Mercurial > repos > iuc > mageck_mle

annotate test-data/out.count.log.txt @ 1:93f268840b0c 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 10:41:41 -0500
parents eab37e8fea75
children 9cd937788131
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eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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1 INFO @ Wed, 14 Feb 2018 01:52:58: Parameters: /home/maria/miniconda3/envs/mulled-v1-0142cfe25b04f0c1d6899e250fb2f311b2d84778259938a0f6bd1d2ee743fa71/bin/mageck count -l /tmp/tmpqZ84Xc/files/000/dataset_7.dat --fastq input.gz -n output --pdf-report --keep-tmp --unmapped-to-file --norm-method median --sgrna-len 20
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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2 INFO @ Wed, 14 Feb 2018 01:52:58: Welcome to MAGeCK v0.5.7. Command: count
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
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3 INFO @ Wed, 14 Feb 2018 01:52:58: Loading 2550 predefined sgRNAs.
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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4 WARNING @ Wed, 14 Feb 2018 01:52:58: There are 0 sgRNAs with duplicated sequences.
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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5 INFO @ Wed, 14 Feb 2018 01:52:58: Parsing FASTQ file input.gz...
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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6 INFO @ Wed, 14 Feb 2018 01:52:58: Determining the trim-5 length of FASTQ file input.gz...
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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7 INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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8 INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ...
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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9 INFO @ Wed, 14 Feb 2018 01:52:58: Read length:30
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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10 INFO @ Wed, 14 Feb 2018 01:52:58: Total tested reads: 2500, mapped: 1453(0.5812)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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11 INFO @ Wed, 14 Feb 2018 01:52:58: --trim-5 test data: (trim_length reads fraction)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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12 INFO @ Wed, 14 Feb 2018 01:52:58: 0 1453 1.0
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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13 INFO @ Wed, 14 Feb 2018 01:52:58: Auto determination of trim5 results: 0
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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14 INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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15 INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ..
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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16 INFO @ Wed, 14 Feb 2018 01:52:58: Total: 2500.
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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17 INFO @ Wed, 14 Feb 2018 01:52:58: Mapped: 1453.
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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18 DEBUG @ Wed, 14 Feb 2018 01:52:58: Initial (total) size factor: 1.0
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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19 DEBUG @ Wed, 14 Feb 2018 01:52:58: Median factor: 2.0
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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20 INFO @ Wed, 14 Feb 2018 01:52:58: Final size factor: 2.0
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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21 INFO @ Wed, 14 Feb 2018 01:52:58: Summary of file input.gz:
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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22 INFO @ Wed, 14 Feb 2018 01:52:58: label sample1
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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23 INFO @ Wed, 14 Feb 2018 01:52:58: reads 2500
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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24 INFO @ Wed, 14 Feb 2018 01:52:58: mappedreads 1453
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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25 INFO @ Wed, 14 Feb 2018 01:52:58: totalsgrnas 2550
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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26 INFO @ Wed, 14 Feb 2018 01:52:58: zerosgrnas 1276
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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27 INFO @ Wed, 14 Feb 2018 01:52:58: giniindex 0.5266899931488773
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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28 INFO @ Wed, 14 Feb 2018 01:52:58: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-0142cfe25b04f0c1d6899e250fb2f311b2d84778259938a0f6bd1d2ee743fa71/lib/python3.6/site-packages/mageck/fastq_template.Rnw.
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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29 DEBUG @ Wed, 14 Feb 2018 01:52:58: Setting up the visualization module...
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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30 INFO @ Wed, 14 Feb 2018 01:52:58: Running command: cd ./; Rscript output_countsummary.R
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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31 INFO @ Wed, 14 Feb 2018 01:52:58: Command message:
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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32 INFO @ Wed, 14 Feb 2018 01:52:58: Writing to file output_countsummary.tex
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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33 INFO @ Wed, 14 Feb 2018 01:52:58: Processing code chunks with options ...
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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34 INFO @ Wed, 14 Feb 2018 01:52:58: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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35 INFO @ Wed, 14 Feb 2018 01:52:58: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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36 INFO @ Wed, 14 Feb 2018 01:52:58: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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37 INFO @ Wed, 14 Feb 2018 01:52:58: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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38 INFO @ Wed, 14 Feb 2018 01:52:58: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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39 INFO @ Wed, 14 Feb 2018 01:52:58: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228)
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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40 INFO @ Wed, 14 Feb 2018 01:52:58:
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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41 INFO @ Wed, 14 Feb 2018 01:52:58: You can now run (pdf)latex on ‘output_countsummary.tex’
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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42 INFO @ Wed, 14 Feb 2018 01:52:58: Error in texi2dvi("output_countsummary.tex", pdf = TRUE) :
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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43 INFO @ Wed, 14 Feb 2018 01:52:58: pdflatex is not available
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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44 INFO @ Wed, 14 Feb 2018 01:52:58: Execution halted
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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45 INFO @ Wed, 14 Feb 2018 01:52:58:
eab37e8fea75 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
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46 INFO @ Wed, 14 Feb 2018 01:52:58: End command message.