Hi guys,

I am working on RNA structures of viral genomes and tried to use RNAforester to numerically confirm difference in RNA structure between two genomic fragments; however when I try to analyse two sequences containing ~4k nts I get following error (I am copying entire readout):

* Scoring parameters *

Scoring type: global similarity

Scoring parameters:

pair match: 10

pair indel: -5

base match: 1

base replacement: 0

base indel: -10

Error: Maximum array size of 2GB exceeded due to large input data. Calculation terminated.

Is there a limit to the length of RNA fragments one can compare using RNAforester (analysis of shorter fragments works fine in my hands)? I do not think that there is an issue with the memory space of the computer which I use for this analysis as I run RNAforester from a Linux cluster available at my institute (unless someone put some limits while installing RNAforester). If this is an issue with the size of the RNA string, is there a way I can overwrite it? While I can split the genomic region into smaller fragments, from the biological perspective I would rather compare the entire region.

Many thanks in advance!

Lidia