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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping #1614

Closed PietroCrivello closed 3 weeks ago

PietroCrivello commented 3 weeks ago

log_2024-06-06_10-51-35.txt

Hi,

I am running Fragpipe to identify HLA peptides using a large database and group specific FDR analysis. The workflow crashed at the MSbooster step.

Initially I thought that the issue might be related to the relatively old version of Fragpipe (v20.0), I have now run the version v22 which is giving the same issue. Can anybody help to solve this problem?

Many thanks in advance, Pietro

yangkl96 commented 3 weeks ago

Hi Pietro,

Could you please attach one PIN file here or at this DropBox link for me to help troubleshoot?

Thanks, Kevin

PietroCrivello commented 3 weeks ago

Thank you very much for your help. I uploaded one of the pin file as requested.

I also recognized yesterday that my fasta file not clear how, included the symbol " for delimiting some of the sequence names (not sure now if it was the same even for some of the actual sequences. Can this cause the issue somehow?

PietroCrivello commented 3 weeks ago

Apparently the problem was indeed caused by the wrong sequence headers. It worked fine with a clean fasta and finished all jobs in a couple of hours. Thanks.