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