ani_rep

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

Arguments

Files output

• [prefix].ani_closest.tsv

• [prefix].ani_summary.tsv

• [prefix].log

• [prefix].warnings.log

• [prefix].warnings.log

• intermediate_results/mash/

  • [prefix].gtdb_ref_sketch.msh

  • [prefix].mash_distances.msh

  • [prefix].user_query_sketch.msh

Example

Input

gtdbtk ani_rep --genome_dir genomes/ --out_dir ani_rep/ --cpus 70

Output

[2020-04-13 10:51:58] INFO: GTDB-Tk v1.1.0
[2020-04-13 10:51:58] INFO: gtdbtk ani_rep --genome_dir genomes/ --out_dir ani_rep/ --cpus 70
[2020-04-13 10:51:58] INFO: Using GTDB-Tk reference data version r89: /release89
[2020-04-13 10:51:59] INFO: Using Mash version 2.2.2
[2020-04-13 10:51:59] INFO: Creating Mash sketch file: ani_rep/intermediate_results/mash/gtdbtk.user_query_sketch.msh
==> Sketching 3 of 3 (100.0%) genomes
[2020-04-13 10:51:59] INFO: Creating Mash sketch file: ani_rep/intermediate_results/mash/gtdbtk.gtdb_ref_sketch.msh
==> Sketching 24706 of 24706 (100.0%) genomes
[2020-04-13 10:53:13] INFO: Calculating Mash distances.
[2020-04-13 10:53:14] INFO: Calculating ANI with FastANI.
==> Processing 874 of 874 (100.0%) comparisons.
[2020-04-13 10:53:23] INFO: Summary of results saved to: ani_rep/gtdbtk.ani_summary.tsv
[2020-04-13 10:53:23] INFO: Closest representative hits saved to: ani_rep/gtdbtk.ani_closest.tsv
[2020-04-13 10:53:23] INFO: Done.