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denisekuehnert / bdmm

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
http://mbe.oxfordjournals.org/content/early/2016/05/20/molbev.msw064
GNU General Public License v3.0
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Start likelihood:-Infinity after 50 initialisation attempts #33

Open Omnipotent32 opened 3 years ago

Omnipotent32 commented 3 years ago

Hi, I'm a fresh guy in using BDMM. I want to calculate the R0 of 5 large HIV-1 clusters identified by transmission network analysis, so I set the cluster serial number as demes. All I need to analyze are 5 cluster, then I set demes to 5. After finished other settings, I ran the BEAST, the I have the next warning. Could anyone tell me how to figure out this problem? 5MOTBP7VX5MO%8ZN)U2S0ED GNDCJ~ 86M2BXN1Z$ @JMPX

Omnipotent32 commented 3 years ago

Oh the problem is done, I found I set the wrong sampling change time which not early than the height of the first sample

ntakebay commented 1 year ago

I'm having a similar problem. I'm trying to follow BDMM Beginner's Tutorial: https://github.com/denisekuehnert/bdmm/wiki/Beginner's-Tutorial with BEAST 2.6.7.

I think I followed BEAUti configuration there, but I get the same error as Omnipotent32:

P(birthDeathMigration.t:h3n2_2deme) = -Infinity (was -Infinity)

The first figure in Adjusting Priors section has "Sampling change time:" of 2.63, but the paragraph before that seems to indicate that this value should be 5.57. I tried 2.63 and 5.57, but they give the same error.

What am I doing wrong?

Thank you, Naoki

Below is some relevant part of error message.

                  BEAST v2.6.7, 2002-2022

Random number seed: 1668648561137

Alignment(h3n2_2deme) 60 taxa 1762 sites 211 patterns

CY002938_NewZealand_2004.68767123 = NewZealand (NaN) CY007011_NewZealand_2003.61917808 = NewZealand (NaN) CY007059_NewZealand_2003.50958904 = NewZealand (NaN) CY007203_NewZealand_2003.53972603 = NewZealand (NaN) CY007227_NewZealand_2003.54246575 = NewZealand (NaN) CY007267_NewZealand_2003.62739726 = NewZealand (NaN) CY007395_NewZealand_2004.63287671 = NewZealand (NaN) CY007667_NewZealand_2002.35616438 = NewZealand (NaN) CY007795_NewZealand_2005.17534247 = NewZealand (NaN) CY007923_NewZealand_2002.48219178 = NewZealand (NaN) 50 more... CY002938_NewZealand_2004.68767123 = 2004.68767123 (0.9808219199999257) CY007011_NewZealand_2003.61917808 = 2003.61917808 (2.0493150699999205) CY007059_NewZealand_2003.50958904 = 2003.50958904 (2.1589041099998667) CY007203_NewZealand_2003.53972603 = 2003.53972603 (2.128767119999793) CY007227_NewZealand_2003.54246575 = 2003.54246575 (2.1260273999998844) CY007267_NewZealand_2003.62739726 = 2003.62739726 (2.0410958899999514) CY007395_NewZealand_2004.63287671 = 2004.63287671 (1.0356164400000125) CY007667_NewZealand_2002.35616438 = 2002.35616438 (3.3123287699997945) CY007795_NewZealand_2005.17534247 = 2005.17534247 (0.4931506799998715) CY007923_NewZealand_2002.48219178 = 2002.48219178 (3.18630136999991) 50 more... Using BEAGLE version: 4.0.0 (PRE-RELEASE) resource 0: CPU (x86_64) with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

: :

=============================================================================== Start likelihood: -Infinity after 10 initialisation attempts P(posterior) = -Infinity (was -Infinity) P(prior) = -Infinity (was -Infinity) P(birthDeathMigration.t:h3n2_2deme) = -Infinity (was -Infinity) P(RPrior.t:h3n2_2deme) = -3.7046244414474376 (was -3.7046244414474376) P(becomeUninfectiousRatePrior.t:h3n2_2deme) = -1.8378770664093453 (was -1.8378770664093453) P(ClockPrior.c:h3n2_2deme) = 0.0 (was 0.0) P(FrequenciesPrior.s:h3n2_2deme) = 0.0 (was 0.0) P(GammaShapePrior.s:h3n2_2deme) = -1.0 (was -1.0) P(KappaPrior.s:h3n2_2deme) = -1.8653600339742873 (was -1.8653600339742873) P(PropInvariantPrior.s:h3n2_2deme) = 0.0 (was 0.0) P(rateMatrixPrior.t:h3n2_2deme) = -0.2 (was -0.2) P(samplingProportionPrior.t:h3n2_2deme) = 1.7763568394002497E-15 (was 1.7763568394002497E-15) P(likelihood) = NaN (was NaN) P(treeLikelihood.h3n2_2deme) = NaN (was NaN) Fatal exception: Could not find a proper state to initialise. Perhaps try another seed. See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions. java.lang.RuntimeException: Could not find a proper state to initialise. Perhaps try another seed. See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions. at beast.core.MCMC.run(Unknown Source) at beast.app.BeastMCMC.run(Unknown Source) at beast.app.beastapp.BeastMain.(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at beast.app.beastapp.BeastLauncher.run(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source) Fatal exception: Could not find a proper state to initialise. Perhaps try another seed. See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.

BEAST has terminated with an error. Please select QUIT from the menu.