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annotate 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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a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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1 PLINK v1.90p 64-bit (16 Jun 2020)
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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2 Options in effect:
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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3 --adjust gc log10 qq-plot
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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4 --assoc mperm=10000 fisher-midp
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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5 --bfile plink_input/plink_input
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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6 --logistic perm genedrop perm-count dominant hide-covar beta intercept
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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7 --make-bed
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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8 --out plink_output/plink_output
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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9
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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10 Hostname: p-body.local
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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11 Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmp78g2r600/job_working_directory/000/94/working
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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12 Start time: Wed Sep 16 16:43:34 2020
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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13
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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14 Random number seed: 1600299814
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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15 32768 MB RAM detected; reserving 16384 MB for main workspace.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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16 50 variants loaded from .bim file.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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17 200 people (0 males, 200 females) loaded from .fam.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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18 200 phenotype values loaded from .fam.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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19 Using up to 11 threads (change this with --threads).
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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20 Before main variant filters, 200 founders and 0 nonfounders present.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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21 Calculating allele frequencies... done.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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22 50 variants and 200 people pass filters and QC.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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23 Among remaining phenotypes, 101 are cases and 99 are controls.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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24 --make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim +
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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25 plink_output/plink_output.fam ... done.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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26 Writing C/C --assoc report to plink_output/plink_output.assoc.fisher ...
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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27 done.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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28 --adjust: Genomic inflation est. lambda (based on median chisq) = 1.22743.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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29 --adjust values (50 variants) written to
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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30 plink_output/plink_output.assoc.fisher.adjusted .
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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31 10000 max(T) permutations complete.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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32 Permutation test report written to plink_output/plink_output.assoc.fisher.mperm
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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33 .
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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34 Writing logistic model association results to
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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35 plink_output/plink_output.assoc.logistic ... done.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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36 --adjust: Genomic inflation est. lambda (based on median chisq) = 1.16136.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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37 --adjust values (50 variants) written to
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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38 plink_output/plink_output.assoc.logistic.adjusted .
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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39 579 (adaptive) permutations complete.
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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40 Permutation test report written to plink_output/plink_output.assoc.logistic.perm .
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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41
a98caf1d69ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
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42 End time: Wed Sep 16 16:43:34 2020