HELP - how to execute mothur on sun grid engine?

I’ve been working with mothur for a few weeks now (awesome program, btw) on a cluster - but I’m only able to access 8 processors currently since I’m not actually using qsub to submit the job. I’ve tried a few simple scripts to execute a batch but they all seem to fail. Has anyone successfully run mothur on a Sun grid engine in parallel mode? And if you have, would you be willing to share some scripting examples? :slight_smile:

Here’s the PBS script that I use (it is a bit of a handme down…)

#PBS -l nodes=1:ppn=8
#PBS -l mem=10gb
#PBS -l walltime=500:00:00
#PBS -j oe
#PBS -m abe
#PBS -q first

echo "ncpus-2.pbs"
qstat -f $PBS_JOBID


NCPUS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

mothur "#classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta,, cutoff=80, processors=8)"

echo "qsub working directory absolute is"

This works on our cluster, but I’m not sure how it will work on yours. You would change the mothur line to run you commands.