qsub submission script

bigblast.qsub:

    #!/bin/sh
    #$ -N Big_Blast
    #$ -m e
    #$ -e sge.err
    #$ -o sge.out
    #$ -pe threaded 8

    JOB_ID=bigblast

    echo Running blast $1 vs $2 

    #Blastx=/usr/adavisr/ncbi/blastx

    /home/adavisr/ncbi/blastx -query $1 -db $2 -out $1.out -num_threads 8 -outfmt 6 -evalue 0.01 -num_descriptions 1 -num_alignments 1


Command to submit:
    
    for i in *.ffn; do qsub bigblast.qsub $i SEED.fasta; done;


This submits a qsub job for each *.ffn file in your directory.  The second argument is the database.

I should I have made sge.out unique for each job incase one crashes.

just change line 7 to

#$ -e $1.sge.out 

or something