Rpsblast And Formatrpsdb Problems

Question

[James Smith]

I'm trying to install the CDD database locally using rpsblast. However, I've run into several problems. I can't seem to find formatrpsdb after compiling BLAST 2.2.24 from source. Has it been replaced with something else?

Since I couldn't get this to work, I tried using the preformatted CDD databases. However, rpsblast can't seem to open this database and get this error:

RPSBLAST 2.2.25+

Database: CDD.v2.29
           39,844 sequences; 10,209,221 total letters

BLAST engine error: Cannot memory map RPS-BLAST database file: db/cdd/Cdd.rps

The other database, like SMART works, but the Cdd one does not.

[James Smith]

Michael's right on this, I needed a 64 bit machine. Also, please note that formatrpsdb is in the legacy BLAST package and NOT in BLAST+. Also to format your own Cdd dataset, you need to run it on a 64 but machine.

Answer 1

[Michael Schubert]

If I recall correctly, this is either a memory or a 32 bit issue (the whole CDD being too big).

You can either:

• switch to a 64 bit machine with enough RAM or
• format your own CDD with cd* entries only (normally the "Cdd" has PFAM, SMART, etc. as well)