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abyss

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Abyss

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. You can fins more information on abyss here.

Environment Setup

To work with abyss first we need to load abyss and it's dependencies. The easiest way to do this is to modify the .bashrc file in your $HOME directory.

module load gcc
module load mpi
module load openmpi
module load intel/13.1.0
module load abyss/2.0.2

Create a directory in your $HOME directory where you can submit and run the example job. Copy the fastaq files used for the example job from the examples directory located with the abyss software.

razor-l1:jokinsey:~$ mkdir ABYSS-JOBS
razor-l1:jokinsey:~$ cp /share/apps/abyss/examples/SRR001665_* ABYSS-JOBS/

Example Job

To run the example job create a PBS script file with the information below that we can submit to run the job.

#!/bin/bash
#PBS -N abyss
#PBS -q tiny12core
#PBS -j oe
#PBS -o abyss.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=1:00:00

cd $PBS_O_WORKDIR
cp SRR001665_1.fastq  SRR001665_2.fastq /scratch/$PBS_JOBID

cd /scratch/$PBS_JOBID

abyss-pe mpirun='mpirun -v -machinefile $(PBS_NODEFILE)' name=ecoli k=31 in='SRR001665_1.fastq  SRR001665_2.fastq'
mkdir $PBS_O_WORKDIR/abyss.$PBS_JOBID
cd $PBS_O_WORKDIR/abyss.$PBS_JOBID
cp -r /scratch/$PBS_JOBID/* 

This script will produce a directory with the output in the submission directory. You can find information on the output here.

Alls thats left to do is submit the job.

razor-l1:jokinsey:~/ABYSS-JOBS$ qsub abyss.pbs 

Once you have your output for this given example try running the command below on the file ecoli-1.fa and verify your output.

razor-l1:jokinsey:~/ABYSS-JOBS/abyss.3539296.sched$ abyss-fac ecoli-1.fa 
n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
1833	414	71	518	8892	18242	36985	23425	67081	4512653	ecoli-1.fa
abyss.txt · Last modified: 2017/11/07 23:53 by jokinsey