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