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Description:
A general user list for discussion about the BEAST MCMC program.
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error in *BEAST in 1.7.2
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When using BEAUTI 1.7.2 for new *BEAST runs, I consistently get the
following error when starting the run using beast.jar:
...
Unexpected element in taxa:taxa: dr.util.Attribute$Default ####many of
these lines followed by...
Parsing error - poorly formed BEAST file, tamiasshortmtDNA_1.xml:
Error parsing '<taxa>' element with id, 'taxa':... more »
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Continuous ancestral reconstruction using BEAUTi 1.7.2?
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Hello, I am trying to use BEAUti 1.7.2 for comparative analysis - reconstructing continuous ancestral traits and looking at the correlations between them. The release notes for 1.7.2 indicate bug fixes for multivariate traits and the availibility of Pearson correlation statistics, but I'm still having... more »
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Failure to merge trees after 1000 tries - Exponential Model
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I'm getting this error message when I try to run my xml file using
exponential model.
Fatal exception: failed to merge trees after 1000 tries!
java.lang.RuntimeException: failed to merge trees after 1000 tries!
I could perfectly run the same data set using constant and BSP model,... more »
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models, clock and skyride results
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Dear all,
I have been recently using Beast, specifically the skyride analysis to
inspect demography through time of a fish population based on a mtDNA
gene. I have two main questions:
1. When I choose either TrN or HKY (I did not try with GTR, but maybe
it also holds), but without G+I parameterization, plus a strict... more »
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some questions regarding EBSP
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Dear Beast users,
I am new to extended bayesian skyline plots and I would like to ask some
questions that could be very basic but that I would like to understand. I
am running an analysis with 16 nuclear loci, and I have an estimate of
0.004 substitutions per million year for the species which I have included... more »
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Help with Beauti input file
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Dear Beast users
I have a dataset that contains sequences of different lengths.I do not want
to trim these to be the same length as all the samples are full coding
region. Is there any way to incorporate these sequences into a nexus file
so that beauti will accept this?
I get the following error: error parsing imported file:... more »
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difficulty running microsatellite analysis
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Hi, I have been encountering crashes while attempting to run a 14 locus, 280 individual dataset. Basically, after the taxa are read, and the tree models are created, the output reads as follows: ... tree height = 8.5930192959888 Using strict molecular clock model. Using strict molecular clock model.... more »
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Problem saving substitution trees
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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"... more »
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Underflow issue with Beast v1.7.2... not with v1.7.1
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Hi there...
Just wanted to mention about an underflow "issue" I have while using
Beast v1.7.2 (with Beagle CPU, precision double, scaling always) ...
90% lines on the screen are "Underflow calculating like likelihood...
attempting a rescaling"... Yet my analyses run until the end and
finally reach a very decent result...... more »
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Problem in using different calibration schemes
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Hi all
I am using 5 different calibration schemes in my analysis. Estimated
ages are slightly different from one another especially between two
particular schemes . Is there any criteria to make a choice between
these two?
Details: In scheme 1, I used fossil calibrations plus root prior and... more »
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