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WU-Blast Error - should I worry?

Betastar nospam at newsranger.com
Tue May 8 04:55:26 EST 2001

I've got Wu-Blast running on a Linux box (Redhat 7 Kernel 2.2.16-22enterprise on
a 4-processor i686) and I seem to be able
to take a nucleotide sequence and run blastx against genbank's nr database just

But when I try to run a tblastx against the nt database (also downloaded from
Genbank) I get the following error message:

WARNING:  The associated FASTA-format database file is too large and will be
ignored:  /usr/ncbi/blast/db/nt

Strangely enough, though, it still gives me results in my output file.

Not knowing if I should worry about this error message, I ran setdb on nt to try
to create a protein database from nt,
and then ran blastx against it with my nucelotide sequence - and I got no
matches (where I did get matches from the tblastx, even though it tells me its
ignoring the database.)

I guess I'm wondering two things:

1. Should I worry about this error message?  (In other words, can I trust the
results its giving me, despite this error message)

2. If I have to worry about it (which for now I assume I do) is there any way to
get around this?

I didn't set up the Linux machine myself, and I'm not sure how I can
double-check my swap space, but when the machine was set up
they did ask me how much swap space I wanted, and I asked for 2 Gig.  I'm
assuming that's what's there.  

If anyone can help me with this, I'd greatly appreciate it!




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