PLINK v2.00a6 64-bit (5 Feb 2024)
Options in effect:
  --out tests/testthat//data.hg38.renamed
  --pfile tests/testthat//data.hg38.renamed
  --read-freq /Users/syed/Documents/meyerlab/Aim1/plinkQC/extdata/all_hg38_maf_first_pca.acount
  --score /Users/syed/Documents/meyerlab/Aim1/plinkQC/extdata/all_hg38_maf_first_pca.eigenvec.allele 2 6 header-read no-mean-imputation variance-standardize
  --score-col-nums 7-26

Hostname: SBS2022-05.cshl.edu
Working directory: /Users/syed/Documents/meyerlab/Aim1/plinkQC
Start time: Mon Aug 26 14:38:35 2024

Random number seed: 1724697515
16384 MiB RAM detected; reserving 8192 MiB for main workspace.
Using up to 8 compute threads.
200 samples (111 females, 89 males; 200 founders) loaded from
tests/testthat//data.hg38.renamed.psam.
9994 variants loaded from tests/testthat//data.hg38.renamed.pvar.
Note: No phenotype data present.
--read-freq: PLINK 2 --freq file detected.
--read-freq: Frequencies for 1417 variants loaded.
Warning: 1858207 entries skipped due to missing variant IDs, mismatching allele
codes, and/or zero observations.
Calculating allele frequencies... done.
Warning: --score: 3716414 entries in
/Users/syed/Documents/meyerlab/Aim1/plinkQC/extdata/all_hg38_maf_first_pca.eigenvec.allele
were skipped due to missing variant IDs.
(Add the 'list-variants' modifier to see which variants were actually used for
scoring.)
--score: 1417 variants processed.
--score: Results written to tests/testthat//data.hg38.renamed.sscore .

End time: Mon Aug 26 14:38:35 2024