[Bioclusters] ncbi blast

Chris Dwan bioclusters@bioinformatics.org
Wed, 16 Jun 2004 10:27:14 -0500

Please forward an example of the error-provoking query sequence.  I'm 
curious to see if I can replicate this behavior.

-Chris Dwan
  University of Minnesota

> I'm experiencing trouble with blastall 2.2.9 running blastn on a linux
> cluster against a recently downloaded version of the 'nt' database from
> ncbi.  Intermittently I get a segmentation fault partway through the
> search.
> This happens both with precompiled blast and blast I compile myself. It
> happens on a two dual xeon systems running redhat9.0 and a dual athlon
> system running redhat7.1.  Both systems have 4GB ram. It happens with
> several different query sequences, but never with the est nucleotide
> database. It also happens if I use fastacmd to dump the ncbi nt 
> database
> into fasta format and then formatdb it myself. Blastdbs are kept 
> locally
> so its not a networking issue.
> Strangely this also happens with blastall2.2.6 on the athlon system, 
> I've
> not tested it on the xeon systems (or other releases).
> So I would guess, given the variety of systems, that its a bug which nt
> provokes specifically - but then I assume huge numbers of people must 
> use
> blast to search nt on linux boxes and would have noticed already if 
> this
> were the case. Anyone have any ideas what might be going on?
> Justin
> jacp1@mole.bio.cam.ac.uk
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