WU-Blast Error - should I worry?

Betastar insq at yahoo.com
Wed May 9 04:11:26 EST 2001


I've fixed the problem in the 4 days it took for my original post to
reach this newsgroup.

Thanks anyway

Betastar


On 8 May 2001 10:55:25 +0100, nospam at newsranger.com (Betastar) wrote:

>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
>fine.
>
>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!
>
>Thanks!
>
>Betastar
>
>---
>





More information about the Bio-soft mailing list