{
    "fasta_txt": "five-genomes-fasta.txt",
    "anvi_run_hmms": {
        "run": true,
        "threads": 5,
        "--installed-hmm-profile": "",
        "--hmm-profile-dir": ""
    },
    "anvi_run_ncbi_cogs": {
        "run": false
    },
    "anvi_script_reformat_fasta": {
        "run": false
    },
    "anvi_get_sequences_for_gene_clusters": {
        "--min-num-genomes-gene-cluster-occurs": 5,
        "--max-num-genes-from-each-genome": 1,
        "--add-into-items-additional-data-table": "GCs_for_phylogeny",
        "--align-with": "famsa",
        "--concatenate-gene-clusters": true
    },
    "import_phylogenetic_tree_to_pangenome": {
        "tree_name": "phylogeny_gene_clusters"
    },
    "project_name": "FIVE_TEST",
    "internal_genomes": "",
    "external_genomes": "five-external-genomes.txt",
    "sequence_source_for_phylogeny": "gene_clusters",
    "output_dirs": {
        "FASTA_DIR": "01_FASTA_FIVE_PAN",
        "CONTIGS_DIR": "02_CONTIGS_FIVE_PAN",
        "PHYLO_DIR": "01_PHYLOGENOMICS_FIVE_PAN",
        "PAN_DIR": "03_PAN_FIVE_PAN",
        "LOGS_DIR": "00_LOGS_FIVE_PAN"
    }
}
