gnomad_exome ggb randomly fails on chr1

[naumenko-sa]

gnomad_exome ggb randomly fails on chr1

[chapmanb]

Sergey;
Thanks for working on this and for the heads up. Happy to convert over to bcftools annotate for this if it works more cleanly in your tests. I appreciate you testing and working on the fixes.

[naumenko-sa]

Hi Brad!

The problem is definitely gone with the help of bcftools in chr1 test. Please merge and I will run the entire installation to make sure everything works for all chr.
#299

Sergey

[chapmanb]

Thanks so much, merged your fix. Fingers crossed it's all running cleanly now.

[naumenko-sa]

It works, but it is really slow. 2 chrs in 2 days for gnomad_genome for me. I will be lucky if the installation finishes in 1 week. Probably, we just need to push the resulting file in the cloud to make life easier for other people.

[lbeltrame]

The script also fails for downloading exomes:

2019-05-10 12:37:58 (347 KB/s) - 'gnomad.exomes.r2.1.sites.chr1_noVEP.vcf.gz.tbi' saved [90750/90750]

/opt/bcbio/genomes/Hsapiens/hg19/txtmp/ggd-run.sh: line 23: fields_to_keep: unbound variable
> gsort version 0.0.6