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BEAUti incorrectly generate the xml file after unlinking the trees

Open carlopacioni opened this issue 3 years ago • 0 comments

I have a nexus file with multiple partitions in nexus format. I have imported it, linked the substitution, clock and trees. Then in the prior tab, I have selected the EBSP prior (the idea being that so I don't have to select this prior for each of the multiple partitions I have - the data are short reads used to generate genomewide SNP, so lots of partitions!) and, returned to the first tab, I have unlinked the trees. As expected the EBSP tree prior gets populated for all partitions, but the XML is incorrectly generated (I get the error: "Fatal exception: 204"). I believe that the error stems from the fact that BEAUti progressively insert the previous treeIntervals in the EBS block (see below how treeIntervals.t:64668207 is inserted in the last block). This does not happen (and the XML runs normally) if I don't link the partitions before selecting the tree prior, but I manually select the tree prior for each partition.

` <distribution id="ExtendedBayesianSkyline.t:64668207" spec="Coalescent" treeIntervals="@treeIntervals.t:64668207"> <populationModel id="scaledDemo.t:64668207" spec="ScaledPopulationFunction" factor="@RealParameter.14"> <population id="demographic.alltrees.64668207" spec="CompoundPopulationFunction" populationIndicators="@indicators.alltrees" populationSizes="@popSizes.alltrees"> </populationModel>

        <distribution id="ExtendedBayesianSkyline.t:64669187" spec="Coalescent" treeIntervals="@treeIntervals.t:64669187">
            <populationModel id="scaledDemo.t:64669187" spec="ScaledPopulationFunction" factor="@RealParameter.14">
                <population id="demographic.alltrees.64669187" spec="CompoundPopulationFunction" populationIndicators="@indicators.alltrees" populationSizes="@popSizes.alltrees">
                    <itree idref="treeIntervals.t:64669187"/>
                </population>
            </populationModel>
        </distribution>

        <distribution id="ExtendedBayesianSkyline.t:64669554" spec="Coalescent" treeIntervals="@treeIntervals.t:64669554">
            <populationModel id="scaledDemo.t:64669554" spec="ScaledPopulationFunction" factor="@RealParameter.14">
                <population id="demographic.alltrees.64669554" spec="CompoundPopulationFunction" populationIndicators="@indicators.alltrees" populationSizes="@popSizes.alltrees">
                    <itree idref="treeIntervals.t:64669554"/>
                    <itree idref="treeIntervals.t:64668207"/>
                </population>
            </populationModel>
        </distribution>` 

carlopacioni avatar Jun 15 '21 08:06 carlopacioni