Question: (Closed) Running Trinity on a server using PBS job script
gravatar for seta
5.2 years ago by
seta1.3k wrote:

Dear all,

I'm trying to submit my trinity job in the PBS to a server with 256 GB of RAM and two CPUs, each with 12 cores and 24 threads, yielding 48 computing units. I attempt to create this script file to perform de novo transcriptome assembly of about 350 million PE reads, but I'm not sure about it as I'm basically a biologist and have never such the experiences. I would be highly appreciate if you, my expert friends, could please take a look at the following PBS file to correct my possible mistakes and help me how I should submit it using qsub command. As the various stages of trinity is dependent on an output of another, I think submitting it to the server cannot be using a simple command of qsub. Your feedback would be highly welcomed.


#PBS -N run_trinity
#PBS -l nodes=1:ppn=6
#PBS -l walltime=100:00:00
#PBS -l mem=200gb
#PBS -j oe

#Set stack size to unlimited
ulimit -s unlimited

cd /home/seta/software/trinityrnaseq_r20140717

perl/home/seta/software/trinityrnaseq_r20140717/ --seqType fq --JM 200G --normalize_reads --left reads8_1.fq.gz --right reads8_2.fq.gz --SS_lib_type FR --CPU 6 --full_cleanup --output /home/seta/software/trinityrnaseq_r20140717

rna-seq alignment assembly • 2.8k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by seta1.3k

Hello seta!

Fundamentally this is a question about using PBS, and whilst it involves bioinformatics tools, it is not a bioinformatics question, so I'm going to close it.  I think you should do some reading around the job scheduling system, as if you've not done this before you will want to take advice on resource utilisation. And you can generally submit jobs that recapitulate a command line that you would run on the server.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Daniel Swan13k

Hi Daniel,

sorry for the question. I indeed read and read to write the above script file, but I just wanna it's correct to submit the job as it's my first experience.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by seta1.3k

Then you should be talking to the person who administers your HPC facilities.. :)

ADD REPLYlink written 5.2 years ago by Daniel Swan13k
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