Unexpected end of file

[anoronh4]

I am working with a conda installation of this tool in a docker image. I downloaded the reference package and on that I ran:

/opt/conda/envs/hlala/opt/hla-la/bin/HLA-LA \
--action prepareGraph \
--PRG_graph_dir ../../../HLA-LA/graphs/PRG_MHC_GRCh38_withIMGT

This completed without errors. However when I ran HLA-LA it failed. The command was:

env SINGULARITYENV_LC_ALL=C singularity exec \
-B /path 
/path/to/singularity_images/cmopipeline-hlala-0.0.1-test.img HLA-LA.pl \
--BAM /path/to/my.bam \
--graph PRG_MHC_GRCh38_withIMGT \
--sampleID sample \
--maxThreads 20 \
--workingDir ./ \
--customGraphDir ../../../HLA-LA/graphs/

And in the error file I see:

BWTIncConstructFromPacked() : Can't read from /path/to/mydir/../../../HLA-LA/graphs//PRG_MHC_GRCh38_withIMGT/extendedReferenceGenome/extendedReferenceGenome.fa.pac : Unexpected end of file
terminate called after throwing an instance of 'std::runtime_error'
  what():  Command /opt/conda/envs/hlala/bin/bwa index /path/to/mydir/../../../HLA-LA/graphs//PRG_MHC_GRCh38_withIMGT/extendedReferenceGenome/extendedReferenceGenome.fa returned code 256

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

[AlexanderDilthey]

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