search

pwilmart / PAW_pipeline

A Comet-based, best practices proteomics pipeline.
MIT License
33 stars 9 forks source link

Comet Run not Converting SQT Files #2

Closed gmhernandezneu closed 3 years ago

gmhernandezneu commented 4 years ago

Hello Phil,

I am running into trouble running the Comet command. After I hit run, I immediately receive the error as pictured below in my idle console "Warning - folder does not contain any SQT files." How do I remedy this problem? Could it stem from how I set up the program command? Thank you for your help!

image

Best, Gabby

pwilmart commented 4 years ago

Hi Gabby, Look at this and see if the Comet command is set up correctly. The error occurs when each Comet command fails. The launching a Windows command shell kind of happens in the background and I do not have a mechanism in place to capture any of the Comet error messages and pass them on in the GUI. All of the failed Comet commands can happen quickly, then there are no SQT output files, and you get the error message. Let me know how it goes. Cheers, Phil

pwilmart commented 4 years ago

oops, here is the link: https://github.com/pwilmart/PAW_pipeline/blob/master/docs/Comet.md

gmhernandezneu commented 4 years ago

Hi Phil, I re-setup the Comet command and it worked. Thank you for your help! Best, Gabby