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comparison test-data/plink_output.log @ 0:a98caf1d69ab 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 10:09:22 +0000
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-1:000000000000 0:a98caf1d69ab
1 PLINK v1.90p 64-bit (16 Jun 2020)
2 Options in effect:
3 --adjust gc log10 qq-plot
4 --assoc mperm=10000 fisher-midp
5 --bfile plink_input/plink_input
6 --logistic perm genedrop perm-count dominant hide-covar beta intercept
7 --make-bed
8 --out plink_output/plink_output
9
10 Hostname: p-body.local
11 Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmp78g2r600/job_working_directory/000/94/working
12 Start time: Wed Sep 16 16:43:34 2020
13
14 Random number seed: 1600299814
15 32768 MB RAM detected; reserving 16384 MB for main workspace.
16 50 variants loaded from .bim file.
17 200 people (0 males, 200 females) loaded from .fam.
18 200 phenotype values loaded from .fam.
19 Using up to 11 threads (change this with --threads).
20 Before main variant filters, 200 founders and 0 nonfounders present.
21 Calculating allele frequencies... done.
22 50 variants and 200 people pass filters and QC.
23 Among remaining phenotypes, 101 are cases and 99 are controls.
24 --make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim +
25 plink_output/plink_output.fam ... done.
26 Writing C/C --assoc report to plink_output/plink_output.assoc.fisher ...
27 done.
28 --adjust: Genomic inflation est. lambda (based on median chisq) = 1.22743.
29 --adjust values (50 variants) written to
30 plink_output/plink_output.assoc.fisher.adjusted .
31 10000 max(T) permutations complete.
32 Permutation test report written to plink_output/plink_output.assoc.fisher.mperm
33 .
34 Writing logistic model association results to
35 plink_output/plink_output.assoc.logistic ... done.
36 --adjust: Genomic inflation est. lambda (based on median chisq) = 1.16136.
37 --adjust values (50 variants) written to
38 plink_output/plink_output.assoc.logistic.adjusted .
39 579 (adaptive) permutations complete.
40 Permutation test report written to plink_output/plink_output.assoc.logistic.perm .
41
42 End time: Wed Sep 16 16:43:34 2020