Reference data

CheckM relies on a number of precalculated data files which can be downloaded from either:

The reference data (checkm_data_2015_01_16.tar.gz) must be decompressed into a directory. For example:

mkdir -p ~/.checkm   # or wherever you want to put it
cd ~/.checkm
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -xzf checkm_data_2015_01_16.tar.gz

Setting the location of the reference data

The recommended way to tell CheckM where the reference data is located is the CHECKM_DATA_PATH environment variable:

export CHECKM_DATA_PATH=/path/to/my_checkm_data

Alternatively, the location can be stored in CheckM’s DATA_CONFIG file with the data command:

checkm data setRoot <checkm_data_dir>

checkm data setRoot must be able to write to the DATA_CONFIG file (located in the installed checkm Python package, unless a different file is given as a second argument) and to the reference data directory, as it creates a manifest file (.dmanifest) in this directory.

CheckM determines the location of the reference data in the following order:

  1. the CHECKM_DATA_PATH environment variable, if it is set (checkm data setRoot has no effect while it is set)

  2. the directory stored in DATA_CONFIG by checkm data setRoot

  3. ~/.checkm (after printing a message about it)

The location of the reference data used by a run is written to the CheckM log.