run-dbCAN

Introduction

run_dbCAN using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes. This is a standalone tool of http://bcb.unl.edu/dbCAN2/. Details aobut its uage can be found in its Github repository.

Versions

  • 3.0.2

  • 3.0.6

Commands

run_dbcan

Database

Latest version of database has been downloaded and setup, including CAZyDB.09242021.fa, dbCAN-HMMdb-V10.txt, tcdb.fa, tf-1.hmm, tf-2.hmm, and stp.hmm.

Module

You can load the modules by:

module load biocontainers
module load run_dbcan/3.0.2

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 run_dbcan on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=run_dbcan
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers run_dbcan/3.0.2

run_dbcan protein.faa protein --out_dir test1_dbcan
run_dbcan genome.fasta prok --out_dir test2_dbcan