MAKER is a popular genome annotation pipeline for both prokaryotic and eukaryotic genomes. This guide describes best practices for running MAKER on RCAC clusters. For detailed information about MAKER, see its offical website (


  • 2.31.11

  • 3.01.03


  • cegma2zff

  • chado2gff3

  • compare

  • cufflinks2gff3

  • evaluator

  • fasta_merge

  • fasta_tool

  • genemark_gtf2gff3

  • gff3_merge

  • iprscan2gff3

  • iprscan_wrap

  • ipr_update_gff

  • maker

  • maker2chado

  • maker2eval_gtf

  • maker2jbrowse

  • maker2wap

  • maker2zff

  • maker_functional

  • maker_functional_fasta

  • maker_functional_gff

  • maker_map_ids

  • map2assembly

  • map_data_ids

  • map_fasta_ids

  • map_gff_ids

  • tophat2gff3


You can load the modules by:

module load biocontainers
module load maker/2.31.11 # OR maker/3.01.03


Dfam release 3.5 (October 2021) downloaded from Dfam website ( that required by RepeatMasker has been set up for users. The RepeatMakser library is stored here /depot/itap/datasets/Maker/RepeatMasker/Libraries.


  1. After loading MAKER modules, users can create MAKER control files by the folowing comand:

    maker -CTL

    This will generate three files:

  • maker_opts.ctl (required to be modified)

  • maker_exe.ctl (do not need to modify this file)

  • maker_bopts.ctl (optionally modify this file)

  1. maker_opts.ctl: - If not using RepeatMasker, modify model_org=all to model_org= - If not using RepeatMasker, modify model_org=all to an appropriate family/genus/species.

Example job non-mpi


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 MAKER on our cluster:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH --job-name=MAKER
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers maker/2.31.11  # or maker/3.01.03

maker -c 24

Example job mpi

To use MAKER in MPI mode, we cannot use the maker modules. Instead we have to use the singularity image files stored in /apps/biocontainers/images:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 5:00:00
#SBATCH -n 24
#SBATCH -c 8
#SBATCH --job-name=MAKER_mpi
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

mpirun -n 24 singularity exec /apps/biocontainers/images/maker_2.31.11.sif maker -c 8

mpirun -n 24 singularity exec /apps/biocontainers/images/maker_3.01.03.sif maker -c 8