--pca ending in Segmentation Fault (core dump)

[Letitia Sng]

Hi, I am trying to calculate PCs of the 1000 Genomes using the following command:

plink2 \

    --vcf chrALL.1000g.ukbb.recode.vcf.gz \

    --extract chrALL.1000g.ukbb.prune.in \

    --freq counts \

    --pca allele-wts vzs \

    --out chrALL.1000g.ukbb.pruned \

    --memory 128000 \

    --threads 15 \

    --debug

But once the GRM has been constructed, I get a segmentation fault with a core dump, ending my run prematurely. 

I have been running Plink version: PLINK v2.00a3 AVX2 (28 Oct 2020). I've also included the log file. Any help would be greatly appreciated! 

[Christopher Chang]

This is definitely a bug, but I haven't been able to replicate it.  What operating system are you running on?  Is it possible for you to send me a set of input files that I can use to try to replicate the crash?

[Letitia Sng]

It's running on:

Distributor ID: SUSE

Description:    SUSE Linux Enterprise Server 12 SP4

Release:        12.4

The (.gz) input files are quite large to send, but I could upload it somewhere. It's the publicly available 1000 Genomes Phase3 Autosomal vcfs that have been filtered to common variant locations. 

[Christopher Chang]

Ok, it should be sufficient to post the output of --write-snplist on the original VCF, and the .prune.in file, then.

Do you know how this plink2 build was compiled?  Its version string does not correspond to the Linux precompiled binary (no "Intel"), so I should try to link to the same linear algebra library, etc.

[Letitia Sng]

A .zip of the output of --write-snplist and the prune.in file can be found here. 

This job is being run on my organisation's HPC, so I don't have the details on how the build was compile, but I can find that out. It might take some time though.

[Christopher Chang]

Ok, let me know when you have that information, I'm still unable to reproduce the segfault.

[Letitia Sng]

It looks like this issue was due to the compilation on the cluster. The commands now work with no segmentation fault. Thanks for help and quick responses!