mhm2.rst

Mhm2

Introduction ~~~~~~~~ MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes.

For more information, please check:
Home page: https://bitbucket.org/berkeleylab/mhm2/wiki/Home.md

Versions

• 2.0.0

Commands ~~~~~~~ - mhm2.py

Module

You can load the modules by:

module load biocontainers
module load mhm2

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 mhm2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mhm2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mhm2

mhm2.py -r input_1.fastq,input_2.fastq