search

beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
188 stars 71 forks source link

Check parser loading warning messages #996

Closed rambaut closed 6 years ago

rambaut commented 6 years ago

A number of warning messages about parsers not loading come up. These should be fixed.

rambaut commented 6 years ago

For release parsers, we get the following:

Failed to load parser: dr.inferencexml.model.FastBUTMPParser
line = dr.inferencexml.model.FastBUTMPParser

Failed to load parser: dr.evomodelxml.branchratemodel.RandomDiscretizedBranchRatesParser
line = dr.evomodelxml.branchratemodel.RandomDiscretizedBranchRatesParser

Failed to load parser: dr.evomodel.trace.DnDsPerSiteAnalysis
line = dr.evomodel.trace.DnDsPerSiteAnalysis

Failed to load parser: dr.evomodel.trace.CnCsPerSiteAnalysis
line = dr.evomodel.trace.CnCsPerSiteAnalysis

Failed to load parser: dr.evomodel.trace.CnCsToDnDsPerSiteAnalysis
line = dr.evomodel.trace.CnCsToDnDsPerSiteAnalysis

Failed to load parser: dr.evomodelxml.continuous.hmc.BranchRateGradientParser
line = dr.evomodelxml.continuous.hmc.BranchRateGradientParser
rambaut commented 6 years ago

developer parses give the additional:

Failed to load parser: dr.evomodel.branchratemodel.TimeDependentBranchRates
line = dr.evomodel.branchratemodel.TimeDependentBranchRates

Failed to load parser: dr.evomodel.continuous.MissingInjection
line = dr.evomodel.continuous.MissingInjection

Failed to load parser: dr.evomodel.continuous.MissingInjectionLogger
line = dr.evomodel.continuous.MissingInjectionLogger
rambaut commented 6 years ago

Removing lines from the parser list where the parsers don't exist (it is possible that they exist in a different branch but will be merged back in at somepoint).

joelnitta commented 2 years ago

This seems to persist in thorney beast v0.1.1, here using the XML file from the tutorial

root@cafd6a4ba153:/wd# beast 1K_SARS-CoV-2_SG-thorney.xml

        BEAST v1.10.5 Prerelease #16d1c75, 2002-2019
       Bayesian Evolutionary Analysis Sampling Trees
                 Designed and developed by
   Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard

               Department of Computer Science
                   University of Auckland
                  alexei@cs.auckland.ac.nz

             Institute of Evolutionary Biology
                  University of Edinburgh
                     a.rambaut@ed.ac.uk

              David Geffen School of Medicine
           University of California, Los Angeles
                     msuchard@ucla.edu

                Downloads, Help & Resources:
                        http://beast.community

Source code distributed under the GNU Lesser General Public License:
                http://github.com/beast-dev/beast-mcmc

                     BEAST developers:
        Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall,
        Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
        Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
                Oliver Pybus, Chieh-Hsi Wu, Walter Xie

                         Thanks to:
        Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Using BEAGLE library v4.0.0 (PRE-RELEASE) for accelerated, parallel likelihood evaluation
2009-, BEAGLE Working Group - https://beagle-dev.github.io/
Citation: Ayres et al (2019) Systematic Biology 68: 1052-1061 | doi:10.1093/sysbio/syz020

Random number seed: 1656392462421

Failed to load parser: New parser (gmrfSkygridBlockUpdateOperator) in {interface dr.inference.operators.MCMCOperator} cannot replace existing parser (gmrfSkygridBlockUpdateOperator) in {interface dr.inference.operators.MCMCOperator}
line = dr.evomodelxml.coalescent.operators.GMRFSkygridBlockUpdateOperatorParser

Failed to load parser: dr.evomodelxml.coalescent.GMRFTestLikelihoodParser
line = dr.evomodelxml.coalescent.GMRFTestLikelihoodParser

Failed to load parser: dr.inference.trace.DnDsPerSiteAnalysis
line = dr.inference.trace.DnDsPerSiteAnalysis

Failed to load parser: dr.inference.trace.CnCsPerSiteAnalysis
line = dr.inference.trace.CnCsPerSiteAnalysis

Failed to load parser: dr.inference.trace.CnCsToDnDsPerSiteAnalysis
line = dr.inference.trace.CnCsToDnDsPerSiteAnalysis

Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

Failed to load parser: dr.evomodel.continuous.hmc.TaskPool
line = dr.evomodel.continuous.hmc.TaskPool

Failed to load parser: dr.inferencexml.operators.RepeatOperatorParser
line = dr.inferencexml.operators.RepeatOperatorParser

Parsing XML file: 1K_SARS-CoV-2_SG-thorney.xml
  File encoding: ASCII
Looking for plugins in /wd/plugins
Using node heights.

Creating the constrained tree model based on big fast tree model, 'treeModel'
  taxon count = 1000
  tree height = 0.498275193936914
The gmrfSkyrideLikelihood has time aware smoothing
Creating a GMRF smoothed skyride model for multiple loci (SkyGrid)
        Population sizes: 39
Optimization Schedule: default

Likelihood computation is using an auto sizing thread pool.

Creating the MCMC chain:
  chain length = 100000000
  operator adaption = true
  adaptation delayed for 1000000 steps

Citations for this analysis: 

FRAMEWORK
BEAST primary citation:
        Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution. vey016. DOI:10.1093/ve/vey016

TREE DENSITY MODELS
Skyride coalescent:
        Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA (2013) Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol. 30, 713-724
        Minin VN, Bloomquist EW, Suchard MA (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol. 25, 1459-1471. DOI:10.1093/molbev/msn090

# BEAST v1.10.5 Prerelease #16d1c75
# Generated Tue Jun 28 05:01:03 GMT 2022 [seed=1656392462421]
# 1K_SARS-CoV-2_SG-thorney.xml
# keywords: skygrid
state   Joint           Prior           Likelihood      age(root)       clock.rate  
0       -9366.6712      -5385.5575      -3981.1137      2019.97         7.5E-4          -
10000   -4991.1842      -2518.1066      -2473.0777      2019.95         6.96064E-4      -
20000   -4824.3229      -2602.5833      -2221.7396      2019.94         7.69432E-4      0.77 minutes/million states
30000   -4769.7949      -2609.3291      -2160.4658      2019.95         7.65565E-4      0.64 minutes/million states

Running BEAST in docker container joelnitta/thorney_beast:0.1.1 (github, docker hub)