[Bioc-devel] pairwiseAlignment strings too long?

[Vincent Carey]

On Fri, Jun 18, 2021 at 5:06 AM csmatyi via Bioc-devel <
bioc-devel using r-project.org> wrote:

> 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.
>

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.


> Can someone help me? Are the sequences too long perchance?
>
> Thanks, Matthew
>
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