User Tools

Site Tools


blast

This is an old revision of the document!


blast

The Intel processors on the razor cluster will run blast+ faster than the AMD processors on trestles. 12-core nodes are sufficient since blast+ is not very scalable. If doing a number of runs, it may be worthwhile to copy the database to your area of the local scratch disk, as shown. For a single run it is probably faster to read from the reference copy. If copying the database please remember to remove it at the end of the job. Please note the difference in paths between the clusters. The latest 2.3.0 version is considerably faster multi-threaded than earlier versions.

trestles

$ rsync -a /share/apps/bioinformatics/blast/db20150912/nt /local_scratch/rfeynman/
$ export BLASTDB=/local_scratch/rfeynman/nt
$ export PATH=$PATH:/share/apps/bioinformatics/blast/ncbi-blast-2.3.0+/bin
$ time  blastn -num_threads 32 -query queries/blastn/NM_001005648 -db $BLASTDB/nt >blast.output

real	0m11.438s
user	1m28.905s
sys	0m11.403s

razor

$ rsync -a /share/apps/blast/db20150912/nt /local_scratch/rfeynman
$ export BLASTDB=/local_scratch/rfeynmann/nt
$ export PATH=$PATH:/share/apps/blast/ncbi-blast-2.3.0+/bin
$ time  blastn -num_threads 16 -query queries/blastn/NM_001005648 -db $BLASTDB/nt >blast.output

real 0m5.917s user 0m48.965s sys 0m6.227s

blast.1455574939.txt.gz · Last modified: 2016/02/15 22:22 by root