Mercurial > repos > iuc > mageck_gsea
view test-data/out.pathway.log.txt @ 2:82a180e6b582 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
author | iuc |
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date | Wed, 04 Apr 2018 11:03:05 -0400 |
parents | d95eae71878e |
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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 INFO @ Mon, 12 Feb 2018 04:19:29: Welcome to MAGeCK v0.5.7. Command: pathway 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 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 INFO @ Mon, 12 Feb 2018 04:19:29: Command message: INFO @ Mon, 12 Feb 2018 04:19:29: GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat INFO @ Mon, 12 Feb 2018 04:19:29: Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat INFO @ Mon, 12 Feb 2018 04:19:29: Output file: sample1.pathway.low.txt INFO @ Mon, 12 Feb 2018 04:19:29: pathway size:1 INFO @ Mon, 12 Feb 2018 04:19:29: rank size:101 INFO @ Mon, 12 Feb 2018 04:19:29: Permutations:1000 INFO @ Mon, 12 Feb 2018 04:19:29: . INFO @ Mon, 12 Feb 2018 04:19:29: INFO @ Mon, 12 Feb 2018 04:19:29: End command message. 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 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 INFO @ Mon, 12 Feb 2018 04:19:29: Command message: INFO @ Mon, 12 Feb 2018 04:19:29: GMT file: /tmp/tmpd9LSrs/files/000/dataset_20.dat INFO @ Mon, 12 Feb 2018 04:19:29: Rank file: /tmp/tmpd9LSrs/files/000/dataset_19.dat INFO @ Mon, 12 Feb 2018 04:19:29: Output file: sample1.pathway.high.txt INFO @ Mon, 12 Feb 2018 04:19:29: pathway size:1 INFO @ Mon, 12 Feb 2018 04:19:29: rank size:101 INFO @ Mon, 12 Feb 2018 04:19:29: Permutations:1000 INFO @ Mon, 12 Feb 2018 04:19:29: . INFO @ Mon, 12 Feb 2018 04:19:29: INFO @ Mon, 12 Feb 2018 04:19:29: End command message. INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.tmp INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.tmp INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.low.txt INFO @ Mon, 12 Feb 2018 04:19:29: Running command: rm sample1.pathway.high.txt