{
    "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_hmm_hits": {
        "--return-best-hit": true,
        "--align-with": "muscle",
        "--concatenate-genes": true,
        "--get-aa-sequences": true,
        "--hmm-sources": "Campbell_et_al",
        "--min-num-bins-gene-occurs": 5
    },
    "import_phylogenetic_tree_to_pangenome": {
        "tree_name": "phylogeny_hmms"
    },
    "project_name": "FIVE_TEST",
    "internal_genomes": "",
    "external_genomes": "five-external-genomes.txt",
    "sequence_source_for_phylogeny": "hmm",
    "output_dirs": {
        "FASTA_DIR": "01_FASTA_FIVE_PAN",
        "CONTIGS_DIR": "02_CONTIGS_FIVE_PAN",
        "PHYLO_DIR": "01_PHYLOGENOMICS_FIVE_PAN_hmms",
        "PAN_DIR": "03_PAN_FIVE_PAN",
        "LOGS_DIR": "00_LOGS_FIVE_PAN"
    }
}
