Mercurial > repos > iuc > mageck_test

comparison 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
comparison
equal deleted inserted replaced
1:5e2a28bee02d 2:81bbbddcf285
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 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
2 INFO @ Wed, 14 Feb 2018 01:52:58: Welcome to MAGeCK v0.5.7. Command: count 2 INFO @ Sun, 25 Mar 2018 15:51:06: Welcome to MAGeCK v0.5.7. Command: count
3 INFO @ Wed, 14 Feb 2018 01:52:58: Loading 2550 predefined sgRNAs. 3 INFO @ Sun, 25 Mar 2018 15:51:06: Loading 2550 predefined sgRNAs.
4 WARNING @ Wed, 14 Feb 2018 01:52:58: There are 0 sgRNAs with duplicated sequences. 4 WARNING @ Sun, 25 Mar 2018 15:51:06: There are 0 sgRNAs with duplicated sequences.
5 INFO @ Wed, 14 Feb 2018 01:52:58: Parsing FASTQ file input.gz... 5 INFO @ Sun, 25 Mar 2018 15:51:06: Parsing FASTQ file input_0.gz...
6 INFO @ Wed, 14 Feb 2018 01:52:58: Determining the trim-5 length of FASTQ file input.gz... 6 INFO @ Sun, 25 Mar 2018 15:51:06: Determining the trim-5 length of FASTQ file input_0.gz...
7 INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 7 INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20
8 INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ... 8 INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ...
9 INFO @ Wed, 14 Feb 2018 01:52:58: Read length:30 9 INFO @ Sun, 25 Mar 2018 15:51:06: Read length:30
10 INFO @ Wed, 14 Feb 2018 01:52:58: Total tested reads: 2500, mapped: 1453(0.5812) 10 INFO @ Sun, 25 Mar 2018 15:51:06: Total tested reads: 2500, mapped: 1453(0.5812)
11 INFO @ Wed, 14 Feb 2018 01:52:58: --trim-5 test data: (trim_length reads fraction) 11 INFO @ Sun, 25 Mar 2018 15:51:06: --trim-5 test data: (trim_length reads fraction)
12 INFO @ Wed, 14 Feb 2018 01:52:58: 0 1453 1.0 12 INFO @ Sun, 25 Mar 2018 15:51:06: 0 1453 1.0
13 INFO @ Wed, 14 Feb 2018 01:52:58: Auto determination of trim5 results: 0 13 INFO @ Sun, 25 Mar 2018 15:51:06: Auto determination of trim5 results: 0
14 INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 14 INFO @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20
15 INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads .. 15 INFO @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ..
16 INFO @ Wed, 14 Feb 2018 01:52:58: Total: 2500. 16 INFO @ Sun, 25 Mar 2018 15:51:06: Total: 2500.
17 INFO @ Wed, 14 Feb 2018 01:52:58: Mapped: 1453. 17 INFO @ Sun, 25 Mar 2018 15:51:06: Mapped: 1453.
18 DEBUG @ Wed, 14 Feb 2018 01:52:58: Initial (total) size factor: 1.0 18 DEBUG @ Sun, 25 Mar 2018 15:51:06: Initial (total) size factor: 1.0
19 DEBUG @ Wed, 14 Feb 2018 01:52:58: Median factor: 2.0 19 DEBUG @ Sun, 25 Mar 2018 15:51:06: Median factor: 2.0
20 INFO @ Wed, 14 Feb 2018 01:52:58: Final size factor: 2.0 20 INFO @ Sun, 25 Mar 2018 15:51:06: Final size factor: 2.0
21 INFO @ Wed, 14 Feb 2018 01:52:58: Summary of file input.gz: 21 INFO @ Sun, 25 Mar 2018 15:51:06: Summary of file input_0.gz:
22 INFO @ Wed, 14 Feb 2018 01:52:58: label sample1 22 INFO @ Sun, 25 Mar 2018 15:51:06: label test1_fastq_gz
23 INFO @ Wed, 14 Feb 2018 01:52:58: reads 2500 23 INFO @ Sun, 25 Mar 2018 15:51:06: reads 2500
24 INFO @ Wed, 14 Feb 2018 01:52:58: mappedreads 1453 24 INFO @ Sun, 25 Mar 2018 15:51:06: mappedreads 1453
25 INFO @ Wed, 14 Feb 2018 01:52:58: totalsgrnas 2550 25 INFO @ Sun, 25 Mar 2018 15:51:06: totalsgrnas 2550
26 INFO @ Wed, 14 Feb 2018 01:52:58: zerosgrnas 1276 26 INFO @ Sun, 25 Mar 2018 15:51:06: zerosgrnas 1276
27 INFO @ Wed, 14 Feb 2018 01:52:58: giniindex 0.5266899931488773 27 INFO @ Sun, 25 Mar 2018 15:51:06: giniindex 0.5266899931488773
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. 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.
29 DEBUG @ Wed, 14 Feb 2018 01:52:58: Setting up the visualization module... 29 DEBUG @ Sun, 25 Mar 2018 15:51:06: Setting up the visualization module...
30 INFO @ Wed, 14 Feb 2018 01:52:58: Running command: cd ./; Rscript output_countsummary.R 30 INFO @ Sun, 25 Mar 2018 15:51:06: Running command: cd ./; Rscript output_countsummary.R
31 INFO @ Wed, 14 Feb 2018 01:52:58: Command message: 31 INFO @ Sun, 25 Mar 2018 15:51:11: Command message:
32 INFO @ Wed, 14 Feb 2018 01:52:58: Writing to file output_countsummary.tex 32 INFO @ Sun, 25 Mar 2018 15:51:11: Writing to file output_countsummary.tex
33 INFO @ Wed, 14 Feb 2018 01:52:58: Processing code chunks with options ... 33 INFO @ Sun, 25 Mar 2018 15:51:11: Processing code chunks with options ...
34 INFO @ Wed, 14 Feb 2018 01:52:58: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) 34 INFO @ Sun, 25 Mar 2018 15:51:11: 1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28)
35 INFO @ Wed, 14 Feb 2018 01:52:58: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) 35 INFO @ Sun, 25 Mar 2018 15:51:11: 2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156)
36 INFO @ Wed, 14 Feb 2018 01:52:58: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) 36 INFO @ Sun, 25 Mar 2018 15:51:11: 3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174)
37 INFO @ Wed, 14 Feb 2018 01:52:58: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) 37 INFO @ Sun, 25 Mar 2018 15:51:11: 4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188)
38 INFO @ Wed, 14 Feb 2018 01:52:58: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221) 38 INFO @ Sun, 25 Mar 2018 15:51:11: 5 : keep.source term verbatim pdf (output_countsummary.Rnw:221)
39 INFO @ Wed, 14 Feb 2018 01:52:58: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228) 39 INFO @ Sun, 25 Mar 2018 15:51:11: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228)
40 INFO @ Wed, 14 Feb 2018 01:52:58: 40 INFO @ Sun, 25 Mar 2018 15:51:11:
41 INFO @ Wed, 14 Feb 2018 01:52:58: You can now run (pdf)latex on ‘output_countsummary.tex’ 41 INFO @ Sun, 25 Mar 2018 15:51:11: You can now run (pdf)latex on ‘output_countsummary.tex’
42 INFO @ Wed, 14 Feb 2018 01:52:58: Error in texi2dvi("output_countsummary.tex", pdf = TRUE) : 42 INFO @ Sun, 25 Mar 2018 15:51:11:
43 INFO @ Wed, 14 Feb 2018 01:52:58: pdflatex is not available 43 INFO @ Sun, 25 Mar 2018 15:51:11: End command message.
44 INFO @ Wed, 14 Feb 2018 01:52:58: Execution halted
45 INFO @ Wed, 14 Feb 2018 01:52:58:
46 INFO @ Wed, 14 Feb 2018 01:52:58: End command message.