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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.

MetaBAT

MetaBAT is a tool for the accurate and efficient binning of metagenomic contigs into genome bins (metagenome-assembled genomes) using tetranucleotide frequencies and contig abundances. On Roihu it is provided as MetaBAT2.

License

Free to use and open source. See the MetaBAT license.

Available

  • Roihu: 2.15, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load metabat/2.15

MetaBAT2 takes an assembly and a per-contig depth file (computed from BAM alignments with jgi_summarize_bam_contig_depths):

jgi_summarize_bam_contig_depths --outputDepth depth.txt aln.sorted.bam
metabat2 -i assembly.fa -a depth.txt -o bins/bin -t 8

Example batch script

#!/bin/bash
#SBATCH --job-name=metabat2
#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 metabat/2.15

metabat2 -i assembly.fa -a depth.txt -o bins/bin -t $SLURM_CPUS_PER_TASK

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