Mercurial > repos > iuc > mageck_gsea
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 |
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| date | Wed, 14 Feb 2018 06:41:59 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:d95eae71878e |
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| 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 |