seg fault using --fast-epistasis with parallel with some values of je-cellmin

[Peter Andrews]

PLINK v1.90b1g 64-bit (10 Jun 2014)\

Note: toy file is too small to test epistasis because 'Error: --fast-epistasis requires at least two cases and two controls.'. Would be nice to make it tiny bit bigger

With the attached files I get a segfault when I use parallel with some settings of --je-cellmin

--je-cellmin 2 works but 3 does not.

~/bin> ./plink --fast-epistasis joint-effects --je-cellmin 2 --bfile pandrews_test --parallel 1 2
PLINK v1.90b1g 64-bit (10 Jun 2014)        https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
16011 MB RAM detected; reserving 8005 MB for main workspace.
15 variants loaded from .bim file.
2228 people (1960 males, 268 females) loaded from .fam.
2228 phenotype values loaded from .fam.
Using up to 8 threads (change this with --threads).
Calculating allele frequencies... done.
Total genotyping rate is 0.999431.
15 variants and 2228 people pass filters and QC.
Among remaining phenotypes, 1145 are cases and 1083 are controls.
--fast-epistasis: Skipping 1 site due to --je-cellmin setting.
--fast-epistasis joint-effects to plink.epi.cc.1... done.
31 valid tests performed, summary written to plink.epi.cc.summary.1 .
~/bin>


~/bin> ./plink --fast-epistasis joint-effects --je-cellmin 3 --bfile pandrews_test --parallel 1 2
PLINK v1.90b1g 64-bit (10 Jun 2014)        https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.log.
16011 MB RAM detected; reserving 8005 MB for main workspace.
15 variants loaded from .bim file.
2228 people (1960 males, 268 females) loaded from .fam.
2228 phenotype values loaded from .fam.
Using up to 8 threads (change this with --threads).
Calculating allele frequencies... done.
Total genotyping rate is 0.999431.
15 variants and 2228 people pass filters and QC.
Among remaining phenotypes, 1145 are cases and 1083 are controls.
--fast-epistasis: Skipping 1 site due to --je-cellmin setting.
--fast-epistasis joint-effects to plink.epi.cc.1... 0% [writing]Segmentation fault (core dumped)
~/bin>

[Christopher Chang]

Okay, I've replicated this; will try to post a fixed development build today.

[Christopher Chang]

This should be fixed in the 19 Jun development build; let me know if you still encounter any problems.

On Thursday, June 19, 2014 5:46:02 AM UTC+8, Peter Andrews wrote:

[Peter Andrews]

Fixed!