Augustus

Introduction

Augustus is a program that predicts genes in eukaryotic genomic sequences.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/augustus

Home page: http://bioinf.uni-greifswald.de/augustus/

Note

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

Versions

Cluster	Version(s)
ANVIL	3.4.0, 3.5.0
BELL	3.4.0, 3.5.0
GAUTSCHI	3.4.0, 3.5.0
NEGISHI	3.4.0, 3.5.0
SCHOLAR	3.4.0, 3.5.0

Commands

• aln2wig

• augustus

• bam2hints

• bam2wig

• bam2wig-dist

• consensusFinder

• curve2hints

• etraining

• fastBlockSearch

• filterBam

• getSeq

• getSeq-dist

• homGeneMapping

• joingenes

• prepareAlign

Module

You can load the modules by:

module load biocontainers
module load augustus

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 augustus on our clusters:

Anvil

#!/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=augustus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers augustus

# Your augustus workflow...

Bell, Gautschi, or Negishi

#!/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=augustus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers augustus

# Your augustus workflow...

Gautschi-AI

#!/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=augustus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers augustus

# Your augustus workflow...

Gilbreth

#!/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=augustus
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers augustus

# Your augustus workflow...

Scholar

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

module --force purge
module biocontainers augustus

# Your augustus workflow...