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Question: Biostrings - size limits
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gravatar for Erik Wright
7.4 years ago by
Erik Wright210
Erik Wright210 wrote:
Hello, What limits the number of sequences and size of sequences that are part of a DNAStringSet? Are there any way to change these limits? On my home laptop I can create a DNAStringSet of about sixty thousand sequences of length 1500. On my desktop I can only make a DNAStringSet of twenty thousand sequences. Does anyone know what is creating this difference is maximum size? Is there any way I can "up" the amount of memory available to a sequence set? I would like to be able to have at least one hundred thousand sequences (of width 1500 nucleotides) in memory. Thanks!, Erik > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base
ADD COMMENTlink modified 7.4 years ago by Steve Lianoglou12k • written 7.4 years ago by Erik Wright210
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gravatar for Steve Lianoglou
7.4 years ago by
Genentech
Steve Lianoglou12k wrote:
Hi, On Thu, Jun 24, 2010 at 9:24 AM, Erik Wright <eswright at="" wisc.edu=""> wrote: > Hello, > > What limits the number of sequences and size of sequences that are part of a DNAStringSet? (1) the amount of RAM on your computer, and; (2) the architecture (32 bit vs. 64 bit) that R is running on/in. > ?Are there any way to change these limits? Yes, adjust (1) and (2) from above. > On my home laptop I can create a DNAStringSet of about sixty thousand sequences of length 1500. ?On my desktop I can only make a DNAStringSet of twenty thousand sequences. What's the error you get when you try to create these large DNAStringSets on your desktop? >?Does anyone know what is creating this difference is maximum size? What are the differences between the computers, specifically with respect to RAM and architecture? > Is there any way I can "up" the amount of memory available to a sequence set? ?I would like to be able to have at least one hundred thousand sequences (of width 1500 nucleotides) in memory. R wouldn't limit the amount of memory on a per object basis[*] -- it just takes as much RAM as it can get from the OS. [*] with the exception of the number of elements in a vector, which is limited to 2^(32-1) due to R's 32bit addressing for vectors, but AFAIK (i) Biostrings runs an end-around on this to avoid this problem, and (ii) you're only talking about 100,000 elements anyway, so this isn't your problem. >> sessionInfo() >R version 2.11.0 (2010-04-22) >x86_64-apple-darwin9.8.0 Is this for your laptop, desktop, or both? Also, R 2.11.1 is out -- never hurts to upgrade ;-) -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
ADD COMMENTlink written 7.4 years ago by Steve Lianoglou12k
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