger_output\G4Gr_SDS_Mix-101_tst]


~~~~~~Sample of T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas~~~~~~~
>rev_sp|A0A1D5XGW0|DMS1B_WHEAT Deoxymugineic acid synthase 1-B OS=Triticum aestivum OX=4565 GN=DMAS1-B PE=2 SV=1
>rev_tr|A0A3B5YRT6|A0A3B5YRT6_WHEAT Germin-like protein OS=Triticum aestivum OX=4565 GN=CFC21_005332 PE=3 SV=1
>rev_tr|A0A3B6B4G7|A0A3B6B4G7_WHEAT Uncharacterized protein OS=Triticum aestivum OX=4565 GN=CFC21_018623 PE=4 SV=1
>rev_tr|A0A3B6EE08|A0A3B6EE08_WHEAT SHSP domain-containing protein OS=Triticum aestivum OX=4565 GN=CFC21_034399 PE=3 SV=1
>rev_tr|A0A3B6H3M7|A0A3B6H3M7_WHEAT Cysteine-rich receptor-like protein kinase OS=Triticum aestivum OX=4565 GN=CFC21_050286 PE=4 SV=1
>rev_tr|A0A3B6JPQ9|A0A3B6JPQ9_WHEAT Homeobox-leucine zipper protein OS=Triticum aestivum OX=4565 GN=CFC21_062916 PE=3 SV=1
>rev_tr|A0A3B6MPX0|A0A3B6MPX0_WHEAT GATA-type domain-containing protein OS=Triticum aestivum OX=4565 GN=CFC21_076754 PE=4 SV=1
>rev_tr|A0A3B6QAT8|A0A3B6QAT8_WHEAT F-box domain-containing protein OS=Triticum aestivum OX=4565 GN=CFC21_090674 PE=4 SV=1
>rev_tr|A0A3B6SNT7|A0A3B6SNT7_WHEAT Uncharacterized protein OS=Triticum aestivum OX=4565 GN=CFC21_104105 PE=4 SV=1
>rev_tr|A0A9R1DWY0|A0A9R1DWY0_WHEAT OVATE domain-containing protein OS=Triticum aestivum OX=4565 GN=CFC21_015409 PE=4 SV=1
>rev_tr|X5JTT4|X5JTT4_WHEAT HKT protein (Fragment) OS=Triticum aestivum OX=4565 GN=HKT PE=2 SV=1
>tr|A0A3B5YRT3|A0A3B5YRT3_WHEAT Uncharacterized protein OS=Triticum aestivum OX=4565 GN=CFC21_004999 PE=3 SV=1
>tr|A0A3B6B4G5|A0A3B6B4G5_WHEAT RBR-type E3 ubiquitin transferase OS=Triticum aestivum OX=4565 GN=CFC21_018816 PE=3 SV=1
>tr|A0A3B6EE06|A0A3B6EE06_WHEAT Uncharacterized protein OS=Triticum aestivum OX=4565 GN=CFC21_034655 PE=4 SV=1
>tr|A0A3B6H3M4|A0A3B6H3M4_WHEAT t-SNARE coiled-coil homology domain-containing protein OS=Triticum aestivum OX=4565 PE=4 SV=1
>tr|A0A3B6JPQ7|A0A3B6JPQ7_WHEAT glutathione gamma-glutamylcysteinyltransferase OS=Triticum aestivum OX=4565 GN=CFC21_063547 PE=4 SV=1
>tr|A0A3B6MPW8|A0A3B6MPW8_WHEAT DNA2/NAM7 helicase helicase domain-containing protein OS=Triticum aestivum OX=4565 GN=CFC21_077141 PE=4 SV=1
>tr|A0A3B6QAT6|A0A3B6QAT6_WHEAT Photosystem II reaction center protein K OS=Triticum aestivum OX=4565 GN=CFC21_091495 PE=3 SV=1
>tr|A0A3B6SNT3|A0A3B6SNT3_WHEAT Uncharacterized protein OS=Triticum aestivum OX=4565 GN=CFC21_105453 PE=4 SV=1
>tr|A0A9R1DWU4|A0A9R1DWU4_WHEAT HECT-type E3 ubiquitin transferase OS=Triticum aestivum OX=4565 GN=CFC21_015015 PE=3 SV=1
>tr|X5I1U0|X5I1U0_WHEAT Inactive poly [ADP-ribose] polymerase RCD1-like (Fragment) OS=Triticum aestivum OX=4565 PE=2 SV=1

# FragPipe v21.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=T\:\\Databases\\Wheat_UniProt\\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.generate-msstats=true
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.quantification-strategy-2=QuantUMS (high precision)
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=false
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=
diaumpire.DeltaApex=
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=false
diaumpire.Q2=false
diaumpire.Q3=false
diaumpire.RFmax=
diaumpire.RPmax=
diaumpire.RTOverlap=
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=
diaumpire.SE.MS1PPM=
diaumpire.SE.MS2PPM=
diaumpire.SE.MS2SN=
diaumpire.SE.MassDefectFilter=false
diaumpire.SE.MassDefectOffset=
diaumpire.SE.NoMissedScan=
diaumpire.SE.SN=
diaumpire.run-diaumpire=false
fpop.fpop-tmt=false
fpop.label_control=
fpop.label_fpop=
fpop.region_size=1
fpop.run-fpop=false
fpop.subtract-control=false
fragpipe-config.bin-diann=C\:\\MyPrograms\\FragPipe21\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe
fragpipe-config.bin-ionquant=C\:\\MyPrograms\\FragPipe21\\tools\\IonQuant-1.10.12.jar
fragpipe-config.bin-msfragger=C\:\\MyPrograms\\FragPipe21\\tools\\MSFragger-4.0\\MSFragger-4.0.jar
fragpipe-config.bin-philosopher=C\:\\MyPrograms\\FragPipe21\\tools\\philosopher_v5.1.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\MyPrograms\\Python\\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=1
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=100000
ionquant.medium=
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=4
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.5
ionquant.run-ionquant=true
ionquant.tp=5
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=1
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.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=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.mass_offsets_detailed=
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
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=trypsin
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
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.output_report_topN_dda_plus=5
msfragger.output_report_topN_dia1=5
msfragger.override_charge=false
msfragger.precursor_mass_lower=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
msfragger.precursor_true_tolerance=10
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.require_precursor=false
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
msfragger.run-msfragger=false
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=trypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=P
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; 57.021465,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,true,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_detailed_offsets=false
msfragger.use_topN_peaks=150
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=HCD
opair.filterOxonium=true
opair.glyco_db=
opair.max_glycans=2
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=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
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 --razor --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=true
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 20
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
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.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=15
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=0.01
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
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=true
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=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.run_diagextract_mode=false
ptmshepherd.run_diagmine_mode=false
ptmshepherd.run_glyco_mode=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
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=0.01
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=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.extraction_tool=IonQuant
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=D\:\\Fragger_output\\G4Gr_SDS_Mix-101_tst
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.misc.save-sdrf=true
workflow.ram=0
workflow.threads=55

CheckCentroid C:\MyPrograms\FragPipe21\jre\bin\java.exe -Xmx117G -cp C:\MyPrograms\FragPipe21\lib\fragpipe-21.0.jar;C:\MyPrograms\FragPipe21\tools\batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_A100_01.raw 55 Done in 0,0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:11] Executing Workspace v5.1.0
INFO[16:45:11] Removing workspace
INFO[16:45:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\e42db50b-a67b-4646-a68e-817dd5416825 INFO[16:45:11] Executing Workspace v5.1.0
INFO[16:45:11] Creating workspace
INFO[16:45:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:11] Executing Workspace v5.1.0
INFO[16:45:11] Removing workspace
INFO[16:45:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\f18943b0-596f-48e7-896c-040b2db43f4c INFO[16:45:11] Executing Workspace v5.1.0
INFO[16:45:11] Creating workspace
INFO[16:45:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:11] Executing Workspace v5.1.0
INFO[16:45:11] Removing workspace
INFO[16:45:11] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\29886699-bdfc-4281-9176-ce1834c35879 INFO[16:45:12] Executing Workspace v5.1.0
INFO[16:45:12] Creating workspace
INFO[16:45:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:12] Executing Workspace v5.1.0
INFO[16:45:12] Removing workspace
INFO[16:45:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\8ae7af7b-d63c-4146-884e-5fbef1f3219a INFO[16:45:12] Executing Workspace v5.1.0
INFO[16:45:12] Creating workspace
INFO[16:45:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:12] Executing Workspace v5.1.0
INFO[16:45:12] Removing workspace
INFO[16:45:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\e7f295f3-bc29-4056-b6e7-b1828b17d7a4 INFO[16:45:12] Executing Workspace v5.1.0
INFO[16:45:12] Creating workspace
INFO[16:45:12] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:13] Executing Workspace v5.1.0
INFO[16:45:13] Removing workspace
INFO[16:45:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\9a447ff3-9ede-46c7-accd-bd4775bdca0d INFO[16:45:13] Executing Workspace v5.1.0
INFO[16:45:13] Creating workspace
INFO[16:45:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:13] Executing Workspace v5.1.0
INFO[16:45:13] Removing workspace
INFO[16:45:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\05ffd3de-42ee-4a3e-9a31-70d148a39ff0 INFO[16:45:13] Executing Workspace v5.1.0
INFO[16:45:13] Creating workspace
INFO[16:45:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[16:45:13] Executing Workspace v5.1.0
INFO[16:45:13] Removing workspace
INFO[16:45:13] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\b587a705-9574-40e4-89bd-918f56c138bf INFO[16:45:14] Executing Workspace v5.1.0
INFO[16:45:14] Creating workspace
INFO[16:45:14] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1\fragpipe-G4Gr_SDS_A100_01.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\39bc6f53-c445-4831-b95f-08f71800c028 INFO[16:45:14] Executing Workspace v5.1.0
INFO[16:45:14] Creating workspace
INFO[16:45:14] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\fragpipe-G4Gr_SDS_A100_02.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\faeb94f2-a6bd-416e-ab97-4cd546f302cf INFO[16:45:14] Executing Workspace v5.1.0
INFO[16:45:14] Creating workspace
INFO[16:45:14] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\fragpipe-G4Gr_SDS_A100_03.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\163b13f6-d374-4b3d-bba7-219571fcde3d INFO[16:45:14] Executing Workspace v5.1.0
INFO[16:45:14] Creating workspace
INFO[16:45:14] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1\fragpipe-G4Gr_SDS_A101_01.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\2663bebe-7cfb-466f-900d-795cc8cc4c6c INFO[16:45:15] Executing Workspace v5.1.0
INFO[16:45:15] Creating workspace
INFO[16:45:15] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3\fragpipe-G4Gr_SDS_A101_03.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\93cd70d9-06a6-457e-896f-2f1015c3cadf INFO[16:45:15] Executing Workspace v5.1.0
INFO[16:45:15] Creating workspace
INFO[16:45:15] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\fragpipe-G4Gr_SDS_A101_5x.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\70d7c78e-8f6b-43d0-bd0e-e4ef81484253 INFO[16:45:15] Executing Workspace v5.1.0
INFO[16:45:15] Creating workspace
INFO[16:45:15] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_5.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\cfb30a49-9afc-4a26-a340-0b1fe964171e INFO[16:45:15] Executing Workspace v5.1.0
INFO[16:45:15] Creating workspace
INFO[16:45:15] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet: Workspace init [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_6.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ameri001\AppData\Local\Temp\f03c9df8-ee93-435d-9568-208177f2dd95 INFO[16:45:15] Executing Workspace v5.1.0
INFO[16:45:15] Creating workspace
INFO[16:45:15] Done
Process 'PeptideProphet: Workspace init' finished, exit code: 0 PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_1\fragpipe-G4Gr_SDS_A100_01.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A100_01.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\fragpipe-G4Gr_SDS_A100_02.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A100_02.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_3\fragpipe-G4Gr_SDS_A100_03.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A100_03.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_1\fragpipe-G4Gr_SDS_A101_01.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A101_01.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_3\fragpipe-G4Gr_SDS_A101_03.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A101_03.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A101_5\fragpipe-G4Gr_SDS_A101_5x.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_A101_5x.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_5.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_Amix5_5.pepXML PeptideProphet [Work dir: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\Amix5_5\fragpipe-G4Gr_SDS_Amix5_6.pepXML-temp] C:\MyPrograms\FragPipe21\tools\philosopher_v5.1.0_windowsamd64\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database T:\Databases\Wheat_UniProt\2023-12-18-decoys-contam-uniprot-TritAestivum_taxon_4565_18dec23_152264entries.fasta.fas ..\G4Gr_SDS_Amix5_6.pepXML Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. Please wait. PeptideProphet is running. It can take a long time. INFO[16:45:16] Executing PeptideProphet v5.1.0
Unknown file type. No file loaded.D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2/G4Gr_SDS_A100_02.raw Unknown file type. No file loaded.D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2/G4Gr_SDS_A100_02.raw file 1: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\G4Gr_SDS_A100_02.pepXML processed altogether 34989 results INFO: Results written to file: D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\interact-G4Gr_SDS_A100_02.pep.xml

D:\Fragger_output\G4Gr_SDS_Mix-101_tst\A100_2\interact-G4Gr_SDS_A100_02.pep.xml
Building Commentz-Walter keyword tree...
Searching the tree...
Linking duplicate entries...
Printing results...

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: 0.0 init with X! Tandem trypsin PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) @.*** read in 1141 1+, 12567 2+, 13975 3+, 7306 4+, 0 5+, 0 6+, and 0 7+ spectra. Found 8548 Decoys, and 26441 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 (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+). model complete after 27 iterat

fcyu commented 10 months ago

You need to rerun from scratch,

ProteomicsPSG commented 10 months ago

started a new search from scratch, with "deselected" single combined pepXML file.... Same error message

Again NB the inconsistent forward and backslashes in the last output path in the log file. Could taht hint to an error?? ..... Fixing pepxml: D:\Fragger_output\G4Gr_SDS_Mix-101_2ndtst\A101_1\interact-G4Gr_SDS_A101_01.pep.xml Didn't find correct mapping for raw file path in pepxml: D:\Fragger_output\G4Gr_SDS_Mix-101_2ndtst\A101_1/G4Gr_SDS_A101_01Writing output to: D:\Fragger_output\G4Gr_SDS_Mix-101_2ndtst\A101_1\interact-G4Gr_SDS_A101_01.pep.xml349473914224268326.temp-rewrite Process 'Rewrite pepxml' finished, exit code: 1 Process returned non-zero exit code, stopping ...... log_2024-01-08_17-10-17.txt

fcyu commented 10 months ago

Then, I am clueless now unless taking a look at your files. If you like, please upload all files to https://www.dropbox.com/request/jtkhkVvxGfsh5lBLsRad

Again NB the inconsistent forward and backslashes in the last output path in the log file. Could taht hint to an error??

Although I don't know what "NB" means, I don't think this is the cause of the error.

Best,

Fengchao

ProteomicsPSG commented 10 months ago

I have now re-run the search with only 2 files. Then zipped the complete FragPipe output folder plus the zippped .raw files together and uploaded them to the given Dropbox.

Also these 2 files give the same error message: ... Didn't find correct mapping for raw file path in pepxml: ......

Thanks for your help.

fcyu commented 10 months ago

Thanks for your files. Something does not seem right in your *.pep.xml files:

<msms_run_summary base_name="D:\Fragger_output\G4Gr_SDS_Mix2fileTst\Amix5_6/G4Gr_SDS_Amix5_6" raw_data_type="raw" raw_data="raw">

The above like should be

<msms_run_summary base_name="F:\github_issues\github_fragpipe_1401\G4Gr_SDS_Amix5_6_uncalibrated" raw_data_type="mzML" raw_data="mzML">

I don't know why it happened. Maybe some files were messed up (one indication is that your log has the messages printed by logback, which there should not be). I suggest you delete all FragPipe, MSFragger, Philosopher, and IonQuant folders. Download new ones to new folders. And then use the new downloaded FragPipe. If the error persists, please convert your raw files to mzML format according to the tutorial: https://fragpipe.nesvilab.org/docs/tutorial_convert.html

Best,

Fengchao

ProteomicsPSG commented 10 months ago

Hi Fengchao, Thank you for your efforts and suggestion. I completely new installation of FragPipe + modules in itself was not enough. But after delecting the (un)calibrated mzML files and runnign with Peptide/ProteinProhet validation, the search was succesfull. I have now also tried some other files which were succesful.

\Halas, \ With MS booster and percolator (not PEPTIDEPROPHET) I still run into an error.:
last lines: Found 23307 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 32968 target PSMs and 9311 decoy PSMs. Calculating q values. Final list yields 23313 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 7.9960 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: D:\Fragger_output\G4Gr_SDS_Mix_Nw2fileTst_BoosterPercolator\Amix5_5] C:\MyPrograms\FragPipe21p1\jre\bin\java.exe -cp C:\MyPrograms\FragPipe21p1\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML G4Gr_SDS_Amix5_5.pin G4Gr_SDS_Amix5_5 G4Gr_SDS_Amix5_5_percolator_target_psms.tsv G4Gr_SDS_Amix5_5_percolator_decoy_psms.tsv interact-G4Gr_SDS_Amix5_5 DDA 0.5 D:\Data_Proteomics\Data_G4Gr_SDS_dec23\G4Gr_SDS_Amix5_5_calibrated.mzML Exception in thread "main" java.lang.NumberFormatException: For input string: "0,6299" at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source) at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source) at java.base/java.lang.Float.parseFloat(Unknown Source) at com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML.percolatorToPepXML(PercolatorOutputToPepXML.java:340) at com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML.main(PercolatorOutputToPepXML.java:59) Process 'Percolator: Convert to pepxml' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 16 remaining tasks

fcyu commented 10 months ago

This is a known issue: https://github.com/Nesvilab/FragPipe/issues/1378

Please follow the instruction in https://github.com/Nesvilab/FragPipe/issues/1378#issuecomment-1864566848 to resolve it.

Best,

Fengchao

ProteomicsPSG commented 10 months ago

Hi Fengchao, Thank you for your help. Changing the location and number notation (again) helped indeed to get MS Booster and Percolator working again.

Thank you, a lot, for developing such a great software environment as FragPipe and its tools. 😉

Cheers, Twan

From: Fengchao @.> Sent: 09 January 2024 13:59 To: Nesvilab/FragPipe @.> Cc: America, Twan @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Messed up files broke FragPipe (Issue #1401)

This is a known issue: #1378https://github.com/Nesvilab/FragPipe/issues/1378

Please follow the instruction in #1378 (comment)https://github.com/Nesvilab/FragPipe/issues/1378#issuecomment-1864566848 to resolve it.

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1401#issuecomment-1883023826, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AXSSINGM4NCIB5VD2S2WXQTYNU5J5AVCNFSM6AAAAABBRUV4EGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBTGAZDGOBSGY. You are receiving this because you authored the thread.Message ID: @.**@.>>

fcyu commented 10 months ago

Hi Twan,

You are welcome.

I will close this ticket but feel free to contact us if you have any questions in the future.

Best,

Fengchao

Nesvilab / FragPipe

Messed up files broke FragPipe #1401