MaxQuant for Label-Free quantification

usegalaxy.org support
1

Hi, I am having some problems with MaxQuant.
I followed the steps in the tutorial “Label-free data analysis using MaxQuant” but I got an error that I could not get the peptide, PTXQC and protein reports.

“Unhandled Exception:
System.Exception: Exception during execution of external process: 159891
at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 thre”.

In this case, I have downloaded from the UniProt database the fasta: UniProtKB reviewed (Swiss-Prot).

My files come from an agilent QToF (mzxml), so I selected the input extensions.

Identifiers parse rule: >.|(.)|
Description parse rule: >.|.|[^ ]+ (.*) OS

Variable modifications: Oxidation (M), Carbamidomethyl (C), Phsopho (STY), Gln → pyro-Glu

I hope you can help me…

Regards

2

Hi @jsalasm
I tested MaxQuant on the main Galaxy server using data and settings from “Label-free data analysis using MaxQuant” tutorial. I don’t see any issue with the software. The job has been completed. It suggests that the cause of the error might be in settings or/and input files.
Have you examined the log files? Click at any output from the failed job, click at info icon, and in the middle window examine the standard output and standard error log files.
Kind regards,
Igor