Mercurial > repos > iuc > plink
diff test-data/stats.log @ 0:a98caf1d69ab draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
author | iuc |
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date | Mon, 21 Sep 2020 10:09:22 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.log Mon Sep 21 10:09:22 2020 +0000 @@ -0,0 +1,40 @@ +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