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Error: unhandled exception: Not a zip archive
Hi @brentp
I am having the same issue reported on issue#94.
I downloaded gnomad v3.1.1, and concat all the chr VCF into one file, around 2.3T.
I used following command to generate the "gnomad-3.1.1-cadd.zip"
slivar make-gnotate --prefix gnomad-3.1.1-cadd \
--field nhomalt_popmax:gnomad_nhomalt \
--field AF_popmax:gnomad_popmax_af \
--field cadd_phred:caddv16 \
$dir/gnomad.genomes.v3.1.1.sites.chrAll.vcf.bgz
However, when I use this dataset for gnotate, it gave me the error
Error: unhandled exception: Not a zip archive
The docker I am using is the latest one
docker(brentp/slivar:latest)
v0.2.7
Here is the command I ran the gnotate:
slivar expr --vcf $vcf --ped $ped --gnotate $gnomadv3 --gnotate $topmed --js $js --out-vcf $out --info "variant.call_rate > 0.9" --family-expr "test:kid.het"
Thanks
thanks for reporting. can you try running slivar expr with the binary from the releases, instead of the one inside the container?
Yes, I tried this one
https://github.com/brentp/slivar/releases/download/v0.2.7/slivar
It works well. Do you happen to know why the docker version didn't work?
Thanks,
David
Hi, thanks for following up. I don't know why this happens. Maybe it's something with the compiler used for the docker version or something with docker itself? You can, of course, make a new dockerfile and container that simply adds the release version of slivar.
Cool, thanks.