view test-data/plink_output.log @ 4:ac16d24f0d9d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 577ea693a59004c6fa892d079cd0b2b835ee59bf"

PLINK v1.90p 64-bit (16 Jun 2020)
Options in effect:
  --adjust gc log10 qq-plot
  --assoc mperm=10000 fisher-midp
  --bfile plink_input/plink_input
  --logistic perm genedrop perm-count dominant hide-covar beta intercept
  --make-bed
  --out plink_output/plink_output

Hostname: p-body.local
Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmp78g2r600/job_working_directory/000/94/working
Start time: Wed Sep 16 16:43:34 2020

Random number seed: 1600299814
32768 MB RAM detected; reserving 16384 MB for main workspace.
50 variants loaded from .bim file.
200 people (0 males, 200 females) loaded from .fam.
200 phenotype values loaded from .fam.
Using up to 11 threads (change this with --threads).
Before main variant filters, 200 founders and 0 nonfounders present.
Calculating allele frequencies... done.
50 variants and 200 people pass filters and QC.
Among remaining phenotypes, 101 are cases and 99 are controls.
--make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim +
plink_output/plink_output.fam ... done.
Writing C/C --assoc report to plink_output/plink_output.assoc.fisher ...
done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.22743.
--adjust values (50 variants) written to
plink_output/plink_output.assoc.fisher.adjusted .
10000 max(T) permutations complete.
Permutation test report written to plink_output/plink_output.assoc.fisher.mperm
.
Writing logistic model association results to
plink_output/plink_output.assoc.logistic ... done.
--adjust: Genomic inflation est. lambda (based on median chisq) = 1.16136.
--adjust values (50 variants) written to
plink_output/plink_output.assoc.logistic.adjusted .
579 (adaptive) permutations complete.
Permutation test report written to plink_output/plink_output.assoc.logistic.perm .

End time: Wed Sep 16 16:43:34 2020