MAKER

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on subsequent runs. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.


External Links:
MAKER website
MAKER Tutorial


Both serial and parallel MAKER are installed on HPC systems. To use serial MAKER, you need to set up the MAKER environment first using the command

module load maker/2.31.10-serial

To use parallel MAKER, you need to set up the MAKER environment first using the command

module load maker

Below are two simple sample run scripts that demonstrate the uses MAKER, with the first one for serial MAKER and the second one for parallel MAKER:

#!/bin/bash

#BSUB -n 1
#BSUB -W 120
#BSUB -o outLog.%J
#BSUB -e errLog.%J

module load maker/2.31.10-serial

maker

#!/bin/bash

#BSUB -n 16
#BSUB -W 120
#BSUB -o outLog.%J
#BSUB -e errLog.%J

module load maker

mpirun maker

You need to replace <MAKER command> by your actual MAKER command.

In the scripts,

#BSUB -n <a number>

indicates number of cores you request for running MAKER.

In the scripts,

#BSUB -W 120

means that the time limit (Wall time) set for the job is 120 minutes. You need to change that to a number that you expect as the upper time limit for your job.

In the scripts,

#BSUB -o outLog.%J
#BSUB -e errLog.%J

set the files that will contain standard output and standard errors, where "%J" will be the LSF job ID number when the files are finally generated. The error file may be empty if there are no errors at all in running your job.

Last modified: March 20 2026 07:39:23.