analyze

Identify marker genes in bins and calculate genome statistics.

Identifies the marker genes in a marker file within each bin. The marker file can be a lineage-specific marker file produced by lineage_set, a taxonomic-specific marker file produced by taxon_set, or a HMM file of custom marker genes. Completeness and contamination are then estimated with the qa command.

• --ali: generate a HMMER alignment file for each bin in <output folder>/bins/<bin id>/hmmer.analyze.ali.txt.gz.

• --nt: generate nucleotide gene sequences for each bin in <output folder>/bins/<bin id>/genes.fna.gz.

• --genes: bins contain genes as amino acids instead of nucleotide contigs.

Outputs:

• called gene files are placed in <output folder>/bins/<bin id>/genes.*.gz (see Output files)

• HMMER result files are placed in <output folder>/bins/<bin id>/hmmer.*

Genes are called with Prodigal as described for the tree command.

Arguments

usage: checkm analyze [-h] [--ali] [--nt] [-g] [-x EXTENSION] [-t THREADS] [-q] [--tmpdir TMPDIR]
                      marker_file bin_input output_dir

Identify marker genes in bins and calculate genome statistics.

positional arguments:
  marker_file           markers for assessing bins (marker set or HMM file)
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  output_dir            directory to write output files

options:
  -h, --help            show this help message and exit
  --ali                 generate HMMER alignment file for each bin
  --nt                  generate nucleotide gene sequences for each bin
  -g, --genes           bins contain genes as amino acids instead of nucleotide contigs
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -t, --threads THREADS
                        number of threads (default: 1)
  -q, --quiet           suppress console output
  --tmpdir TMPDIR       specify an alternative directory for temporary files

Example: checkm analyze lineage.ms ./bins ./output

Example

checkm analyze ./output/lineage.ms ./bins ./output
checkm analyze -t 8 -x fa bacteria.ms ./bins ./output