RepeatModeler-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.0.11

Author / Distributor

RepeatModeler

Description

"RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats." More details are at RepeatModeler

Running Program

The last version of this application is at /usr/local/apps/eb/RepeatModeler/1.0.11-foss-2016b

To use this version, please load the module with

ml RepeatModeler/1.0.11-foss-2016b 

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

#!/bin/bash
#SBATCH --job-name=j_RepeatModeler
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=RepeatModeler.%j.out
#SBATCH --error=RepeatModeler.%j.err

cd $SLURM_SUBMIT_DIR
ml RepeatModeler/1.0.11-foss-2016b
RepeatModeler [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_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml RepeatModeler/1.0.11-foss-2016b 
RepeatModeler -h
No database indicated

NAME
    RepeatModeler - Model repetitive DNA

SYNOPSIS
      RepeatModeler [-options] -database <XDF Database>

DESCRIPTION
    The options are:

    -h(elp)
        Detailed help

    -database
        The prefix name of a XDF formatted sequence database containing the
        genomic sequence to use when building repeat models. The database
        may be created with the WUBlast "xdformat" utility or with the
        RepeatModeler wrapper script "BuildXDFDatabase".

    -engine <abblast|wublast|ncbi>
        The name of the search engine we are using. I.e abblast/wublast or
        ncbi (rmblast version).

    -pa #
        Specify the number of shared-memory processors available to this
        program. RepeatModeler will use the processors to run BLAST searches
        in parallel. i.e on a machine with 10 cores one might use 1 core for
        the script and 9 cores for the BLAST searches by running with "-pa
        9".

    -recoverDir <Previous Output Directory>
        If a run fails in the middle of processing, it may be possible
        recover some results and continue where the previous run left off.
        Simply supply the output directory where the results of the failed
        run were saved and the program will attempt to recover and continue
        the run.

    -srand #
        Optionally set the seed of the random number generator to a known
        value before the batches are randomly selected ( using Fisher Yates
        Shuffling ). This is only useful if you need to reproduce the sample
        choice between runs. This should be an integer number.

SEE ALSO
        RepeatMasker, WUBlast

COPYRIGHT
     Copyright 2005-2017 Institute for Systems Biology

AUTHOR
     Robert Hubley <rhubley@systemsbiology.org>
     Arian Smit <asmit@systemsbiology.org>

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Installation

Source code is obtained from RepeatModeler

System

64-bit Linux