Mercurial > repos > frogs > frogs_3_1_0

view test-data/references/14-phylo_import.log @ 0:59bc96331073 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
parents
children
line wrap: on
line source

## Application
Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py (version : 3.1)
Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py --biomfile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/chaillou.biom --samplefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/sample_metadata.tsv --treefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/tree.nwk --rdata res/14-phylo_import.Rdata --html res/14-phylo_import.html --log-file res/14-phylo_import.log

########################################################################################################
# Run r_import_data.Rmd (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
[1] "Rmarkdown version:  1.10"
[1] "Phyloseq version:  1.19.1")
Command:
	Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_import_data.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.html', params=list(biomfile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/chaillou.biom', samplefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/tree.nwk', normalization=FALSE, outputRdata='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549620116.55_23941_rmarkdown.stderr

Execution:
	start: 08 Feb 2019 11:02:03
	end:   08 Feb 2019 11:02:13

## Application
Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py (version : 3.1)
Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/r_import_data.py --biomfile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/chaillou.biom --samplefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/sample_metadata.tsv --treefile /home/maria/workspace/git/FROGS/FROGS_master/test/../test/data/tree.nwk --rdata res/14-phylo_import.Rdata --html res/14-phylo_import.html --log-file res/14-phylo_import.log

########################################################################################################
# Run r_import_data.Rmd (Rscript version : [1] "R version 3.4.4 (2018-03-15)"
[1] "Rmarkdown version:  1.10"
[1] "Phyloseq version:  1.19.1")
Command:
	Rscript -e "rmarkdown::render('/home/maria/workspace/git/FROGS/FROGS_master/app/r_import_data.Rmd',output_file='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.html', params=list(biomfile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/chaillou.biom', samplefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/sample_metadata.tsv', treefile='/home/maria/workspace/git/FROGS/FROGS_master/test/data/tree.nwk', normalization=FALSE, outputRdata='/home/maria/workspace/git/FROGS/FROGS_master/test/res/14-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/maria/workspace/git/FROGS/FROGS_master/lib/external-lib'), intermediates_dir='/home/maria/workspace/git/FROGS/FROGS_master/test/res')" 2> /home/maria/workspace/git/FROGS/FROGS_master/test/res/1549623006.35_25404_rmarkdown.stderr

Execution:
	start: 08 Feb 2019 11:50:09
	end:   08 Feb 2019 11:50:16