Mercurial > repos > iuc > mageck_mle
view 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 |
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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.