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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_* .


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

#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

cp ecoli_1K_* /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID --pe1-1 ecoli_1K_1.fq.gz --pe1-2 ecoli_1K_2.fq.gz -o spades_test

mkdir $PBS_O_WORKDIR/spades.$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 $HOME/SPADES-JOBS/spades.$PBS_JOBID/spades_test/, a good place to start would be the file spades.log in that given directory.

spades.txt · Last modified: 2020/09/21 21:15 by root