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PoonLab / vindels

Developing an empirical model of sequence insertion and deletion in virus genomes
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Skygrid tree priors fail on the cluster, not Lio #78

Closed jpalmer37 closed 5 years ago

jpalmer37 commented 5 years ago

The following error is thrown when trying to run BEAST with a Skygrid coalescent tree prior on the cluster. 

SEVERE: Parsing error - poorly formed BEAST file, QT-b.xml:
The '<dirichletPrior>' element with id, 'null', is incorrectly constructed.
The following was expected:
ATTRIBUTE Array of Double; counts REQUIRED
java.lang.RuntimeException: Terminate
    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)
dr.xml.XMLParseException: The '<dirichletPrior>' element with id, 'null', is incorrectly constructed.
The following was expected:
ATTRIBUTE Array of Double; counts REQUIRED
    at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
    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.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)

Strangely, no error messages are seen at all when I run the same files locally on my machine (Lio). The BEAST runs seem to be progressing normally. I'm currently running a few instances of both Skyride and Skygrid tree priors on my machine to see how they fare.

jpalmer37 commented 5 years ago

I found that this was being caused by my incorrect use of a newer parameterization (which utilizes the dirichletPrior element) used in BEAST v1.10 and onwards. Reversion to the original uniformPrior element allowed BEAST to run on the cluster normally.