Skip to content

Docs CSC now features an automatic Finnish translation. Click here for more information.

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.

eggNOG-mapper

eggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs.

License

Free to use and open source under GNU GPLv3.

Available

  • Roihu: 2.1.15, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load eggnog-mapper/2.1.15

Databases

eggNOG-mapper requires the eggNOG reference databases, which 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 download_eggnog_data.py and point eggNOG-mapper at them with --data_dir (or the EGGNOG_DATA_DIR environment variable):

download_eggnog_data.py -y --data_dir /scratch/<project>/eggnog_db

The -y flag in the above command can be included e.g. in scripts and batch jobs to skip a confirmation prompt before the download proceeds.

Running eggNOG-mapper

eggNOG-mapper is run with the emapper.py command:

#!/bin/bash
#SBATCH --job-name=emapper
#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 eggnog-mapper/2.1.15

emapper.py --cpu $SLURM_CPUS_PER_TASK \
    --data_dir /scratch/<project>/eggnog_db \
    -i proteins.fasta -o annotation

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