comparison test-data/out.pathway.log.txt @ 0:d95eae71878e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
author iuc
date Wed, 14 Feb 2018 06:41:59 -0500
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-1:000000000000 0:d95eae71878e
1 INFO @ Mon, 12 Feb 2018 04:19:29: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck pathway --gene-ranking /tmp/tmpd9LSrs/files/000/dataset_19.dat --gmt-file /tmp/tmpd9LSrs/files/000/dataset_20.dat -n sample1 --method gsea --sort-criteria neg --ranking-column 2 --ranking-column-2 8 --pathway-alpha 0.25 --permutation 1000
2 INFO @ Mon, 12 Feb 2018 04:19:29: Welcome to MAGeCK v0.5.7. Command: pathway
3 INFO @ Mon, 12 Feb 2018 04:19:29: GSEA command for negative selection: mageckGSEA -s -c 2 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.low.txt
4 INFO @ Mon, 12 Feb 2018 04:19:29: Running command: mageckGSEA -s -c 2 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.low.txt
5 INFO @ Mon, 12 Feb 2018 04:19:29: Command message:
6 INFO @ Mon, 12 Feb 2018 04:19:29: GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat
7 INFO @ Mon, 12 Feb 2018 04:19:29: Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat
8 INFO @ Mon, 12 Feb 2018 04:19:29: Output file: sample1.pathway.low.txt
9 INFO @ Mon, 12 Feb 2018 04:19:29: pathway size:1
10 INFO @ Mon, 12 Feb 2018 04:19:29: rank size:101
11 INFO @ Mon, 12 Feb 2018 04:19:29: Permutations:1000
12 INFO @ Mon, 12 Feb 2018 04:19:29: .
13 INFO @ Mon, 12 Feb 2018 04:19:29:
14 INFO @ Mon, 12 Feb 2018 04:19:29: End command message.
15 INFO @ Mon, 12 Feb 2018 04:19:29: GSEA command for positive selection: mageckGSEA -s -c 8 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.high.txt
16 INFO @ Mon, 12 Feb 2018 04:19:29: Running command: mageckGSEA -s -c 8 -p 1000 -g "/tmp/tmpd9LSrs/files/000/dataset_20.dat" -r "/tmp/tmpd9LSrs/files/000/dataset_19.dat" -o sample1.pathway.high.txt
17 INFO @ Mon, 12 Feb 2018 04:19:29: Command message:
18 INFO @ Mon, 12 Feb 2018 04:19:29: GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat
19 INFO @ Mon, 12 Feb 2018 04:19:29: Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat
20 INFO @ Mon, 12 Feb 2018 04:19:29: Output file: sample1.pathway.high.txt
21 INFO @ Mon, 12 Feb 2018 04:19:29: pathway size:1
22 INFO @ Mon, 12 Feb 2018 04:19:29: rank size:101
23 INFO @ Mon, 12 Feb 2018 04:19:29: Permutations:1000
24 INFO @ Mon, 12 Feb 2018 04:19:29: .
25 INFO @ Mon, 12 Feb 2018 04:19:29:
26 INFO @ Mon, 12 Feb 2018 04:19:29: End command message.
27 INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.tmp
28 INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.tmp
29 INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.txt
30 INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.txt