Updated 2019-02-14

Run IDBA on the Cluster

Summary

  • IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. More information can be found on the IDBA github
  • Use module avail idba to see all the available versions of IDBA on the cluster
  • To load IDBA in you PBS script:
    • Load with module load idba/1.1.1. Replace the version number with the version you want to load.
  • To run IDBA:
    • In your PBS script, put all the lines to execute IDBA after the module load lines that load IDBA

Warning

you must set the --num_threads option to the number of processors you requested in the #PBS directives portion of your PBS script. Example: if you requested 16 processors (2 nodes and 8 proc. per node), you would set the --num_threads option as --num_threads 16

Example PBS Script

#PBS -N idbaTest
#PBS -l nodes=2:ppn=8
#PBS -l walltime=1:00:00
#PBS -q iw-shared-6
#PBS -j oe
#PBS -o idbaResult.out

cd $PBS_O_WORKDIR
module load idba/1.1.1
idba_ud -r read.fa -o output_dir --num_threads 16
  • The #PBS directives are standard, requesting 1 hour of walltime and 2 nodes with 8 cores per node. More on #PBS directives can be found in the PBS guide

Note

If using $PBS_O_WORKDIR, the .fa files, as well as any other files required for the job, must be stored in the same folder as the PBS script

  • $PBS_O_WORKDIR is simply a variable that represents the folder you submit the PBS script from. Make sure the .fa files, and any other files you need are in the same folder you put the PBS script in. This line tells the cluster to enter this directory where you have stored the PBS script, and look for all the files for the job. If you use $PBS_O_WORKDIR, you need to have all your files in the same folder as your PBS script otherwise the cluster won't be able to find the files it needs.
  • Output Files will also show up in the same folder as the PBS script
  • The module load line loads IDBA
  • The idba_ud line executes IDBA. Note, this is just a general template. More info on IDBA can be found by running idba without any arguments.
  • There are a couple important things to point out in the execution line:
    • It is placed after the module load line, as well as the cd $PBS_O_WORKDIR line
    • --num_threads 16 is set to the same number of processors requested in the PBS script (16).

Submit Job and Check Status

  • Make sure you're in the directory that contains the PBS script, the sequence files, and any other files you need.
  • Submit with qsub <pbs script name>. In this case qsub idba.pbs or whatever you called the PBS script. You can name the PBS scripts whatever you want, just keep the .pbs at the end
  • Check job status with qstat -u username3 -n, replacing "username3" with your gt username
  • You can delete the job with qdel 22182721, replacing the number with the jobid returned after running qsub
  • Depending on the resources requested and queue the job is run on, it may take varying amounts of time for the job to start. To estimate the time until the job executes, run showstart 22182721, replacing the number with the jobid returned after running qsub. More helpful commands can be found in this guide

Collecting Results

  • After the job finishes running, all files created will be in the same folder where your PBS script is (same directory you ran qsub from)
  • The .out file will be found here as well. It contains the results of the job, as well as diagnostics and a report of resources used during the job. If the job fails or doesn't produce the result your were hoping for, the .out file is a great debugging tool.
  • You can transfer the resulting files off the cluster using scp or a file transfer service