[Bioclusters] BioPerl 1.2.3 and memory handling

Mike Cariaso cariaso at yahoo.com
Tue Nov 30 16:10:02 EST 2004


While I'm certainly learning a bit from the
bioperlers, we seem to have strayed a bit from your
original question. 

If you don't need to see the alignments, you might
wish to investigate if your software can be made to
use blast's table output ("blastall -m 8" I believe).
Perhaps the bioperl parser will recognize the format,
and will be able to complete since it will have no
alignments to eat up memory. If its not automatically
recognized writing a parser for this might be pretty

If you need the alignments but don't need all the
statistics, you might wish to use the BPLite parser,
which manages to handle some reports that the SearchIO
parser cannot.

If you need both, you can probably still use BPLite,
but you'll need to do a bit more work.

Sadly, I don't believe that the XML (-m 7) format is
handled by bioperl yet. That would probably solve all
of these issues.

That'll teach you to ask a question! ;)
Mike Cariaso

--- Al Tucker <act at comm.rockefeller.edu> wrote:

> Hi everybody.
> We're new to the Inquiry Xserve scientific cluster
> and trying to iron 
> out a few things.
> One thing is we seem to be coming up against is an
> out of memory 
> error when getting large sequence analysis results
> (5,000 seq - at 
> least- and above) back from BTblastall. The problem
> seems to be with 
> BioPerl.
> Might anyone here know if BioPerl is knows enough
> not to try and 
> access more than 4gb of RAM in a single process (an
> OS X limit)? I'm 
> told Blastall and BTblastall are and will chunk
> problems accordingly, 
> but we're not certain if BioPerl is when called to
> merge large Blast 
> results back together. It's the default version
> 1.2.3 that's supplied 
> btw, and OS X 10.3.5 with all current updates just
> short of the 
> latest 10.3.6 update.
> - Al Tucker

Mike Cariaso

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