[BioC] memory exhausted for readAligned

[Patrick Aboyoun]

Lana,
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.


Patrick


Lana Schaffer wrote:
> Patrick,
> Yes, I am on a 32-bit machine.
> length=35bp
> 298,610kb  50% PF and 12% Align
>  R version 2.9.0 Under development (unstable) (2009-02-12 r47905) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base   
> Thanks,
> Lana
>
> -----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
>
> Lana,
> 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.
>
>
> Patrick
>
>
>
> Lana Schaffer wrote:
>   
>> Hi,
>> I am trying to read the alignment in a lane of Solexa data and ran out
>>     
>
>   
>> of memory.
>> I have 3.2G memory on my desktop computer.
>> Is there a setting I can use to have enough memory for the readAligned
>>     
>
>   
>> command?
>> How much memory do i need?
>>
>> Lana Schaffer
>> Biostatistics/Informatics
>> 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
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>   
>>     
>
>