comparison test-data/out.count.log.txt @ 0:eab37e8fea75 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
author iuc
date Wed, 14 Feb 2018 06:42:36 -0500
parents
children 9cd937788131
comparison
equal deleted inserted replaced
-1:000000000000 0:eab37e8fea75
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
2 INFO @ Wed, 14 Feb 2018 01:52:58: Welcome to MAGeCK v0.5.7. Command: count
3 INFO @ Wed, 14 Feb 2018 01:52:58: Loading 2550 predefined sgRNAs.
4 WARNING @ Wed, 14 Feb 2018 01:52:58: There are 0 sgRNAs with duplicated sequences.
5 INFO @ Wed, 14 Feb 2018 01:52:58: Parsing FASTQ file input.gz...
6 INFO @ Wed, 14 Feb 2018 01:52:58: Determining the trim-5 length of FASTQ file input.gz...
7 INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20
8 INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ...
9 INFO @ Wed, 14 Feb 2018 01:52:58: Read length:30
10 INFO @ Wed, 14 Feb 2018 01:52:58: 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)
12 INFO @ Wed, 14 Feb 2018 01:52:58: 0 1453 1.0
13 INFO @ Wed, 14 Feb 2018 01:52:58: Auto determination of trim5 results: 0
14 INFO @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20
15 INFO @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ..
16 INFO @ Wed, 14 Feb 2018 01:52:58: Total: 2500.
17 INFO @ Wed, 14 Feb 2018 01:52:58: Mapped: 1453.
18 DEBUG @ Wed, 14 Feb 2018 01:52:58: Initial (total) size factor: 1.0
19 DEBUG @ Wed, 14 Feb 2018 01:52:58: Median factor: 2.0
20 INFO @ Wed, 14 Feb 2018 01:52:58: Final size factor: 2.0
21 INFO @ Wed, 14 Feb 2018 01:52:58: Summary of file input.gz:
22 INFO @ Wed, 14 Feb 2018 01:52:58: label sample1
23 INFO @ Wed, 14 Feb 2018 01:52:58: reads 2500
24 INFO @ Wed, 14 Feb 2018 01:52:58: mappedreads 1453
25 INFO @ Wed, 14 Feb 2018 01:52:58: totalsgrnas 2550
26 INFO @ Wed, 14 Feb 2018 01:52:58: zerosgrnas 1276
27 INFO @ Wed, 14 Feb 2018 01:52:58: 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.
29 DEBUG @ Wed, 14 Feb 2018 01:52:58: Setting up the visualization module...
30 INFO @ Wed, 14 Feb 2018 01:52:58: Running command: cd ./; Rscript output_countsummary.R
31 INFO @ Wed, 14 Feb 2018 01:52:58: Command message:
32 INFO @ Wed, 14 Feb 2018 01:52:58: Writing to file output_countsummary.tex
33 INFO @ Wed, 14 Feb 2018 01:52:58: 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)
35 INFO @ Wed, 14 Feb 2018 01:52:58: 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)
37 INFO @ Wed, 14 Feb 2018 01:52:58: 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)
39 INFO @ Wed, 14 Feb 2018 01:52:58: 6 : keep.source term verbatim pdf (output_countsummary.Rnw:228)
40 INFO @ Wed, 14 Feb 2018 01:52:58:
41 INFO @ Wed, 14 Feb 2018 01:52:58: 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) :
43 INFO @ Wed, 14 Feb 2018 01:52:58: pdflatex is not available
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.