Problem saving substitution trees

[Justin]

When saving trees with branch lengths in substitutions the following error comes up:

Error parsing '<logTree>' element with id, 'substTreeFileLog':

To log trees in units of substitutions a BranchRateModel must be provided

The logTree element is output from Beauti.

<logTree id="substTreeFileLog" logEvery="1000" nexusFormat="true" fileName="Tree.(subst).trees" branchLengths="substitutions">

<treeModel idref="treeModel"/>

<trait name="rate" tag="rate">

<discretizedBranchRates idref="branchRates"/>

</trait>

</logTree>

It appears that trees will be saved by modifying the element as follows:

<logTree id="substTreeFileLog" logEvery="1000" nexusFormat="true" fileName="Tree.(subst).trees" branchLengths="substitutions">

<treeModel idref="treeModel"/>

<discretizedBranchRates idref="branchRates"/>

</logTree>

Is this ok, or should something else be identified in the xml.

J

[Andrew Rambaut]

Dear Justin,

This is a case of fix one thing, break another. You are correct that the second of the two examples will work but I will file a bug report that the former should work.

Andrew

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___________________________________________________________________
 Andrew Rambaut                
 Institute of Evolutionary Biology       University of Edinburgh
 Ashworth Laboratories                         Edinburgh EH9 3JT
 EMAIL - a.ra...@ed.ac.uk                TEL - +44 131 6508624  

[BEAST007]

Dear Andrew

Is it possible to draw chronogram/evolutionary lineage tree using
housekeeping genes?? with date included.

Want some help.

Shree

On May 30, 2:37 am, Andrew Rambaut <a.ramb...@ed.ac.uk> wrote:
> Dear Justin,
>
> This is a case of fix one thing, break another. You are correct that the second of the two examples will work but I will file a bug report that the former should work.
>
> Andrew
>
> On 29 May 2012, at 18:12, Justin wrote:
>
>
>
>
>
> > When saving trees with branch lengths in substitutions the following error comes up:
>
> > Error parsing '<logTree>' element with id, 'substTreeFileLog':
> > To log trees in units of substitutions a BranchRateModel must be provided
>
> > The logTree element is output from Beauti.
>
> >            <logTree id="substTreeFileLog" logEvery="1000" nexusFormat="true" fileName="Tree.(subst).trees" branchLengths="substitutions">
> >                    <treeModel idref="treeModel"/>
> >                    <trait name="rate" tag="rate">
> >                            <discretizedBranchRates idref="branchRates"/>
> >                    </trait>
> >            </logTree>
>
> > It appears that trees will be saved by modifying the element as follows:
>
> >            <logTree id="substTreeFileLog" logEvery="1000" nexusFormat="true" fileName="Tree.(subst).trees" branchLengths="substitutions">
> >                    <treeModel idref="treeModel"/>
> >                    <discretizedBranchRates idref="branchRates"/>
> >            </logTree>
>
> > Is this ok, or should something else be identified in the xml.
>
> > J
>
> > --
> > You received this message because you are subscribed to the Google Groups "beast-users" group.

> > To view this discussion on the web visithttps://groups.google.com/d/msg/beast-users/-/fXnmPDly9o4J.

> > To post to this group, send email to beast...@googlegroups.com.
> > To unsubscribe from this group, send email to beast-users...@googlegroups.com.

> > For more options, visit this group athttp://groups.google.com/group/beast-users?hl=en.

>
> ___________________________________________________________________
>  Andrew Rambaut
>  Institute of Evolutionary Biology       University of Edinburgh
>  Ashworth Laboratories                         Edinburgh EH9 3JT

>  EMAIL - a.ramb...@ed.ac.uk                TEL - +44 131 6508624
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

[Rachel]

Hi all-
I'm getting a similar error when I use the XSEDE platform for my BEAST analysis.

Parsing error - poorly formed BEAST file, infile.xml:

Error parsing '<logTree>' element with id, 'substTreeFileLog':
To log trees in units of substitutions a BranchRateModel must be provided

so I'm speaking up in case the bug fix is still in the queue.

Rachel

[Jason Tokayer]

Regarding Justin's XML below - is there a clear difference between logging (in the treeLog) something as a trait or simply logging the element? I've seen it done both ways and I'm not sure when/why one would be preferred over the other.