Genemark

Introduction

GeneMark-ES/ET/EP is package including GeneMark-ES, GeneMark-ET and GeneMark-EP+ algorithms.

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/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster	Version(s)
ANVIL	4.68, 4.69
BELL	4.68, 4.69
GAUTSCHI	4.68, 4.69
NEGISHI	4.68, 4.69
SCHOLAR	4.68, 4.69

Commands

• bed_to_gff.pl

• bp_seq_select.pl

• build_mod.pl

• calc_introns_from_gtf.pl

• change_path_in_perl_scripts.pl

• compare_intervals_exact.pl

• gc_distr.pl

• get_below_gc.pl

• get_sequence_from_GTF.pl

• gmes_petap.pl

• hc_exons2hints.pl

• histogram.pl

• make_nt_freq_mat.pl

• parse_by_introns.pl

• parse_ET.pl

• parse_gibbs.pl

• parse_set.pl

• predict_genes.pl

• reformat_gff.pl

• rescale_gff.pl

• rnaseq_introns_to_gff.pl

• run_es.pl

• run_hmm_pbs.pl

• scan_for_bp.pl

• star_to_gff.pl

• verify_evidence_gmhmm.pl

• gmhmme3

Module

You can load the modules by:

module load biocontainers
module load genemark

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 genemark on our clusters:

Anvil

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

module --force purge
module biocontainers genemark

# Your genemark workflow...

Bell, Gautschi, or Negishi

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genemark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers genemark

# Your genemark workflow...

Gautschi-AI

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genemark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers genemark

# Your genemark workflow...

Gilbreth

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genemark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers genemark

# Your genemark workflow...

Scholar

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

module --force purge
module biocontainers genemark

# Your genemark workflow...