Braker3

Introduction

BRAKER3 enables the usage of RNA-seq and protein data in a fully automated pipeline to train and predict highly reliable genes with GeneMark-ETP and AUGUSTUS. The result of the pipeline is the combined gene set of both gene prediction tools, which only contains genes with very high support from extrinsic evidence.

For more information, please check:
BioContainers: https://hub.docker.com/r/teambraker/braker3
Home page: https://github.com/Gaius-Augustus/BRAKER Note: Since BRAKER is a pipeline that trains AUGUSTUS, i.e. writes species specific parameter files, BRAKER needs writing access to the configuration directory of AUGUSTUS that contains such files. This installation comes with a stub of AUGUSTUS coniguration files, but you must copy them out from the container into a location where you have write permissions. A helper command ‘copy_augustus_config’ is provided to simplify the task. Follow the procedure below to put the config files in your scratch space: $ mkdir -p $RCAC_SCRATCH/augustus $ copy_augustus_config $RCAC_SCRATCH/augustus $ export AUGUSTUS_CONFIG_PATH$RCAC_SCRATCH/augustus/config You would also pass the value via command-line (use the FULL path) switch: $ braker.pl –AUGUSTUS_CONFIG_PATH$RCAC_SCRATCH/augustus/config ….. Note: If this is your first time using BRAKER3, register at https://exon.gatech.edu/GeneMark/license_download.cgi to obtain a GeneMark-ES/ET/EP+ ver 4.72_lic license for Linux 64 kernel 3.10
5. Download the license file as gm_key_64 and place it in your home directory as follows: gunzip gm_key_64.gz mv gm_key_64 ~/.gm_key

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

v3.0.7.5, 3.0.3

BELL

v3.0.7.5, 3.0.3

GAUTSCHI

v3.0.7.5, 3.0.3

NEGISHI

v3.0.7.5, 3.0.3

Commands

  • braker.pl

Module

You can load the modules by:

module load biocontainers
module load braker3

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run braker3 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=braker3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers braker3

# Your braker3 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=braker3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers braker3

# Your braker3 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=braker3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers braker3

# Your braker3 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=braker3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers braker3

# Your braker3 workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=braker3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers braker3

# Your braker3 workflow...