decorate

Decorate a tree with the GTDB-Tk taxonomy.

Arguments

usage: gtdbtk decorate --input_tree INPUT_TREE --output_tree OUTPUT_TREE
                       [--gtdbtk_classification_file GTDBTK_CLASSIFICATION_FILE]
                       [--custom_taxonomy_file CUSTOM_TAXONOMY_FILE]
                       [--tmpdir TMPDIR] [--debug] [-h]

required named arguments

--input_tree

path to the unrooted tree in Newick format

--output_tree

path to output the tree

Named Arguments

--gtdbtk_classification_file

file with GTDB-Tk classifications produced by the classify command

--custom_taxonomy_file

file indicating custom taxonomy strings for user genomes, that should contain any genomes belonging to the outgroup. Format: GENOME_ID<TAB>d__;p__;c__;o__;f__;g__;s__

--tmpdir

specify alternative directory for temporary files

Default: “/tmp”

--debug

create intermediate files for debugging purposes

Example

Input

gtdbtk decorate --input_tree input.tree --output_tree output.tree

Output

[2020-04-14 08:20:51] INFO: GTDB-Tk v1.1.0
[2020-04-14 08:20:51] INFO: gtdbtk decorate --input_tree input.tree --output_tree output.tree
[2020-04-14 08:20:51] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-14 08:20:51] WARNING: DECORATE NOT YET IMPLEMENTED!
[2020-04-14 08:20:51] INFO: Done.