Parallel blasting of bacterial sequences, inspired by: http://students.washington.edu/bowmanjs/wordpress/?p=737

blast_unassigned_otus.sh

#!/bin/bash                                                                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                  
number_of_jobs=4                                                                                                                                                                                                                                                                  
# Opts for fast blasting, http://www.biostars.org/p/16425/#16431                                                                                                                                                                                                                  
blastopts="-num_alignments 20 -num_threads 4 -word_size 50"                                                                                                                                                                                                                       
                                                                                                                                                                                                                                                                                  
# Job script                                                                                                                                                                                                                                                                      
if [[ $1 ]]; then                                                                                                                                                                                                                                                                 
        # Extract sequences                                                                                                                                                                                                                                                       
        for otu in $(cat $1); do                                                                                                                                                                                                                                                  
                samtools faidx otus/rep_set/seqs_rep_set.fasta ${otu} >> $1.fasta                                                                                                                                                                                                 
        done                                                                                                                                                                                                                                                                      
        blastn -task megablast -db /resources/blast/nt -outfmt 5 -query $1.fasta -out $1.xml ${blastopts}                                                                                                                                                                         
        exit 0                                                                                                                                                                                                                                                                    
fi

# Index original FASTA
samtools faidx otus/rep_set/seqs_rep_set.fasta

# Find unassigned sequences and split into number_of_jobs
grep -i unassigned  otus/uclust_assigned_taxonomy/seqs_rep_set_tax_assignments.txt | awk '{ print $1; }' >> unassigned.$$
split -n l/${number_of_jobs} unassigned.$$ part
rm unassigned.$$

# Submit jobs
for part in part??; do
        qsub -terse -sync y -b y -V -cwd $0 ${part} &
done
wait
rm part?? part??.fasta