Updated 2021-05-17
Run Bowtie2 on the Cluster¶
Summary¶
- Use
module avail bowtie2
to see all the available versions of Bowtie2 on the cluster - Load Bowtie2 with
module load bowtie2/<your version>
- Run Bowtie2 with
bowtie2 -x <.genomes file> -U <.fq file> -S <allignment .sam file>
. Bowtie2 has many options and can be run many ways. The line above is simply a general template. When you login on the head node, load Bowtie2 and typebowtie2
. A more detailed explanation on all the possible run options should appear.
Warning
In your PBS
script, you must load Bowtie2 before you run Bowtie2
Example PBS Script¶
#PBS -N bowtie2Test
#PBS -A [Account]
#PBS -l nodes=2:ppn=8
#PBS -l walltime=2:00
#PBS -q inferno
#PBS -j oe
#PBS -o bt2Result.out
cd $PBS_O_WORKDIR
module load bowtie2/2.3.2
bowtie2 -x <.genomes file> -U <.fq file> -S <allignment .sam file>
- The
#PBS
directives are standard, requesting 2 hours of walltime and 2 nodes with 8 cores per node. More on#PBS
directives can be found in the PBS guide $PBS_O_WORKDIR
is simply a variable that represents the directory you submit the PBS script from. Make sure the.fastq
.sam
, and any other files you need are in the same directory you put thePBS
script in. This line tells the cluster to enter this directory where you have stored thePBS
script, and look for all the files for the job. If you use$PBS_O_WORKDIR
, you need to have all your files in the same folder as yourPBS
script otherwise the cluster won't be able to find the files it needs.- Output Files, will also show up in the same directory as the
PBS
script. module load bowtie2/2.3.2
loads Bowtie2bowtie2 -x <.genomes file> -U <.fq file> -S <allignment .sam file>
runs Bowtie2. Again, this is just a general template. This line will vary based on what you are running.
Submit Job & Check Job Status¶
- Make sure you're in the directory that contains the
PBS
script, the.fasq
files, the.sam
file, and any other files you need. - Submit as normal, with
qsub <pbs script name>
. In this caseqsub bowtie2.pbs
or whatever you called thePBS
script. You can name thePBS
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
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 you 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