Re: problem with TreeAnnotator and java.lang.NumberFormatException

[Andrés Parada]

Further details, the version employed is Beast  2.3.2. Thanks for your help

El lunes, 4 de abril de 2016, 15:39:30 (UTC-3), Andrés Parada escribió:

I don't know if this issue was already reported or solved but I am having problems with a 7 loci dataset. 

I linked the trees in the Partition tab, the clock model is also identical for the partitions, the only difference is 7  distinct site models.

Now I checked and I got 5 trees for each STATE like, tree STATE_0 (the tree):0.0;tree STATE_0 (another tree), etc. 

Was the xml poorly formed? Is the whole analysis wrong? 

When I try to use TreeAnnotator (either on the combined trees or on a single .trees file) I get this error

java.lang.NumberFormatException: For input string: "#NEXUS"
 at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
 at java.lang.Integer.parseInt(Integer.java:569)
 at java.lang.Integer.<init>(Integer.java:867)
 at beast.app.treeannotator.TreeSetParser.parseFile(Unknown Source)
 at beast.app.treeannotator.TreeAnnotator$FastTreeSet.<init>(Unknown Source)
 at beast.app.treeannotator.TreeAnnotator.<init>(Unknown Source)
 at beast.app.treeannotator.TreeAnnotator.main(Unknown Source)
 at beast.app.treeannotator.TreeAnnotatorLauncher.main(Unknown Source)

This is the end of the xml after the data block

<map name="Uniform" >beast.math.distributions.Uniform</map>
<map name="Exponential" >beast.math.distributions.Exponential</map>
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal" >beast.math.distributions.Normal</map>
<map name="Beta" >beast.math.distributions.Beta</map>
<map name="Gamma" >beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
<map name="prior" >beast.math.distributions.Prior</map>
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
<map name="OneOnX" >beast.math.distributions.OneOnX</map>




<run id="mcmc" spec="MCMC" chainLength="30000000" preBurnin="1">
    <state id="state" storeEvery="1000">
        <tree id="Tree.t:nomok11" name="stateNode">
            <taxonset id="TaxonSet.nomok51" spec="TaxonSet">
                <alignment idref="nomok51"/>
            </taxonset>
        </tree>
        <parameter id="rateAC.s:nomok11" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateAG.s:nomok11" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateAT.s:nomok11" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateCG.s:nomok11" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateGT.s:nomok11" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="proportionInvariant.s:nomok11" lower="0.0" name="stateNode" upper="1.0">1.0E-7</parameter>
        <parameter id="gammaShape.s:nomok11" name="stateNode">1.0</parameter>
        <parameter id="kappa.s:nomok21" lower="0.0" name="stateNode">2.0</parameter>
        <parameter id="proportionInvariant.s:nomok21" lower="0.0" name="stateNode" upper="1.0">1.0E-7</parameter>
        <parameter id="gammaShape.s:nomok21" name="stateNode">1.0</parameter>
        <parameter id="rateAC.s:nomok31" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateCG.s:nomok31" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="proportionInvariant.s:nomok31" lower="0.0" name="stateNode" upper="1.0">1.0E-7</parameter>
        <parameter id="rateAT.s:nomok31" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateGT.s:nomok31" lower="0.0" name="stateNode">1.0</parameter>
        <parameter id="rateAG.s:nomok31" lower="0.0" name="stateNode"

...

[Andrés Parada]

I fixed this using Beauti & Beast 2.4 altogether.