PLINK v1.9.0-b.7.11 64-bit (19 Aug 2025)
Options in effect:
  --allow-extra-chr
  --bfile /mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset
  --distance square ibs
  --geno 0.5
  --mind 0.9
  --out /mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/ibs
  --threads 32

Hostname: n3469
Working directory: /mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants
Start time: Sat Nov 22 11:21:05 2025

Random number seed: 1763839265
1547837 MB RAM detected; reserving 773918 MB for main workspace.
7865 variants loaded from .bim file.
112 people (0 males, 0 females, 112 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/ibs.nosex
.
2 people removed due to missing genotype data (--mind).
IDs written to
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/ibs.irem
.
Using up to 32 threads (change this with --threads).
Before main variant filters, 110 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate in remaining samples is 0.966681.
118 variants removed due to missing genotype data (--geno).
7747 variants and 110 people pass filters and QC.
Note: No phenotypes present.
Distance matrix calculation complete.
IDs written to
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/ibs.mibs.id
.
IBS matrix written to
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/ibs.mibs
.

End time: Sat Nov 22 11:21:05 2025