Open chrisclarkson opened 2 years ago
@chrisclarkson The most concerning thing I see is that it identified 0 variants:
present in both bcf and bed file.
0 total variants on selected chromosomes.
This is likely why it later failed when processing the genotype data:
Processed genotype data for 0Segmentation fault (core dumped)
Your BED file uses chromosome names with the "chr" prefix, e.g. "chr1". What chromosome names are used in your VCF file? If they don't match, that might be the problem.
For context, here is what I see when attempted to run apex store
. It identified variants and shared samples, but then segfaulted:
bin/apex/apex store \
--vcf data/genotypes/genotypes.chr22.vcf.gz \
--bed data/expression/adipose_subcutaneous.bed.gz \
--cov data/covariates/covariates.txt.gz \
--prefix test-apex
Using 2 threads.
chr22 present in both bcf and bed file.
633161 total variants on selected chromosomes.
Found 838 samples in bcf file ...
Found 581 samples in covariate file ...
Found 663 samples in expression bed file ...
Found 581 samples in common across all files.
Segmentation fault
Quick update. From Chris' output, I guessed that apex store
failed while processing the covariates file. Thus I focused my attention there, and confirmed it was not formatted correctly. Once I fixed that, now it's running!
I downloaded the precompiled binary of this program and tried to run it on my own data- which look as follows:
BED:
... PCA (made using QTLtools):
...
VCF (bgzipped and tabix indexed)
I get an error when I try to run a cis MR on this:
Is it just the case that the software is not compatible with my system?