Closed seboyden closed 3 years ago
Yeah. You probably have too many values, causing a single chromosome to be more than 4.2GB uncompressed. I don't know how to fix this. You can use less annotations or split them to 2 different files to circumvent.
This turned out to be a permissions issue unrelated to Slivar. A cron job was resetting file ownership in my output directory overnight. I reran with a different output directory and it worked, even extracting all 20 fields at once.
I'm getting the same error reported in Issue 27 but using
slivar make-gnotate
notslivar expr
I downloaded gnomad v3.1.1 and concatenated per-chr VCFs. It is a gigantic 2.3 Tb VCF (compressed). I ran the following using slivar v0.2.1:
I got this error:
I ran the exact same command a second time and got the same error, but at a different place:
Then I tried the dev slivar v0.2.2 from Issue 27, and got the same thing: