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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
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State 0 to 1 takes too long (stuck?) with Thorney BEAST #1139

Closed abulenciamiguel closed 2 years ago

abulenciamiguel commented 2 years ago

Hello.

I am running Thorney BEAST with 4238 taxa and 162 discrete traits. Is it normal that it takes too long (maybe it's stuck) for State 0 to proceed to State 1?

I have here the preliminary output in case you need some information.

Thank you very much.

Creating the MCMC chain:
  chain length = 10000000
  operator adaption = true
  adaptation delayed for 100000 steps
Underflow calculating likelihood. Attempting a rescaling...

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
Using BEAGLE likelihood calculation library:
    Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA (2019) BEAGLE 3: Improved performance, scaling and usability for a high-performance computing library for statistical phylogenetics. Systematic Biology. 68, 1052-1061

TREE DENSITY MODELS
Bayesian Skyline Coalescent:
    Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22, 1185-1192

SUBSTITUTION MODELS
Complex-diagonalizable, irreversible substitution model:
    Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG, Shapiro B (2011) Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology. 21, 1251-1258

PRIOR MODELS
CTMC Scale Reference Prior model:
    Ferreira MAR, Suchard MA (2008) Bayesian analysis of elapsed times in continuous-time Markov chains. Canadian Journal of Statistics. 36, 355-368

# BEAST v1.10.5 Prerelease #16d1c75
# Generated Thu Jul 21 16:57:44 CST 2022 [seed=1658393840110]
# -window -working -options
# keywords: skyline
state   Joint           Prior           Likelihood      age(root)       location.clock.rate
0   -609085.9936    -409853.7509    -199232.2427    2019.95         1.00000         -
jtmccr1 commented 2 years ago

Hello, I think this is expected. 162 discrete states is a lot and calculating that likelihood is likely taking the majority of the compute time.