MAKER

Introduction

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 (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018).

Versions

  • 2.31.11

  • 3.01.03

Commands

  • 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

Module

You can load the modules by:

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

Note

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

Prerequisites

  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

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 MAKER on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=MAKER
#SBATCH --mail-type=FAIL,BEGIN,END
#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:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 5:00:00
#SBATCH -N 2
#SBATCH -n 24
#SBATCH -c 8
#SBATCH --job-name=MAKER_mpi
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --mail-user=UserID@purdue.edu
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

## MAKER2
mpirun -n 24 singularity exec /apps/biocontainers/images/maker_2.31.11.sif maker -c 8

## MAKER3
mpirun -n 24 singularity exec /apps/biocontainers/images/maker_3.01.03.sif maker -c 8