Updated 2021-05-17
Run Blat on the Cluster¶
Summary¶
- Blat is a suite of programs that produces alignments at different DNA levels
- The Blat suite is available on the cluster by loading the
Blat
module - Use
module avail blat
to see all the available versions of blat on the cluster - To load bedtools in your
PBS
script:- Load with
module load blat/35
. Replace the version with any version you prefer that is available on the cluster (found withmodule avail blat
)
- Load with
- To run bedtools:
- In your
PBS
script, put all lines execuing blat or one of blat's programs after themodule load
lines that load blat - Example: If you wanted to use
pslReps
, the linepslReps in.psl out.psl out.psr
would go in thePBS
script after the lines that load the correct module for blat.
- In your
Example PBS Script¶
#PBS -N blatTest
#PBS -A [Account]
#PBS -l nodes=1:ppn=16
#PBS -l walltime=1:00:00
#PBS -q inferno
#PBS -j oe
#PBS -o blatResult.out
cd $PBS_O_WORKDIR
module load blat/35
pslReps in.psl out.psl out.psr
- The
#PBS
directives are standard, requesting 1 hour of walltime and 1 node with 16 cores per node. More on#PBS
directives can be found in the PBS guide
Note
If using $PBS_O_WORKDIR
, the .psl
files, as well as any other files required for the job, must be stored in the same folder as the PBS
script
$PBS_O_WORKDIR
is simply a variable that represents the folder you submit the PBS script from. Make sure the.psl
files, and any other files you need are in the same folder you put thePBS
script in. This line tells the cluster to enter this directory where you have stored thePBS
script, and look for all the files for the job. If you use$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.- The
module load
line loads blat - The
pslReps
line is just a general example showing how a program in the blat suite might be executed. The line is from the blat user guide which includes much more information on the capabilities of blat. The point is to show that the execution lines must be included after:- Entering the correct folder with all the files, data, and
PBS
script, in this case achieved withcd $PBS_O_WORKDIR
- blat is loaded with the
module load
line
- Entering the correct folder with all the files, data, 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 blat.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¶
- After the job finishes running, 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