I usually use less number of generations e.g. 50 million for my BEAST analysis because of my large number of taxa and then I run about three times and use the log combiner to combine my logs and tree files with the aim of getting better effective sampling sizes. When annotating the tree file using tree annotator, I get error messages such as "java heap space error" anyone knows how I can solve this problem?
Please visit the - www.pnas.org/cgi/content/short/1007606107. You may got your answer.
This error basically means that your .trees files are too large. This can be solved by subsampling from the original .trees files when you combine them using LogCombiner. For instance subsampling every 100,000 generations will give you 1500 trees (minus burnin), which should be plenty.
Hi Chantal, you have just to use log combiner and resample a smallest number of tree.
Hope this help
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