annotate test-data/stats.log @ 0:a98caf1d69ab draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"

PLINK v1.90p 64-bit (16 Jun 2020)
Options in effect:
  --bfile plink_input/plink_input
  --check-sex ycount 0.2 0.8 10 200
  --freq
  --hardy
  --het
  --make-bed
  --missing
  --out plink_output/plink_output

Hostname: p-body.local
Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmpzq_so7fd/job_working_directory/000/89/working
Start time: Tue Sep 15 10:53:23 2020

Random number seed: 1600192403
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 1 thread (no multithreaded calculations invoked).
Before main variant filters, 200 founders and 0 nonfounders present.
Calculating allele frequencies... done.
--freq: Allele frequencies (founders only) written to
plink_output/plink_output.frq .
--missing: Sample missing data report written to
plink_output/plink_output.imiss, and variant-based missing data report written
to plink_output/plink_output.lmiss.
--hardy: Writing Hardy-Weinberg report (founders only) to
plink_output/plink_output.hwe ... done.
50 variants and 200 people pass filters and QC.
Among remaining phenotypes, 101 are cases and 99 are controls.
Warning: No Y chromosome data for --check-sex ycount.
--check-sex: 26 Xchr and 0 Ychr variant(s) scanned, 31 problems detected.
Report written to plink_output/plink_output.sexcheck .
--make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim +
plink_output/plink_output.fam ... done.
--het: 24 variants scanned, report written to plink_output/plink_output.het .

End time: Tue Sep 15 10:53:23 2020