Closed Mxrcon closed 1 year ago
This seems related https://github.com/ngs-fzb/MTBseq_source/issues/23 and reported for a conda_env, which I haven't been able to reproduce on my setup yet.
Note that I haven't been able to reproduce this issue using the docker
container, either.
I can't agree with classifying this as a bug
since this relates to an underlying tool, which we happen to use i.e. gatk
, maybe it should be called known_issue
.
I'm testing the GATKjar version 3.8.1 (GenomeAnalysisTK-3.8-1-0-gf15c1c3ef), avaible on this link: https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
As suggested on this issue, so we can see if updating the jar solves the problem with mtbseq
After a long test on IEC Cluster the issue seems to be fixed, If it's okay to you @abhi18av, I'll close this issue and keep it as a possible troubleshooting for future use.
Brilliant!
@Mxrcon , would you mind adding a general outline of the solution please?
Sure!
wget https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
[ ] Untar the GATK.jar
tar -xvf GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
[ ] Register the new GATK and use on the pipeline as usual
gatk-register GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar
Hmm, I see.
In that case, do you think it's worth upgrading the default gatk version within the pipeline?
I have updated the title of this issue to help anyone discover the cause of this issue earlier.
I'm trying to run the pipeline on a PBS cluster and during the TBBWA step, I'm getting this very odd error:
I'm using a new conda environtment provided by the recipe on this repository, I'm also using the correct GATK jar.