Segmentation fault (core dumped)

[jwestmeier]

I have been trying to set up eCAVIAR and getting it to run on the sample data. Unfortunately, I get an error message that doesn't help much and the website for documentation is not available.

This is the command I used: ./eCAVIAR -z ./sample_data/GWAS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.Z.txt -ld ./sample_data/GWAS.ADGC.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld -z ./sample_data/eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.ILMN_1810712.NM_015313.1.ARHGEF12.Z.txt -ld ./sample_data/eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld -f 1 -c 2 -o ./sample_data/Coloc_test

And this is the error I get: @-------------------------------------------------------------@	eCAVIAR!	v2.2	10/Apr/2018
(C) 2018 Farhad Hormozdiari, GNU General Public License, v2
-------------------------------------------------------------
For documentation, citation & bug-report instructions:
http://genetics.cs.ucla.edu/caviar/

@-------------------------------------------------------------@ Segmentation fault (core dumped)

Is there any way to find out what the problem is?

[fhormoz]

This generally happen for two reasons:

1) One of the input files have nan. Can you check your Z-score file and LD-file and make sure there is no nan?

2) The number of variants do not match. Can you make sure. you have the same number of line in both Z-score files and the number of rows and columns in the LD file matches as well.

so:

wc -l /sample_data/GWAS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.Z.txt wc -l ./sample_data/GWAS.ADGC.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld wc -l ./sample_data/eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.ILMN_1810712.NM_015313.1.ARHGEF12.Z.txt wc -l ./sample_data/eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld awk '{print NF}' ./sample_data/GWAS.ADGC.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld | sort | uniq awk '{print NF}' ./sample_data/eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.LD.ld | sort | uniq

all the above commands should give the same output value.

[jwestmeier]

The output of the commands is always the same (75) and the don't contain any NAs. Could there be another reason for the error?

[fhormoz]

It is possible to email me a sample data. My email is farhad.hormozdiari@gmail.com

[tingqi]

I had the same issue when I used the example data. Have you got the solution? @juschroeder. Any comments/suggestions would be appreciated.

[Daphne-myue]

Have you got the solution? I have the same issue even I put only 10 SNPs data with the same lines of .ld/gwas.zscore/*qtl.zscore. Please feel free to contact me if you have any idea. @fhormozdiari @juschroeder

[fhormoz]

Can you make sure your GSL version is 2.6? If you are using GSL 2.6 you can send me an input example. My email is farhad.hormozdiari@gmail.com

[hailingfang]

Hi, I met this problem too when I compile it under centos8. And I compile it under Freebsd 13, and the problem gone.

Update: I update armadillo to 10.7.3 and the problem solved, But I still confuse, and don't know why.