[Bioclusters] BLAT users?

David Adelson bioclusters@bioinformatics.org
Fri, 29 Oct 2004 10:52:50 -0500

This may be the wrong forum to look for an answer, but I thought I 
would start here.

We have been using BLAT on G4 Xserves (2GB RAM) for some time now.  
Given the memory limitations, we carve up the database into chunks so 
that we don't get a malloc error message telling us we have run out of 
huge memory.  We then parallelize the job and run the chunks in 
parallel on our cluster.  This works for modest query sizes (15,000 
ESTs vs 1.2GB database-hs_chroms1-6).  However, when we scaled up to 
larger queries (493365 ESTs vs 1.3GB database-bovine genome 
200,000scaffolds) we see blat just sort of stop working after a while.  
I ran the leaks program and found 91832 memory leaks, so the problem 
seems to be memory related.  I would be curious to know if anyone else 
has seen this type of behavior with BLAT.  I am in the process of 
contacting Jim Kent about this, but thought it would not hurt to ask 
some other knowledgeable computational biologists about this.

thanks in advance,

Dave Adelson
Texas A&M University