I recently posted that I had encountered two problems while working with Beauti to build a Starbeast xml input file. One problem was that I was not seeing a dialog box to establish a taxon set in the priors panel. Remco fixed this bug for an upcoming release. My other problem was that I had an issue with my Beauti-generated xml file such that my Beast run would end on an error with the screen output pasted in below. Note that 'volans' is the first species in my taxon set. Remco could not duplicate this problem and it disappeared for me when I opened another instance of Beauti out of another directory. I therefore thought my problem might be a 'one off'. However, I have now experienced this again. I don't know exactly which moves that I made in Beauti that initiated the problem, but it might be the result of switching back and forth between tree prior or other prior settings. I reach this conclusion because I had opened Beauti, successfully generated a working xml file, and then changed the prior settings and exported again only to find that the xml file throws the error pasted in below. My only recourse is to again start over in Beauti, which is a simple enough fix except that my data set has 162 terminals and each has to be manually renamed in the taxon set. To avoid this issue, I've been trying to reload my working .beauti file (which is simply my working xml file with the suffix changed from .xml to .beauti). The file appears to load properly, bringing up my saved taxon sets and model settings, but the sequence alignment is not loaded. I have tried reload the alignment after reloading the .beauti but this hangs on a series of java heap space errors. Loading the alignment first and then attempting to load the .beauti file just ends up in the alignmentless .beauti settings again.
This seems like another bug in Beauti but is just as likely another example of 'user error' on my part. Any feedback would again be appreciated!
Jim
error message:
java.lang.Exception: Cannot find species with name volans in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: Cannot find species with name volans in species tree
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:Contig139' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
