Illegals storage access. (Attempt to read from nil)
vdejager opened this issue · comments
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
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).
Hi, can you share the input VCF file?
I've send the link through your gmail account
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.
ah OK I see, i'll rename the samples and try again
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.