dfam in newest developer version

[Jiawen Chen]

Hi,

I try to use dfam to analyze parent and sibling data. Here is the ouput file.

PLINK v1.90p 64-bit (28 Oct 2019)              www.cog-genomics.org/plink/1.9/

(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to /z/Comp/lu_group/Members/jiawen/ASD/TDT/result/1mv3.log.

Options in effect:

  --allow-no-sex

  --bfile /z/Comp/lu_group/Members/jiawen/ASD/TDT/bfile_sibling/1mv3_sibling

  --debug

  --dfam

  --out /z/Comp/lu_group/Members/jiawen/ASD/TDT/result/1mv3

773800 MB RAM detected; reserving 386900 MB for main workspace.

111439 variants loaded from .bim file.

85680 people (840 males, 840 females, 84000 ambiguous) loaded from .fam.

Ambiguous sex IDs written to

/z/Comp/lu_group/Members/jiawen/ASD/TDT/result/1mv3.nosex .

85680 phenotype values loaded from .fam.

Using 1 thread (no multithreaded calculations invoked).

Before main variant filters, 1680 founders and 84000 nonfounders present.

Calculating allele frequencies... done.

Total genotyping rate is 0.99985.

111439 variants and 85680 people pass filters and QC.

Among remaining phenotypes, 0 are cases and 85680 are controls.

Segmentation fault (core dumped)

I try to open all the access for both plink and result folder, it still does not work... Could you please check that?

[Christopher Chang]

Can you post a test dataset I can use to replicate the segfault? Thanks.

[Christopher Chang]

For what it's worth, this bug should be fixed in today's build; it'll consistently print the correct error message (at least one case is needed for --dfam) instead of possibly segfaulting.