Closed kguehrs closed 3 years ago
fcyu
commented
3 years ago If you are using DIA-Umpire, then MSFragger. You should choose "DDA" as the data type in MSFragger because the pseudo-spectra from DIA-Umpire are like DDA spectra. Could you please load the corresponding workflow (DIA-Umpire_Speclib), do not change any parameters other than those related to digestion and modification, and try again?
Best,
Fengchao
kguehrs
commented
3 years ago Hello Fengchao,
Thanks for the response.
The default workflow worked for me for a small dataset now. There is some “Time outwaiting for sequential executor shutdown “ notice after the DONE was printed that I cannot fully understand but I will go into the data now to compare the results with those of other approaches.
Perhaps, it would be a good idea to make options of the real “master workflows” that should not be touched unchangeable or even hidden. If one can kind of clone a workflow from the “master” and save differently flagged using a different name this could be used as an user adaptable template. I know that this is lot of scripting but shall help you and the users to keep track with all settings that can go wrong.
Mit freundlichen Grüßen/Best regards
Dr. Karl-Heinz Gührs CF Proteomics
Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) Beutenbergstraße 11 07745 Jena, Germany Phone: +49(0)3641-65-6433 Email: @.*** WWW: http://www.leibniz-fli.de Scientific Director: Prof. Dr. Alfred Nordheim Administrative Director: Dr. Daniele Barthel Chairman of the Board of Trustees: Burkhard Zinner Register of Associations: No. 230296 at Amtsgericht Jena VAT No.: DE 153 925 464
From: Fengchao @.> Sent: Friday, June 11, 2021 13:45 To: Nesvilab/FragPipe @.> Cc: Karl-Heinz Gührs @.>; Author @.> Subject: [External] Re: [Nesvilab/FragPipe] error in extracting isolation windows: Cannot get isolation window info from scan (#390)
If you are using DIA-Umpire, then MSFragger. You should choose "DDA" as the data type in MSFragger because the pseudo-spectra from DIA-Umpire are like DDA spectra. Could you please load the corresponding workflow (DIA-Umpire_Speclib), do not change any parameters other than those related to digestion and modification, and try again?
Best,
Fengchao
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/390#issuecomment-859523170, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AE7U6YTY2BUL2QZ34YZ55BTTSHZLRANCNFSM46QJDTDA.
fcyu
commented
3 years ago Hi Karl-Heinz,
"Time out waiting for sequential executor shutdown" is kind of debug message and it won't affect the result. You can ignore it,
All those built-in workflows cannot be overwritten inside FragPipe. Users can make some changes and create a custom workflow.
Best,
Fengchao
log_2021-06-11_10-52-33.zip Pipe/files/6637097/log_2021-06-11_10-14-33.txt)
Describe the issue or question:
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.)