Annotate ORFs with kingdom-specific marker information

optional arguments:
  -h, --help            show this help message and exit
  --orfs ORFS           Path to a fasta file containing amino acid sequences
                        of open reading frames (default: None)
  --kingdom {bacteria,archaea}
                        kingdom to search for markers (default: bacteria)
  --hmmscan HMMSCAN     Path to hmmscan output table containing the respective
                        `kingdom` single-copy marker annotations. (default:
  --out OUT             Path to write filtered annotated markers corresponding
                        to `kingdom`. (default: None)
  --dbdir DBDIR         Path to directory containing the single-copy marker
                        HMM databases. (default: MARKERS_DIR)
  --hmmdb HMMDB         Path to single-copy marker HMM databases. (default:
  --cutoffs CUTOFFS     Path to single-copy marker cutoff tsv. (default: None)
  --force               Whether to overwrite existing provided annotations.
                        (default: False)
  --parallel            Whether to use hmmscan parallel option. (default:
  --gnu-parallel        Whether to run hmmscan using GNU parallel. (default:
  --cpus CPUS           Number of cores to use for parallel execution.
                        (default: 8)
  --seed SEED           Seed to set random state for hmmscan. (default: 42)