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comparison test-data/stats.log @ 0:940df46cf76a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
author iuc
date Mon, 21 Sep 2020 10:08:35 +0000
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-1:000000000000 0:940df46cf76a
1 PLINK v1.90p 64-bit (16 Jun 2020)
2 Options in effect:
3 --bfile plink_input/plink_input
4 --check-sex ycount 0.2 0.8 10 200
5 --freq
6 --hardy
7 --het
8 --make-bed
9 --missing
10 --out plink_output/plink_output
11
12 Hostname: p-body.local
13 Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmpzq_so7fd/job_working_directory/000/89/working
14 Start time: Tue Sep 15 10:53:23 2020
15
16 Random number seed: 1600192403
17 32768 MB RAM detected; reserving 16384 MB for main workspace.
18 50 variants loaded from .bim file.
19 200 people (0 males, 200 females) loaded from .fam.
20 200 phenotype values loaded from .fam.
21 Using 1 thread (no multithreaded calculations invoked).
22 Before main variant filters, 200 founders and 0 nonfounders present.
23 Calculating allele frequencies... done.
24 --freq: Allele frequencies (founders only) written to
25 plink_output/plink_output.frq .
26 --missing: Sample missing data report written to
27 plink_output/plink_output.imiss, and variant-based missing data report written
28 to plink_output/plink_output.lmiss.
29 --hardy: Writing Hardy-Weinberg report (founders only) to
30 plink_output/plink_output.hwe ... done.
31 50 variants and 200 people pass filters and QC.
32 Among remaining phenotypes, 101 are cases and 99 are controls.
33 Warning: No Y chromosome data for --check-sex ycount.
34 --check-sex: 26 Xchr and 0 Ychr variant(s) scanned, 31 problems detected.
35 Report written to plink_output/plink_output.sexcheck .
36 --make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim +
37 plink_output/plink_output.fam ... done.
38 --het: 24 variants scanned, report written to plink_output/plink_output.het .
39
40 End time: Tue Sep 15 10:53:23 2020