Seg fault on --make-bed

[chrchang]

Seg fault on --make-bed

[chrchang]

1. Check whether the latest stable build also segfaults here.
2. If it does, check whether the --make-bed component fails in isolation, with --bfile [plink-temporary file] --allow-extra-chr --make-bed after the first crash; this should indicate whether the bug is in the --bcf or the --make-bed code.

[ryanlayer]

Latest version has the same result:

$ time ~/src/plink1.90b2t/plink     --make-bed     --bcf ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf     --out ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink     --allow-extra-chr
PLINK v1.90b2t 64-bit (20 Dec 2014)        https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.log.
32054 MB RAM detected; reserving 16027 MB for main workspace.
--bcf: 84739k variants complete.
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.bed
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.bim
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary.fam
written.
84739846 variants loaded from .bim file.
2504 people (0 males, 0 females, 2504 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.nosex
.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 2504 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.980324.
84739846 variants and 2504 people pass filters and QC.
Note: No phenotypes present.
--make-bed to
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.bed
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.bim
+
ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink.fam
Segmentation fault (core dumped)

real    43m27.661s
user    37m54.756s
sys     1m6.058s

When I try your suggestion to run --make-bed using --bfile on the tmp file I get another seg fault:

$ time ~/src/plink1.90b2t/plink     --make-bed     --bfile ALL.phase3_shapeit2_mvncall_integrated_v5_extra_anno.20130502.genotypes.bcf.plink-temporary     --out plink.test     --allow-extra-chr
PLINK v1.90b2t 64-bit (20 Dec 2014)        https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink.test.log.
32054 MB RAM detected; reserving 16027 MB for main workspace.
84739846 variants loaded from .bim file.
2504 people (0 males, 0 females, 2504 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.test.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 2504 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.980324.
84739846 variants and 2504 people pass filters and QC.
Note: No phenotypes present.
Segmentation fault (core dumped)

real    3m3.203s
user    0m40.631s
sys     0m13.533s

[chrchang]

Thanks, I will try to reproduce and fix this tonight, and let you know if I need any more information to do so.

[chrchang]

The January 8 development build should fix this; let me know if you still have any problems. (This was actually supposed to crash, but with a "sorting of files too large to fit in RAM has not been implemented yet" error message, rather than a segfault. The multipass sorting code was already 90% written, though, so I went ahead and added the last 10%.)