SEVERE: Parsing error - poorly formed BEAST file, UCE_const_PWL184.xml: Object with idref=branchRates has not been previously declared.

[hejm...@umn.edu]

Hello - 

I have been running *BEAST 1.8.4 without any issues until I changed the settings in Beauti to link the clock models. (I did this because I'm using a lot of loci and my runs weren't going to stationarity)

Once I made this change, I'm getting the following error sequence:

Is there something else I need to do if I'm linking clock models? I can email the XML file if necessary

Thanks!

Creating state frequencies model 'frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25}

Creating HKY substitution model. Initial kappa = 2.0

Creating site model.

  with initial relative rate = 1.0

  4 category discrete gamma with initial shape = 0.5

dr.xml.XMLParseException: Object with idref=branchRates has not been previously declared.

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.convert(Unknown Source)

at dr.xml.XMLParser.parse(Unknown Source)

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

BEAST has terminated with an error. Please select QUIT from the menu.

Nov 02, 2017 5:05:57 PM dr.app.beast.BeastMain <init>

SEVERE: Parsing error - poorly formed BEAST file, UCE_const_PWL184.xml:

Object with idref=branchRates has not been previously declared.

java.lang.RuntimeException: Terminate

at dr.app.beast.BeastMain.<init>(Unknown Source)

at dr.app.beast.BeastMain.main(Unknown Source)

[hejm...@umn.edu]

Update: I switched my Beauti settings to have unlinked clocks, strict clocks for all my partitions. It is working just fine.  Is there a bug in BEAST 1.8.4 that has a problem with linking the molecular clock models?

[hejm...@umn.edu]

I am still getting this error when I try to link the clock models (uncorrelated relaxed clock lognormal) - and I need to link clock models because I already have too many parameters. Does anyone know what I would need to do to the XML file to fix this? apparently someone had the same problem with 1.8.1 in 2014, but I can't tell what she did to her xml file to fix it. 

Shanta

On Friday, November 3, 2017 at 1:44:16 AM UTC-5, hejm...@umn.edu wrote:

[Steen]

Where you able to solve this ?

I am removed a single partition inside beauti, and this generated an xml file that I was able to run in v1.8.4,

Yesterday I installed v1.10.4 and I tried removing a partition, and now I get this error:

Object with idref=p3.branchRates has not been previously declared.

'p3' is the partition I have deleted inside beauti.

[Shanta Hejmadi]

I don't think I ever did solve it, but we moved on to analyzing the data a different way. Thanks

Shanta

----------------------------

Shanta Hejmadi

PhD Candidate

Ecology, Evolution, and Behavior

University of Minnesota

Office: 113 Ecology Building

Mail: 1479 Gortner Ave, St Paul, MN 55108

hejm...@umn.edu ~ twitter: @hejma002

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