Error: Failed to create thread

[Jill Rabinowitz]

Hi there,

I am running the following line of code in PLINK and I am getting an error message I have never seen before.

[compute-127 /legacy/amber2/scratch/bmaher/ALIVEMethyl/PRS]$ plink --bfile c1c2_miss_mfa_hwe2_hetero_AA --extract indepSNPs2_AA.prune.in --genome --min 0.2 --out pihat_min0.2_2_AA
PLINK v1.90b6.6 64-bit (10 Oct 2018)           www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to pihat_min0.2_2_AA.log.
Options in effect:
  --bfile c1c2_miss_mfa_hwe2_hetero_AA
  --extract indepSNPs2_AA.prune.in
  --genome
  --min 0.2
  --out pihat_min0.2_2_AA

1031995 MB RAM detected; reserving 515997 MB for main workspace.
Allocated 2907 MB successfully, after larger attempt(s) failed.
5911520 variants loaded from .bim file.
829 people (0 males, 0 females, 829 ambiguous) loaded from .fam.
Ambiguous sex IDs written to pihat_min0.2_2_AA.nosex .
--extract: 426770 variants remaining.
Using up to 255 threads (change this with --threads).
Before main variant filters, 829 founders and 0 nonfounders present.
Calculating allele frequencies... done.
426770 variants and 829 people pass filters and QC.
Note: No phenotypes present.

Error: Failed to create thread.

Do you know why I am getting this message?

Warmly,

Jill

[Christopher Chang]

0. --genome/--min is less reliable and useful than plink 2.0's --make-king-table/--king-table-filter.

1. It looks like you're running on a shared machine, and there may have simply been too many other threads running on the system at the time.  You can add e.g. "--threads 8" to your command line to limit how many threads plink tries to create.