BEAST2 BASTA error

carla

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Oct 25, 2018, 4:43:49 PM10/25/18

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Hi All,

I have followed the tutorials to set up the xml with BEAST2 and then change it to set up the BASTA analysis, however it gives me a random error (<run> should terminate with </run> which of course does).

anyone can help me?

Thanks,

Carla

attaching here the xml lines

<run id="mcmc" spec="MCMC" chainLength="10000000" numInitializationAttempts="100" storeEvery="-10">
    <state id="state" storeEvery="5000">
        <stateNode id="Tree.t:126G_output" spec="beast.evolution.tree.StructuredCoalescentMultiTypeTreeVolz">
            <migrationModelVolzVolz id="migModelInit.t:126G_output" spec="beast.evolution.tree.MigrationModelVolz">
                <parameter id="RealParameter.0" dimension="2" estimate="false" name="rateMatrix">1.0 1.0</parameter>
                <parameter id="RealParameter.1" estimate="false" name="rateMatrixScaleFactor">1.0</parameter>
                <parameter id="RealParameter.2" dimension="2" estimate="false" name="popSizes">1.0 1.0</parameter>
                <parameter id="RealParameter.3" estimate="false" name="popSizesScaleFactor">1.0</parameter>
                <typeSet id="typeSet.t:126G_output" spec="beast.evolution.tree.TypeSet" value="">
                    <typeTraitSet id="typeTraitSetInput.t:126G_output" spec="beast.evolution.tree.TraitSet" traitname="type" value="seq"

<taxa id="taxonsSet.t:126G_output" spec="TaxonSet">
                            <alignment idref="126G_output"/>
                        </taxa>
                    </typeTraitSet>
                </typeSet>
            </migrationModelVolzVolz>
            <typeTrait idref="typeTraitSetInput.t:126G_output"/>
            <typeSet idref="typeSet.t:126G_output"/>
            <trait id="dateTrait.t:126G_output" spec="beast.evolution.tree.TraitSet" taxa="@taxonsSet.t:126G_output" traitname="date" units="day" value="seq"

Alexei Drummond

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Oct 25, 2018, 4:49:53 PM10/25/18

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Dear Carla,

This is the sort of error you will get when some of the XML tags in between the pair name aren't closed properly or there are extraneous close tags present in between.

In your case it looks like there is a </operator> tag without a matching <operator> tag preceding it in the XML snippet you have posted. Is this snippet hand-coded or generated by BEAUti?

Cheers

Alexei

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Carla Mavian

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Oct 25, 2018, 4:58:25 PM10/25/18

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Hi Alexei,

I did the first xml with beauty and then hand change it to incorporate BASTA requirements. I might deleted involuntarily the <operator> one while I was changing those!

would be this one correct then?

Thanks so much for your fast reply!

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Carla Mavian

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Oct 25, 2018, 5:09:48 PM10/25/18

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I have re-run it correcting <operator> and now I have a new error and I am not sure how to proceed:

Error 130 parsing the xml input file

This BEASTInterface (migModelInit.t:126G_output) has no input with name rateMatrixScaleFactor. Choose one of these inputs: rateMatrix,popSizes,nTypes,rateMatrixFlags

Error detected about here:

<beast>

Tim Vaughan

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Oct 25, 2018, 8:19:17 PM10/25/18

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Hi Carla,

if the tutorial you're talking about is the one on the MultiTypeTree wiki, then this is probably because the tutorial there is out of date. I'm very sorry for this, the problem is that MTT has been improved/changed substantially since I wrote the MTT->BASTA tutorial, so the conversation process is quite a bit more complicated. Instead you'll have to follow the instructions on the BASTA page or perhaps contact Nicola directly for information on how to set to the analysis. I will (as I should have done already) post a note to this effect on the MTT wiki.

I hope this didn't waste to much of your time!

Tim

Carla Mavian

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Oct 25, 2018, 9:38:09 PM10/25/18

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Tim

Indeed I was using the MTT tutorial, I will follow the BASTA page instructions as you say and if I don’t succeed I will contact Nicola,

Hope to make it work :)

Thank you,

Carla

carla

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Oct 26, 2018, 10:45:58 AM10/26/18

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Dear Tim,

I have used the BASTA xml examples from the paper to create my own with my dataset, however I get this error:

Error 110 parsing the xml input file

validate and intialize error: Input 'nTypes' must be specified.

Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>

          <init id='tree' spec='StructuredCoalescentMultiTypeTreeVolz'>
              <migrationModelVolz spec='MigrationModelVolz'>

Validation error when initializing object beast.evolution.tree.MigrationModelVolz (id null):
java.lang.IllegalArgumentException: Input 'nTypes' must be specified.
    at beast.core.Input.validate(Unknown Source)
    at beast.core.BEASTInterface.validateInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseRunElement(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)

I then try to run the original xml from the paper (the ones that have BASTA in the title) and they also give me the same error using BEAST2 v2.5.0,

I have no clue on what to do. I woud really like to implement BASTA for my analysis since I have uneven sampling, and I would like to compare BASTA to the results obtained with BEAST1.

I checked the xml and nTypes is actually there, is there anywhere else where I should add nTypes?

Thanks for your help

here the xml:

</frequencies>
     </substModel>
   </siteModel>

   
   <migrationModelVolz spec='MigrationModelVolz' id='migModel'>
     <rateMatrix spec='RealParameter' value="0.00001 1.0" dimension="2" id="rateMatrix"/>
     <popSizes spec='RealParameter' value="1.0" dimension="2" id="popSizes"/>
   </migrationModelVolz>

   
   <input spec='CompoundDistribution' id='parameterPriors'>
     <distribution spec='beast.math.distributions.Prior' x="@mutationRate">
       <distr spec='LogNormalDistributionModel' M="0.0" S="4.0"/>
     </distribution>

     <distribution spec='beast.math.distributions.Prior' x="@hky.kappa">
       <distr spec='LogNormalDistributionModel' M="0.0" S="4.0"/>
     </distribution>

   

     <distribution spec='beast.math.distributions.Prior' x="@rateMatrix">
       <distr spec='Exponential'/>
     </distribution>

     <distribution spec='beast.math.distributions.Prior' x="@popSizes">
       <distr spec="LogNormalDistributionModel" M="0.0" S="4.0"/>
     </distribution>
   </input>

   


   <input spec='TreeLikelihood' id="treeLikelihood1">
     <data idref="alignment"/>
     <tree idref="tree"/>
     <siteModel idref='siteModel'/>   </input>


   

   <input spec='StructuredCoalescentTreeDensityVolz' id='treePrior'>
     <multiTypeTreeVolz idref="tree"/>
     <migrationModelVolz idref="migModel"/>
   </input>

   <run spec="MCMC" id="mcmc" chainLength="100000000" storeEvery="1000">

     

     <init spec='StructuredCoalescentMultiTypeTreeVolz' id='tree' nTypes="2">
         <migrationModelVolz spec='MigrationModelVolz'>
             <rateMatrix spec='RealParameter' value="0.00001 1.0" dimension="2"/>
             <popSizes spec='RealParameter' value="1.0" dimension="2"/>
         </migrationModelVolz>
         <trait idref='typeTraitSet'/>
         <trait idref='timeTraitSet'/>
     </init>



     <state>

       <stateNode idref="tree"/>
       
       <stateNode idref="rateMatrix"/>
       <stateNode idref="popSizes"/>
       <stateNode idref="mutationRate"/>
       <stateNode idref="hky.kappa"/>
       <stateNode idref="hky.freq"/>
     </state>

     <distribution spec='CompoundDistribution' id='posterior'>

       <distribution idref="treeLikelihood1"/>
       <distribution idref="treeLikelihood2"/>
       <distribution idref='treePrior'/>

       <distribution idref="parameterPriors"/>
     </distribution>

     

     <operator spec='ScaleOperator' id='RateScaler' scaleAll='True'
           parameter="@rateMatrix"
           scaleFactor="0.8" weight="3">
           
     </operator>

     <operator spec="ScaleOperator" id="PopSizeScaler"
           parameter="@popSizes"
          scaleFactor="0.8" weight="3"/>


     <operator spec="ScaleOperator" id="muRateScaler"
           parameter="@mutationRate"
           scaleFactor="0.8" weight="0.1"/>

     <operator spec='ScaleOperator' id='kappaScaler'
           parameter="@hky.kappa"
           scaleFactor="0.8" weight="0.1">
     </operator>

     <operator spec="DeltaExchangeOperator" id="freqExchanger"
           parameter="@hky.freq"
           delta="0.01" weight="0.1"/>



     


     <operator spec='TypedSubtreeExchangeVolz' id='STX' weight="10" multiTypeTree="@tree" migrationModel="@migModel"/>
     <operator spec="TypedWilsonBaldingVolz" id="TWB" weight="10" multiTypeTree="@tree" migrationModel="@migModel" alpha="0.2"/>
     <operator spec="MultiTypeUniformVolz" id="MTU" weight="10" multiTypeTree="@tree" includeRoot="true" rootScaleFactor="0.9"/>
     <operator spec="MultiTypeTreeScaleVolz" id="MTTS2" weight="10" multiTypeTree="@tree" scaleFactor="0.98" useOldTreeScaler="true"/>


      

     

     <logger logEvery="1000" fileName="Ebola_withBats_BASTA.log">

       <model idref='posterior'/>
       <log idref="posterior"/>
       <log spec='TreeRootTypeLoggerVolz' multiTypeTreeVolz='@tree'/>
       <log idref="rateMatrix"/>
       <log idref="popSizes"/>
       
       <log idref="mutationRate"/>
       <log idref="hky.kappa"/>
     </logger>


     <logger logEvery="10000" fileName="Ebola_withBats_BASTA.trees" mode="tree">
       <log idref="tree"/>
     </logger>

     <logger logEvery="100000">
       <model idref='posterior'/>
       <log idref="posterior"/>
       <log idref="rateMatrix"/>
       
       <log idref="popSizes"/>

       <log idref="mutationRate"/>
       <ESS spec='ESS' name='log' arg="@rateMatrix"/>

     </logger>



   </run>

</beast>

Thank you,
Carla

Tim

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Nicola de maio

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Oct 27, 2018, 11:29:43 AM10/27/18

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Hi Carla,

From what I can see, it seems that the problem is that nTypes should go in the next line, like for example:

<migrationModelVolz spec='MigrationModelVolz' nTypes="2">

Cheers,
Nicola

Thank you,
Carla

Tim

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