convert_to_species

Replace the GTDB genome accessions at the leaves of a GTDB-Tk tree with their GTDB species names.

Leaves that are not GTDB genomes (e.g. user genomes) are left unchanged, unless they are listed in a --custom_taxonomy_file (same format as in de_novo_wf); entries in that file take precedence over the GTDB taxonomy. With --all_ranks, the full 7-rank taxonomy is used as the leaf label instead of the species name.

Arguments

usage: gtdbtk convert_to_species --input_tree INPUT_TREE --output_tree
                                 OUTPUT_TREE
                                 [--custom_taxonomy_file CUSTOM_TAXONOMY_FILE]
                                 [--all_ranks] [--debug] [-h]

required named arguments

--input_tree

path to the unrooted tree in Newick format

--output_tree

path to output the tree

optional arguments

--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__

--all_ranks

add all missing ranks to the leaf nodes if they are present in the reference tree.

--debug

create intermediate files for debugging purposes

Example

gtdbtk convert_to_species --input_tree gtdbtk.bac120.classify.tree --output_tree species.tree