Checkm-genome

Introduction

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/checkm-genome

Home page: https://github.com/Ecogenomics/CheckM

Versions

• 1.2.0

• 1.2.2

Commands

• checkm-genome

Module

You can load the modules by:

module load biocontainers
module load checkm-genome

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run checkm-genome on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=checkm-genome
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers checkm-genome

checkm lineage_wf -t 8 -x fa bins checkm