Comments (6)
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.
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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).
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Hi, can you share the input VCF file?
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I've send the link through your gmail account
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ah OK I see, i'll rename the samples and try again
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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.
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Related Issues (20)
- Sex QC for one sample HOT 7
- Legend results in relatedness plot HOT 2
- [Question]: difference between sites.hg38.vcf.gz and sites.hg38.rna.vcf.gz HOT 2
- Re-use of inferred parent names in large families HOT 1
- SIGSEGV: Illegal storage access. (Attempt to read from nil?) HOT 2
- Failing to run find-sites HOT 10
- sex check HOT 6
- How sex is inferred HOT 1
- Why this is a male? HOT 1
- Relatedness color pattern issue in plot HOT 6
- IBS1 count
- Extracted genotypes format? HOT 2
- Inference questions
- sm1.somalier and no other output HOT 5
- [error] SIGSEGV: Illegal storage access. (Attempt to read from nil?) Segmentation fault (core dumped) ( HOT 14
- Scaled mean depth on X - how to calculate? HOT 1
- chrX sites count
- Reading .somalier binary files - how is the SNP order determined? HOT 2
- `Argument list too long' on 90k samples running ancestry HOT 1
- Somalier with pooled parents HOT 1
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