Mercurial > repos > iuc > mageck_gsea
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 |
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--- 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.