Mercurial > repos > iuc > mageck_test

annotate test-data/out.count.log.txt @ 2:81bbbddcf285 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
author iuc
date Wed, 04 Apr 2018 11:03:59 -0400
parents b8da4d41aa1d
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
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1 INFO @ Sun, 25 Mar 2018 15:51:06: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-5ed9647f14e9d3e99564d31bed2eb19cd32ee8b9da66a89bea59b64a8983b1d6/bin/mageck count -l /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmp0EKzNL/files/000/dataset_2.dat --fastq input_0.gz --sample-label test1_fastq_gz -n output --pdf-report --keep-tmp --unmapped-to-file
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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2 INFO @ Sun, 25 Mar 2018 15:51:06: Welcome to MAGeCK v0.5.7. Command: count
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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3 INFO @ Sun, 25 Mar 2018 15:51:06: Loading 2550 predefined sgRNAs.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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4 WARNING @ Sun, 25 Mar 2018 15:51:06: There are 0 sgRNAs with duplicated sequences.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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5 INFO @ Sun, 25 Mar 2018 15:51:06: Parsing FASTQ file input_0.gz...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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6 INFO @ Sun, 25 Mar 2018 15:51:06: Determining the trim-5 length of FASTQ file input_0.gz...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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7 INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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8 INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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9 INFO @ Sun, 25 Mar 2018 15:51:06: Read length:30
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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10 INFO @ Sun, 25 Mar 2018 15:51:06: Total tested reads: 2500, mapped: 1453(0.5812)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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11 INFO @ Sun, 25 Mar 2018 15:51:06: --trim-5 test data: (trim_length reads fraction)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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12 INFO @ Sun, 25 Mar 2018 15:51:06: 0 1453 1.0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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13 INFO @ Sun, 25 Mar 2018 15:51:06: Auto determination of trim5 results: 0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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14 INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20
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 INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ..
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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16 INFO @ Sun, 25 Mar 2018 15:51:06: Total: 2500.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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17 INFO @ Sun, 25 Mar 2018 15:51:06: Mapped: 1453.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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18 DEBUG @ Sun, 25 Mar 2018 15:51:06: Initial (total) size factor: 1.0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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19 DEBUG @ Sun, 25 Mar 2018 15:51:06: Median factor: 2.0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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20 INFO @ Sun, 25 Mar 2018 15:51:06: Final size factor: 2.0
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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21 INFO @ Sun, 25 Mar 2018 15:51:06: Summary of file input_0.gz:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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22 INFO @ Sun, 25 Mar 2018 15:51:06: label test1_fastq_gz
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 INFO @ Sun, 25 Mar 2018 15:51:06: reads 2500
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 @ Sun, 25 Mar 2018 15:51:06: mappedreads 1453
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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25 INFO @ Sun, 25 Mar 2018 15:51:06: totalsgrnas 2550
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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26 INFO @ Sun, 25 Mar 2018 15:51:06: zerosgrnas 1276
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 INFO @ Sun, 25 Mar 2018 15:51:06: giniindex 0.5266899931488773
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 INFO @ Sun, 25 Mar 2018 15:51:06: Loading Rnw template file: /Users/doylemaria/miniconda3/envs/mulled-v1-5ed9647f14e9d3e99564d31bed2eb19cd32ee8b9da66a89bea59b64a8983b1d6/lib/python3.6/site-packages/mageck/fastq_template.Rnw.
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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29 DEBUG @ Sun, 25 Mar 2018 15:51:06: Setting up the visualization module...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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30 INFO @ Sun, 25 Mar 2018 15:51:06: Running command: cd ./; Rscript output_countsummary.R
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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31 INFO @ Sun, 25 Mar 2018 15:51:11: 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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32 INFO @ Sun, 25 Mar 2018 15:51:11: Writing to file output_countsummary.tex
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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33 INFO @ Sun, 25 Mar 2018 15:51:11: Processing code chunks with options ...
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
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34 INFO @ Sun, 25 Mar 2018 15:51:11: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
35 INFO @ Sun, 25 Mar 2018 15:51:11: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
36 INFO @ Sun, 25 Mar 2018 15:51:11: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174)
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 @ Sun, 25 Mar 2018 15:51:11: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
38 INFO @ Sun, 25 Mar 2018 15:51:11: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
39 INFO @ Sun, 25 Mar 2018 15:51:11: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228)
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
40 INFO @ Sun, 25 Mar 2018 15:51:11:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
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41 INFO @ Sun, 25 Mar 2018 15:51:11: You can now run (pdf)latex on ‘output_countsummary.tex’
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
42 INFO @ Sun, 25 Mar 2018 15:51:11:
81bbbddcf285 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 0
diff changeset
43 INFO @ Sun, 25 Mar 2018 15:51:11: End command message.