Mercurial > repos > iuc > mageck_test

annotate test-data/out.test.log.txt @ 3:afa81ef5f1c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
author iuc
date Thu, 19 Apr 2018 05:35:12 -0400
parents 81bbbddcf285
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
1 INFO @ Mon, 26 Mar 2018 08:37:53: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/bin/mageck test -k /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpTX65kA/files/000/dataset_4.dat -t HL60_final,KBM7_final -c HL60_initial,KBM7_initial -n output --normcounts-to-file --pdf-report --norm-method median --adjust-method fdr --sort-criteria neg --remove-zero both --gene-lfc-method median
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
2 INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to MAGeCK v0.5.7. Command: test
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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3 INFO @ Mon, 26 Mar 2018 08:37:53: Loading count table from /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpTX65kA/files/000/dataset_4.dat
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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4 INFO @ Mon, 26 Mar 2018 08:37:53: Processing 1 lines..
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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5 DEBUG @ Mon, 26 Mar 2018 08:37:53: Parsing error in line 1 (usually the header line). Skip this line.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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6 INFO @ Mon, 26 Mar 2018 08:37:53: Loaded 999 records.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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7 INFO @ Mon, 26 Mar 2018 08:37:53: Loading R template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template.RTemplate.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
8 INFO @ Mon, 26 Mar 2018 08:37:53: Loading R template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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9 INFO @ Mon, 26 Mar 2018 08:37:53: Loading Rnw template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template.Rnw.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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10 DEBUG @ Mon, 26 Mar 2018 08:37:53: Setting up the visualization module...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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11 DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_final,KBM7_final
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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12 DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 2 3
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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13 INFO @ Mon, 26 Mar 2018 08:37:53: Treatment samples:HL60_final,KBM7_final
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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14 INFO @ Mon, 26 Mar 2018 08:37:53: Treatment sample index:2,3
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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15 DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_initial,KBM7_initial
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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16 DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 0 1
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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17 INFO @ Mon, 26 Mar 2018 08:37:53: Control samples:HL60_initial,KBM7_initial
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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18 INFO @ Mon, 26 Mar 2018 08:37:53: Control sample index:0,1
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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19 DEBUG @ Mon, 26 Mar 2018 08:37:53: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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20 DEBUG @ Mon, 26 Mar 2018 08:37:53: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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21 INFO @ Mon, 26 Mar 2018 08:37:53: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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22 INFO @ Mon, 26 Mar 2018 08:37:53: Writing normalized read counts to output.normalized.txt
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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23 DEBUG @ Mon, 26 Mar 2018 08:37:53: Adjusted model: 1.1175084644498339 3.4299551007579927
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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24 INFO @ Mon, 26 Mar 2018 08:37:53: Raw variance calculation: 0.5 for control, 0.5 for treatment
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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25 INFO @ Mon, 26 Mar 2018 08:37:53: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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26 INFO @ Mon, 26 Mar 2018 08:37:53: Use qnorm to reversely calculate sgRNA scores ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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27 DEBUG @ Mon, 26 Mar 2018 08:37:53: lower test FDR cutoff: 0.3283283283283283
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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28 DEBUG @ Mon, 26 Mar 2018 08:37:53: higher test FDR cutoff: 0.34534534534534533
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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29 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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30 INFO @ Mon, 26 Mar 2018 08:37:53: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
31 INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
32 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
33 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
34 INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
35 INFO @ Mon, 26 Mar 2018 08:37:53: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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36 INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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37 INFO @ Mon, 26 Mar 2018 08:37:53: Computing false discovery rate...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
38 INFO @ Mon, 26 Mar 2018 08:37:53: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
39 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
40 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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41 INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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42 INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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43 INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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44 INFO @ Mon, 26 Mar 2018 08:37:53:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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45 INFO @ Mon, 26 Mar 2018 08:37:53: End command message.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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46 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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47 INFO @ Mon, 26 Mar 2018 08:37:53: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
48 INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
49 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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50 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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51 INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
52 INFO @ Mon, 26 Mar 2018 08:37:53: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
53 INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
54 INFO @ Mon, 26 Mar 2018 08:37:53: Computing false discovery rate...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
55 INFO @ Mon, 26 Mar 2018 08:37:53: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
56 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
57 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
58 INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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59 INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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60 INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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61 INFO @ Mon, 26 Mar 2018 08:37:53:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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62 INFO @ Mon, 26 Mar 2018 08:37:53: End command message.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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63 DEBUG @ Mon, 26 Mar 2018 08:37:53: Sorting the merged items by negative selection...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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64 INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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65 DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:3
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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66 INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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67 DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:9
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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68 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.plow.txt
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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69 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.phigh.txt
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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70 INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.low.txt
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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71 INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.high.txt
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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72 INFO @ Mon, 26 Mar 2018 08:37:54: Running command: cd ./; Rscript output.R
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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73 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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74 INFO @ Mon, 26 Mar 2018 08:37:59: null device
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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75 INFO @ Mon, 26 Mar 2018 08:37:59: 1
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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76 INFO @ Mon, 26 Mar 2018 08:37:59: Writing to file output_summary.tex
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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77 INFO @ Mon, 26 Mar 2018 08:37:59: Processing code chunks with options ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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78 INFO @ Mon, 26 Mar 2018 08:37:59: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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79 INFO @ Mon, 26 Mar 2018 08:37:59: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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80 INFO @ Mon, 26 Mar 2018 08:37:59: 3 : keep.source term verbatim (output_summary.Rnw:77)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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81 INFO @ Mon, 26 Mar 2018 08:37:59: 4 : keep.source term verbatim pdf (output_summary.Rnw:83)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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82 INFO @ Mon, 26 Mar 2018 08:37:59: 5 : keep.source term verbatim pdf (output_summary.Rnw:201)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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83 INFO @ Mon, 26 Mar 2018 08:37:59: 6 : keep.source term verbatim pdf (output_summary.Rnw:345)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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parents: 0
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84 INFO @ Mon, 26 Mar 2018 08:37:59: 7 : keep.source term verbatim pdf (output_summary.Rnw:489)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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85 INFO @ Mon, 26 Mar 2018 08:37:59: 8 : keep.source term verbatim (output_summary.Rnw:567)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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86 INFO @ Mon, 26 Mar 2018 08:37:59: 9 : keep.source term verbatim pdf (output_summary.Rnw:573)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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parents: 0
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87 INFO @ Mon, 26 Mar 2018 08:37:59: 10 : keep.source term verbatim pdf (output_summary.Rnw:691)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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88 INFO @ Mon, 26 Mar 2018 08:37:59: 11 : keep.source term verbatim pdf (output_summary.Rnw:835)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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89 INFO @ Mon, 26 Mar 2018 08:37:59: 12 : keep.source term verbatim pdf (output_summary.Rnw:979)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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90 INFO @ Mon, 26 Mar 2018 08:37:59:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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91 INFO @ Mon, 26 Mar 2018 08:37:59: You can now run (pdf)latex on ‘output_summary.tex’
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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92 INFO @ Mon, 26 Mar 2018 08:37:59:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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93 INFO @ Mon, 26 Mar 2018 08:37:59: End command message.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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94 INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary-*.pdf
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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95 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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96 INFO @ Mon, 26 Mar 2018 08:37:59:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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97 INFO @ Mon, 26 Mar 2018 08:37:59: End command message.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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98 INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.aux
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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99 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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100 INFO @ Mon, 26 Mar 2018 08:37:59:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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101 INFO @ Mon, 26 Mar 2018 08:37:59: End command message.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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102 INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.tex
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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103 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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104 INFO @ Mon, 26 Mar 2018 08:37:59:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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105 INFO @ Mon, 26 Mar 2018 08:37:59: End command message.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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106 INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.toc
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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107 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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108 INFO @ Mon, 26 Mar 2018 08:37:59:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
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109 INFO @ Mon, 26 Mar 2018 08:37:59: End command message.