GeneMarkES-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

4.57

Author / Distributor

GeneMarkES

Description

"Gene Prediction in Eukaryotes. Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training." More details are at GeneMarkES

Running Program

Also refer to Running Jobs on Sapelo2 Also refer to Run X window Jobs and Run interactive Jobs

In order to use geneMarker you will need to download a key and put it into your home directory. Instructions to download the key can be found here: https://github.com/ablab/quast/issues/97

From the above link:

1.)Go to http://exon.gatech.edu/GeneMark/license_download.cgi, fill the requested fields are read the license text. Note: you can select any tool and platform actually, e.g. GeneMark-ES / ET v.4.33 and LINUX64.

2.)After pressing "I agree ..." button you will be redirected to a download page. You will need to download the key only (either 32bit or 64bit depending on your platform, I think now everyone has 64bit), the software is in Quast package already.

3.)The key is in gzip format, you should unpack it (with gunzip) and move to ~/.gm_key (the name should be exactly like this, with a dot in the beginning).

~/ is your home directory. i.e /home/ugamyid . Once the .gm_key file has been placed there you should be able to run GeneMarker.

Version 4.57

Version 4.57 is at /apps/eb/GeneMark-ET/4.57-GCCcore-8.3.0 It can be loaded with: module load GeneMark-ET/4.57-GCCcore-8.3.0

Here is an example of a shell script sub.sh to run on at the batch queue:

#!/bin/bash
#SBATCH --job-name=geneMarkJob
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem10gb
#SBATCH --time=08:00:00
#SBATCH --output=RAxML.%j.out
#SBATCH --error=RAxML.%j.err

cd $SLURM_SUBMIT_DIR

module load GeneMark-ET/4.57-GCCcore-8.3.0

gmes_petap.pl [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running Jobs on Sapelo2.

Documentation

module load GeneMark-ET/4.57-GCCcore-8.3.0
gmes_petap.pl 
# -------------------
# -------------------
Usage:  /apps/eb/GeneMark-ET/4.57-GCCcore-8.3.0/gmes_petap.pl  [options]  --sequence [filename]

GeneMark-ES Suite version 4.57_lic
Suite includes GeneMark.hmm, GeneMark-ES, GeneMark-ET and GeneMark-EP algorithms.

Input sequence/s should be in FASTA format.

Select one of the gene prediction algorithm

To run GeneMark-ES self-training algorithm
  --ES

To run GeneMark-ET with hints from transcriptome splice alignments
  --ET           [filename]; file with intron coordinates from RNA-Seq read splice alignment in GFF format
  --et_score     [number]; default 10; minimum score of intron in initiation of the ET algorithm

To run GeneMark-EP with hints from protein splice alignments
  --EP           
  --dbep         [filename]; file with protein database in FASTA format
  --ep_score     [number,number]; default 4,0.25; minimum score of intron in initiation of the EP algorithm
or
  --EP           [filename]; file with intron coordinates from protein splice alignment in GFF format

To run GeneMark.hmm predictions using previously derived model
  --predict_with [filename]; file with species specific gene prediction parameters

To run ES, ET or EP with branch point model. This option is most useful for fungal genomes
  --fungus

To run hmm, ES, ET or EP in PLUS mode (prediction with hints)
  --evidence     [filename]; file with hints in GFF format

Masking option
  --soft_mask    [number] or [auto]; default auto; to indicate that lowercase letters stand for repeats;
                 masks only lowercase repeats longer than specified length
                 In 'auto' mode length is adjusted based on the size of the input genome

Run options
  --cores        [number]; default 1; to run program with multiple threads
  --pbs          to run on cluster with PBS support
  --v            verbose

Optional sequence pre-processing parameters
  --max_contig   [number]; default 5000000; will split input genomic sequence into contigs shorter then max_contig
  --min_contig   [number]; default 50000; will ignore contigs shorter then min_contig in training 
  --max_gap      [number]; default 5000; will split sequence at gaps longer than max_gap
                 Letters 'n' and 'N' are interpreted as standing within gaps 
  --max_mask     [number]; default 5000; will split sequence at repeats longer then max_mask
                 Letters 'x' and 'X' are interpreted as results of hard masking of repeats

Optinal algorithm parameters
  --max_intron            [number]; default 10000 (3000 fungi); maximum length of intron
  --max_intergenic        [number]; default 50000; maximum length of intergenic regions
  --min_contig_in_predict [number]; default 500; minimum allowed length of contig in prediction step
  --min_gene_in_predict   [number]; default 300 (120 fungi); minimum allowed gene length in prediction step
  --gc_donor              [value];  default 0.001; transition probability to GC donor in the range 0..1; 'auto' mode detects probability from training; 'off' switches GC donor model OFF

Developer options
  --gc3          [number]; GC3 cutoff in training for grasses
  --training     to run only training step of algorithms; applicable to ES, ET or EP
  --prediction   to run only prediction step of algorithms using species parameters from previously executed training; applicable to ES, ET or EP
  --usr_cfg      [filename]; use custom configuration from this file
  --ini_mod      [filename]; use this file with parameters for algorithm initiation
  --test_set     [filename]; to evaluate prediction accuracy on the given test set
  --key_bin
  --debug
# -------------------

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Installation

source code from GeneMarkES

System

64-bit Linux