From mpiBLAST

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User's Guide

In order to perform a search with mpiBLAST, the target BLAST database must first be formatted and segmented using mpiformatdb. Then, mpiexec can be used to execute mpiblast in parallel on several cluster nodes.

Formatting a database

Before processing blast queries the sequence database must be formatted with mpiformatdb. The command line syntax looks like this:
mpiformatdb -N 16 -i nt -o T

The above command would format the nt database into 16 fragments. Note that currently mpiformatdb does not support multiple input files.

mpiformatdb places the formatted database fragments in the same directory as the FASTA database. To specify a different target location, use the "-n" option as what is available in the NCBI formatdb.

Querying the database

mpiblast command line syntax is nearly identical to NCBI's blastall program. Running a query on 18 nodes would look like:
mpiexec -n 18 mpiblast -p blastn -d nt -i blast_query.fas -o blast_results.txt

The above command would query the sequences in blast_query.fas against the nt database and write out results to the blast_results.txt file in the current working directory. By default, mpiBLAST reads configuration information from ~/.ncbirc. Furthermore, mpiBLAST needs at least 3 processes to perform a search: two processes dedicated for scheduling tasks and coordinating file output, while any additional processes actually perform search tasks.

Extra options to mpiblast

Please refer to the README file in the mpiBLAST package for performance tuning guide.

Removing a database

The --removedb command line option will cause mpiBLAST to do all work in a temporary directory that will get removed from each node's local storage directory upon successful termination. For example:
mpiexec -n 18 mpiblast -p blastx -d yeast.aa -i ech_10k.fas -o results.txt --removedb

The above command would perform a 18 node (16 worker) search of the yeast.aa database, writing the output to results.txt. Upon completion, worker nodes would delete the yeast.aa database fragments from their local storage.

Databases can also be removed without performing a search in the following manner:
mpiexec -n 18 mpiblast_cleanup

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Page last modified on March 27, 2011, at 11:37 PM