Mercurial > repos > iuc > mageck_gsea

annotate test-data/out.test.log.txt @ 1:80cf607159ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
author iuc
date Sat, 17 Feb 2018 10:41:13 -0500
parents d95eae71878e
children 82a180e6b582
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d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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1 INFO @ Mon, 12 Feb 2018 03:40:01: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck test -k /tmp/tmp0xS0Jl/files/000/dataset_21.dat -t HL60.final,KBM7.final -c HL60.initial,KBM7.initial -n output --normcounts-to-file --pdf-report --norm-method median --gene-test-fdr-threshold 0.25 --adjust-method fdr --sort-criteria neg --remove-zero none --gene-lfc-method median
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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2 INFO @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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3 INFO @ Mon, 12 Feb 2018 03:40:01: Loading count table from /tmp/tmp0xS0Jl/files/000/dataset_21.dat
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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4 INFO @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines..
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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5 DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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6 INFO @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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7 INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.RTemplate.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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8 INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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9 INFO @ Mon, 12 Feb 2018 03:40:01: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.Rnw.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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10 DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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11 DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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12 DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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13 INFO @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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14 INFO @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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15 DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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16 DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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17 INFO @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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18 INFO @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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19 DEBUG @ Mon, 12 Feb 2018 03:40:01: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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20 DEBUG @ Mon, 12 Feb 2018 03:40:01: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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21 INFO @ Mon, 12 Feb 2018 03:40:01: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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22 INFO @ Mon, 12 Feb 2018 03:40:01: Writing normalized read counts to output.normalized.txt
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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23 DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339 3.4299551007579927
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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24 INFO @ Mon, 12 Feb 2018 03:40:01: Raw variance calculation: 0.5 for control, 0.5 for treatment
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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25 INFO @ Mon, 12 Feb 2018 03:40:01: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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26 INFO @ Mon, 12 Feb 2018 03:40:01: Use qnorm to reversely calculate sgRNA scores ...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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27 DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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28 DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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29 INFO @ Mon, 12 Feb 2018 03:40:01: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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30 INFO @ Mon, 12 Feb 2018 03:40:02: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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31 INFO @ Mon, 12 Feb 2018 03:40:02: Welcome to RRA v 0.5.7.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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32 INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene NA for permutation ...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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33 INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene na for permutation ...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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34 INFO @ Mon, 12 Feb 2018 03:40:02: Reading input file...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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35 INFO @ Mon, 12 Feb 2018 03:40:02: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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36 INFO @ Mon, 12 Feb 2018 03:40:02: Computing lo-values for each group...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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37 INFO @ Mon, 12 Feb 2018 03:40:02: Computing false discovery rate...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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38 INFO @ Mon, 12 Feb 2018 03:40:02: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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39 INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 9 sgRNAs...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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40 INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 10 sgRNAs...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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41 INFO @ Mon, 12 Feb 2018 03:40:02: Number of genes under FDR adjustment: 100
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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42 INFO @ Mon, 12 Feb 2018 03:40:02: Saving to output file...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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43 INFO @ Mon, 12 Feb 2018 03:40:02: RRA completed.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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44 INFO @ Mon, 12 Feb 2018 03:40:02:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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45 INFO @ Mon, 12 Feb 2018 03:40:02: End command message.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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46 INFO @ Mon, 12 Feb 2018 03:40:02: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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47 INFO @ Mon, 12 Feb 2018 03:40:03: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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48 INFO @ Mon, 12 Feb 2018 03:40:03: Welcome to RRA v 0.5.7.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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49 INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene NA for permutation ...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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50 INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene na for permutation ...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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51 INFO @ Mon, 12 Feb 2018 03:40:03: Reading input file...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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52 INFO @ Mon, 12 Feb 2018 03:40:03: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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53 INFO @ Mon, 12 Feb 2018 03:40:03: Computing lo-values for each group...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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54 INFO @ Mon, 12 Feb 2018 03:40:03: Computing false discovery rate...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
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55 INFO @ Mon, 12 Feb 2018 03:40:03: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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56 INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 9 sgRNAs...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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57 INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 10 sgRNAs...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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58 INFO @ Mon, 12 Feb 2018 03:40:03: Number of genes under FDR adjustment: 100
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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59 INFO @ Mon, 12 Feb 2018 03:40:03: Saving to output file...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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60 INFO @ Mon, 12 Feb 2018 03:40:03: RRA completed.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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61 INFO @ Mon, 12 Feb 2018 03:40:03:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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62 INFO @ Mon, 12 Feb 2018 03:40:03: End command message.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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63 DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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64 INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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65 DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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66 INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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67 DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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68 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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69 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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70 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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71 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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72 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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73 INFO @ Mon, 12 Feb 2018 03:40:04: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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74 INFO @ Mon, 12 Feb 2018 03:40:04: null device
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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75 INFO @ Mon, 12 Feb 2018 03:40:04: 1
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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76 INFO @ Mon, 12 Feb 2018 03:40:04: Writing to file output_summary.tex
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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77 INFO @ Mon, 12 Feb 2018 03:40:04: Processing code chunks with options ...
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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78 INFO @ Mon, 12 Feb 2018 03:40:04: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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79 INFO @ Mon, 12 Feb 2018 03:40:04: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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80 INFO @ Mon, 12 Feb 2018 03:40:04: 3 : keep.source term verbatim (output_summary.Rnw:77)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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81 INFO @ Mon, 12 Feb 2018 03:40:04: 4 : keep.source term verbatim pdf (output_summary.Rnw:83)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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82 INFO @ Mon, 12 Feb 2018 03:40:04: 5 : keep.source term verbatim pdf (output_summary.Rnw:201)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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83 INFO @ Mon, 12 Feb 2018 03:40:04: 6 : keep.source term verbatim pdf (output_summary.Rnw:345)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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84 INFO @ Mon, 12 Feb 2018 03:40:04: 7 : keep.source term verbatim pdf (output_summary.Rnw:489)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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85 INFO @ Mon, 12 Feb 2018 03:40:04: 8 : keep.source term verbatim (output_summary.Rnw:567)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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86 INFO @ Mon, 12 Feb 2018 03:40:04: 9 : keep.source term verbatim pdf (output_summary.Rnw:573)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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87 INFO @ Mon, 12 Feb 2018 03:40:04: 10 : keep.source term verbatim pdf (output_summary.Rnw:691)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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88 INFO @ Mon, 12 Feb 2018 03:40:04: 11 : keep.source term verbatim pdf (output_summary.Rnw:835)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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89 INFO @ Mon, 12 Feb 2018 03:40:04: 12 : keep.source term verbatim pdf (output_summary.Rnw:979)
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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90 INFO @ Mon, 12 Feb 2018 03:40:04:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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91 INFO @ Mon, 12 Feb 2018 03:40:04: You can now run (pdf)latex on ‘output_summary.tex’
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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92 INFO @ Mon, 12 Feb 2018 03:40:04: Error in texi2dvi("output_summary.tex", pdf = TRUE) :
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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93 INFO @ Mon, 12 Feb 2018 03:40:04: pdflatex is not available
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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94 INFO @ Mon, 12 Feb 2018 03:40:04: Execution halted
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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95 INFO @ Mon, 12 Feb 2018 03:40:04:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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96 INFO @ Mon, 12 Feb 2018 03:40:04: End command message.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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97 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary-*.pdf
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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98 INFO @ Mon, 12 Feb 2018 03:40:04: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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99 INFO @ Mon, 12 Feb 2018 03:40:04:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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100 INFO @ Mon, 12 Feb 2018 03:40:04: End command message.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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101 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.aux
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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102 INFO @ Mon, 12 Feb 2018 03:40:04: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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103 INFO @ Mon, 12 Feb 2018 03:40:04:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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104 INFO @ Mon, 12 Feb 2018 03:40:04: End command message.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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105 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.tex
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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106 INFO @ Mon, 12 Feb 2018 03:40:04: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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107 INFO @ Mon, 12 Feb 2018 03:40:04:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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108 INFO @ Mon, 12 Feb 2018 03:40:04: End command message.
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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109 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.toc
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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110 INFO @ Mon, 12 Feb 2018 03:40:04: Command message:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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111 INFO @ Mon, 12 Feb 2018 03:40:04:
d95eae71878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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112 INFO @ Mon, 12 Feb 2018 03:40:04: End command message.