gtdbtk.json

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

Produced by

• align

• align

• classify

• classify_wf

• de_novo_wf

• identify

• infer

Example

{
    "version": "2.1.1",
    "command_line": "gtdbtk classify_wf --batchfile /srv/projects/gtdbtk/test_new_features/gems_benchmark/3lines_batchfile.tsv --out_dir /srv/projects/gtdbtk/test_new_features/gems_benchmark/classify_wf_outdir_prescreen_3lines/ --keep_intermediates --cpus 20 --mash_db /srv/projects/gtdbtk/test_new_features/gems_benchmark/mash_sketch/cli/",
    "database_version": "r207",
    "database_path": "/srv/projects/gtdbtk/test_new_features/release207_v2/",
    "steps": [
        {
            "name": "ANI screen",
            "input": "/srv/projects/gtdbtk/test_new_features/gems_benchmark/3lines_batchfile.tsv",
            "output_dir": "/srv/projects/gtdbtk/test_new_features/gems_benchmark/classify_wf_outdir_prescreen_3lines/",
            "output_files": {
                "bac120": "/srv/projects/gtdbtk/test_new_features/gems_benchmark/classify_wf_outdir_prescreen_3lines/classify/ani_screen/gtdbtk.bac120.ani_summary.tsv"
            },
            "starts_at": "2023-02-01T08:02:17.814231",
            "ends_at": "2023-02-01T08:02:27.782442",
            "duration": "0:00:09",
            "status": "completed",
            "mash_k": 16,
            "mash_s": 5000,
            "mash_v": 1.0,
            "mash_max_dist": 0.1,
            "mash_db": "/srv/projects/gtdbtk/test_new_features/gems_benchmark/mash_sketch/cli/"
        },