Segfault after calling

Hi,

I’m getting a segfault running sniffles from commit 53b7500 on Ubuntu 20.04 with the following command:

sniffles \
    -m path/to/sorted.bam \
    -v path/to/sniffles.vcf \
    --tmp_file /path/to/tmp/tmpn81h96mu \
    -t 64 \
    &> logs/sniffles.log

I mapped the reads with minimap2 using the --MD flag.

Calling seems to finish but then sniffles segfaults. I can’t see any problems in the output VCF and there’s no error in the stdout/stderr. The final message is:

	Finalizing  ..

I’ve pasted the full output here.

Thanks!

[TomHarrop]

Hi Fritz, yep, it does finish if I don’t specify --tmp_file. Thanks for the help.

[fritzsedlazeck]

Thanks for the confirmation. The temp file is not large… So I never use that option 😃. Thanks for letting me know