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CheckM works on a directory of genome bins in FASTA format. By default, CheckM assumes genomes consist of contigs/scaffolds in nucleotide space and that the files to process end with the extension fna. You can specify a different extension with the –x flag. CheckM calls genes internally using prodigal, taking care to identify genes with recoded stop codons. You can call genes externally and provide CheckM with FASTA files containing genes in amino acid space. To specify this, use the --genes flag. Again, you may need to change the extension CheckM looks for (e.g., -x faa).

Required Modules


  • checkm

System Variables

  • HPC_CHECKM_DIR - installation directory