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.

#!/bin/bash
#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/Trinity.pl --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