Updated 2021-05-17
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 typevim <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 -A [Account]
#PBS -l nodes=2:ppn=8
#PBS -l walltime=2:00
#PBS -q inferno
#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 thePBS
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 scythescythe -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 caseqsub scythe.pbs
or whatever you called thePBS
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 ranqsub
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