gtdbtk.json¶
The console output of GTDB-Tk saved to disk in a JSON format.
Produced by¶
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"