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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Error parsing '<scaleOperator>' element with id, 'null': #1198

Open dskwei opened 3 months ago

dskwei commented 3 months ago

Using TreeDataLikelihood Branch rate model used: strictClockBranchRates Using BEAGLE DataLikelihood DelegAug 15, 2024 6:05:44 PM dr.app.beast.BeastMain SEVERE: Parsing error - poorly formed BEAST file, 123.xml: Error parsing '' element with id, 'null': Scale operator can only be used on parameters constrained to be strictly positive or negative (demographic.popSize) Error thrown at: dr.inferencexml.operators.ScaleOperatorParser.parseXMLObject(Unknown Source) ate Using BEAGLE resource 0: CPU (x86_64) with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_CPP PROCESSOR_CPU FRAMEWORK_CPU Ignoring ambiguities in tree likelihood. With 93 unique site patterns. Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow) Using TreeDataLikelihood Branch rate model used: strictClockBranchRates BEAST has terminated with an error. Please select QUIT from the menu.

dskwei commented 3 months ago

I am currently conducting an EBSP analysis with four gene partitions and have generated the configuration file (.xml). However, I encountered an error when running the configuration file, and I’m not sure where the problem lies. I would appreciate your guidance and assistance.

GuyBaele commented 3 months ago

Can you share the XML you are using? Which version of BEAST are you running? The recent beta4 version?