Updated 2019-02-21

Run MASH on the Cluster


  • This guide will cover how to load and use mash/1.0.2
  • mash requires multiple other modules to be loaded before it itself can be loaded.

Load Mash

  • To use Mash, load these module in your PBS script using module load:
    • module load gcc/4.9.0
    • module load capnproto-c++/0.53
    • module load boost/1.57.0
    • module load zlib/1.2.8
    • module load autoconf/2.6

Walkthrough: Run Mash on the Cluster

Part 1: The PBS Script

#PBS -N mashTest
#PBS -l nodes=2:ppn=4
#PBS -l pmem=2gb
#PBS -l walltime=2:00
#PBS -q iw-shared-6
#PBS -j oe
#PBS -o mashTest.out

module load gcc/4.9.0
module load capnproto-c++/0.5.3
module load boost/1.57.0
module load zlib/1.2.8
module load autoconf/2.69
module load mash

mash sketch genome1.fna
mash sketch genome2.fna
mash dist genome1.fna.msh genome2.fna.msh
  • The #PBS directives are standard, requesting just 1 minute of walltime and 2 node with 4 cores. More on #PBS directives can be found in the PBS guide
  • $PBS_O_WORKDIR is simply a variable that represents the directory you submit the PBS script from.


Make sure the .fna files you want to run are in the same directory you put the PBS script.

  • Output Files will also show up in this dir as well
  • module load lines load the dependent programs as well as Mash
  • Lines that begin with mash execute the program

Part 2: Submit Job and Check Status

  • Make sure you're in the directory that contains the PBS script and the .fna files
  • Submit as normal, with qsub <pbs script name>. In this case qsub mash.pbs
  • Check job status with qstat -u username3 -n, replacing "username3" with your gtusername
  • You can delete the job with qdel 22182721, replacing the number with the jobid returned after running qsub

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see a couple of newly generated files, including genome1.fna.msh and mashTest.out
  • Open mashTest.out in a text editor to take a look, using Vim this would be vim mashTest.out
  • mashTest.out should look something like this:
Job name:   mashTest
Queue:      iw-shared-6
End PBS Prologue Fri Nov  9 09:43:47 EST 2018
Sketching genome1.fna...
Writing to genome1.fna.msh...
Sketching genome2.fna...
Writing to genome2.fna.msh...
genome1.fna genome2.fna 0.0222766   0   456/1000
Begin PBS Epilogue Fri Nov  9 09:43:49 EST 2018
Job ID:     22865014.shared-sched.pace.gatech.edu
  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran a Mash program on the cluster.