Proovread-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=proovread.%j.out<br>
<nowiki>#</nowiki>SBATCH --output=proovread.%j.out<br>
<nowiki>#</nowiki>SBATCH --error=proovread.%j.err<br>
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
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<pre  class="gcommand">
<pre  class="gcommand">
ml proovread/2.14.1-foss-2016b  
ml proovread/2.14.1-foss-2016b  
NA NA  
NA  


</pre>
</pre>

Revision as of 14:05, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

2.14.1

Author / Distributor

proovread

Description

"PacBio hybrid error correction through iterative short read consensus" More details are at proovread

Running Program

The last version of this application is at /usr/local/apps/eb/proovread/2.14.1-foss-2016b

To use this version, please load the module with

ml proovread/2.14.1-foss-2016b 

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

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

cd $SLURM_SUBMIT_DIR
ml proovread/2.14.1-foss-2016b
NA [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 proovread/2.14.1-foss-2016b 
NA 

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Installation

Source code is obtained from proovread

System

64-bit Linux