view test-data/out.count.log.txt @ 0:d95eae71878e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe

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.