[BioC] memory exhausted for readAligned
schaffer at scripps.edu
Fri Feb 13 01:58:59 CET 2009
Do I need a 64-bit windows computer?
Where is the code for the R v2.9.0dev Unix version?
From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org]
Sent: Thursday, February 12, 2009 4:32 PM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] memory exhausted for readAligned
Given that there is typically a trade-off between memory and speed and
the ubiquity of 64-bit machines, most of the Bioconductor sequencing
software was designed with 64-bit architectures in mind in order to
minimize computation time. Once you move to a 64-bit machine for this
work, I'm pretty sure this issue will go away.
Lana Schaffer wrote:
> Yes, I am on a 32-bit machine.
> 298,610kb 50% PF and 12% Align
> R version 2.9.0 Under development (unstable) (2009-02-12 r47905)
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> -----Original Message-----
> From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org]
> Sent: Thursday, February 12, 2009 4:20 PM
> To: Lana Schaffer
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] memory exhausted for readAligned
> Could you provide your session information for you R session as well
> as the number of alignments you are trying to read in? My first guess
> is that you are running on a 32-bit architecture, but without more
> information we on the list can't help you very much.
> Lana Schaffer wrote:
>> I am trying to read the alignment in a lane of Solexa data and ran
>> of memory.
>> I have 3.2G memory on my desktop computer.
>> Is there a setting I can use to have enough memory for the
>> How much memory do i need?
>> Lana Schaffer
>> The Scripps Research Institute
>> DNA Array Core Facility
>> La Jolla, CA 92037
>> (858) 784-2263
>> (858) 784-2994
>> schaffer at scripps.edu
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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