unable to import alignment file into beauti

[nadi dixit]

Hello!

I am trying to use SNAPP for my GBS-derived SNP data, but the nexus alignment file (~50 MB) won't import into beauti. The program doesn't close, but it doesn't do anything either, it just gets stuck. I access the program through the command line and I can see that the program is still running through the terminal. I am guessing it takes an incredibly large amount of time to import such a huge file? I only waited an hour or so though. I tried to import a very small nexus file, and it works. Is there a workaround to importing a really huge file into beauti?  

Also, complete BEAST noob here. It is my first time with the program. 

Thanks!
Cheers

Nadi

[Shannon]

I had this issue - for me it was a problem with my Nexus file. I was able to increase the memory to Beauti in order to get it to open but it never really ran well or was able to save. But I fixed the NEXUS file - either my SNPs weren't in binary format, or included all my non-polymorphic sites, I can't remember which. I correctly re-converted it (from the original VCF) using PGDSpider and it shrunk the size by a huge amount, and then Beauti was able to manage it. I'm not sure if it makes sense for a SNP-containing NEXUS file to be 50 MB. Good luck!