BEAST ARG bug

[GoogleCodeExporter]

[seed=1259701539023] state  Posterior       ARG1            ARG2            ARG3  
        TotalLength     TreeHeight      taxa1       taxa2       taxa3       taxa4  
    taxa5       taxa6       taxa7       taxa8       taxa9       taxa10     0
-7,530.8032     0E0             0.769           1.565E-2        3.993           1.000  
        0.0         0.0         0.0         0.0         0.0         0.0         0.0
        0.0         0.0         0.0         - 2/12/2009 10:05:52
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: dr.evomodel.arg.operators.ARGAddRemoveEventOperator@345619
ARGEventOperator 2/12/2009 10:05:52 dr.inference.markovchain.MarkovChain
runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1590.3713,
ARGLikelihood(argTreeLikelihood)=-1356.8762,
ARGLikelihood(argTreeLikelihood)=-1706.111,
ARGLikelihood(argTreeLikelihood)=-1781.841) 2/12/2009 10:05:52
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1590.3713,
ARGLikelihood(argTreeLikelihood)=-1356.8762,
ARGLikelihood(argTreeLikelihood)=-1706.111,
ARGLikelihood(argTreeLikelihood)=-1781.841) 2/12/2009 10:05:53
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:54
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: scaleOperator(mu.prec [0.75, 1.3333333333333333] scale(mu.prec)
2/12/2009 10:05:54 dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:55
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:56
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:56
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: uniformOperator(nodeHeights) uniform(nodeHeights) 2/12/2009
10:05:57 dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:57
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:58
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:05:59
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: dr.evomodel.arg.operators.ARGSwapOperator@1d35698 bifurcationSwap
2/12/2009 10:05:59 dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:00
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:00
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:01
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: dr.evomodel.arg.operators.ARGSwapOperator@1d35698 bifurcationSwap
2/12/2009 10:06:01 dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:02
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:03
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:03
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: dr.evomodel.arg.operators.ARGSwapOperator@1ec72a6
reassortmentSwap 2/12/2009 10:06:04 dr.inference.markovchain.MarkovChain
runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:04
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:05
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:06
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: dr.evomodel.arg.operators.ARGSwapOperator@2b26f1 narrowSwap
2/12/2009 10:06:06 dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:07
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:08
dr.inference.markovchain.MarkovChain runChain SEVERE:
CompoundLikelihood(compoundModel)=(DistributionLikelihood=-8.6037,
ARGUniformPrior(argUniformPrior)=-10.0894, DistributionLikelihood=-8.7995,
DistributionLikelihood(logNormalDistributionModel)=-5.8694,
DistributionLikelihood(logNormalDistributionModel)=-7.8179,
DistributionLikelihood(logNormalDistributionModel)=2.5674,
DistributionLikelihood=-16.5725, DistributionLikelihood=-16.6837,
UniformPartitionLikelihood(partLike)=-3.2958),
CompoundLikelihood(compoundModel)=(ARGLikelihood(argTreeLikelihood)=-1682.9485,
ARGLikelihood(argTreeLikelihood)=-1362.665,
ARGLikelihood(argTreeLikelihood)=-1777.8586,
ARGLikelihood(argTreeLikelihood)=-1619.7831) 2/12/2009 10:06:08
dr.inference.markovchain.MarkovChain runChain SEVERE: State was not
correctly restored after reject step.
Likelihood before: -6510.363975547812 Likelihood after: -6518.419763260694
Operator: dr.evomodel.arg.operators.ARGSwapOperator@2b26f1 narrowSwap
2/12/2009 10:06:08 

Original issue reported on code.google.com by dong.w.xie@gmail.com on 2 Dec 2009 at 10:14

[GoogleCodeExporter]

What file was being run here? 

Original comment by ramb...@gmail.com on 3 Dec 2009 at 12:53

[GoogleCodeExporter]

/release/common/examples

Original comment by dong.w.xie@gmail.com on 3 Dec 2009 at 9:18

Attachments:

• arg-ecoli.xml

[GoogleCodeExporter]

Original comment by dong.w.xie@gmail.com on 27 Aug 2010 at 4:31

• Changed state: Fixed
• Added labels: 1.6
• Removed labels: 1.5.2