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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Will answer today at around 17:00 Amsterdam time 👍

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Note to self: TaxonSet.G_VII_pre2003_msa is probably a left-over from the tests. This is probably the first user that ever uses this feature (including me) 😎

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Note to self: Created repo richelbilderbeek/babette_issue_87

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Note to self: here is the bug:

<run id="mcmc" spec="MCMC" chainLength="3000" storeEvery="1000">
    <state id="state" storeEvery="5000">
        <tree id="Tree.t:cluster_10_dates" name="stateNode">
            <trait id="dateTrait.t:cluster_10_dates" spec="beast.evolution.tree.TraitSet" traitname="date-forward" value="2134-20-03-18-L-DNA-MTB-008988-S53-2017-06-22=2017,4151-13-03-18-L-DNA-MTB-008940-S13-2017-11-09=2017,4423-13-03-18-L-DNA-MTB-008950-S258-2017-10-10=2017,L-14-3447-S97-2014-07-11=2014,L-15-1237-S32-2015-06-03=2015,L-16-606-S90-2015-09-28=2015,T1-XX-2016-726-S164-2016-08-05=2016">
                <taxa id="TaxonSet.cluster_10_dates" spec="TaxonSet">
                    <alignment idref="cluster_10_dates"/>
                </taxa>
            </trait>
            <taxonset idref="TaxonSet.
        cluster_10_dates
        "/>
        </tree>
        <parameter id="clockRate.c:cluster_10_dates" name="stateNode">1.0</parameter>
        <parameter id="birthRate.t:cluster_10_dates" name="stateNode">1.0</parameter>
    </state>

Didn't immediately spot it? It's here:

            <taxonset idref="TaxonSet.
        cluster_10_dates
        "/>

That should have been one line. It appears cluster_10_dates has tabs at the start and end of it. Those should be removed 👍

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Issue is fixed, I contacted and thanked @ksw9 for her help.

Done!

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ksw9 avatar ksw9 commented on August 19, 2024

Thank you very much for the quick response! Tested and working! Best,

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richelbilderbeek avatar richelbilderbeek commented on August 19, 2024

Awesome, thanks 👍

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