Sorting large VCF file fails

[sa9]

I am trying to annotate a 5+ Gb compressed VCF file with vcfanno but it fails at the sorting (after 10 min or so) with this message sort: write failed: /tmp/sortTH9eaK: No space left on device

I tried fews things like

• changing the TMP folders for the sort command ($TMP=/new_temp_folder)
• adding -T option to sort (alias sort='sort -T /media/BML/tmp')

But the same issue persists. I know this is an OS issue not a vcfanno specific but I wonder where does vcfanno invoke the sort command and how can we change the default behavior?

• the command used to invoke vcfanno ./vcfanno_0.1.1 af_v1.tmol d.vcf.gz | bgzip -c > o.vcf.gz

• conf file. [[annotation]] file="ExAC.r0.3.sites.vep.decom_normalized_vt.vcf.gz" fields = ["AF"] names=["EXAC_AF"]

• the full error message

vcfanno version 0.1.1 [built with go1.8]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:114: found 2 sources from 2 files
sort -k1,1d -k2,2n
sort: write failed: /tmp/sortTH9eaK: No space left on device```

[brentp]

Hi, this isn't a vcfanno problem, your drive is full. You can see if there are other drives with more space with df -h

vcfanno doesn't call sort, so you must be doing that in the command-line, though it's not shown in your invocation above.