Table of Contents

Spades

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. You can find more information on SPAdes here.

Environment Setup

To use spades edit your $HOME/.bashrc to include the spades module. 

module load spades

Create a folder in your $HOME directory that you will submit the jobs from. 

razor-l1:jokinsey:~$ mkdir SPADES-JOBS
razor-l1:jokinsey:~$ cd SPADES-JOBS/

Copy the example files for the test from the spades documentation. 

razor-l1:jokinsey:~$ cp /share/apps/spades/SPAdes-3.6.0/test_dataset/ecoli_1K_* .

Example

Create a PBS file that will run the test job, which looks like the one below. 

#!/bin/bash
#PBS -N spades
#PBS -q tiny12core
#PBS -j oe
#PBS -o spades.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=0:05:00

cd $PBS_O_WORKDIR
cp ecoli_1K_* /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

spades.py --pe1-1 ecoli_1K_1.fq.gz --pe1-2 ecoli_1K_2.fq.gz -o spades_test

mkdir $PBS_O_WORKDIR/spades.$PBS_JOBID
cd $PBS_O_WORKDIR/$PBS_JOBID
cp -r /scratch/$PBS_JOBID/* .

You can find more information on the commands being run here.

All thats left to do is submit the job. 

razor-l1:jokinsey:~/SPADES-JOBS$ qsub spades.pbs

The important output will be in the directory $HOME/SPADES-JOBS/spades.$PBSJOBID/spadestest/, a good place to start would be the file spades.log in that given directory.