gemma error when I used the parameters -gs ???

[xinwang-bio]

Hi Author, When I used the gemma for GWAS analysis (Version 0.96, 05/17/2017), I encountered the errors below. How can I fix it?

Thanks Xin

############################################################################
## number of analyzed individuals = 88
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs = 9457536
## number of analyzed SNPs = 4586358
Calculating the S Matrix ... 
Reading SNPs  ==================================================100.00%
*** Error in `gemma.linux': double free or corruption (!prev): 0x000000006df031b0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x77d9e)[0x7fe503e3cd9e]
/lib64/libc.so.6(cfree+0x5b5)[0x7fe503e489f5]
/home/xinwang/software/gemma.linux[0x501ff2]
/home/xinwang/software/gemma.linux[0x4c99a9]
/home/xinwang/software/gemma.linux[0x423c2f]
/home/xinwang/software/gemma.linux[0x4050ac]
/lib64/libc.so.6(__libc_start_main+0xf0)[0x7fe503de4fe0]
/home/xinwang/software/gemma.linux[0x4054b1]
======= Memory map: ========
00400000-00962000 r-xp 00000000 fd:01 27000875                           /home/xinwang/software/gemma.linux
00b62000-00b67000 r--p 00562000 fd:01 27000875                           /home/xinwang/software/gemma.linux
00b67000-00b6a000 rw-p 00567000 fd:01 27000875                           /home/xinwang/software/gemma.linux
00b6a000-00b6b000 rw-p 00000000 00:00 0 
01b36000-7fe4a000 rw-p 00000000 00:00 0                                  [heap]
7fe443cfc000-7fe4a3cfd000 rw-p 00000000 00:00 0 
7fe4fdb85000-7fe501b86000 rw-p 00000000 00:00 0 
7fe503b87000-7fe503bc4000 r-xp 00000000 fd:01 27793980                   /usr/lib64/libquadmath.so.0.0.0
7fe503bc4000-7fe503dc3000 ---p 0003d000 fd:01 27793980                   /usr/lib64/libquadmath.so.0.0.0
7fe503dc3000-7fe503dc4000 r--p 0003c000 fd:01 27793980                   /usr/lib64/libquadmath.so.0.0.0
7fe503dc4000-7fe503dc5000 rw-p 0003d000 fd:01 27793980                   /usr/lib64/libquadmath.so.0.0.0
7fe503dc5000-7fe503f78000 r-xp 00000000 fd:01 27787842                   /usr/lib64/libc-2.20.so
7fe503f78000-7fe504178000 ---p 001b3000 fd:01 27787842                   /usr/lib64/libc-2.20.so
7fe504178000-7fe50417c000 r--p 001b3000 fd:01 27787842                   /usr/lib64/libc-2.20.so
7fe50417c000-7fe50417e000 rw-p 001b7000 fd:01 27787842                   /usr/lib64/libc-2.20.so
7fe50417e000-7fe504182000 rw-p 00000000 00:00 0 
7fe504182000-7fe504199000 r-xp 00000000 fd:01 27787868                   /usr/lib64/libpthread-2.20.so
7fe504199000-7fe504398000 ---p 00017000 fd:01 27787868                   /usr/lib64/libpthread-2.20.so
7fe504398000-7fe504399000 r--p 00016000 fd:01 27787868                   /usr/lib64/libpthread-2.20.so
7fe504399000-7fe50439a000 rw-p 00017000 fd:01 27787868                   /usr/lib64/libpthread-2.20.so
7fe50439a000-7fe50439e000 rw-p 00000000 00:00 0 
7fe50439e000-7fe5043b4000 r-xp 00000000 fd:01 27792474                   /usr/lib64/libgcc_s-4.9.2-20150212.so.1
7fe5043b4000-7fe5045b3000 ---p 00016000 fd:01 27792474                   /usr/lib64/libgcc_s-4.9.2-20150212.so.1
7fe5045b3000-7fe5045b4000 r--p 00015000 fd:01 27792474                   /usr/lib64/libgcc_s-4.9.2-20150212.so.1
7fe5045b4000-7fe5045b5000 rw-p 00016000 fd:01 27792474                   /usr/lib64/libgcc_s-4.9.2-20150212.so.1
7fe5045b5000-7fe5046bc000 r-xp 00000000 fd:01 27787850                   /usr/lib64/libm-2.20.so
7fe5046bc000-7fe5048bb000 ---p 00107000 fd:01 27787850                   /usr/lib64/libm-2.20.so
7fe5048bb000-7fe5048bc000 r--p 00106000 fd:01 27787850                   /usr/lib64/libm-2.20.so
7fe5048bc000-7fe5048bd000 rw-p 00107000 fd:01 27787850                   /usr/lib64/libm-2.20.so
7fe5048bd000-7fe5049ad000 r-xp 00000000 fd:01 27787890                   /usr/lib64/libstdc++.so.6.0.20
7fe5049ad000-7fe504bad000 ---p 000f0000 fd:01 27787890                   /usr/lib64/libstdc++.so.6.0.20
7fe504bad000-7fe504bb5000 r--p 000f0000 fd:01 27787890                   /usr/lib64/libstdc++.so.6.0.20
7fe504bb5000-7fe504bb7000 rw-p 000f8000 fd:01 27787890                   /usr/lib64/libstdc++.so.6.0.20
7fe504bb7000-7fe504bcc000 rw-p 00000000 00:00 0 
7fe504bcc000-7fe504cf1000 r-xp 00000000 fd:01 27793985                   /usr/lib64/libgfortran.so.3.0.0
7fe504cf1000-7fe504ef1000 ---p 00125000 fd:01 27793985                   /usr/lib64/libgfortran.so.3.0.0
7fe504ef1000-7fe504ef2000 r--p 00125000 fd:01 27793985                   /usr/lib64/libgfortran.so.3.0.0
7fe504ef2000-7fe504ef4000 rw-p 00126000 fd:01 27793985                   /usr/lib64/libgfortran.so.3.0.0
7fe504ef4000-7fe504f09000 r-xp 00000000 fd:01 27788022                   /usr/lib64/libz.so.1.2.8
7fe504f09000-7fe505108000 ---p 00015000 fd:01 27788022                   /usr/lib64/libz.so.1.2.8
7fe505108000-7fe505109000 r--p 00014000 fd:01 27788022                   /usr/lib64/libz.so.1.2.8
7fe505109000-7fe50510a000 rw-p 00015000 fd:01 27788022                   /usr/lib64/libz.so.1.2.8
7fe50510a000-7fe50512b000 r-xp 00000000 fd:01 27787835                   /usr/lib64/ld-2.20.so
7fe505309000-7fe505311000 rw-p 00000000 00:00 0 
7fe505324000-7fe505327000 rw-p 00000000 00:00 0 
7fe505327000-7fe505329000 r--p 00000000 00:00 0                          [vvar]
7fe505329000-7fe50532b000 r-xp 00000000 00:00 0                          [vdso]
7fe50532b000-7fe50532c000 r--p 00021000 fd:01 27787835                   /usr/lib64/ld-2.20.so
7fe50532c000-7fe50532d000 rw-p 00022000 fd:01 27787835                   /usr/lib64/ld-2.20.so
7fe50532d000-7fe50532e000 rw-p 00000000 00:00 0 
7fff615d6000-7fff615f8000 rw-p 00000000 00:00 0                          [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[1]+  Aborted                 (core dumped) gemma.linux -bfile all_for_fastlmm -gs -o gemma.kinship

[pjotrp]

Please try running the latest gemma from https://github.com/genetics-statistics/GEMMA/issues/90.

[pcarbo]

@wangxinbio What is the command you ran? Maybe try with a smaller number of SNPs (e.g., 1000) to start? Perhaps there is a memory issue with loading >9 million SNPs into memory.

[pjotrp]

Please run the latest gemma as pointed to above. Any discussion that does not refer to development of gemma should be on the mailing list: https://groups.google.com/forum/#!forum/gemma-discussion

[xinwang-bio]

@pjotrp @pcarbo Thanks. I will try it.

[pcarbo]

@wangxinbio To clarify, we are migrating all Q&A and discussion (except for bug reports and development-related discussion) to the GEMMA mailing list. I encourage you to subscribe to the mailing list and post your question there. Please see:

https://groups.google.com/group/gemma-discussion

(Note it is easy to unsubcribe at any point.)