Illegals storage access. (Attempt to read from nil)

[vdejager]

Hi Brent,

I'm trying to compare two VCFs (hg19) for relatedness and stumbled on your tool.

somalier extract -d extracted/ --sites /home/victor/commondata/sites.hg19.vcf.gz -f /home/victor/commondata/human_g1k_v37_decoy.fasta 071181/071181_xAtlas.recode.sorted.vcf.gz
somalier version: 0.2.10
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
[somalier] FORMAT field 'AD' not found for depth information. using genotype only
[somalier] found 10531 sites
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

any ideas how to resolve this? its probably a file that cannot be accessed similar to one ticked reported for slivar

[vdejager]

Hi Brent, the problem seems to be in the VCF file. If I run somalier with GATK3 VCF files it works perfectly. the xAtlas VCF file shows the above issue (tested with a variety of xAtlas files and GATK3 & 4 files. The same occurs with multisample VCF files, GATK derived multisample files work fine, xAtlas multisample files crash somalier).

[brentp]

Hi, can you share the input VCF file?

[vdejager]

I've send the link through your gmail account

[brentp]

Got it. Thanks for sending.
Your sample name is a long path, e.g. /path/to/SNVCalling_20190403_xatlas/071180. somalier tries to use that as part of a file to open (assuming it would be something like sample_0711801). I'll try to give a better error message for this, but even then you'll have to change your sample name to something that's not path-like.

[vdejager]

ah OK I see, i'll rename the samples and try again

[brentp]

I am making a change so you'll see:

Error: unhandled exception: somalier: error opening file: extracted///path/to/xatlas/071180.somalier [IOError]

which will at least give a little more insight into what is going on.