Genemarks-2

Introduction

GeneMarkS-2 combines GeneMark.hmm (prokaryotic) and GeneMark (prokaryotic) with a self-training procedure that determines parameters of the models of both GeneMark.hmm and GeneMark.

For more information, please check:

The users need to download your own licence key from GeneMark website and copy key “gm_key” into users’ home directory as: cp gm_key ~/.gm_key | Home page: http://opal.biology.gatech.edu/GeneMark/

Versions

  • 1.14_1.25

Commands

  • gms2.pl

  • biogem

  • compp

  • gmhmmp2

Module

You can load the modules by:

module load biocontainers
module load genemarks-2

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 genemarks-2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genemarks-2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers genemarks-2