BEAST Documentation->Error Messages
"Parsing error - the input file is not a valid XML file"
This error is most likely because the input file was not actually an XML file.
"Parsing error - poorly formed XML (possibly not an XML file):: The markup in the document following the root element must be well-formed."
The input file was recognized as an XML document but the document broke some fundemental rules for XML (it was not "well-formed").
"Parsing error - poorly formed BEAST file"
The input file was recognized as an XML file but the content was not as expected by BEAST. The exact element in the file will be listed along with details of the problem. For example,
Parsing error - poorly formed BEAST file: The '<alignment>' element with id, 'alignment1', is incorrectly constructed. The following was expected: One of ATTRIBUTE String dataType REQUIRED ELEMENT of type dataType REQUIRED
In this case, although the input file was a valid XML document, there was an error in the syntax that BEAST requires. For example, above, an element of type <alignment> does not conform to the requirement that it either has an attribute called 'dataType' or contains an element called '<dataType>'.
"Initial Likelihood is Zero"
Look at the answer to this FAQ question for possible reasons for this error and solutions.
"java.lang.OutofMemoryError Java heap space"
Look at the Increasing Memory Usage page for details of increasing the memory available to BEAST and the other programs.