Segmentation faults when running example in demo.txt #36
Description
I've been going through the demo and have experienced segmentation faults for one of the example processes. The rest worked fine.
On command line:
> ../bin/gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt -n 1 6 -a mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8MCH_lmm
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1197
## number of covariates = 1
## number of phenotypes = 2
## number of total SNPs = 12226
## number of analyzed SNPs = 10758
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
1.3940
-0.2267 2.0817
se(Vg):
0.1567
0.1363 0.2359
REMLE estimate for Ve in the null model:
0.3489
0.0491 0.4144
se(Ve):
0.0206
0.0166 0.0267
REMLE likelihood = -2855.1664
MLE estimate for Vg in the null model:
1.3959
-0.2267 2.0854
se(Vg):
0.1568
0.1365 0.2361
MLE estimate for Ve in the null model:
0.3483
0.0490 0.4136
se(Ve):
0.0206
0.0166 0.0266
MLE likelihood = -2856.0280
Reading SNPs ==================================================100.00%
Segmentation fault (core dumped)
Running on gdb:
(gdb) file ../bin/gemma
Reading symbols from ../bin/gemma...done.
(gdb) run -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt -n 1 6 -a mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8MCH_lmm
Starting program: /home/ubuntu/Nic/Programs/bugwas/GEMMA/bin/gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt -n 1 6 -a mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8MCH_lmm
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1197
## number of covariates = 1
## number of phenotypes = 2
## number of total SNPs = 12226
## number of analyzed SNPs = 10758
Start Eigen-Decomposition...
REMLE estimate for Vg in the null model:
1.3940
-0.2267 2.0817
se(Vg):
0.1567
0.1363 0.2359
REMLE estimate for Ve in the null model:
0.3489
0.0491 0.4144
se(Ve):
0.0206
0.0166 0.0267
REMLE likelihood = -2855.1664
MLE estimate for Vg in the null model:
1.3959
-0.2267 2.0854
se(Vg):
0.1568
0.1365 0.2361
MLE estimate for Ve in the null model:
0.3483
0.0490 0.4136
se(Ve):
0.0206
0.0166 0.0266
MLE likelihood = -2856.0280
Reading SNPs ==================================================100.00%
Program received signal SIGSEGV, Segmentation fault.
0x000000000046d369 in MVLMM::WriteFiles() ()
I got a similar error after using the down-loadable executable and compiling it myself.
If anyone can help me understand what this means and what I can do that would be great.
Thanks!