Mercurial > repos > iuc > mageck_test
view test-data/out.count.log.txt @ 2:81bbbddcf285 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
| author | iuc |
|---|---|
| date | Wed, 04 Apr 2018 11:03:59 -0400 |
| parents | b8da4d41aa1d |
| children |
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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.