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Taming-the-BEAST / FBD-tutorial

Dating Species Divergences with the Fossilized Birth-Death Process
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error "negative branch length found in tree" #8

Open kq1986 opened 1 year ago

kq1986 commented 1 year ago

Hi Louis,

I am following the FBD tutorial for practice. I used BEAST v.2.7.5 and the .xml files you provided. However, every time there is a similar error:

... 1940000 -5521.8582 -5419.0703 -102.7878 15s/Msamples 1950000 -5533.9924 -5412.6830 -121.3093 15s/Msamples 1960000 -5541.1663 -5419.5117 -121.6546 15s/Msamples 1970000 -5560.4289 -5414.4138 -146.0150 15s/Msamples 1980000 -5523.2824 -5416.1242 -107.1582 15s/Msamples 1990000 -5510.2942 -5420.2680 -90.0262 15s/Msamples 2000000 -5504.5693 -5417.7088 -86.8604 15s/Msamples 2010000 -5524.2829 -5417.8299 -106.4529 15s/Msamples 2020000 -5528.9979 -5417.2854 -111.7124 15s/Msamples 2030000 -5514.8036 -5421.9378 -92.8657 15s/Msamples 2040000 -5524.1484 -5423.1224 -101.0259 15s/Msamples 2050000 -5532.8400 -5414.0342 -118.8057 15s/Msamples 2060000 -5528.4930 -5412.6332 -115.8597 15s/Msamples java.lang.IllegalArgumentException: negative branch length found in tree at beastlabs.evolution.tree.RNNIMetric.minHeight(Unknown Source) at beastlabs.evolution.tree.RNNIMetric.distance(Unknown Source) at beastlabs.evolution.tree.RNNIMetric.distance(Unknown Source) at beast.base.evolution.operator.AdaptableOperatorSampler.computeSS(Unknown Source) at beast.base.evolution.operator.AdaptableOperatorSampler.accept(Unknown Source) at beast.base.inference.MCMC.propagateState(Unknown Source) at beast.base.inference.MCMC.doLoop(Unknown Source) at beast.base.inference.MCMC.run(Unknown Source) at beastfx.app.beast.BeastMCMC.run(Unknown Source) at beastfx.app.beast.Controller$2.run(Unknown Source)

I tried with different versions (2.7.x) and platforms (Windows, Linux), but this error still exists. Could you please help me to find out the problem?

Thanks. Qi

laduplessis commented 1 year ago

Hi Qi, There is an error arising from the default operators introduced by the ORC package being incompatible with sampled ancestors trees. We will fix the error soon.

In the meantime you can solve the issue by using an uncorrelated lognormally distributed relaxed clock model instead (as in older versions of the tutorial).

Louis

kq1986 commented 1 year ago

Hi Louis,

Thanks for your reply! I will try with the uncorrelated lognormally distributed relaxed clock model.

Thanks for your help!

Qi