Comments (8)
Just wanted to add my recent experience with plink on WSL (Ubuntu 16.04.4 LTS).
I had an issue with the precompiled Linux 64bit version (PLINK v1.90p 64-bit (7 Aug 2018)) on WSL - Core dump upon execution with a bed file (e.g. plink --bfile cohort --make-bed --out test2). However, with the same version compiled from source the operation could be completed successfully.
from plink-ng.
It worked on my Windows 10 laptop the last time I tried it; I don't know whether that's because I was using a newer version of WSL, or there's some other reason.
Is there a reason you can't use the regular Windows 32- or 64-bit builds?
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The strange thing is, the Windows 64-bit version of PLINK 1.9 runs in WSL, whereas the Linux 64-bit version doesn't (gives the segmentation fault).
The reason why I'd like to use the Linux version, is to program a script that works on both Windows and Ubuntu. I could program a workaround, but it would be awesome to get the Linux version to run on WSL.
from plink-ng.
Well, I actually got the Windows 10 laptop for the explicit purpose of investigating a WSL crash report a while ago, but "unfortunately" the Linux build ran fine... If you're familiar with C, you could try inserting debug print statements and/or using a debugger to try to isolate where the segfault is occurring.
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@chrchang Are you sure that Plink 1.9 is working fine on WSL?
I have a new laptop now, I installed WSL, downloaded the latest Plink 1.9 stable beta, and then ran the toy example command
./plink --file toy --freq --out toy_analysis
which gives me the error
PLINK v1.90p 64-bit (10 Apr 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)
The same command ran perfectly fine when using CMD Plink on the same laptop.
Edit: For the record: plink2 seems to work so far on WSL.
from plink-ng.
As I stated above, plink 1.9 appears to work on some WSL setups and not others, and unfortunately, the Windows 10 laptop I bought for the express purpose of trying to replicate WSL bug reports was not able to reproduce this.
Unless you can provide me a remote login which lets me e.g. inspect the core dump, and/or insert debug-prints and recompile until I've isolated the cause, you'll have to do that yourself and tell me what you find; it is not reasonable for me to spend thousands of dollars buying Windows machines with different configurations until I run into one that's similar enough to yours.
from plink-ng.
That's perfectly understandable. Unfortunately I'm not proficient enough to do debug prints, but I'm lucky and PLINK2 alpha seems to work and also have all features that I currently need, so I guess I'll stick with PLINK2 for now.
Anyway, thanks for your responses!
from plink-ng.
Closing this since WSL2 exists, which should have improved compatibility across the board.
from plink-ng.
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