ERROR: Alignment must have at least 3 sequences

[GonzaloYebra]

Hi everyone,

First of all, thanks so much for such an amazing tool!

I'm having trouble running Civet3 whenever I use an alignment that includes both sequences in the background and not. The logfile that contains the error says:

ERROR: Alignment must have at least 3 sequences

I've tried increasing the SNP distance cutoff so that more sequences would be included in the catchment but that sadly doesn't solve the problem.

Any help would be appreciated.

Best,

Gonzalo