Alexander Churbanov wrote:
We've heard of this before - this *may* be due to an old bug that was *supposed* to have been fixed in the biojava code base long ago i.e. something not getting popped of a stack when it should be. Should be easy to fix if this bug is somehow still in the biojava code.Hello Matthew or Thomas,I just use SAX BLAST parser to parse a massive of BLAST output. Unfortunately this package does a really poor job in a batch mode. It runs out of memory because of the recursive self-calls which adversely affects the heap. I know that you have borrowed this from another team, but are there any ways to fix it, outherwise I run into strange situation while parsing 18,000 Blast runs.
If could e-mail the code of the ContentHandler you are using it would be helpful. It would be useful to confirm that the problem you are experiencing is nothing to do with object creation *outside* of the SAX driver itself.
An obvious work around for your problem is to split the blast output into smaller chunks.
Simon
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