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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#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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