[Rmannounce] WUBlast "out of memory" bugfix

Robert Hubley rhubley at systemsbiology.org
Tue Sep 28 15:44:38 PDT 2004


A bugfix is available for RepeatMasker open-3.0 which corrects a problem 
with short sequences run with the WUBlast option.

If a search is performed on a large sequence file containing many short 
( less than 100bp sequences ) *and* during batching one of these 
sequences ends up being placed as the last entry in a particular batch 
you may see the following error messages:

identifying full-length ALUs in batch # of #
ERROR from search engine (16)
retrying comparison with smaller bandwidth

This is not a memory problem, rather a problem with the way we handled 
exceptions returned by WUBlast. The fix is to replace the 
WUBlastSearchEngine.pm file in your RepeatMasker installation directory 
with the new version available here: 
http://www.repeatmasker.org/WUBlastSearchEngine.pm



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