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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 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 (~3 GB), which is not bundled with the module.

Shared reference databases

CSC plans to provide shared reference databases at a central location on Roihu. This is still being set up. Until it is available, download your own copy to a writable location (for example your project's /scratch).

Download the database with:

checkm2 database --download --path /scratch/<project>/checkm2_db

You can then point CheckM2 at it with --database_path, or set the CHECKM2DB environment variable to the downloaded .dmnd file.

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 \
    --database_path /scratch/<project>/checkm2_db/CheckM2_database/*.dmnd \
    --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