robertsmac:bin sr320$ ./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OlyOys_contigs41136.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/pfu_aug1.0_Nall -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Oly_Pinc_blastout 



robertsmac:bin sr320$ ./blastx -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OlyOys_contigs41136.fa -db /Volumes/Bay3/CLC_blastdatabases/swissprot -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Oly_SP_blastout 



issue, 
2.2.6 commandline produces significantly less hits than local blast in CLC (400v4000).
Running OlyOys against Pearl Oyster

Will try to recreate and maybe run elsewhere


tao@gizmo:/home/tao$ tar zxvpf ncbi-blast-2.2.23-x64-linux.tar.gz

Documentation available in http://www.ncbi.nlm.nih.gov/books/NBK1762





task
WEDNESDAY

robertsmac:bin sr320$ ./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/OlyOys_contigs41136.fa -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/pfu_aug1.0_Nall -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Oly_Pinc_blastout_tskblastn -task blastn -max_target_seqs 1