CheckM2

CheckM2 is a tool that uses machine learning to determine the quality of genome bins.

Availability

Cluster	Module/Version
BOSE	checkm2/1.1.0
BGSC	N/A

Note: You can simply use module load checkm2 to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the checkm2 command that we wanted to highlight. Look at the project README for a full list.

Option	Description
predict --threads	Number of CPUs to use for calculation
predict --database_path	Path to DIAMOND database (default to /data/software/default/checkm2/1.1.0/databases/)
predict --input	Provide a file or directory to be processed
predict --output_directory	Provide a directory for CheckM2 output

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load checkm2/1.1.0      # Load CheckM2 module
checkm2 testrun --threads 16   # Execute a test run of CheckM2 using 16 CPU cores

Real Example

Has your research group used CheckM2 in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of CheckM2.

Chklovski, Alex, Donovan H. Parks, Ben J. Woodcroft, and Gene W. Tyson. n.d. “CheckM2: A Rapid, Scalable and Accurate Tool for Assessing Microbial Genome Quality Using Machine Learning.” https://doi.org/10.1101/2022.07.11.499243.