geNomad#

Introduction#

geNomad: Identification of mobile genetic elements.

Versions#

1.8.1

Commands#

genomad

Database#

The genomad database has been downloaded for users. The current version is v1.7. The database is stored in /cluster/tufts/biocontainers/datasets/genomad_db/v1.7. Users can follow the below example to run genomad with the downloaded database.

Example job#

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=genomad     # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load fqtk/XXXX  ### Latest version is recommended.

genomad end-to-end --cleanup --splits 8 genome.fa genomad_output /cluster/tufts/biocontainers/datasets/genomad_db/v1.7/