gtdbtk.json

The console output of GTDB-Tk saved to disk in a JSON format.

Example

{
"version": "2.5.0",
"command_line": "gtdbtk classify_wf --batchfile genomes/3_batchfile.tsv --out_dir classify_wf_3_genomes --cpus 20",
"database_version": "r226",
"database_path": "/srv/db/gtdbtk/official/release226",
"steps": [
    {
        "name": "ANI screen",
        "output_dir": "classify_wf_3_genomes",
        "starts_at": "2025-08-05T20:31:02.156781",
        "ends_at": "2025-08-05T20:35:27.198873",
        "duration": "0:04:25",
        "status": "completed",
        "genome_dir": null,
        "batchfile": "genomes/3_batchfile.tsv",
        "min_af": 0.5,
        "output_files": {}
    },
    {
        "name": "identify",
        "output_dir": "classify_wf_3_genomes",
        "starts_at": "2025-08-05T20:35:27.270095",
        "ends_at": "2025-08-05T20:36:15.865020",
        "duration": "0:00:48",
        "status": "completed",
        "genes": false,
        "extension": "fna",
        "write_single_copy_genes": false,
        "genome_dir": null,
        "batchfile": "genomes/3_batchfile.tsv",
        "output_files": {
            "all": [
                "classify_wf_3_genomes/identify/gtdbtk.failed_genomes.tsv",
                "classify_wf_3_genomes/identify/gtdbtk.translation_table_summary.tsv"
            ],
            "ar53": [
                "classify_wf_3_genomes/identify/gtdbtk.ar53.markers_summary.tsv"
            ],
            "bac120": [
                "classify_wf_3_genomes/identify/gtdbtk.bac120.markers_summary.tsv"
            ]
        }
    },
    {
        "name": "align",
        "output_dir": "classfiy_wf_3_genomes",
        "starts_at": "2025-08-05T20:36:15.865242",
        "ends_at": "2025-08-05T20:41:38.376388",
        "duration": "0:05:22",
        "status": "completed",
        "identify_dir": "classfiy_wf_3_genomes",
        "skip_gtdb_refs": false,
        "taxa_filter": null,
        "min_perc_aa": 10,
        "custom_msa_filters": false,
        "skip_trimming": false,
        "rnd_seed": null,
        "cols_per_gene": null,
        "min_consensus": null,
        "max_consensus": null,
        "min_perc_taxa": null,
        "outgroup_taxon": null,
        "output_files": {
            "bac120": [
                "classfiy_wf_3_genomes/align/gtdbtk.bac120.filtered.tsv",
                "classfiy_wf_3_genomes/align/gtdbtk.bac120.msa.fasta",
                "classfiy_wf_3_genomes/align/gtdbtk.bac120.user_msa.fasta"
            ]
        }
    },
    {
        "name": "classify",
        "output_dir": "classfiy_wf_3_genomes",
        "starts_at": "2025-08-05T20:41:38.377084",
        "ends_at": "2025-08-05T21:08:25.704484",
        "duration": "0:26:47",
        "status": "completed",
        "align_dir": "classfiy_wf_3_genomes",
        "genome_dir": null,
        "batchfile": "genomes/3_batchfile.tsv",
        "scratch_dir": null,
        "debug_option": false,
        "full_tree": false,
        "skip_ani_screen": true,
        "output_files": {
            "bac120": [
                "classify_wf_3_genomes/classify/gtdbtk.backbone.bac120.classify.tree",
                "classify_wf_3_genomes/classify/gtdbtk.bac120.classify.tree.7.tree",
                "classify_wf_3_genomes/classify/gtdbtk.bac120.classify.tree.2.tree",
                "classify_wf_3_genomes/classify/gtdbtk.bac120.tree.mapping.tsv",
                "classify_wf_3_genomes/classify/gtdbtk.bac120.summary.tsv"
            ]
        }
    }
],
"output_dir": "classify_wf_3_genomes",
"path": "classify_wf_3_genomes/gtdbtk.json"