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We use a PBS Pro submission script to submit jobs to the HPC cluster. Above the Create a file called ‘launch_blastN.pbs’ can be used to submit the job. This file has the following informationand fill it with this content, substituting email@host for your email address, and the files used as input to blastn:
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#!/bin/bash -l
#PBS -N blastN
#PBS -l walltime=10:00:00
#PBS -l mem=8gb
#PBS -l ncpus=4
#PBS -m bae
#PBS -M email@host
#PBS -j oe
cd $PBS_O_WORKDIR
#define variables. For example name of the fasta file to use. Note: it can be either with a suffix .fa or .fasta or other.
QUERY=query_sample.fa
REFERENCE=MsiMV_genome.fasta
EVALUE=1e-10
#run blastn search
blastn -query $QUERY \
-subject $REFERENCE \
-out blastN_${QUERY}_vs_${REFERENCE}.out \
-outfmt 6 \
-evalue $EVALUE \
-num_threads 4 |
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qjobs #alternatively use: qstatsqstat -u USERNAME |
How to interpret the result? check this tutorial.
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