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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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SIGSEGV: Illegal storage access. (Attempt to read from nil?) #130

Closed zeliasoo closed 2 years ago

zeliasoo commented 2 years ago

While trying to run slivar v0.2.4, we encountered the following error:

Command error:

slivar version: 0.2.4 d64b67c51ab4f3323e08caf65f2bb9aeb3aab285 [slivar] no ped file specified, not able to determine family relationships. SIGSEGV: Illegal storage access. (Attempt to read from nil?)

We run slivar in our bioinformatic pipeline and everything goes smoothly, but filtered list to tsv part failed and we can't solve it. Can anyone help us solve this?

brentp commented 2 years ago

Hi, can you try with the latest version (v0.2.7) of slivar and see if that resolves it? If not, we can debug further if you can send the full command that you ran.

zeliasoo commented 2 years ago

Hi Brent, sorry I only just saw this. When I tried to run 0.2.7, it has a slightly different error message and stops at the same stage of running. 

Command error:
  > slivar version: 0.2.7 71af7d12881ae0590c6d2a97ef2b282cc93fe7c6
  [slivar] no ped file specified, not able to determine family relationships.
  warning: unknown impact "@17397477" from csq "@17397477" please report the variant at https://github.com/brentp/slivar/issues
  SIGSEGV: Illegal storage access. (Attempt to read from nil?)

Hope you can help

brentp commented 2 years ago

Hi, this is because of the way that you ran bcftools CSQ the @17397477 is a reference to another entry. You'll need to run bcftool csq something like this:

bcftools csq -s - --ncsq 40 -g $gff -l -f $fasta $vcf -O u -o $vcf_with_csq