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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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RUN error #1428

Closed RaquelVA closed 7 months ago

RaquelVA commented 7 months ago

I feel I have a problem with the installation of the MSfragger or something else. I downloaded fragpipe v21.0.

C:\Users\SCIEXProc\Desktop\fragpipe\tools\MSFragger-4.0\MSFragger-4.0.jar C:\Users\SCIEXProc\Desktop\fragpipe\tools\IonQuant-1.10.12.jar C:\Users\SCIEXProc\Desktop\fragpipe\tools\philosopher_v5.1.0_windows_amd64\philosopher.exe C:\Users\SCIEXProc\Desktop\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe C:\Users\SCIEXProc\AppData\Local\Programs\Python\Python39\pythonw.exe

I have a known workflow and a correct file from someone who has this program, and it works for him. So I'm pretty sure all parameters and the files conversion are correct. I'm using MSFragger for a DDA experiment. All the validation tools aren't working at all, and when I want to activate MSBooster, it says that is not compatible with an open search and it should be disabled, but this is strange for me because all parameters come from a known correct workflow (dafault, closed search). Without the MSbooster and any validation tool, I'm allowed to RUN the file, but percolator shouldn't be activated or any PTM or any tool after the validations tools. If I activate the prophet or the percolator stops the RUN and the remaining tasks are cancelled.

I'm pretty sure I have an informatic problem or something like this because this person RUN my files with the same workflow and it works for him, but not for me. I don't know how to fix this. Thanks for your attention.

I'm going to copy one example RUN (a part of, without MSbooster):

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: 1_1 (if "spectral library generation" is enabled, all files will be analyzed together)

[ ... ]

MSFragger move pin C:\Users\SCIEXProc\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\SCIEXProc\Desktop\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/SCIEXProc/Desktop/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\PROTEOMICS\FILES_CONVERTER\211129_PeptideMapping_Proves-HSA_Option_A_20uL.pin D:\PROTEOMICS\MS_FRAGGER\OUTPUT7\4_1\211129_PeptideMapping_Proves-HSA_Option_A_20uL.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\SCIEXProc\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\SCIEXProc\Desktop\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/SCIEXProc/Desktop/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\PROTEOMICS\FILES_CONVERTER\211129_PeptideMapping_Proves-HSA_Option_A_5uL.pepXML D:\PROTEOMICS\MS_FRAGGER\OUTPUT7\5_1\211129_PeptideMapping_Proves-HSA_Option_A_5uL.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\SCIEXProc\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\SCIEXProc\Desktop\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/SCIEXProc/Desktop/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\PROTEOMICS\FILES_CONVERTER\211129_PeptideMapping_Proves-HSA_Option_A_5uL.pin D:\PROTEOMICS\MS_FRAGGER\OUTPUT7\5_1\211129_PeptideMapping_Proves-HSA_Option_A_5uL.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml C:\Users\SCIEXProc\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\SCIEXProc\Desktop\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/SCIEXProc/Desktop/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\PROTEOMICS\FILES_CONVERTER\211129_PeptideMapping_Proves-HSA_Option_A_80min.pepXML D:\PROTEOMICS\MS_FRAGGER\OUTPUT7\6_1\211129_PeptideMapping_Proves-HSA_Option_A_80min.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin C:\Users\SCIEXProc\Desktop\fragpipe\jre\bin\java.exe -cp C:\Users\SCIEXProc\Desktop\fragpipe\lib\fragpipe-21.0.jar;/C:/Users/SCIEXProc/Desktop/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err D:\PROTEOMICS\FILES_CONVERTER\211129_PeptideMapping_Proves-HSA_Option_A_80min.pin D:\PROTEOMICS\MS_FRAGGER\OUTPUT7\6_1\211129_PeptideMapping_Proves-HSA_Option_A_80min.pin Process 'MSFragger move pin' finished, exit code: 0 Percolator [Work dir: D:\PROTEOMICS\MS_FRAGGER\OUTPUT7\2_1] C:\Users\SCIEXProc\Desktop\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms 211129_PeptideMapping_Proves-HSA_OptionA(2)_percolator_target_psms.tsv --decoy-results-psms 211129_PeptideMapping_Proves-HSA_OptionA(2)_percolator_decoypsms.tsv --protein-decoy-pattern rev 211129_PeptideMapping_Proves-HSA_OptionA(2).pin Protein decoy-prefix used is All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 13:59:29 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Users\SCIEXProc\Desktop\fragpipe\tools\percolator_3_6_4\windows\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms 211129_PeptideMapping_Proves-HSA_OptionA(2)_percolator_target_psms.tsv --decoy-results-psms 211129_PeptideMapping_Proves-HSA_OptionA(2)_percolator_decoypsms.tsv --protein-decoy-pattern rev 211129_PeptideMapping_Proves-HSA_OptionA(2).pin Started Tue Jan 30 16:23:07 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 211129_PeptideMapping_Proves-HSA_OptionA(2).pin Features:

ERROR: Reading tab file, too few features present. No-terminate flag set: ignoring error and using a pseudo-feature of zeroes. Exception caught: ERROR: Reading tab file, error reading PSM on line 2. Could not read PSMid.

Process 'Percolator' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 54 remaining tasks
fcyu commented 7 months ago

I am pretty sure you messed up the configurations and parameters ;)

Could you

  1. Share the whole workflow file
  2. Sent the screenshots of the "config" and "workflow" tab.

Best,

Fengchao

RaquelVA commented 7 months ago

Capture Capture JPG2 Capture JPG3 Capture JPG4 Capture JPG5 Capture JPG6 Capture JPG7 Capture JPG8

Parameter without run, I cant with MSbooster

RaquelVA commented 7 months ago

Its okey with this? If you have an email I can send you the workflow.

fcyu commented 7 months ago

Thanks for the screenshots. I took a brief look and the following are the errors I found

  1. In the "MSFragger" tab, the precursor mass tolerance was set to Da, which made FragPipe think it was an open search. This was also why you saw the warning "MSBooster is incompatible with open search....".
  2. The "PTMs" tab is for open or mass-offset search, you should disable all panels in thie tab

You did not show the screenshots of the other tabs such as "Glyco", "Quant(MS1)" etc. I am not sure if you have messed up other parameters. But I am pretty sure that what you were using is not "default, closed search" as you described in the first message.

Please select and load the "default" workflow by clicking "Load" (I saw many users forgot clicking that "Load" button) if you want to perform a "closed, default search".

Best,

Fengchao

RaquelVA commented 7 months ago

Thank you so much, and I did not put the sother creenshots because right now arent activated. However, I completely missed this load. So sorry and thank you so much for your work and this wonderful platform, with which one Im trying to learn to work with.