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Rpsblast And Formatrpsdb Problems

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.

blast blast
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updated by Michael Schubert Michael Schubert • written by James Smith • 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.

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written by James Smith • James Smith

1 answer

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)
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written by Michael Schubert Michael Schubert

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