Multitrait GWAS (-lmm) has NaN values for Se(Ve) #45
Description
Hello,
I have attempted multitrait GWAS with two traits and a kinship matrix (no other covariates) and I think something must be wrong with my input data. Here's the command line output:
lindroth@lindroth-5810:/usr/share/gemma_program$ ./gemma -bfile WisAsp_BCFfiltered_VCFfiltered_vcf-merge_VCFfiltered-take2_maf05_plink_LinkImpute_LDprune -k output/kinship.cXX.txt -lmm 4 -n 13 15 -o wisasp_multitrait
Reading Files ...
## number of total individuals = 446
## number of analyzed individuals = 445
## number of covariates = 1
## number of phenotypes = 2
## number of total SNPs = 139570
## number of analyzed SNPs = 139570
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
2.0034
-0.2032 2.0683
se(Vg):
1.5507
1.0244 0.9791
REMLE estimate for Ve in the null model:
0.4170
-0.4272 0.4377
se(Ve):
0.4100
0.2699 0.2571
REMLE likelihood = -1177.0001
MLE estimate for Vg in the null model:
2.2770
-0.4818 2.3521
se(Vg):
0.2408
0.1944 0.2496
MLE estimate for Ve in the null model:
0.3447
-0.3532 0.3618
se(Ve):
-nan
-nan 0.0000
MLE likelihood = -684011.4970
Reading SNPs 0.00%
The se(Ve) has NaNs and the "Reading SNPs" does not advance from 0.00%. The command does not execute fully. Do you have any suggestions for what could be wrong with the input data? I can attach the data as a zip if needed.
Thank you very much!
Hilary