I attempted to run MaxQuant (v2.0.3) within Galaxy for an LFQ proteomics analysis using 18 Thermo .raw files. I uploaded all raw files, created a dataset collection, and provided a correctly formatted experimental design file (Name, Fraction, Experiment, PTM) with filenames matching the .raw files exactly. The job starts normally and progresses through many MaxQuant steps (feature detection, searches, recalibration, PEP calculation), but fails before producing any outputs. The job terminates with the error: “Exception during execution of external process: no /proc/self/maps, not on linux?”. This appears to be an environment-related issue rather than a problem with inputs or parameters, as MaxQuant requires access to the Linux /proc filesystem, which seems to be unavailable or restricted on the Galaxy execution node where the job is run. Is there something i can do about it ?
Welcome @Sofia_Orfanou
This is an interesting error and might be due to the job configuration on the cluster, and maybe with just the newest version of the tool, and possibly at just one server and not the others. We can get this ticketed if reproducible.
To do that, I’ll need enough specifics to trigger the error. Then, if this can’t be reproduced, we can look into how the job is set up (inputs, parameters), since there can sometimes be what appears to be a technical error that is instead rooted in data (not just input formats, but the content).
I will also suggest that you send in a bug report to the administrators. You can include a link to this topic in the comments for extra context.
Then, for a possible quick workaround, you can try using the prior version of the tool. You can navigate under the Versions menu on the tool form. FAQ: Changing the tool version
And finally, for me to run a test, I’ll need to know the exact version of the tool wrapper and the server you are working at. Inputs and parameters would also be helpful. You can do this by generating and posting back a shared history link. You can unshare once we are done.
These are the versions currently hosted at UseGalaxy.eu. The underlying version of MaxQuant is v 2.0.3 but around that is the Galaxy wrapper, and these also have a version! How the job is submitted to the cluster depends on the wrapper, so knowing which is presenting with an issue is needed for this.
I’ll start up a quick tool test with the most current version at this server. More soon and I’ll watch for your reply. Thanks! 
Xref → 
GTN Tutorials for MaxQuant → Galaxy Training!