ani_rep¶

Compute the ANI of input genomes to all GTDB-Tk representative genomes.

Arguments¶

usage: gtdbtk ani_rep (--genome_dir GENOME_DIR | --batchfile BATCHFILE)
                      --out_dir OUT_DIR [--min_af MIN_AF] [-x EXTENSION]
                      [--prefix PREFIX] [--cpus CPUS] [--tmpdir TMPDIR]
                      [--debug] [-h]

mutually exclusive required arguments¶

--genome_dir: directory containing genome files in FASTA format
--batchfile: path to file describing genomes - tab separated in 2 or 3 columns (FASTA file, genome ID, translation table [optional])

required named arguments¶

--out_dir: directory to output files

optional clustering arguments¶

--min_af

minimum alignment fraction to assign genome to a species cluster

Default: 0.5

Named Arguments¶

-x, --extension

extension of files to process, gz = gzipped

Default: “fna”

--prefix

prefix for all output files

Default: “gtdbtk”

--cpus

number of CPUs to use

Default: 1

--tmpdir

specify alternative directory for temporary files

Default: “/tmp”

--debug

create intermediate files for debugging purposes

Files output¶

Example¶

Input¶

gtdbtk ani_rep --batchfile genomes/500_batchfile.tsv -x fa --out_dir test_ani_reps --cpus 90

Output¶

[2025-08-05 17:13:33] INFO: GTDB-Tk v2.5.0
[2025-08-05 17:13:33] INFO: gtdbtk ani_rep --batchfile genomes/500_batchfile.tsv -x fa --out_dir test_ani_reps --cpus 90
[2025-08-05 17:13:33] INFO: Using GTDB-Tk reference data version r226: /srv/db/gtdbtk/official/release226
[2025-08-05 17:13:34] INFO: Loading reference genomes.
[2025-08-05 17:13:39] INFO: Calculating all vs all ANI with skani v0.2.1.
[2025-08-05 17:13:40] INFO: Sketching genomes
[2025-08-05 17:15:52] INFO: Sketches done: 2min 11secs
[2025-08-05 17:15:52] INFO: Running comparisons
[2025-08-05 17:21:15] INFO: Comparisons finished, capturing results.
[2025-08-05 17:23:26] INFO: Summary of results saved to: test_ani_reps/gtdbtk.ani_summary.tsv
[2025-08-05 17:23:27] INFO: Closest representative hits saved to: test_ani_reps/gtdbtk.ani_closest.tsv
[2025-08-05 17:23:27] INFO: Done.