mpiBLAST and PBS

you need a work directory (/work/$USER) and sufficient space allocated. defualt is 5GB

to load the mpiblast-tools, run "module load mpiblast"

you need a .ncbirc file in you home directory:

[mpiBLAST]
Shared=/work/$USER/mblast
Local=/work/$USER/mblast

you need a database, and to put it in the correct directory /work/$USER/mblast

This example uses the the sample from:

cd /work/$USER
mkdir mblast
cd mblast
wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/drosoph.nt.gz
gunzip dropsoph.nt.gz

then you need to format the database correctly, using mpiformat, something like this:

mpiformat -i drosoph.nt --nfrags=4 -pF

create a test input file "test.in":

>Test
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT

and create your qsub script:

#!/bin/sh
#
#This is an example script mpiblast.sh
#
#These commands set up the Grid Environment for your job:
#PBS -N mpiblast
#PBS -l nodes=4:ppn=12
#PBS -q default
mpiexec -np 4 /share/apps/modulessoftware/mpiblast/mpiblast-1.5.0/bin/mpiblast -
d drosoph.nt -i /work/einjen/mblast/test.in -p blastn -o /work/einjen/mblast/res
ults.txt

Then submit your job:

qsub mpiblast.sh

and your results should be output to results.txt