Open anoronh4 opened 1 year ago
Hey @anoronh4,
I am no Docker expert, but is it possible for you to delete the file extendedReferenceGenome/extendedReferenceGenome.fa.pac
and re-execute the inference command (on one sample only, i.e. do not try to process multiple samples in parallel)? When you do this, HLAL*LA will try to re-execute the bwa index
command, which may solve your issue.
Best,
Alex
I am working with a conda installation of this tool in a docker image. I downloaded the reference package and on that I ran:
This completed without errors. However when I ran HLA-LA it failed. The command was:
And in the error file I see:
I am using the bwa that with the conda package, version
0.7.12-r1039
I was hoping someone could help to debug this. anyone can access the container as well, since it is public: docker://cmopipeline/hlala:0.0.1-test