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