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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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"hangup" error #188

Open cfz1998 opened 2 years ago

cfz1998 commented 2 years ago

When i try: [smoove annotate --gff $gff3 join_call.smoove.square.vcf.gz | bgzip -c > join_call.smoove.square.anno.vcf.gz ]

It always give me: [smoove] 2022/02/17 11:08:27 starting with version 0.2.5 hangup

I don't know the reasons. Is it because I don't have enough memory? Or caused by other reasons? Thanks for your reply.

brentp commented 2 years ago

I don't see anything obviously wrong with that. Can you run with /usr/bin/time -v smoove annotate ... and check the memory use?

you could also check if you get any output by viewing stdout instead of piping. perhaps these bits of information can help us diagnose.

brentp commented 2 years ago

Oh. Somehow I missed the "hangup" part of your message. Check here: https://en.wikipedia.org/wiki/SIGHUP this means the terminal where you are running your process got disconnected. I'd just run it in screen submit job to a compute node.