[Bioc-sig-seq] scanBam memory issue

[Francesco Lescai]

Hi there,
I know this issue has been already touched, perhaps several times, but 
the solutions I found in the list (i.e. param=ScanBamParam(which=<...>) 
doesn't seem to work. 
(https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2010-December/001755.html)

I have bam files from Human Exomes, about 45 millions reads.
I imported RefSeq exons as genomic ranges using the import function of 
rtracklayer from the bed file.

This is my command and the error I get
 > load("refseq.exon.fixed.RData")
 > UCLG_20_1<-scanBam("UCLG_20_1.fq.novo.rmdup.bam_sorted.bam", 
param=ScanBamParam(which=refseq.exon.fixed))
Error: cannot allocate vector of size 156 Kb
Execution halted

My R version is
R version 2.11.1 (2010-05-31)
running on linux machines within a cluster environment.

Any idea? being it in a cluster it becomes a bit difficult to tweak 
memory settings..

cheers,
Francesco