Software: run_dbCAN
Description
run_dbCAN using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
Available Versions
| Unspecified: | 3.0.2 3.0.6 |
|---|
This is a standalone tool of http://bcb.unl.edu/dbCAN2/. Details about its usage can be found in its Github repository.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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