Updated 2021-05-17
Run Bedtools on the Cluster¶
Summary¶
- Bedtools contains a multitude of tools used for genomic analysis and allows for functionality such as shuffling, merging, and intersecting genomic intervals.
- Use
module avail bedtools
to see all the available versions of bedtools on the cluster - To load bedtools in your
PBS
script:- Load its dependent module first with
module load gcc/4.9.0
- Load bedtools with
module load bedtools/2.25
. Replace the version number with any version you prefer that is available on the cluster (found withmodule avail
)
- Load its dependent module first with
- To run bedtools:
- In your
PBS
script, put all lines executing bedtools after themodule load
lines that load bedtools - Example: using the intersect tool, the line
bedtools intersect -a <filename>.bed -b genes.bed
would go in thePBS
script after the lines that load the correct modules for bedtools.
- In your
Example PBS Script¶
#PBS -N bedtoolsTest
#PBS -A [Account]
#PBS -l nodes=2:ppn=4
#PBS -l walltime=20:00
#PBS -q inferno
#PBS -j oe
#PBS -o bedtoolsResult.out
cd $PBS_O_WORKDIR
module load gcc/4.9.0
module load bedtools/2.25
bedtools intersect -a reads.bed -b genes.bed
- The
#PBS
directives are standard, requesting 20 min of walltime and 2 nodes with 4 cores per node. More on#PBS
directives can be found in the PBS guide
Note
If using $PBS_O_WORKDIR
,the .bed
files, as well as any other files required for the job, must be stored in the same folder as the PBS
script
$PBS_O_WORKDIR
is simply a variable that represents the directory you submit the PBS script from. Make sure the.bed
files, and any other files you need are in the same directory you put thePBS
script in. This line tells the cluster to enter this directory where you have stored thePBS
script, and look for all the files for the job. If you use$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: Any files generated by the job will also show up in the same directory as the
PBS
script. - The
module load
lines load bedtools and its dependent module - The
bedtools intersect
line is just a general example showing how bedtools might be executed. The line is from the bedtools documentation which includes much more information on the capabilities of bedtools. The point is to show that the execution lines must be included after:- Entering the correct folder with all the files and
PBS
script, in this case achieved withcd $PBS_O_WORKDIR
- bedtools is loaded with the
module load
lines
- Entering the correct folder with all the files and
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 caseqsub bedtools.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 - 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¶
- 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