diff test-data/out.count.log.txt @ 2:82a180e6b582 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
author iuc
date Wed, 04 Apr 2018 11:03:05 -0400
parents d95eae71878e
children
line wrap: on
line diff
--- a/test-data/out.count.log.txt	Sat Feb 17 10:41:13 2018 -0500
+++ b/test-data/out.count.log.txt	Wed Apr 04 11:03:05 2018 -0400
@@ -1,46 +1,43 @@
-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 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Welcome to MAGeCK v0.5.7. Command: count 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Loading 2550 predefined sgRNAs. 
-WARNING @ Wed, 14 Feb 2018 01:52:58: There are 0 sgRNAs with duplicated sequences. 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Parsing FASTQ file input.gz... 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Determining the trim-5 length of FASTQ file input.gz... 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads ... 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Read length:30 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Total tested reads: 2500, mapped: 1453(0.5812) 
-INFO  @ Wed, 14 Feb 2018 01:52:58: --trim-5 test data: (trim_length reads fraction) 
-INFO  @ Wed, 14 Feb 2018 01:52:58: 0	1453	1.0 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Auto determination of trim5 results: 0 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Possible gRNA lengths:20 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Processing 0M reads .. 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Total: 2500. 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Mapped: 1453. 
-DEBUG @ Wed, 14 Feb 2018 01:52:58: Initial (total) size factor: 1.0 
-DEBUG @ Wed, 14 Feb 2018 01:52:58: Median factor: 2.0 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Final size factor: 2.0 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Summary of file input.gz: 
-INFO  @ Wed, 14 Feb 2018 01:52:58: label	sample1 
-INFO  @ Wed, 14 Feb 2018 01:52:58: reads	2500 
-INFO  @ Wed, 14 Feb 2018 01:52:58: mappedreads	1453 
-INFO  @ Wed, 14 Feb 2018 01:52:58: totalsgrnas	2550 
-INFO  @ Wed, 14 Feb 2018 01:52:58: zerosgrnas	1276 
-INFO  @ Wed, 14 Feb 2018 01:52:58: giniindex	0.5266899931488773 
-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. 
-DEBUG @ Wed, 14 Feb 2018 01:52:58: Setting up the visualization module... 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Running command: cd ./; Rscript output_countsummary.R 
-INFO  @ Wed, 14 Feb 2018 01:52:58: Command message: 
-INFO  @ Wed, 14 Feb 2018 01:52:58:   Writing to file output_countsummary.tex 
-INFO  @ Wed, 14 Feb 2018 01:52:58:   Processing code chunks with options ... 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    5 : keep.source term verbatim pdf  (output_countsummary.Rnw:221) 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    6 : keep.source term verbatim pdf  (output_countsummary.Rnw:228) 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    
-INFO  @ Wed, 14 Feb 2018 01:52:58:   You can now run (pdf)latex on ‘output_countsummary.tex’ 
-INFO  @ Wed, 14 Feb 2018 01:52:58:   Error in texi2dvi("output_countsummary.tex", pdf = TRUE) :  
-INFO  @ Wed, 14 Feb 2018 01:52:58:     pdflatex is not available 
-INFO  @ Wed, 14 Feb 2018 01:52:58:   Execution halted 
-INFO  @ Wed, 14 Feb 2018 01:52:58:    
-INFO  @ Wed, 14 Feb 2018 01:52:58: End command message. 
+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 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Welcome to MAGeCK v0.5.7. Command: count 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Loading 2550 predefined sgRNAs. 
+WARNING @ Sun, 25 Mar 2018 15:51:06: There are 0 sgRNAs with duplicated sequences. 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Parsing FASTQ file input_0.gz... 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Determining the trim-5 length of FASTQ file input_0.gz... 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads ... 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Read length:30 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Total tested reads: 2500, mapped: 1453(0.5812) 
+INFO  @ Sun, 25 Mar 2018 15:51:06: --trim-5 test data: (trim_length reads fraction) 
+INFO  @ Sun, 25 Mar 2018 15:51:06: 0	1453	1.0 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Auto determination of trim5 results: 0 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Possible gRNA lengths:20 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Processing 0M reads .. 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Total: 2500. 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Mapped: 1453. 
+DEBUG @ Sun, 25 Mar 2018 15:51:06: Initial (total) size factor: 1.0 
+DEBUG @ Sun, 25 Mar 2018 15:51:06: Median factor: 2.0 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Final size factor: 2.0 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Summary of file input_0.gz: 
+INFO  @ Sun, 25 Mar 2018 15:51:06: label	test1_fastq_gz 
+INFO  @ Sun, 25 Mar 2018 15:51:06: reads	2500 
+INFO  @ Sun, 25 Mar 2018 15:51:06: mappedreads	1453 
+INFO  @ Sun, 25 Mar 2018 15:51:06: totalsgrnas	2550 
+INFO  @ Sun, 25 Mar 2018 15:51:06: zerosgrnas	1276 
+INFO  @ Sun, 25 Mar 2018 15:51:06: giniindex	0.5266899931488773 
+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. 
+DEBUG @ Sun, 25 Mar 2018 15:51:06: Setting up the visualization module... 
+INFO  @ Sun, 25 Mar 2018 15:51:06: Running command: cd ./; Rscript output_countsummary.R 
+INFO  @ Sun, 25 Mar 2018 15:51:11: Command message: 
+INFO  @ Sun, 25 Mar 2018 15:51:11:   Writing to file output_countsummary.tex 
+INFO  @ Sun, 25 Mar 2018 15:51:11:   Processing code chunks with options ... 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    1 : keep.source term verbatim (label = funcdef, output_countsummary.Rnw:28) 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    2 : keep.source term tex (label = tab1, output_countsummary.Rnw:156) 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    3 : keep.source term tex (label = tab2, output_countsummary.Rnw:174) 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    4 : keep.source term tex (label = tab3, output_countsummary.Rnw:188) 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    5 : keep.source term verbatim pdf  (output_countsummary.Rnw:221) 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    6 : keep.source term verbatim pdf  (output_countsummary.Rnw:228) 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    
+INFO  @ Sun, 25 Mar 2018 15:51:11:   You can now run (pdf)latex on ‘output_countsummary.tex’ 
+INFO  @ Sun, 25 Mar 2018 15:51:11:    
+INFO  @ Sun, 25 Mar 2018 15:51:11: End command message.