PLINK v1.9.0-b.7.11 64-bit (19 Aug 2025)
Options in effect:
  --allow-extra-chr
  --double-id
  --make-bed
  --out /mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset
  --set-missing-var-ids @:#:\$1:\$2
  --vcf /mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/subset_for_plink.vcf.gz

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.
--vcf:
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset-temporary.bed
+
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset-temporary.bim
+
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset-temporary.fam
written.
7865 variants loaded from .bim file.
7865 missing IDs set.
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/plink_dataset.nosex
.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 112 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.949419.
7865 variants and 112 people pass filters and QC.
Note: No phenotypes present.
--make-bed to
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset.bed
+
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset.bim
+
/mmfs1/gscratch/scrubbed/sr320/github/oly-lc-WGS/output/01_align_and_visualize/variants/plink_dataset.fam
... done.

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