Updated 2019-02-22

Run Scythe on the Cluster

Summary

  • Currently, Scythe/0.993 is available on the Cluster
  • Load Scythe with module load scythe
  • In your PBS script, the lines to execute Scythe must go after the lines to load scythe
  • The general command to run Scythe is:
  • scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
  • For more options when running scythe, enter the command scythe or visit the github page

Tip: Creating PBS Scripts on the Cluster

  • To create a PBS script on the cluster, enter the folder you want to use then type vim <name.pbs>. Name the file whatever you want, but keep .pbs at the end. Vim is a text editor that is reliable and effecient to use on Linux.
  • You can write the PBS script on your computer and transfer it over with scp or a file transfer service

Example PBS Script

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

cd $PBS_O_WORKDIR
module load scythe
scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
  • The #PBS directives are standard, requesting 2 hours of walltime and 2 node with 8 cores per node. 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 .fastq & .fasta files you want to use are in the same directory you put the PBS script. This line tells the cluster to enter this directory where you have stored the files for the job, so it has access to all the files it needs
  • Output Files, will also show up in the same directory as the PBS script.
  • module load scythe loads scythe
  • scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq runs scythe

Submit Job & Check Job Status

  • Make sure you're in the directory that contains the PBS script and the .fasq and .fasta files
  • Submit as normal, with qsub <pbs script name>. In this case qsub scythe.pbs or whatever you called the PBS script
  • 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

Collect Results

  • 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