Software: CheckM genome
Description
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
Available Versions
Unspecified: | 1.2.0 1.2.2 |
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BioContainers: https://biocontainers.pro/tools/checkm-genome
Home page: https://github.com/Ecogenomics/CheckM
Commands
- checkm-genome
Module
You can load the modules by:
module load biocontainers
module load checkm-genome
Example job
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