search

Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
Other
204 stars 38 forks source link

Error running Glyco-N-HCD workflow - corrupt files error #1736

Closed Dmorgen closed 2 months ago

Dmorgen commented 2 months ago

log_2024-08-19_22-48-50.txt Hi, I'm getting the following error trying to run the set on glyco-N-HCD workflow. If I understand correctly, the claim is that the files are corrupt. I've opened them manually, and they ran well using other software, so I'm not sure where the problem is. the analysis was run on the same computer as the one in issue #1735.

Thanks! David.

fcyu commented 2 months ago

It was due to the Thermo library was not correctly loaded: 2024-08-19 22:48:50 ERROR - Could not find Batmass-IO Thermo binary BatmassIoThermoServer.exe from C:\Users\protolab\Downloads\MSFragger-4.1\ext\thermo, C:\Users\protolab\Downloads\MSFragger-4.1\.\ext\thermo, C:\Users\protolab\Downloads\MSFragger-4.1\..\ext\thermo, C:\Users\protolab\Downloads\MSFragger-4.1\..\..\..\..\ext\thermo, C:\Users\protolab\Downloads\MSFragger-4.1\..\..\..\..\..\ext\thermo.

Could you check if the ext folder is in one of the folder mentioned above? Most likely, you should put it in the folder where MSFragger-4.1.jar is.

Thanks,

Fengchao

Dmorgen commented 2 months ago

Hi Fengchao,

The folder indeed lacked the files. I've corrected that and it's working well now. Thanks! David.

fcyu commented 2 months ago

No problem. I will close this issue but feel free to contact us if you have any questions in the future.

Best,

Fengchao