[Bioc-sig-seq] scanBam memory issue

[Steve Lianoglou]

Hi,

On Wed, Jul 20, 2011 at 7:28 AM, Francesco Lescai <f.lescai at ucl.ac.uk> wrote:
> 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..

It looks like your machines don't have enough memory to load in all
the reads at once -- perhaps you can load in the reads on a chromosome
by chromosome basis.

If your machines are running linux -- I'm pretty sure there is no need
to tweak any memory settings, you just need to have enough physical
memory is all.

Also -- see if you can't get your sysadmins (or whoever) to upgrade to
latest version of R ;-)

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact