Steps

Pick one genome for a specified rank

hatchet pick -d bac -r f -t /srv/db/gtdbtk/official/release202/pplacer/gtdb_r202_bac120.refpkg/bac120_r202_unroot.pplacer.tree -m /srv/db/gtdbtk/official/release202/pplacer/gtdb_r202_bac120.refpkg/bac120_msa_reps_r202.faa --tax /srv/db/gtdbtk/official/release202/taxonomy/gtdb_taxonomy.tsv --out_dir family_level_tree

Regenerate RED values file for the new pruned tree. hatchet red -t /srv/db/gtdbtk/official/release202/pplacer/gtdb_r202_bac120.refpkg/bac120_r202_unroot.pplacer.tree --pruned_tree family_level_tree/gtdb_pruned.tree --red_file /srv/db/gtdbtk/official/release202/mrca_red/gtdbtk_r202_bac120.tsv -o new_red_file.tsv

Split Reference tree into lower ranks subtrees

hatchet split --ref_tree /srv/db/gtdbtk/official/release202/pplacer/gtdb_r202_bac120.refpkg/bac120_r202_unroot.pplacer.tree --taxonomy /srv/db/gtdbtk/official/release202/taxonomy/gtdb_taxonomy.tsv --rank_to_split o -m /srv/db/gtdbtk/official/release202/pplacer/gtdb_r202_bac120.refpkg/bac120_msa_reps_r202.faa --domain bac --out_dir split_trees

Regenerate RED values file for the new low level trees.

hatchet red_low --split_trees_dir split_trees/ --reference_tree release89/pplacer/gtdb_r89_bac120.refpkg/bac120_r89_unroot.pplacer.tree --red_file release89/mrca_red/gtdbtk_r89_bac120.tsv