[BioC] Rsamtools Memory Issue

Hollis Wright wrighth at ohsu.edu
Fri Oct 1 22:12:37 CEST 2010

Hello, all; I am having a problem with the readPileup() function in Rsamtools. I'm trying to read in a pileup file generated by SamTools of about ~4GB in size, on a Mac Pro, OS X 10.5. Top indicates that I have 18 GB of memory free, and I am using a freshly built R 2.11.1 with the x86_64 arch specified. However, when I attempt to read in the file:

lane1 <- readPileup("test.pup", variant="SNP")

I eventually get a malloc error and the error "Cannot allocate vector of size 500 Mb". I have specified ulimit unlimited for the shell that I'm running R in and have difficulty believing that a 500MB contiguous space is unavailable in 18 GB of free RAM. Top only ever indicates that R is using 2-3GB;  Samtools has had no problems processing the files up to this point and a quick inspection seems to indicate that they are proper Pileup files. Any thoughts? 

Hollis Wright, PhD
Oregon Clinical and Translational Research Institute
Oregon Health and Science University

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