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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Segmentation fault when using --vt price #89

Open Thatguy027 opened 5 years ago

Thatguy027 commented 5 years ago

Hello,

I usually run rvtest on a linux cluster, but want to add mac compatibility to my workflow. I downloaded the latest release of RVtests and am trying to run it the same way as I run it on the lcluster:

~/Downloads/rvtests_macos/executable/rvtest --pheno PC1.ped --out PC1 --inVcf WI.20180527.impute.vcf.gz --f
reqUpper 0.05 --freqLower $min_af --geneFile ~/github_repos/cegwas2-nf/bin/refFlat.ws245.txt --vt price --kernel skat

This causes a segmentation fault error:

Matrix() called 393 times
Matrix() called 394 times
Matrix() called 395 times
Matrix() called 396 times
[INFO]  Gene WBGene00008104 has 0 variants, skipping
Segmentation fault: 11

I did some looking at other segmentation issues posted on the github page and thought it might have to do with calling multiple RV tests in a single run. I removed --vt price and just ran with --kernel skat and it worked, but I ran into the same segmentation issue when attempting to run --vt price alone.

Any idea what might be causing this?

pushpinder-bu commented 4 months ago

Hello,

I am getting the same error when I run --vt price. You found any solution?