test

Run CheckM on a test genome (E. coli) to verify operation.

Runs the E. coli K-12 W3110 genome, which is included with the CheckM reference data, through the standard CheckM pipeline and verifies the resulting output files. This verifies that CheckM, its reference data, and all third-party dependencies are installed correctly (see Testing the installation). The output directory can be removed once the test has run.

Arguments

usage: checkm test [-h] [--tmpdir TMPDIR] output_dir

Test CheckM on E. coli genome.

positional arguments:
  output_dir       output directory for test data

options:
  -h, --help       show this help message and exit
  --tmpdir TMPDIR  specify an alternative directory for temporary files

Example: checkm test ~/checkm_test

Example

checkm test ~/checkm_test_results