local_blast.job

#!/bin/csh

#$ -M crivaldi@nd.edu	 # Email address for job notification
#$ -m abe		 # Send mail when job begins, ends and aborts
#$ -q long
#$ -N localblasthmmer	 # Specify job name

module load bio        # Required modules to load


/afs/crc.nd.edu/user/c/crivaldi/local/bin/blastn -query /afs/crc.nd.edu/user/c/crivaldi/data/Hmmer_stuff/outextended_hmmout.fasta -db /scratch365/crivaldi/data/blast_db_nt/nt -num_threads 8 -max_target_seqs 10 -evalue 10e6 -outfmt 6 -out /afs/crc.nd.edu/user/c/crivaldi/data/blast_out/local_extout_dbnt.outfmt6

###from command line
###afs/crc.nd.edu/user/c/crivaldi/local/bin/blastn -query /afs/crc.nd.edu/user/c/crivaldi/data/Hmmer_stuff/outextended_hmmout.fasta -db nt -remotet 6 -evalue 10e6 -out ~/data/blast_out/hmm_extout_blast_outfmt6