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-bs.xml File: RSV2-bs.xml seed: 3908939141388915395 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. Drummond, A. J., Rambaut, A., Shapiro, B, & Pybus, O. G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular biology and evolution, 22(5), 1185-1192. 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: -50635.607091237056 Writing file /Users/yil218/WorkSpace/BEAST-Tutorial/RSV2-bs.log Writing file /Users/yil218/WorkSpace/BEAST-Tutorial/RSV2-bs.trees Sample posterior likelihood prior 0 -50635.6070 -49852.6376 -782.9694 -- 10000 -9331.8475 -8783.9402 -547.9072 -- 20000 -7266.7046 -6681.5951 -585.1094 -- 30000 -6589.1068 -5976.7952 -612.3116 -- 40000 -6238.5965 -5635.7877 -602.8087 -- 50000 -6138.2907 -5554.6277 -583.6629 -- 60000 -6117.7908 -5533.9602 -583.8305 40s/Msamples 70000 -6092.2482 -5502.4114 -589.8367 40s/Msamples 80000 -6097.3356 -5507.5367 -589.7988 41s/Msamples 90000 -6102.1275 -5509.2729 -592.8545 40s/Msamples 100000 -6087.9280 -5496.0240 -591.9040 40s/Msamples 110000 -6092.0718 -5493.1603 -598.9115 39s/Msamples 120000 -6087.1621 -5473.2634 -613.8986 39s/Msamples 130000 -6083.2269 -5471.5794 -611.6474 39s/Msamples 140000 -6074.3728 -5475.9226 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9940000 -6079.7070 -5468.1592 -611.5477 37s/Msamples 9950000 -6057.4274 -5478.1160 -579.3114 37s/Msamples 9960000 -6090.7191 -5483.5709 -607.1481 37s/Msamples 9970000 -6109.3117 -5479.6814 -629.6302 37s/Msamples 9980000 -6087.1194 -5474.5957 -612.5236 37s/Msamples 9990000 -6064.9840 -5465.4047 -599.5793 37s/Msamples 10000000 -6082.4012 -5500.3319 -582.0692 37s/Msamples Operator Tuning #accept #reject Pr(m) Pr(acc|m) AdaptableOperatorSampler(StrictClockRateScaler.c:clock) - 35462 112235 0.01479 0.24010 AdaptableOperatorSampler(strictClockUpDownOperator.c:clock) - 226 147473 0.01479 0.00153 AdaptableOperatorSampler(KappaScaler.s:RSV2_1) - 1438 3613 0.00049 0.28470 AdaptableOperatorSampler(FrequenciesExchanger.s:RSV2_1) - 1606 8049 0.00099 0.16634 beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(FixMeanMutationRatesOperator) 0.20462 55433 141825 0.01971 0.28102 AdaptableOperatorSampler(FrequenciesExchanger.s:RSV2_2) - 1784 7931 0.00099 0.18363 AdaptableOperatorSampler(KappaScaler.s:RSV2_2) - 1542 3297 0.00049 0.31866 AdaptableOperatorSampler(FrequenciesExchanger.s:RSV2_3) - 2257 7440 0.00099 0.23275 AdaptableOperatorSampler(KappaScaler.s:RSV2_3) - 1567 3409 0.00049 0.31491 EpochFlexOperator(BayesianSkylineBICEPSEpochTop.t:tree) 0.02715 48000 149397 0.01971 0.24316 EpochFlexOperator(BayesianSkylineBICEPSEpochAll.t:tree) 0.03225 40411 156496 0.01971 0.20523 TreeStretchOperator(BayesianSkylineBICEPSTreeFlex.t:tree) 0.02329 49040 147976 0.01971 0.24891 kernel.BactrianScaleOperator(BayesianSkylineTreeRootScaler.t:tree) 0.08412 44494 250981 0.02957 0.15058 kernel.BactrianNodeOperator(BayesianSkylineUniformOperator.t:tree) 2.34626 936427 2020105 0.29571 0.31673 kernel.BactrianSubtreeSlide(BayesianSkylineSubtreeSlide.t:tree) 1.69586 234478 1243995 0.14786 0.15859 Exchange(BayesianSkylineNarrow.t:tree) - 367160 1112347 0.14786 0.24816 Exchange(BayesianSkylineWide.t:tree) - 628 294654 0.02957 0.00213 WilsonBalding(BayesianSkylineWilsonBalding.t:tree) - 1497 293874 0.02957 0.00507 kernel.BactrianScaleOperator(popSizesScaler.t:tree) 0.48404 443730 1035180 0.14786 0.30004 beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(groupSizesDelta.t:tree) 17.38134 230056 362488 0.05914 0.38825 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: 377.734 seconds End likelihood: -6082.401200044847