Error: unhandled exception: Not a zip archive

[Drdreammaerd]

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

[brentp]

thanks for reporting. can you try running slivar expr with the binary from the releases, instead of the one inside the container?

[Drdreammaerd]

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

[brentp]

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.

[Drdreammaerd]

Cool, thanks.