Crash for PSM = 0
Closed this issue · 2 comments
Hello,
I did high-pH fractionation on my sample and ran fragpipe using non-specific HLA workflow.
I had the impression that some fractions are empty (have no peptide identifications) and this make crash fragpipe. I'm expecting to have empty fractions because I did an extensive fractionation.
This is not the first time I observe such behavior. Usually, I remove those file with zero identification prior to running again fragpipe or use MaxQuant. Is there a way to continue the analysis even with the presence of zero peptide identified raw files? I suppose this is the error but it could be something else. I then attached the log file. I also had the impression that the process stop or stuck during MSBoost. So I manually stopped.
I look forward to hearing back from you
Best
HuiSong
log_2024-05-24_14-12-03.txt
Hi HuiSong,
I think we have made FragPipe not crash and continue running if there are any files with no IDs. I guess we didn't check each steps carefully.
@yangkl96 , can you take a look? The error was from MSBooster.
Best,
Fengchao
Fixed in the new FragPipe release: https://github.com/Nesvilab/FragPipe/releases/latest
Best,
Fengchao