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Automatically exported from code.google.com/p/beast-classic
Setting a trait value to '?' i the trait editor leads to an extra entry, but it should be interpreted as unknown.
see mail by Brad Endes 6/12/17
Here's the stack trace:
java.lang.NullPointerException
at beast.evolution.tree.coalescent.GMRFSkyrideLikelihood.getCorrectFieldLength(Unknown Source)
at beast.evolution.tree.coalescent.GMRFSkyrideLikelihood.initAndValidate(Unknown Source)
at beast.util.XMLParser.initBEASTObjects(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: null
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='prior' spec='util.CompoundDistribution'>
<distribution id='skyride' spec='beast.evolution.tree.coalescent.GMRFSkyrideLikelihood'>
PrunedAlignment attempts to assign new objects to the Input fields that were made final in a recent commit (CompEvol/beast2@7a7547b).
I am trying to run the discrete mugration model with the package following the tutorial. I did the model construction in BEAUTi word-by-word but got strange results. Actually, the results, trees & logs turned out normal, according to the tutorial. However, I caught the following in stderr
:
Warning: removing transform class beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform because it should have at least 2 dimensions but it has 0
Turning on scaling to prevent numeric instability 1.0201
…
0 NaN
1 NaN
2 NaN
3 NaN
4 NaN
java.lang.Error: randomChoiceUnnormalized falls through -- negative components in input distribution?
Please report error to Marc
You may find all files here
I see such the first time and do not understand the reason. Moreover, I have compared my XML with the example from the package GitHub repository and did not detect the difference, of course, besides new BEAST 2.7 default operators. I tried to run the example unsuccessfully; it falls with:
Error 1017 parsing the xml input file
Class could not be found. Did you mean beast.base.inference.MCMC?
Perhaps a package required for this class is not installed?
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
May this error influence the results of real analyses? How to correct my XMLs to eradicate it?
What steps will reproduce the problem?
1. Run a discrete trait analysis
What is the expected output? What do you see instead?
Expect that the log file will contain samples from the posterior for geographic
transition rates. Instead, the log file contains the rate and indicator
variables used by BSSVS, and an additional step is required to transform this
into the rate posteriors.
It's probably dangerous to expose users to the BSSVS rate and indicator
variables, as this makes it possible for users to treat the BSSVS rate variable
as the actual transition rate - which it is not.
What version of the product are you using? On what operating system?
BEAST_CLASSIC v1.1.8 on GNu/Linux.
Please provide any additional information below.
Original issue reported on code.google.com by tgvaughan
on 15 May 2015 at 12:41
When trying to run testSkyRide.xml as it is, the GMRFSkyrideBlockUpdateOperator is never accepted.
After changing its scale factor to <1 (e.g. 0.9 or 0.1) and setting initial values for the skyrideLogPopSize to 1, both skyrideLogPopSize and skyridePrecision seem to mix well.
The GMRFSkyrideBlockUpdateOperator in BEAST1 doesn't accept scale factors <1 so I wonder if there is a problem somewhere or if this is an expected difference in the BEAST2 implementation.
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