Closed xtmgah closed 3 years ago
fhormoz
commented
5 years ago I think most probability your LD or Z-score file has nan. Can you convert nan to 0? Please let me know if you still have the Segmentation fault. I will try to fix this in the next version to output a warning if the files have nan.
zpliu
commented
5 years ago I think most probability your LD or Z-score file has nan. Can you convert nan to 0? Please let me know if you still have the Segmentation fault. I will try to fix this in the next version to output a warning if the files have nan.
@fhormoz Thanks for the reply. I think it is caused by nan value. I did not check the LD matrix very carefully at the beginning. Later, I only pick SNPs that existed in the 1KG data (thus no nan value), it works fine.
BTW, I noticed in the latest version, there are sample data for colocalization analysis (eQTL.CARDIOGENICS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.ILMN_1810712.NM_015313.1.ARHGEF12.Z.txt and GWAS.MC.AD.IGAP.stage1.hg19.chr.11.121344805.121517613.CHRPOSREFALT.Z.txt). They have the exactly same SNPs but rho values in ld files are different. Why is this?
Hello:
I am trying the caivar on the eQTL and GWAS data for few GWAS loci. However, some loci are completed and some loci had a error information like "segmentation fault"... Here i gave a example. Here is the output from my command. Could you help to check and fix this error? Thanks so much.
eCAVIAR -l test_GWAS.ld -l test_eQTL.ld -z test_GWAS.z -z test_eQTL.z -o output
@-------------------------------------------------------------@ -0 0 add 0 0.1 add 0 0.2 add 0 0.3 add 0 0.4 add 0 0.5 add 4.94066e-324 0.6 FINISH reach=2659 2659 Max Causal=2 Total=3536471 0 5.67241e-23 100000 4.2641e-17 200000 4.98178e-17 300000 5.67564e-17 400000 6.55714e-17 500000 7.24377e-17 600000 8.29678e-17 700000 9.06624e-17 800000 9.79103e-17 900000 1.03529e-16 1000000 1.09101e-16 1100000 1.15797e-16 1200000 1.22241e-16 1300000 1.29166e-16 1400000 1.36004e-16 1500000 1.47125e-16 1600000 1.55799e-16 1700000 1.64667e-16 1800000 1.74226e-16 1900000 1.81991e-16 2000000 1.90807e-16 2100000 2.01153e-16 2200000 2.14104e-16 2300000 2.34897e-16 2400000 3.31121e-16 2500000 7.22409e-13 2600000 7.22409e-13 2700000 7.22409e-13 2800000 7.22409e-13 2900000 7.22409e-13 3000000 7.22409e-13 3100000 7.22409e-13 3200000 7.22409e-13 3300000 7.22409e-13 3400000 7.22409e-13 3500000 7.22409e-13 Total Likelihood= 1.444780e-12 SNP=2659
1183 4.850940e-01
-0 0 add 0 0.1 add 0 0.2 add 0 0.3 add 0 0.4 add 0 0.5 add 4.94066e-324 0.6 Segmentation fault
The data can be download here:
https://www.dropbox.com/sh/d3wspkfm5csknk5/AABAhXeqWbfakgTBX8LJnwPpa?dl=0