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millanek / Dsuite

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
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Program received signal SIGSEGV, Segmentation fault. #104

Open Cjianghao opened 1 month ago

Cjianghao commented 1 month ago

Processed 598000 variants in 151.979secs，Program received signal SIGSEGV, Segmentation fault.I first suspected that it was a problem with my vcf file because I did not filter for missing sites when filtering, but later I used vcftools to filter, and the result was still the same problem. I downloaded your test data on GitHub, and the results are available. It runs smoothly. Then I found that the INFO column was missing from my data, so I used bcftools to supplement it, bcftools_pluginCommand=plugin fill-tags -Oz -o， But it still doesn't work, and then I found out that my vcf may not be a phased VCF file. I used java - jar beamle.28Jun21.220.jar gt=input.vcf.gz out=phased vcf_file。After processing, it still doesn't work. The information in the picture is my VCF file。Do you know what's going on?

Cjianghao commented 1 month ago

1 11298 1_11298 G A . . PR;AN=382;AF=0.136126;AC=52;F_MISSING=0;NS=191;MAF=0.136126;AC_Het=52;AC_Hom=0;AC_Hemi=0;HWE=0.0282798;ExcHet=0.0178012 GT 0/1 0/0 0/0 0/1 0/0
1 11338 1_11338 A G . . PR;AN=382;AF=0.0575916;AC=22;F_MISSING=0;NS=191;MAF=0.0575916;AC_Het=22;AC_Hom=0;AC_Hemi=0;HWE=1;ExcHet=0.526683 GT 0/0 0/0 0/0 0/0 0/0
1 15360 1_15360 T G . . PR;AN=382;AF=0.191099;AC=73;F_MISSING=0;NS=191;MAF=0.191099;AC_Het=57;AC_Hom=16;AC_Hemi=0;HWE=0.639715;ExcHet=0.778274 GT 0/1 1/1 0/1 0/0 0/0
1 16576 1_16576 C T . . PR;AN=382;AF=0.123037;AC=47;F_MISSING=0;NS=191;MAF=0.123037;AC_Het=35;AC_Hom=12;AC_Hemi=0;HWE=0.0440633;ExcHet=0.98847 GT 0/0 0/0 0/0 0/0 0/0
1 18308 1_18308 G A . . PR;AN=382;AF=0.32199;AC=123;F_MISSING=0;NS=191;MAF=0.32199;AC_Het=79;AC_Hom=44;AC_Hemi=0;HWE=0.507142;ExcHet=0.824645 GT 0/1 0/0 0/0 0/0 0/0
1 23743 1_23743 G T . . PR;AN=382;AF=0.418848;AC=160;F_MISSING=0;NS=191;MAF=0.418848;AC_Het=88;AC_Hom=72;AC_Hemi=0;HWE=0.459637;ExcHet=0.823084 GT 0/1 1/1 0/1 0/0 0/0
1 27176 1_27176 G A . . PR;AN=382;AF=0.410995;AC=157;F_MISSING=0;NS=191;MAF=0.410995;AC_Het=85;AC_Hom=72;AC_Hemi=0;HWE=0.295124;ExcHet=0.903885 GT 0/1 0/0 0/0 0/0 0/0
1 29968 1_29968 C T . . PR;AN=382;AF=0.078534;AC=30;F_MISSING=0;NS=191;MAF=0.078534;AC_Het=26;AC_Hom=4;AC_Hemi=0;HWE=0.319022;ExcHet=0.907246 GT 0/1 0/0 0/1 0/0 1/1 ，This is my VCF file information