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[Bioc-devel] pairwiseAlignment strings too long?

2 messages · csmatyi, Vincent Carey

Original
csmatyi
# 
Hello,

I am trying to align two sequences, in DNAString format using the R command pairwiseAlignment.
I keep getting this error:

pairwiseAlignment(si,sj)
Error in .Call2("XStringSet_align_pairwiseAlignment", pattern, subject,  :
  max(nchar(pattern) * nchar(subject)) is too big (must be <= 2147483647)

The 2 DNAstrings are si and sj, and are 108,007 bp and 120,698 bp long, respectively.

Can someone help me? Are the sequences too long perchance?

Thanks, Matthew

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1 day later
Vincent Carey
# 
On Fri, Jun 18, 2021 at 5:06 AM csmatyi via Bioc-devel <
bioc-devel at r-project.org> wrote:

            

      
      
      
    

        
The error message states the limitation of the function: the product of
string lengths cannot
exceed  2147483647 but the product of your string lengths is 13036228886,
almost an
order of magnitude too large.

You may have to find a different tool.