gsl: newton.c:88: ERROR: function value is not finite 3.08%

[jenny315]

Hi, I have the same problem

When run

gemma -bfile gwas_data -k output/Gemm.sXX.txt -lmm 1 -n 4 -o sex

log:

Reading Files ...
## number of total individuals = 19
## number of analyzed individuals = 19
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs = 19464101
## number of analyzed SNPs = 13387718
Start Eigen-Decomposition...
pve estimate =0.99999
se(pve) =0.00396103
gsl: newton.c:88: ERROR: function value is not finite           3.08%
Default GSL error handler invoked.
Aborted (core dumped)

fam file like this

G101 G101 0 0 2 F F9 2 0 1
G136 G136 0 0 2 F F5 2 0 1
G148 G148 0 0 1 M M1 1 1 0
G163 G163 0 0 2 F F2 2 0 1
G181 G181 0 0 1 M M7 1 1 0
G21 G21 0 0 2 F F10 2 0 1
G238 G238 0 0 1 M M5 1 1 0
G267 G267 0 0 2 F F7 2 0 1
G294 G294 0 0 1 M M6 1 1 0
G297 G297 0 0 2 F F3 2 0 1
G301 G301 0 0 1 M M8 1 1 0
G315 G315 0 0 2 F F1 2 0 1
G355 G355 0 0 1 M M3 1 1 0
G360 G360 0 0 2 F F11 2 0 1
G375 G375 0 0 1 M M2 1 1 0
G41 G41 0 0 2 F F6 2 0 1
G54 G54 0 0 2 F F8 2 0 1
G63 G63 0 0 1 M M4 1 1 0
G68 G68 0 0 2 F F4 2 0 1