AUGUSTUS-Teaching: Difference between revisions

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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>   
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>   
<nowiki>#</nowiki>SBATCH --output=AUGUSTUS.%j.out<br>
<nowiki>#</nowiki>SBATCH --output=AUGUSTUS.%j.out<br>
<nowiki>#</nowiki>SBATCH --error=AUGUSTUS.%j.err<br>
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
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<pre  class="gcommand">
<pre  class="gcommand">
ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14  
ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14  
augustus augustus  
augustus  
AUGUSTUS (3.2.3) is a gene prediction tool
AUGUSTUS (3.2.3) is a gene prediction tool
written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

Latest revision as of 14:01, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

3.2.3

Author / Distributor

AUGUSTUS

Description

"AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" More details are at AUGUSTUS

Running Program

The last version of this application is at /usr/local/apps/eb/AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14

To use this version, please load the module with

ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14 

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

#!/bin/bash
#SBATCH --job-name=j_AUGUSTUS
#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=AUGUSTUS.%j.out
#SBATCH --error=AUGUSTUS.%j.err

cd $SLURM_SUBMIT_DIR
ml AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14
augustus [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 AUGUSTUS/3.2.3-foss-2016b-Python-2.7.14 
augustus 
AUGUSTUS (3.2.3) is a gene prediction tool
written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

usage:
augustus [parameters] --species=SPECIES queryfilename

'queryfilename' is the filename (including relative path) to the file containing the query sequence(s)
in fasta format.

SPECIES is an identifier for the species. Use --species=help to see a list.

parameters:
--strand=both, --strand=forward or --strand=backward
--genemodel=partial, --genemodel=intronless, --genemodel=complete, --genemodel=atleastone or --genemodel=exactlyone
  partial      : allow prediction of incomplete genes at the sequence boundaries (default)
  intronless   : only predict single-exon genes like in prokaryotes and some eukaryotes
  complete     : only predict complete genes
  atleastone   : predict at least one complete gene
  exactlyone   : predict exactly one complete gene
--singlestrand=true
  predict genes independently on each strand, allow overlapping genes on opposite strands
  This option is turned off by default.
--hintsfile=hintsfilename
  When this option is used the prediction considering hints (extrinsic information) is turned on.
  hintsfilename contains the hints in gff format.
--AUGUSTUS_CONFIG_PATH=path
  path to config directory (if not specified as environment variable)
--alternatives-from-evidence=true/false
  report alternative transcripts when they are suggested by hints
--alternatives-from-sampling=true/false
  report alternative transcripts generated through probabilistic sampling
--sample=n
--minexonintronprob=p
--minmeanexonintronprob=p
--maxtracks=n
  For a description of these parameters see section 4 of README.TXT.
--proteinprofile=filename
  When this option is used the prediction will consider the protein profile provided as parameter.
  The protein profile extension is described in section 7 of README.TXT.
--progress=true
  show a progressmeter
--gff3=on/off
  output in gff3 format
--predictionStart=A, --predictionEnd=B
  A and B define the range of the sequence for which predictions should be found.
--UTR=on/off
  predict the untranslated regions in addition to the coding sequence. This currently works only for a subset of species.
--noInFrameStop=true/false
  Do not report transcripts with in-frame stop codons. Otherwise, intron-spanning stop codons could occur. Default: false
--noprediction=true/false
  If true and input is in genbank format, no prediction is made. Useful for getting the annotated protein sequences.
--uniqueGeneId=true/false
  If true, output gene identifyers like this: seqname.gN

For a complete list of parameters, type "augustus --paramlist".
An exhaustive description can be found in the file README.TXT.


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Installation

Source code is obtained from AUGUSTUS

System

64-bit Linux