Sequence too long (max 32000000 permitted).

hyattpd / Prodigal

Prodigal Gene Prediction Software

GNU General Public License v3.0

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Sequence too long (max 32000000 permitted). #54

Closed faylward closed 4 years ago

faylward commented 5 years ago

I'm trying to run Prodigal on a very large genome and I keep getting this error. Is there a way to run the algorithm on very large contigs?

tseemann commented 4 years ago

You need to edit this line in the source code and manually recompile:

https://github.com/hyattpd/Prodigal/blob/9b74af5dd408bae27579a78d33aa1a5db48871b4/sequence.h#L32

hyattpd commented 4 years ago

Yeah.... I'm kind of curious how you could ever have a single genome this big that Prodigal actually works on, since the biggest bacterial genome is still only like 13 million bp or something? Anyway...

faylward commented 4 years ago

Thanks for the tip! I am using Prodigal for non-canonical purposes (i.e., non-bacterial genomes) so this comes up every now and again for me. I understand this isn't the intended purpose of this tool, however, and that it is not an issue for regular prokaryotic genomes.

hyattpd commented 4 years ago

Yeah, this won't be an issue in the Go version (won't be arbitrary limits on memory, size, etc.)