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--- howto:bioinformatics:m9000blast [2014/02/25 15:31]
dane [Job script]
+++ — (current)
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-====== Running Blast on the M9000 ======
-One thing to note is that one cannot use scratch on the m9000 -- so jobs must be run in the user's home (or a sub-directory of home).
-===== Job script =====
-Your job script will look something like this((Note you can click on the tab //my_job.qsub// to download this if you wish to use it as a template. Or you can just copy and paste...)):
-<file bash my_job.qsub>
-#! /bin/bash
-#PBS -l select=1:ncpus=128:mpiprocs=128:jobtype=spark
-#PBS -l place=free
-#PBS -l walltime=06:00:00
-#PBS -q spark
-#PBS -o /export/home/username/blastjob/stdout.txt
-#PBS -e /export/home/username/blastjob/stderr.txt
-#PBS -M youremail@address.com
-#PBS -m be
-#PBS -N m9000_blast
-# NOTE: Scratch doesn't exist on m9000 -- so run in your home, or a subdir of home
-cd /export/home/username/blastjob
-NP=`cat $PBS_NODEFILE | wc -l`
-EXE="/opt/gridware/bioinformatics/m9000/ncbi-blast-2.2.24/bin/blastx"
-ARGS="-db /opt/gridware/bioinformatics/db/blast/nr -query my_seqs.fasta -evalue 0.001 -num_alignments 20 -outfmt 5 -num_threads ${NP} > my_results.xml"
-$EXE $ARGS
-</file>
-Of course one should set the parameters as required. (Setting a small evalue is recommended as is limiting the number of alignments). For blast2go users remember to set //-outfmt// to //5// for XML output. Note one should also select the correct **//EXE//**cutable and **//-db//**: //blastx//, //blastn// and //blastp// are available for the former, while //nr// and //nt// are available for the latter.
-===== Submit your job =====
-Finally submit your job using:<code bash>user@login01:~ $ msub my_job.msub</code>

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