Mercurial > repos > iuc > plink
annotate test-data/plink_output.log @ 4:ac16d24f0d9d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 577ea693a59004c6fa892d079cd0b2b835ee59bf"
| author | iuc |
|---|---|
| date | Mon, 28 Sep 2020 17:00:56 +0000 |
| parents | a98caf1d69ab |
| children |
| rev | line source |
|---|---|
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0
a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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1 PLINK v1.90p 64-bit (16 Jun 2020) |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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2 Options in effect: |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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3 --adjust gc log10 qq-plot |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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4 --assoc mperm=10000 fisher-midp |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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5 --bfile plink_input/plink_input |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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6 --logistic perm genedrop perm-count dominant hide-covar beta intercept |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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7 --make-bed |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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8 --out plink_output/plink_output |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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9 |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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10 Hostname: p-body.local |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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11 Working directory: /private/var/folders/f7/p887fr2x6hd_jg712040rl580000gn/T/tmp78g2r600/job_working_directory/000/94/working |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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12 Start time: Wed Sep 16 16:43:34 2020 |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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13 |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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14 Random number seed: 1600299814 |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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15 32768 MB RAM detected; reserving 16384 MB for main workspace. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
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16 50 variants loaded from .bim file. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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17 200 people (0 males, 200 females) loaded from .fam. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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18 200 phenotype values loaded from .fam. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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19 Using up to 11 threads (change this with --threads). |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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20 Before main variant filters, 200 founders and 0 nonfounders present. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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21 Calculating allele frequencies... done. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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22 50 variants and 200 people pass filters and QC. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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23 Among remaining phenotypes, 101 are cases and 99 are controls. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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24 --make-bed to plink_output/plink_output.bed + plink_output/plink_output.bim + |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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25 plink_output/plink_output.fam ... done. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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changeset
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26 Writing C/C --assoc report to plink_output/plink_output.assoc.fisher ... |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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27 done. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
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28 --adjust: Genomic inflation est. lambda (based on median chisq) = 1.22743. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
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29 --adjust values (50 variants) written to |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
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30 plink_output/plink_output.assoc.fisher.adjusted . |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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31 10000 max(T) permutations complete. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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32 Permutation test report written to plink_output/plink_output.assoc.fisher.mperm |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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33 . |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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34 Writing logistic model association results to |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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35 plink_output/plink_output.assoc.logistic ... done. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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36 --adjust: Genomic inflation est. lambda (based on median chisq) = 1.16136. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
changeset
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37 --adjust values (50 variants) written to |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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38 plink_output/plink_output.assoc.logistic.adjusted . |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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39 579 (adaptive) permutations complete. |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
diff
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40 Permutation test report written to plink_output/plink_output.assoc.logistic.perm . |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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41 |
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a98caf1d69ab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 555a851b363c015f26d6fcf1f52bcbf3420a0b3b"
iuc
parents:
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42 End time: Wed Sep 16 16:43:34 2020 |