[Bioclusters] ncbi blast

Susan Chacko bioclusters@bioinformatics.org
Wed, 23 Jun 2004 10:56:58 -0400

I'm seeing exactly this same problem on our systems. It does not appear 
to be related to hardware, as I see it on all of the following:
- 2.8 GHz Xeon, 2 Gb RAM
- 2.8 GHz Xeon, 4 Gb RAM
- 1.8 GHz Athlon, 2 Gb RAM
- 1.4 GHz Athlon, 2 Gb RAM
- 866 MHz Pentium III, 1 Gb RAM

They're all running RH 7.1 with updated kernels. I'm using the NCBI 
blastall and the NCBI nt db. There aren't any missing libraries, 
according to ldd.

Our databases sit on a Netapp 960 Filer, and at first I thought that 
was the problem, but I still see the failures when I copy the db to 
local scratch on the nodes.

The problem appears _only_ with the combination of the nt database and 
the '-a 2' flag on Blast. It is random, in that I get somewhere between 
5 and 20 failures out of 20 Blast runs with the same db+query. I get no 
failures with other dbs (e.g. est) or if I don't use the -a flag.

I've also run Blast with the same db+query on an SGI Origin 3400 with 
no failures, using -a 2, -a 3, -a 4.

I've emailed NCBI about this and am waiting for a response.


On Jun 16, 2004, at 11:21 AM, Justin Powell wrote:

> 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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