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bio-raum / FooDMe2

A nextflow pipeline for the identification of species from mixed samples based on mitochondrial amplicons
https://bio-raum.github.io/FooDMe2/
GNU General Public License v3.0
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[Bug] Java error OverlappingFileLockException #49

Closed gregdenay closed 2 months ago

gregdenay commented 2 months ago

This is new:

ERROR ~ Error executing process > 'FOODME2:ILLUMINA_WORKFLOW:DADA2_WORKFLOW:HELPER_DADA_STATS (1)'

Caused by:
  java.nio.channels.OverlappingFileLockException

Any insights? Google is not very helpful

marchoeppner commented 2 months ago

What kind of file system are you running this on? Is this on a local drive or network-mounted (NFS, BeeGFS or similar?)

Edit: Make sure you don't have a dangling nextflow process running in the same directory; worst case would be to delete the whole thing (work, results, .nextflow*) and try again.

But it could be that if this is an NFS share or similar, that something "hangs" server-side. Maybe try running the same analysis in a newly created folder to see if the error occurs again.

gregdenay commented 2 months ago

This is a VM on the server, I guess similar to a local disc?

I tried removing all the work, results and .nextflow folders, restart the server, clean mamba locks and caches and run the wrkflow in a new folder.

I get the same error on older versions of the pipeline too.

marchoeppner commented 2 months ago

Right, so then it is probably not the pipeline (seeing that it used to work previously) but something about the virtual machine and the attached storage (depending on what your setup looks like exactly). Happy to chat offline, but this might be beyond my area of expertise...

gregdenay commented 2 months ago

Fixed in 5fe9752

The naming of the conda env was the culprit. We have to ensure that the names are unique in the future :)