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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

run_dbcan (dbCAN)

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

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 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

The dbCAN reference databases are not bundled with the module.

Shared reference databases

CSC plans to provide shared reference databases at a central location on Roihu. This is still being set up. Until it is available, download your own copy to a writable location (for example your project's /scratch).

Download the databases with run_dbcan database (or dbcan_build) into a writable directory:

run_dbcan database --db_dir /scratch/<project>/dbcan_db

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 /scratch/<project>/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

More information