Parsing error

[Josh Sealy]

Hi BEAST users,

I am having difficulty with setting up my XML file for discrete phylogeographic analysis. The issue i am having involves setting the dimensions of the rates and indicators using K*(K-1)/2 under the CTMC model. 

I have 26 different sample locations (K) for 71 samples. Using the above equation i get the value 325 to be used as the dimensions for rates and indicators. However, when I run this in BEAST i am given the below message:

"BEAST has terminated with an error. Please select QUIT from the menu.

dr.xml.XMLParseException: Error parsing '<generalSubstitutionModel>' element with id, 'originModel':

Rates parameter in generalSubstitutionModel element should have 324 dimensions. However parameter dimension is 325

at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)"

My question is, does anyone know why i get this error? In light of this, i have run BEAST with an XML file containing 'corrected' values but get further errors associated with the dimensions.

Any help would be much appreciated, i am quite new to BEAST!

Many thanks,

Josh

PhD Student

The Pirbright Institute, UK

joshua...@gmail.com