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comparison test-data/stats.log @ 10:c7d38dcbf02d draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
author iuc
date Sun, 19 Dec 2021 15:52:45 +0000
parents 303123b30425
children
comparison
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9:303123b30425 10:c7d38dcbf02d
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