Testing the installation

A general test of CheckM which verifies all third-party dependencies can be run using the test command:

checkm test ~/checkm_test_results

This runs the E. coli K-12 W3110 genome through the standard CheckM pipeline and verifies the resulting output files. The output directory can be removed once the test has run. The test limits the memory used by gPlace to 6 GB (--gplace_max_memory 6G) and needs approximately 5 GB of memory.

Unit tests

Unit tests are also provided in the checkm/test directory of the source code. These are designed to aid in development and are not needed to verify an installation. They use Python’s unittest module and can be run from the root of a CheckM source checkout. CHECKM_DATA_PATH must be set to the reference data before running them:

export CHECKM_DATA_PATH=/path/to/my_checkm_data
python3 -m unittest discover -s checkm/test -t .