Mercurial > repos > frogs > frogs_3_1_0
diff test-data/references/13-tree-mafft.log @ 0:59bc96331073 draft default tip
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 diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/references/13-tree-mafft.log Thu Feb 28 10:14:49 2019 -0500 @@ -0,0 +1,33 @@ +## Application +Software :/home/maria/workspace/git/FROGS/FROGS_master/test/../app/tree.py (version : 3.1) +Command : /home/maria/workspace/git/FROGS/FROGS_master/test/../app/tree.py --nb-cpus 4 --input-otu res/04-filters.fasta --biomfile res/06-affiliation.biom --out-tree res/13-tree-mafft.nwk --html res/13-tree-mafft.html --log-file res/13-tree-mafft.log + +Number of input OTUs sequences: 86 + +######################################################################################################## +# Mafft multiple alignment. (mafft version : v7.407) +Command: + mafft --maxiterate 1000 --globalpair --thread 4 res/04-filters.fasta > res/1550052877.76_4235_mafft_aligned.fasta 2> res/1550052877.76_4235_mafft.stderr + +Execution: + start: 13 Feb 2019 11:14:37 + end: 13 Feb 2019 11:15:14 + +######################################################################################################## +# reconstruction a phylogenetic tree (FastTree version : 2.1.10) +Command: + FastTree -nt -gtr res/1550052877.76_4235_mafft_aligned.fasta > res/1550052877.76_4235_fasttree.nwk 2> res/1550052877.76_4235_fasttree.stderr + +Execution: + start: 13 Feb 2019 11:15:14 + end: 13 Feb 2019 11:15:19 + +######################################################################################################## +# root newick tree with phangorn R package midpoint function. (root_tree.R version : 1.0.0) +Command: + root_tree.R res/1550052877.76_4235_fasttree.nwk res/13-tree-mafft.nwk + +Execution: + start: 13 Feb 2019 11:15:23 + end: 13 Feb 2019 11:15:25 +