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brentp / somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
MIT License
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Error extracting from a VCF #98

Open marcustutert opened 2 years ago

marcustutert commented 2 years ago

Hi Brent,

Running into a weird issue here. I've tried to run SOMALIER to extract from a VCF using the following command but have received an error that suggests it can't parse the VCF sample. The output of the command results in ~17k samples have a .somalier generated (out of the 22k in the VCF) but for some reason it fails at this sample ID for some strange reason.

/lustre/scratch123/hgi/mdt2/projects/ibdgwas_bioresource/mt27/somalier/somalier extract -s /lustre/scratch123/hgi/projects/ibdgwas_bioresource/mt27/somalier/sites.hg38.nochr.vcf.gz -f /lustre/scratch118/humgen/resources/ref/Homo_sapiens/HS38DH/hs38DH.fa -d /lustre/scratch123/hgi/mdt2/projects/ibdgwas_bioresource/mt27/CSI/Scratch/Somalier_Data/Extracted_Somalier/WES/ /lustre/scratch123/hgi/mdt2/projects/ibdgwas_bioresource/mt27/CSI/Scratch/Somalier_Data/VCF/WES.vcf.gz
somalier version: 0.2.16
[somalier] FORMAT field 'AD' not found for depth information. using genotype only
[somalier] found 344 sites
common.nim(98)           write_counts
Error: unhandled exception: somalier: error opening file: /lustre/scratch123/hgi/mdt2/projects/ibdgwas_bioresource/mt27/CSI/Scratch/Somalier_Data/Extracted_Somalier/WES//EGAN00002847587_EGAN00002847587.somalier [IOError]
brentp commented 2 years ago

is there a limit on disk space at that mount point? (/lustre/scratch123/hgi/mdt2/projects/ibdgwas_bioresource/mt27/CSI/Scratch/Somalier_Data/Extracted_Somalier/WES/)?

or does that file already exist with permissions that won't allow you to overwrite?