Error in MLMA

Hi, I'm working with two data sets I combined; one case-control (though with some hidden relatedness) and one with family data.

After combining them I wanted to do some QC, particularly trying to see if some SNPs were strongly associated with an indicator variable I coded representing each data set (0, 1).

I ran GCTA to get a grm to include in the mlma, then ran the mlma;

gcta64 --mlma --bfile MA-NA-ExomeChip-Merged-maf01-geno01-051916 --grm step1-grm --pheno NAandMA-caseControl-altPheno-forQC.txt --out test

Here is the output:

*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24.7
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Thu May 19 16:43:48 2016

Options:
--mlma
--bfile MA-NA-ExomeChip-Merged-maf01-geno01-051916
--grm step1-grm
--pheno NAandMA-caseControl-altPheno-forQC.txt
--out test

Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine.

Reading PLINK FAM file from [MA-NA-ExomeChip-Merged-maf01-geno01-051916.fam].
1332 individuals to be included from [MA-NA-ExomeChip-Merged-maf01-geno01-051916.fam].
Reading PLINK BIM file from [MA-NA-ExomeChip-Merged-maf01-geno01-051916.bim].
40652 SNPs to be included from [MA-NA-ExomeChip-Merged-maf01-geno01-051916.bim].
Reading PLINK BED file from [MA-NA-ExomeChip-Merged-maf01-geno01-051916.bed] in SNP-major format ...
Genotype data for 1332 individuals and 40652 SNPs to be included from [MA-NA-ExomeChip-Merged-maf01-geno01-051916.bed].
Reading phenotypes from [NAandMA-caseControl-altPheno-forQC.txt].
Non-missing phenotypes of 1332 individuals are included from [NAandMA-caseControl-altPheno-forQC.txt].
Reading IDs of the GRM from [step1-grm.grm.id].
1332 IDs read from [step1-grm.grm.id].
Reading the GRM from [step1-grm.grm.bin].
Pairwise genetic relationships between 1332 individuals are included from [step1-grm.grm.bin].
1332 individuals are in common in these files.

Performing MLM association analyses (including the candidate SNP) ...

Performing REML analysis ... (Note: may take hours depending on sample size).
1332 observations, 1 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 0.107612 0.080076
logL: 614.755
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 711.14 0.10613 0.00000 (1 component(s) constrained)

Error: the variance-covaraince matrix V is not positive definite.

Analysis finished: Thu May 19 16:43:51 2016
Computational time: 0:0:3

I also ran the analysis using the --reml-no-constrain flag. Any ideas why I am getting this error?

Thanks,
Whitney