problems using plink 1.9 with Ubuntu --Segmentation fault (core dumped).

[Sheila Adams-Sapper]

I am running Ubuntu 16.04.2 LTS (x86_64) on my Windows 10 computer (I successfully run myriad linux-based software on it).  I downloaded plink_linux_x86_64.zip and after unzip, moved the plink executable to /usr/local/bin.  To test that it is installed in my path I type 'plink from any directory', I see:

PLINK v1.90b6.5 64-bit (13 Sep 2018)           www.cog-genomics.org/plink/1.9/

(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3

  plink [input flag(s)...] {command flag(s)...} {other flag(s)...}

  plink --help {flag name(s)...}

etc.

which is encouraging. 

the zip folder included toy.map and toy.ped.  The user instructions says to run:

 plink --file toy --freq --out toy_analysis

I did this in the folder that contained the map and ped files.  This is the message I get:

PLINK v1.90b6.5 64-bit (13 Sep 2018)           www.cog-genomics.org/plink/1.9/

(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to toy_analysis.log.

Options in effect:

  --file toy

  --freq

  --out toy_analysis

Segmentation fault (core dumped).

I have also tried 

plink --file HapMap_3_r3_1 --freq --out test_analysis

which represents a file I downloaded for a plink tutorial, but I basically get the same message with the segmentation fault error.

any clues here in regard to what I try next?

Sheila

[Christopher Chang]

Unless you have some experience with C programming and can recompile plink locally in an effort to debug the plink-WSL incompatibility, you'll have to use the Windows build.  (I actually bought a Windows 10 laptop solely for the purpose of trying to reproduce the WSL crash, but 'unfortunately' the Linux plink binary works properly on my laptop, and it's not practical for me to keep buying more Windows machines until I run into one which exhibits the crash.)

[Sheila Adams-Sapper]

Thanks for the quick reply.  I tried it on an AWS instance and it does work fine, so I'll just run it there.

On Wednesday, September 26, 2018 at 8:53:36 PM UTC-7, Sheila Adams-Sapper wrote: