Segmentation faults when running example in demo.txt

[nmc97]

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!

[pcarbo]

Hi @nmc97,

It appears that Xiang introduced a bug in GEMMA sometime between versions 0.94a and 0.95a; I was able to reproduce your bug with GEMMA 0.95a, and I did not get a segmentation fault with GEMMA 0.94a. So one temporary solution would be to download the v0.94 executable from here or here.

@xiangzhou, are you able to reproduce this segmentation fault? If so, could you investigate this bug?

Peter

[xiangzhou]

This bug inside mvlmm.cpp is fixed now.

[nmc97]

Thank you both!