version 1.04 vs. version 1.24 - bugs

Hi,

I used GCTA for over three years and I realized that the new version can't handle files in the same manner as the original version.

Here is an example: 

I started running GCTA 1.24 on a quantitative traits with no covariates and I got this error message:

Error: the X^t * V^-1 * X matrix is not invertible. Please check the covariate(s) and/or the environmental factor(s).

However, when I run GCTA v1.04 - I got no error message but the output is clueless

Source Variance SE
V(G) 955.077654 62.060516
V(e) 0.000486 45.725337
Vp 955.078141 33.530453
V(G)/Vp 0.999999 0.047876
logL -11831.269
logL0 -11830.108
LRT 0.000
df 1
Pval 0.5
n 3292


Now, I am wondering what does this error message mean:

Error: the X^t * V^-1 * X matrix is not invertible. Please check the covariate(s) and/or the environmental factor(s).

If I am not using any covariate but only one quantitative phenotype.

Similarly, this same phenotype work on a large sets of SNPs (11 million SNPs) but get this error message on a smaller sets of SNPs (700K SNPs):

Error: Log-likelihood not converged (stop after 100 iteractions).
You can specify the option --reml-maxit to allow for more iterations.

But after modifying --reml to --reml-maxit 200 - the program do not even run...:


--mgrm XXX
--pheno XXXX
--reml-maxit 200
--out XXXXX
--thread-num 3

Note: the program will be running on 3 threads.


Analysis finished: Fri Jun 6 14:09:40 2014
Computational time: 0:0:0

Thanks for your help