[Bioperl-l] BlastPlus usage inquiry

Chris Fields cjfields at illinois.edu
Fri Apr 2 17:24:28 EDT 2010


On Fri, 2010-04-02 at 22:11 +0100, Peter wrote:
> On Fri, Apr 2, 2010 at 8:41 PM, Chris Fields <cjfields at illinois.edu> wrote:
> > Glad to see it's not just me.  I just asked the same question the other
> > day and got a response (or non-response, dep. on how you look at it);
> > posted below.  This occurs irrespective of using the BioPerl BLAST+
> > modules or not, using -num-threads of 4 and 8.
> >
> > Interestingly, the legacy BLAST and -a works just fine (I'm using a dual
> > quad-core running ubuntu karmic 64-bit, 48G RAM).  It may be the
> > database size as they imply, but I would like to see this behavior
> > documented.  It's certainly unexpected.
> 
> I was running the new blastp tool from BLAST+ today on a local
> copy of NR, and using -num_threads 7 worked fine. This was on
> a Mac Pro, with BLAST+ compiled from source. So it might be
> down to the database size as the NCBI suggested.
> 
> Peter

I may try the same database on Mac to see what happens.  

chris



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