[Bioclusters] ncbi blast

Justin Powell bioclusters@bioinformatics.org
Wed, 16 Jun 2004 16:21:43 +0100

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

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?