Closed medmaca closed 6 months ago
That's very strange... I've not seen that before.
Googling the error looks like it's something to do with Prokka (rather than the pipeline):
https://github.com/tseemann/prokka/issues/557
Could it be your HPC is somehow adding some extra text to stdout logs etc.?
Other pipelines run fine. However, I'll try to have a root around to see what I can find.
This thread: https://nfcore.slack.com/archives/CE9MS66BS/p1681840960696719 contains reports that others are having the same issue.
Do you mean other pipelines run fine with the prokka
module?
Thanks for pointing to the slack threead!
Do you mean other pipelines run fine with the prokka module?
No, sorry, I mean that in general nf-core pipelines work (atacseq, rnaseq etc), it must be something specific to the prokka
module, or the way that its container is being handled.
Yes exactly :/. You could also try running manually prokka from different contexts and see if you get the same error.
If you go into the working directory that the error reports, you should see a hidden file called .command.sh
that has the bash command nextflow is executing.
So you could try running with a locally compiled/downloaded version, with a version installed with conda etc.
If it's neither of those then it is something specific to the container I guess and we will need to investigate it further
We will eventually replace/update all modules anyway which should hopfeully fix this, and as this seems to be possibly be an edge case as it's not being reported by others I will close this for now.
Description of the bug
The pipeline runs until it gets to process NFCORE_MAG:MAG:PROKKA, it then fails with the error shown below.
Command used and terminal output
Relevant files
nf-5IBlscu8mRjHeQ.log nf-5IBlscu8mRjHeQ.txt
System information
The pipeline is run with the following profiles: ebi_codon_slurm, apptainer, test_full. I'm only providing an output directory I'm leaving everything else as set in test_full.