Hi BEAST users,
I've been trying to get SNAPP to run with two modifications to the xml created by BEAUTi. The first modification is an ingroup prior (making most of my taxa monophyletic to ensure the outgroup is an outgroup). When I try to run this with one of my data sets, it fails to initialise:
Start likelihood: -Infinity after 10000 initialisation attempts
P(posterior) = -Infinity (was NaN)
P(prior) = -Infinity (was NaN)
P(lambdaPrior.even_nopoly_data) = 4.605170185988091 (was NaN)
P(snapprior.even_nopoly_data) = -909.0275559506407 (was NaN)
P(uPrior.even_nopoly_data) = 0.5276471940468044 (was NaN)
P(vPrior.even_nopoly_data) = -1.1872459785043712 (was NaN)
P(ingroup.prior) = -Infinity (was NaN)
P(ingroup.prior) = -Infinity (was NaN)
P(likelihood) = NaN (was NaN)
P(treeLikelihood.even_nopoly_data) = NaN (was NaN)
I assume this means that the ingroup is not monophyletic in the starting upgma trees?
To try to get around this, I looked at (
http://beast2.org/fix-starting-tree/) and attempted to make the adjustments to my xml file. I kept running into errors however, and the only way it seemed to work was when I removed the clock.rate parameter. This seems like an undesirable option, and I don't know how SNAPP uses that parameter. Here's what I did:
ORIGINAL XML
<run id="mcmc" spec="MCMC" chainLength="400000" numInitializationAttempts="10000" storeEvery="400">
<state id="state" storeEvery="400">
<stateNode id="Tree.even_nopoly_data" spec="beast.util.ClusterTree" clusterType="upgma" nodetype="snap.NodeData">
<taxa id="snap.even_nopoly_data" spec="snap.Data" dataType="integerdata">
<rawdata idref="even_nopoly_data"/>
<taxonset id="peed" spec="TaxonSet">
<taxon id="peed.Stew11" spec="Taxon"/>
...
</taxa>
<parameter id="RealParameter.0" lower="0.0" name="clock.rate" upper="0.0">1.0</parameter>
</stateNode>
<parameter id="u" lower="0.0" name="stateNode">0.589991473402598</parameter>
<parameter id="v" lower="0.0" name="stateNode">3.27804096929902</parameter>
<parameter id="lambda" lower="0.0" name="stateNode">0.01</parameter>
<parameter id="coalescenceRate" name="stateNode">10.0</parameter>
</state>
MODIFIED XML
<run id="mcmc" spec="MCMC" chainLength="400000" numInitializationAttempts="10000" storeEvery="400">
<state id="state" storeEvery="400">
<stateNode id="Tree.even_nopoly_data" spec="beast.util.TreeParser" IsLabelledNewick="true" adjustTipHeights="false" nodetype="snap.NodeData" newick="((((peed,(shova,(shovb,lan))),bas),(nana,(shovel,war))),con);">
<taxa id="snap.even_nopoly_data" spec="snap.Data" dataType="integerdata">
<rawdata idref="even_nopoly_data"/>
<taxonset id="peed" spec="TaxonSet">
<taxon id="peed.Stew11" spec="Taxon"/>
...
</taxa>
<parameter id="RealParameter.0" lower="0.0" name="clock.rate" upper="0.0">1.0</parameter>
</stateNode>
<parameter id="u" lower="0.0" name="stateNode">0.589991473402598</parameter>
<parameter id="v" lower="0.0" name="stateNode">3.27804096929902</parameter>
<parameter id="lambda" lower="0.0" name="stateNode">0.01</parameter>
<parameter id="coalescenceRate" name="stateNode">10.0</parameter>
</state>
PRODUCES ERROR:
Error 130 parsing the xml input file
This BEASTInterface (Tree.even_nopoly_data) has no input with name clock.rate. Choose one of these inputs: IsLabelledNewick,taxa,newick,offset,threshold,singlechild,adjustTipHeights,scale,initial,trait,taxonset,nodetype,estimate
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<state id='state'>
<stateNode id='Tree.even_nopoly_data' spec='beast.util.TreeParser'>
If I remove the clock.rate parameter line, the run starts without a problem.
Does anyone have a suggestion for properly setting the starting tree without removing the clock.rate parameter? Comments?