Hi David Please elaborate on what does 'stop working' mean. The leaks program can find a lot more memory leaks and the program can still be correct - try looking at the process memory usage, and see if it grows over time, and whether it reaches the size of the physical RAM. Regards, David Adelson wrote: > 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 > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters > > -- Ran Rubinstein Dept. of Molecular Biology Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel Tel +972-2-6757906 Fax +972-2-6758992