run_dbcan (dbCAN)

run_dbcan (dbCAN) is a standalone tool for automated annotation of carbohydrate-active enzymes (CAZymes) in genomes and metagenomes.

run_dbcan (dbCAN)

License

Free to use and open source under GNU GPLv3.

Available

Roihu-CPU: 5.2.9 (module py-dbcan), via the bio-apps module.

Usage

run_dbcan is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load py-dbcan/5.2.9

Databases

CSC provides the dbCAN reference databases for run_dbcan 5.2.9, including the CGC and PUL databases, on Roihu. The py-dbcan module sets the DBCAN_DB environment variable to their location. Give it to run_dbcan with --db_dir $DBCAN_DB, as in the example below.

Running run_dbcan

#!/bin/bash
#SBATCH --job-name=run_dbcan
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load py-dbcan/5.2.9

run_dbcan CAZyme_annotation --input_raw_data proteins.faa --mode protein \
    --db_dir $DBCAN_DB --output_dir dbcan_out --threads $SLURM_CPUS_PER_TASK

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk