PLINK v1.90b3.32 64-bit (24 Feb 2016)
Options in effect:
  --extract plink.prune.in
  --file /broad/GINGER/data/GWAS/gwas_example
  --maf 0.05
  --pca

Hostname: gold.broadinstitute.org
Working directory: /home/unix/hhuang/pca
Start time: Mon Mar 19 17:13:36 2018

Random number seed: 1521494016
7864 MB RAM detected; reserving 3932 MB for main workspace.
Allocated 294 MB successfully, after larger attempt(s) failed.
Scanning .ped file... done.
Performing single-pass .bed write (100310 variants, 200 people).
--file: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam
written.
100310 variants loaded from .bim file.
200 people (101 males, 99 females) loaded from .fam.
200 phenotype values loaded from .fam.
--extract: 57207 variants remaining.
Using up to 2 threads (change this with --threads).
Before main variant filters, 200 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.996241.
13575 variants removed due to minor allele threshold(s)
(--maf/--max-maf/--mac/--max-mac).
43632 variants and 200 people pass filters and QC.
Among remaining phenotypes, 39 are cases and 161 are controls.
Relationship matrix calculation complete.
--pca: Results saved to plink.eigenval and plink.eigenvec .

End time: Mon Mar 19 17:13:37 2018