[BioC] optimizing VariantTools\' performance

[Eric Foss [guest]]

I am running VariantTools on 40 not particularly large bam files (~700 Mb). When running 5 in parallel on the same machine (12 cores, 48 Gig RAM), each running on a single core, it took several hours for the first one to finish, and the other 4 are still running. In total, the remaing 4 are taking up 70% of the RAM. Does anyone have suggestions for how to run VariantTools for optimum speed? I can increase the number of cores, but then I have to run fewer files because otherwise I run out of memory. And if I run 5 at a time each with a single core, I'm coming close to using up all the memory, and I don't know if that will really slow things down and if it would therefore be better to run just 4 at a time. Any suggestions are appreciated. 

Thank you. 

Eric

 -- output of sessionInfo(): 

These are running in batch mode so I don't have that information. 

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