summary.tsv

Classifications provided by GTDB-Tk are in the files <prefix>.bac120.summary.tsv and <prefix>.ar53.summary.tsv for bacterial and archaeal genomes, respectively. These are tab-separated files with one row per genome and the following 20 columns. Empty values are written as N/A.

Genomes are first compared with skani to all GTDB species representative genomes (ANI screen). A genome is assigned to a species when the closest representative with an alignment fraction (AF) ≥ --min_af (default 0.5) has an ANI within that representative’s species-specific ANI circumscription radius. All other genomes are placed in the reference tree with pplacer and classified from their placement and relative evolutionary divergence (RED). Genomes assigned by the ANI screen are only placed in the tree when --place_species is used.

  • user_genome: unique identifier of the query genome, taken from the FASTA file name (or the batch file).

  • classification: GTDB taxonomy string inferred by GTDB-Tk. An unassigned species (s__) means that no reference genome with an AF ≥ --min_af has an ANI within its circumscription radius, or that the genome is placed outside a named genus. Genomes for which gene calling failed or no marker genes were found are reported as Unclassified (in the bac120 file), and genomes removed by --min_perc_aa as Unclassified Bacteria or Unclassified Archaea, with the reason in warnings.

  • closest_genome_reference: accession of the species representative genome to which the query genome was assigned based on ANI and AF. N/A when no species was assigned by ANI.

  • closest_genome_reference_radius: species-specific ANI circumscription radius of the above reference genome.

  • closest_genome_taxonomy: GTDB taxonomy of the above reference genome.

  • closest_genome_ani: ANI between the query and the above reference genome.

  • closest_genome_af: AF between the query and the above reference genome (the larger of the query and reference alignment fractions reported by skani).

  • closest_placement_reference: for genomes assigned by the ANI screen and placed in the tree with --place_species, the accession of the reference genome on the terminal branch where the query genome is placed. N/A otherwise.

  • closest_placement_radius: species-specific ANI circumscription radius of the above reference genome.

  • closest_placement_taxonomy: GTDB taxonomy of the above reference genome.

  • closest_placement_ani: ANI between the query and the above reference genome, when available.

  • closest_placement_af: AF between the query and the above reference genome, when available.

  • pplacer_taxonomy: taxonomy inferred from the pplacer placement of the query genome in the reference tree.

  • classification_method: rule used to classify the genome. One of:

    • ani_screen: species assigned from ANI and AF alone during the ANI screen; the genome is not placed in the reference tree (unless --place_species is used).

    • taxonomic classification defined by topology and ANI: with --place_species, a genome assigned by the ANI screen that was also placed in the reference tree; the species assignment comes from ANI and AF.

    • taxonomic classification fully defined by topology: the classification follows directly from the placement of the genome in the reference tree.

    • taxonomic novelty determined using RED: the placement and the RED value of the genome were used to determine the classification (e.g. a putative novel genus or family).

  • note: additional information about the classification. Several notes are separated by ;. Values:

    • classification based on ANI only: species assigned by the ANI screen.

    • topological placement and ANI have congruent species assignments: the placement reference and the closest reference by ANI/AF are the same species.

    • topological placement and ANI have incongruent species assignments: they differ; the species assignment follows ANI/AF.

    • classification based on placement in backbone tree: in split mode (bacteria, default), the genome was classified on the backbone tree only.

    • classification based on placement in class-level tree: in split mode, the classification comes from the class-level tree.

    • classification based on consensus between backbone and class-level tree: in split mode, the backbone and class-level placements were combined.

  • other_related_references(genome_id,species_name,radius,ANI,AF): other reference genomes found close to the query genome by the ANI screen, separated by ;. Each entry gives the accession, species name, circumscription radius, ANI and AF. Only reported for genomes assigned to a species by ANI.

  • msa_percent: percentage of the multiple sequence alignment spanned by the genome (i.e. percentage of columns with an amino acid).

  • translation_table: translation table used by Prodigal to call genes (11 or 4, or the table given in the batch file).

  • red_value: relative evolutionary divergence (RED) of the query genome, when it was needed for the classification. Not calculated when the genome is classified by ANI.

  • warnings: unusual characteristics of the query genome that may affect the taxonomic assignment, separated by ; (e.g. a high percentage of markers with multiple hits, a questionable domain, or a genome not assigned to the closest species because it falls outside that species’ ANI circumscription radius).

Produced by

Example

genome_2 shows a genome assigned by the ANI screen and placed in the tree with --place_species.

user_genome classification  closest_genome_reference        closest_genome_reference_radius closest_genome_taxonomy closest_genome_ani      closest_genome_af       closest_placement_reference     closest_placement_radius        closest_placement_taxonomy      closest_placement_ani   closest_placement_af    pplacer_taxonomy        classification_method   note    other_related_references(genome_id,species_name,radius,ANI,AF)  msa_percent     translation_table       red_value       warnings
genome_1    d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium GCF_000024185.1 95.0    d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium 100.0   1.0     N/A     N/A     N/A     N/A     N/A     N/A     ani_screen      classification based on ANI only        GCA_900321995.1, s__Methanobrevibacter sp900321995, 95.0, 80.9, 0.7; GCF_900114585.1, s__Methanobrevibacter olleyae, 95.0, 79.96, 0.55  N/A     N/A     N/A     N/A
genome_2    d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365    GCA_002498365.1 95.0    d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365    99.16   0.94    GCA_002498365.1 95.0    d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365    99.16   0.94    d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__ taxonomic classification defined by topology and ANI    topological placement and ANI have congruent species assignments        GCA_002505345.1, s__VadinCA11 sp002505345, 95.0, 89.92, 0.89; GCA_002509405.1, s__VadinCA11 sp002509405, 95.0, 88.13, 0.89      87.1    11      N/A     N/A
genome_3    d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__;s__       N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__;s__       taxonomic novelty determined using RED  N/A     N/A     85.47   11      0.89523 N/A
genome_4    Unclassified    N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     N/A     No bacterial or archaeal marker