BEAST v2.7.8, 2002-2025 Bayesian Evolutionary Analysis Sampling Trees Designed and developed by Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard Centre for Computational Evolution University of Auckland r.bouckaert@auckland.ac.nz 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://beast2.org/ Source code distributed under the GNU Lesser General Public License: http://github.com/CompEvol/beast2 BEAST developers: Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie Thanks to: Roald Forsberg, Beth Shapiro and Korbinian Strimmer Running file /Users/yil218/WorkSpace/BEAST-Tutorial/RSV2-long.xml File: RSV2-long.xml seed: 6211785988508059811 threads: 1 Loading package SSM v1.2.1 feast v10.5.0 flc v1.2.0 LPhyBeastExt v1.0.0 starbeast3 v1.1.9 CCD v1.0.3 Mascot v3.0.7 phylonco v1.2.0 SA v2.1.1 BEAST.base v2.7.8 BEASTLabs v2.0.3 BEAST.app v2.7.8 phylonco.lphybeast v1.2.1 BEAST_CLASSIC v1.6.4 MM v1.2.1 bdtree v0.0.1 ORC v1.2.0 lphybeast v1.2.1 Alignment(RSV2) 129 taxa 629 sites 332 patterns Filter 3::3 129 taxa 209 sites 92 patterns BE8078s92=92 NYCH09s93=93 SE01s92=92 SE05s91=91 MON1s92=92 BE1587s89=89 BE614s93=93 BE12005s94=94 BE174s95=95 BE12350s96=96 BE12216s96=96 BE11600s94=94 SE10s92=92 MAD6s92=92 BE15471s97=97 SE03s91=91 MAD2s93=93 BE10490s93=93 SE11s95=95 NYCH17s93=93 MAD6s93=93 MAD8s92=92 MAD1s93=93 BE13280s99=99 BE13192s99=99 BE1061s100=100 BE16s100=100 BE2122s100=100 BE1556s101=101 BE800s100=100 BE1441s101=101 BE11976s100=100 BE64s101=101 BE822s100=100 BE13281s99=99 BE1936s100=100 BE1835s101=101 BE1937s100=100 BE1224s101=101 BE2149s100=100 BE1343s101=101 BE1836s101=101 BE1717s101=101 BE112s101=101 BE1150s100=100 BE797s100=100 BE944s100=100 BE14536s98=98 BIR6190s89=89 MON1s90=90 WV12342s84=84 BE2584s85=85 BE933s88=88 WV5222s81=81 BE156s84=84 S2s76=76 BE11030s100=100 BE11129s100=100 BE11091s100=100 BE519s101=101 BE13425s99=99 BE004s102=102 SE12s97=97 BE14808s98=98 SE02s98=98 BE11s101=101 BE13393s99=99 BE14898s98=98 BE332s102=102 BE12028s100=100 BE14461s98=98 MON2s88=88 NYCH57s94=94 BE11465s94=94 MON1s89=89 BE15752s97=97 SE05s96=96 BE13551s95=95 BE12895s95=95 SE10s91=91 SE11s92=92 SE12s94=94 BE1591s90=90 BE512s95=95 SE01s95=95 BE4147s87=87 BE071s88=88 BE538s88=88 BE204s84=84 BE183s85=85 BE076s86=86 BE2466s85=85 BE4763s88=88 BE76s86=86 BE339s86=86 BE3252s86=86 BE410s86=86 WV23836s88=88 BE13462s99=99 BE11584s101=101 BE13412s99=99 SE12s95=95 BE12243s96=96 SE08s96=96 SE09s92=92 SE12s92=92 BE6274s91=91 MADs91=91 BE1440s92=92 BE6460s91=91 BE305s89=89 BE3785s87=87 BE307s87=87 BE119s87=87 BE138s90=90 BE191s90=90 BE369s90=90 MON9s91=91 BIR642s89=89 WV19983s87=87 MON5s91=91 MON51s90=90 MON9s92=92 NYCH34s94=94 BIR1734s89=89 WV2780s79=79 WV6973s82=82 AUSA2s61=61 USALongs56=56 AUSA2s61 = 61 (41.0) BE004s102 = 102 (0.0) BE071s88 = 88 (14.0) BE076s86 = 86 (16.0) BE10490s93 = 93 (9.0) BE1061s100 = 100 (2.0) BE11030s100 = 100 (2.0) BE11091s100 = 100 (2.0) BE11129s100 = 100 (2.0) BE112s101 = 101 (1.0) 119 more... Starting frequencies: [0.25, 0.25, 0.25, 0.25] 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 Ignoring ambiguities in tree likelihood. Ignoring character uncertainty in tree likelihood. With 92 unique site patterns. Using rescaling scheme : dynamic Filter 1::3 129 taxa 210 sites 114 patterns Starting frequencies: [0.25, 0.25, 0.25, 0.25] 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 Ignoring ambiguities in tree likelihood. Ignoring character uncertainty in tree likelihood. With 114 unique site patterns. Using rescaling scheme : dynamic Filter 2::3 129 taxa 210 sites 148 patterns Starting frequencies: [0.25, 0.25, 0.25, 0.25] 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 Ignoring ambiguities in tree likelihood. Ignoring character uncertainty in tree likelihood. With 148 unique site patterns. Using rescaling scheme : dynamic =============================================================================== Citations for this model: Bouckaert, Remco, Timothy G. Vaughan, Joￃﾫlle Barido-Sottani, Sebastiￃﾡn Duchￃﾪne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kￃﾼhnert, Nicola De Maio, Michael Matschiner, Fￃﾡbio K. Mendes, Nicola F. Mￃﾼller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology 15, no. 4 (2019): e1006650. Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174. Douglas J, Zhang R, Bouckaert R. Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model. PLoS computational biology. 2021 Feb 2;17(2):e1008322. Bouckaert RR. An efficient coalescent epoch model for Bayesian phylogenetic inference. Systematic Biology, syac015, 2022 =============================================================================== Start likelihood: -50363.44363746524 Writing file /Users/yil218/WorkSpace/BEAST-Tutorial/RSV2-long.log Writing file /Users/yil218/WorkSpace/BEAST-Tutorial/RSV2-long.trees Sample posterior likelihood prior 0 -50363.4436 -50069.9096 -293.5340 -- 10000 -8501.8948 -7943.7190 -558.1757 -- 20000 -6801.1203 -6183.1522 -617.9681 -- 30000 -6485.6567 -5883.3541 -602.3025 -- 40000 -6237.0985 -5654.3737 -582.7247 -- 50000 -6185.0874 -5588.7321 -596.3553 -- 60000 -6124.7793 -5531.0407 -593.7386 43s/Msamples 70000 -6109.0363 -5525.1110 -583.9253 45s/Msamples 80000 -6096.2373 -5502.1163 -594.1209 46s/Msamples 90000 -6093.0187 -5488.4747 -604.5440 45s/Msamples 100000 -6102.0728 -5485.7602 -616.3126 45s/Msamples 110000 -6087.4738 -5488.4340 -599.0397 44s/Msamples 120000 -6073.8489 -5475.4757 -598.3731 44s/Msamples 130000 -6073.8682 -5470.9523 -602.9158 44s/Msamples 140000 -6106.7217 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7870000 -6069.4516 -5475.0769 -594.3747 42s/Msamples 7880000 -6067.8324 -5487.0535 -580.7789 42s/Msamples 7890000 -6073.2695 -5498.8361 -574.4333 42s/Msamples 7900000 -6070.5437 -5490.8413 -579.7024 42s/Msamples 7910000 -6080.8862 -5498.1599 -582.7263 42s/Msamples 7920000 -6048.4848 -5466.9038 -581.5809 42s/Msamples 7930000 -6049.5712 -5482.4878 -567.0833 42s/Msamples 7940000 -6069.5706 -5485.8648 -583.7058 42s/Msamples 7950000 -6076.3554 -5490.8652 -585.4901 42s/Msamples 7960000 -6066.2445 -5464.0679 -602.1765 42s/Msamples 7970000 -6071.7793 -5482.2567 -589.5225 42s/Msamples 7980000 -6079.0314 -5486.0380 -592.9934 42s/Msamples 7990000 -6060.2548 -5483.5499 -576.7048 42s/Msamples 8000000 -6074.3394 -5481.7580 -592.5813 42s/Msamples Operator Tuning #accept #reject Pr(m) Pr(acc|m) AdaptableOperatorSampler(StrictClockRateScaler.c:clock) - 33470 110759 0.01797 0.23206 AdaptableOperatorSampler(strictClockUpDownOperator.c:clock) - 413 143054 0.01797 0.00288 AdaptableOperatorSampler(KappaScaler.s:RSV2_1) - 1441 3403 0.00060 0.29748 AdaptableOperatorSampler(FrequenciesExchanger.s:RSV2_1) - 1761 7946 0.00120 0.18142 beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(FixMeanMutationRatesOperator) 0.20289 54937 137197 0.02397 0.28593 AdaptableOperatorSampler(FrequenciesExchanger.s:RSV2_2) - 1733 7801 0.00120 0.18177 AdaptableOperatorSampler(KappaScaler.s:RSV2_2) - 1437 3410 0.00060 0.29647 AdaptableOperatorSampler(FrequenciesExchanger.s:RSV2_3) - 3103 6310 0.00120 0.32965 AdaptableOperatorSampler(KappaScaler.s:RSV2_3) - 1379 3509 0.00060 0.28212 EpochFlexOperator(CoalescentConstantBICEPSEpochTop.t:tree) 0.03344 37655 153722 0.02397 0.19676 EpochFlexOperator(CoalescentConstantBICEPSEpochAll.t:tree) 0.03032 40540 150662 0.02397 0.21203 TreeStretchOperator(CoalescentConstantBICEPSTreeFlex.t:tree) 0.02330 47527 144165 0.02397 0.24793 kernel.BactrianScaleOperator(CoalescentConstantTreeRootScaler.t:tree) 0.07280 58612 229095 0.03595 0.20372 kernel.BactrianNodeOperator(CoalescentConstantUniformOperator.t:tree) 2.35989 907408 1969044 0.35950 0.31546 kernel.BactrianSubtreeSlide(CoalescentConstantSubtreeSlide.t:tree) 1.72164 223625 1215666 0.17975 0.15537 Exchange(CoalescentConstantNarrow.t:tree) - 355791 1081219 0.17975 0.24759 Exchange(CoalescentConstantWide.t:tree) - 596 286821 0.03595 0.00207 WilsonBalding(CoalescentConstantWilsonBalding.t:tree) - 1457 286168 0.03595 0.00507 kernel.BactrianScaleOperator(PopSizeScaler.t:tree) 0.20732 83774 203391 0.03595 0.29173 Tuning: The value of the operator's tuning parameter, or '-' if the operator can't be optimized. #accept: The total number of times a proposal by this operator has been accepted. #reject: The total number of times a proposal by this operator has been rejected. Pr(m): The probability this operator is chosen in a step of the MCMC (i.e. the normalized weight). Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). Total calculation time: 338.915 seconds End likelihood: -6074.339401518267