Purdue University

maker

Link to section 'Introduction' of '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 official website (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018).

Link to section 'Versions' of 'maker' Versions

• 2.31.11
• 3.01.03

Link to section 'Commands' of 'maker' 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

Link to section 'Module' of 'maker' Module

You can load the modules by:

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

Link to section 'Prerequisites' of 'maker' Prerequisites

1. After loading MAKER modules, users can create MAKER control files by the following comand: maker -CTL This will generate three files:
2. maker_opts.ctl (required to be modified)
3. maker_exe.ctl (do not need to modify this file)
4. maker_bopts.ctl (optionally modify this file)
5. 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.

Link to section 'Example job non-mpi' of 'maker' Example job non-mpi

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

Link to section 'Example job mpi' of 'maker' 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