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Running MitoZ

MitoZ on HOPPER

We have MitoZ available on Hopper as a singularity image. The image is stored under the directory

/containers/hopper/Containers/mitoz

Running in batch mode with Slurm

It can be run in batch mode with a Slurm script as detailed below:

Example Slurm script (run.slurm)

#!/bin/bash 
#SBATCH -p normal                       
#SBATCH -J mitoz_test 
#SBATCH -o mitoz_test_%j.out 
#SBATCH -e mitoz_test_%j.err 
#SBATCH --nodes=1 
#SBATCH --cpus-per-task=12                      
#SBATCH --mem-per-cpu=3500M             
#SBATCH --export=ALL 
#SBATCH -t 0-01:00:00 



module load singularity

SINGULARITY_BASE=/containers/hopper/Containers
CONTAINER=${SINGULARITY_BASE}/mitoz/MitoZ_v3.6.sif 
SINGULARITY_RUN="singularity run --nv -B ${PWD}:/host_pwd --pwd /host_pwd" 


${SINGULARITY_RUN} ${CONTAINER} mitoz [ OPTIONS ]

Runnning the script

To run the script, modify the command with your mitoz options, e.g.:

${SINGULARITY_RUN} ${CONTAINER} mitoz all \
          --fq1 test.1.fq.gz \
          --fq2 test.2.fq.gz \
          --outprefix ttt \
          --clade Arthropoda \
          --data_size_for_mt_assembly 0 \
          --assembler megahit \
          --requiring_taxa Arthropoda
and then submit it with: 
sbatch run.slurm

You may also adjust the other parameters in the Slurm script like the number of cpus, memory, etc.

Github source page: github.com/linzhi2013/MitoZ