[Bioperl-l] BlastPlus usage inquiry

Peter biopython at maubp.freeserve.co.uk
Fri Apr 2 17:11:57 EDT 2010


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



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