CheckM2

CheckM2 provides rapid assessment of genome bin quality using machine learning, predicting the completeness and contamination of metagenome-assembled genomes (MAGs) and other genomes.

• CheckM2
  • License
  • Available
  • Usage
    • Database
    • Example batch script
  • Support
  • More information

License

Free to use and open source under GNU GPLv3.

Available

• Roihu-CPU: 1.1.0, via the bio-apps module.

Usage

CheckM2 is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the CheckM2 module:

module load bio-apps/v202603
module load checkm2/1.1.0

Database

CheckM2 needs a DIAMOND reference database. CSC provides a shared copy (database version 3) on Roihu, and the checkm2 module sets the CHECKM2DB environment variable to it, so CheckM2 finds the database without further options.

To use another copy of the database, give the path to its .dmnd file with --database_path.

Example batch script

#!/bin/bash
#SBATCH --job-name=checkm2
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load checkm2/1.1.0

checkm2 predict --threads $SLURM_CPUS_PER_TASK \
    --input bins/ --output-directory checkm2_out -x fa

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• CheckM2 GitHub repository

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