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gkarthik/BEASTv1.8.4 Error

Created August 19, 2018 22:40
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BEASTv1.8.4 Error
BEAST v1.8.4, 2002-2016
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.bio.ed.ac.uk
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 v2.1.2 for accelerated, parallel likelihood evaluation
2009-2013, BEAGLE Working Group - http://beagle-lib.googlecode.com/
Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100
Random number seed: 1534717956964
Parsing XML file: 2018-08-18_Clade_CA_sampled_1.xml
File encoding: UTF8
Looking for plugins in /Users/karthik/Documents/westnile/phylogenetics/2018.08.18/plugins
Read alignment: alignment1
Sequences = 170
Sites = 10302
Datatype = nucleotide
Read alignment: alignment2
Sequences = 152
Sites = 10302
Datatype = nucleotide
Read alignment: alignment3
Sequences = 186
Sites = 10302
Datatype = nucleotide
Read alignment: alignment4
Sequences = 104
Sites = 10302
Datatype = nucleotide
Read alignment: alignment5
Sequences = 65
Sites = 10302
Datatype = nucleotide
Read alignment: alignment6
Sequences = 77
Sites = 10302
Datatype = nucleotide
Site patterns 'Clade_5_CA_sampled_1.CP1+2.patterns' created by merging 2 pattern lists
pattern count = 4
Site patterns 'Clade_5_CA_sampled_1.CP3.patterns' created from positions 3-10302 of alignment 'alignment1'
only using every 3 site
unique pattern count = 6
Site patterns 'Clade_4_CA_sampled_1.CP1+2.patterns' created by merging 2 pattern lists
pattern count = 4
Site patterns 'Clade_4_CA_sampled_1.CP3.patterns' created from positions 3-10302 of alignment 'alignment2'
only using every 3 site
unique pattern count = 4
Site patterns 'Clade_3_CA_sampled_1.CP1+2.patterns' created by merging 2 pattern lists
pattern count = 4
Site patterns 'Clade_3_CA_sampled_1.CP3.patterns' created from positions 3-10302 of alignment 'alignment3'
only using every 3 site
unique pattern count = 4
Site patterns 'Clade_2_CA_sampled_1.CP1+2.patterns' created by merging 2 pattern lists
pattern count = 4
Site patterns 'Clade_2_CA_sampled_1.CP3.patterns' created from positions 3-10302 of alignment 'alignment4'
only using every 3 site
unique pattern count = 5
Site patterns 'Clade_1_CA_sampled_1.CP1+2.patterns' created by merging 2 pattern lists
pattern count = 4
Site patterns 'Clade_1_CA_sampled_1.CP3.patterns' created from positions 3-10302 of alignment 'alignment5'
only using every 3 site
unique pattern count = 4
Site patterns 'Clade_0_CA_sampled_1.CP1+2.patterns' created by merging 2 pattern lists
pattern count = 4
Site patterns 'Clade_0_CA_sampled_1.CP3.patterns' created from positions 3-10302 of alignment 'alignment6'
only using every 3 site
unique pattern count = 4
Read attribute patterns, 'Location0.pattern' for attribute, Location
Read attribute patterns, 'Location1.pattern' for attribute, Location
Read attribute patterns, 'Location2.pattern' for attribute, Location
Read attribute patterns, 'Location3.pattern' for attribute, Location
Read attribute patterns, 'Location4.pattern' for attribute, Location
Read attribute patterns, 'Location5.pattern' for attribute, Location
Creating the tree model, 'Clade_5_CA_sampled_1.treeModel'
initial tree topology = (((((((((((((((((((W591_2017-07-06_USA_CA_SanDiego_-117.045_32.814,W768_2015-10-04_USA_CA_Sacramento_-121.393_38.588),W336_2012-07-11_USA_CA_Kern_-119.03_35.383),W710_2015-08-20_USA_CA_Yolo_-121.822_38.808),W228_2015-07-22_USA_CA_Alameda_-122.022_37.55),((W095_2017-10-05_USA_CA_SanDiego_-116.626_32.857,W719_2017-07-18_USA_CA_Sacramento_-121.383_38.425),W218_2014-07-15_USA_CA_Alameda_-121.796_37.669)),W736_2011-08-24_USA_CA_Sacramento_-121.388_38.418),(W423_2010-08-25_USA_CA_Kern_-118.815_35.158,W671_2010-07-13_USA_CA_Sacramento_-121.358_38.46)),W673_2010-07-24_USA_CA_Sacramento_-121.325_38.46),(W250_2017-08-03_USA_CA_Stanislaus_-120.824_37.517,W690_2012-08-24_USA_CA_Sacramento_-121.32_38.674)),W655_2007-08-09_USA_CA_Sacramento_-121.495_38.371),W647_2006-08-10_USA_CA_Sacramento_-121.497_38.729),W643_2006-07-26_USA_CA_Sacramento_-121.517_38.513),W811_2008-06-17_USA_CA_Sacramento_-121.51_38.485),(((((((W241_2017-07-06_USA_CA_Stanislaus_-121.166_37.573,W242_2017-07-06_USA_CA_Fresno_-120.222_36.748),W766_2015-08-12_USA_CA_Yolo_-121.745_38.564),W771_2016-06-20_USA_CA_Sacramento_-121.385_38.578),W691_2013-06-21_USA_CA_Sacramento_-121.302_38.716),(W217_2014-07-07_USA_CA_ContraCosta_-122.117_38.036,W703_2014-07-24_USA_CA_Yolo_-121.83_38.619)),W686_2012-06-21_USA_CA_Sacramento_-121.377_38.542),W332_2012-06-18_USA_CA_Kern_-119.051_35.344)),W809_2007-07-24_USA_CA_Sacramento_-121.513_38.532),((((((((((((((W230_2015-07-21_USA_CA_Lake_-122.659_38.937,W246_2017-06-29_USA_CA_Kings_-119.894_36.344),(W760_2014-09-11_USA_CA_Sacramento_-121.29_38.64,W767_2015-09-24_USA_CA_Sacramento_-121.224_38.546)),(W588_2016-04-28_USA_CA_SanDiego_-117.054_32.965,W702_2014-07-24_USA_CA_Sacramento_-121.198_38.448)),W776_2017-05-23_USA_CA_Sacramento_-121.369_38.55),W747_2012-07-02_USA_CA_Sacramento_-121.394_38.605),((W161_2017-06-17_USA_CA_Riverside_-117.542_33.947,W718_2016-08-09_USA_CA_Sacramento_-121.214_38.423),W720_2017-08-01_USA_CA_Sacramento_-121.354_38.51)),((W171_2017-08-03_USA_CA_ContraCosta_-121.98_37.797,W593_2017-08-15_USA_CA_SanDiego_-117.001_33.094),W240_2016-07-07_USA_CA_Kings_-119.696_36.294)),(W198_2012-08-10_USA_CA_Fresno_-119.534_36.667,W315_2010-07-22_USA_CA_Kern_-119.152_35.367)),(((((W231_2016-07-05_USA_CA_Sutter_-121.676_39.093,W236_2016-07-01_USA_CA_Fresno_-119.895_36.839),W220_2014-07-10_USA_CA_Fresno_-119.592_36.503),W340_2013-07-08_USA_CA_Kern_-119.041_35.275),(KR348980_2011-01-09_USA_CA_Kern_-118.9416_35.1364,KR348983_2011-01-09_USA_CA_Kern_-119.2539_35.5022)),(W446_2012-06-19_USA_CA_Kern_-119.021_35.36,W677_2011-07-22_USA_CA_Sacramento_-121.224_38.385))),((KR348984_2011-01-09_USA_CA_Kern_-119.3503_35.5936,W731_2010-09-12_USA_CA_Sacramento_-121.449_38.584),KR348966_2011-10-28_USA_CA_LosAngeles_-118.6183_34.4534)),(W316_2010-07-22_USA_CA_Kern_-119.089_35.33,W674_2010-09-28_USA_CA_Yolo_-121.685_38.54)),W437_2011-08-04_USA_CA_Kern_-118.825_35.166),((((W670_2010-07-09_USA_CA_Sacramento_-121.358_38.46,W681_2011-08-31_USA_CA_Sacramento_-121.44_38.651),W189_2010-08-12_USA_CA_Kings_-119.727_36.226),(KR348982_2011-01-09_USA_CA_Kern_-119.2539_35.5022,W708_2015-07-31_USA_CA_Yolo_-121.976_38.896)),W645_2006-07-26_USA_CA_Yolo_-121.781_38.69)),((((((((((W146_2012-06-21_USA_CA_Tulare_-119.29_36.315,W759_2014-09-07_USA_CA_Sacramento_-121.255_38.649),W740_2011-09-06_USA_CA_Sacramento_-121.426_38.42),(W455_2012-07-19_USA_CA_Kern_-119.111_35.38,W774_2016-07-10_USA_CA_Sacramento_-121.347_38.553)),W713_2016-06-28_USA_CA_Sacramento_-121.375_38.397),W328_2012-06-08_USA_CA_Kern_-119.046_35.356),W142_2011-09-21_USA_CA_Placer_-121.229_38.737),(((W105_2015-10-02_USA_CA_SanDiego_-116.867_33.075,W769_2016-05-19_USA_CA_Sacramento_-121.363_38.564),W098_2017-08-28_USA_CA_SanDiego_-116.876_32.801),(W335_2012-07-10_USA_CA_Kern_-119.03_35.428,W739_2011-09-02_USA_CA_Sacramento_-121.328_38.431))),((W239_2016-07-07_USA_CA_Kings_-119.727_36.226,W775_2016-07-28_USA_CA_Yolo_-121.771_38.669),(W323_2011-08-05_USA_CA_Kern_-119.095_35.412,W432_2011-07-13_USA_CA_Kern_-119.164_35.346))),W199_2012-08-14_USA_CA_Fresno_-120.59_36.953),(((W160_2013-08-26_USA_CA_Shasta_-122.406_40.552,W229_2015-07-15_USA_CA_Butte_-121.884_39.743),W192_2012-09-04_USA_CA_Kings_-119.794_36.319),W429_2011-07-08_USA_CA_Kern_-119.254_35.502)))),((((((((W188_2010-08-12_USA_CA_Fresno_-119.531_36.653,W324_2011-08-08_USA_CA_Kern_-119.068_35.351),(W226_2015-07-14_USA_CA_Fresno_-120.445_36.847,W717_2016-08-05_USA_CA_Yolo_-121.712_38.61)),W823_2009-10-02_USA_CA_Yolo_-121.798_38.659),W642_2006-07-21_USA_CA_Yolo_-121.781_38.69),W438_2011-08-04_USA_CA_Kern_-118.815_35.158),(((W594_2017-08-24_USA_CA_SanDiego_-117.084_33.03,W716_2016-07-29_USA_CA_Sacramento_-121.621_38.698),W193_2012-08-27_USA_CA_Yuba_-121.589_39.19),KR348918_2011-03-10_USA_CA_ContraCosta_-122.0372_38.0092)),(((W149_2012-07-22_USA_CA_Tulare_-119.329_36.333,W319_2010-07-26_USA_CA_Kern_-119.157_35.366),(W741_2012-05-28_USA_CA_Sacramento_-121.374_38.429,W814_2008-07-08_USA_CA_Sacramento_-121.508_38.504)),W644_2006-07-26_USA_CA_Yolo_-121.882_38.797)),(((((W224_2015-06-15_USA_CA_ContraCosta_-121.702_37.997,W721_2017-08-03_USA_CA_Sacramento_-121.444_38.334),W701_2014-07-10_USA_CA_Sacramento_-121.219_38.385),(W140_2011-07-11_USA_CA_SanJoaquin_-121.302_37.971,W454_2012-07-19_USA_CA_Kern_-119.078_35.353)),(W139_2010-08-02_USA_CA_Fresno_-119.756_36.858,W817_2009-07-29_USA_CA_Sacramento_-121.502_38.464)),((W733_2010-09-22_USA_CA_Sacramento_-121.478_38.575,W822_2009-10-02_USA_CA_Sacramento_-121.383_38.407),W819_2009-08-20_USA_CA_Yolo_-121.793_38.55)))),W405_2009-07-15_USA_CA_Kern_-118.825_35.166),((((((((((((W094_2016-08-18_USA_CA_SanDiego_-117.168_32.697,W726_2017-09-12_USA_CA_Yolo_-121.55_38.543),W013_2016-06-30_USA_CA_SanDiego_-117.053_33.015),(W343_2017-07-07_USA_CA_Kern_-119.091_35.351,W714_2016-07-12_USA_CA_Yolo_-121.751_38.571)),W453_2012-07-18_USA_CA_Kern_-118.932_35.283),W424_2010-09-02_USA_CA_Kern_-119.272_35.493),((((W093_2016-08-11_USA_CA_SanDiego_-117.164_32.811,W711_2015-09-09_USA_CA_Sacramento_-121.293_38.444),W758_2014-09-04_USA_CA_Sacramento_-121.291_38.701),W748_2013-05-31_USA_CA_Sacramento_-121.263_38.394),W745_2012-06-23_USA_CA_Sacramento_-121.26_38.384)),(KR348920_2009-03-08_USA_CA_ContraCosta_-121.797_38.0108,W676_2010-10-13_USA_CA_Sacramento_-121.425_38.441)),(((((((W172_2017-08-30_USA_CA_Butte_-122.001_39.859,W724_2017-09-06_USA_CA_Sacramento_-121.414_38.361),(W245_2017-06-30_USA_CA_Kings_-119.839_36.388,W778_2017-06-29_USA_CA_Sacramento_-121.39_38.609)),W779_2017-07-05_USA_CA_Sacramento_-121.4_38.567),W225_2015-07-21_USA_CA_Tulare_-119.266_35.884),W334_2012-07-09_USA_CA_Kern_-119.031_35.386),(((W215_2014-07-03_USA_CA_Stanislaus_-120.852_37.498,W723_2017-08-22_USA_CA_Sacramento_-121.395_38.489),W435_2011-07-15_USA_CA_Kern_-119.1_35.346),((W706_2015-07-16_USA_CA_Yolo_-121.83_38.619,W773_2016-06-30_USA_CA_Sacramento_-121.366_38.543),W678_2011-08-09_USA_CA_Sacramento_-121.169_38.393))),(((W223_2015-06-15_USA_CA_Yuba_-121.534_39.214,W709_2015-08-06_USA_CA_Yolo_-121.969_38.885),W761_2014-09-26_USA_CA_Yolo_-121.748_38.696),W185_2009-07-28_USA_CA_Kings_-119.673_36.423))),(((((W100_2017-10-05_USA_CA_SanDiego_-117.098_32.737,W590_2017-06-09_USA_CA_SanDiego_-117.216_33.235),W214_2014-06-24_USA_CA_Madera_-120.118_37.026),W337_2012-07-31_USA_CA_Kern_-118.984_35.406),(((W234_2016-07-05_USA_CA_Yuba_-121.534_39.214,W777_2017-06-07_USA_CA_Sacramento_-121.37_38.553),(W243_2017-07-06_USA_CA_Fresno_-120.628_36.951,W781_2017-09-08_USA_CA_Sacramento_-121.403_38.306)),(W722_2017-08-08_USA_CA_Yolo_-121.689_38.551,W780_2017-08-03_USA_CA_Sacramento_-121.275_38.594))),W303_2008-09-24_USA_CA_Kern_-119.123_35.404)),W249_2017-08-02_USA_CA_Merced_-120.625_37.363),((((W154_2013-08-07_USA_CA_Butte_-121.596_39.775,W450_2012-07-02_USA_CA_Kern_-119.021_35.36),W425_2010-09-30_USA_CA_Kern_-119.265_35.507),(W331_2012-06-13_USA_CA_Kern_-119.025_35.362,W725_2017-09-12_USA_CA_Yolo_-121.55_38.543)),W128_2008-08-12_USA_CA_Calaveras_-120.712_38.235)),(((((W322_2011-06-17_USA_CA_Kern_-118.938_35.378,W751_2013-07-24_USA_CA_Sacramento_-121.207_38.688),W732_2010-09-17_USA_CA_Sacramento_-121.379_38.419),W665_2009-08-13_USA_CA_Sacramento_-121.44_38.394),((W431_2011-07-13_USA_CA_Kern_-119.164_35.346,W675_2010-10-05_USA_CA_Sacramento_-121.354_38.51),W682_2011-09-08_USA_CA_Sacramento_-121.219_38.385)),KR348915_2011-08-29_USA_CA_ContraCosta_-121.5822_37.975)))
tree height = 172.13337034337454
Creating the tree model, 'Clade_4_CA_sampled_1.treeModel'
initial tree topology = (((((((((((((((W152_2013-08-02_USA_CA_Placer_-121.18_38.808,W715_2016-07-26_USA_CA_Sacramento_-121.354_38.51),W211_2014-06-17_USA_CA_Stanislaus_-120.826_37.511),W683_2011-09-23_USA_CA_Sacramento_-121.332_38.626),W658_2008-07-25_USA_CA_Sacramento_-121.341_38.465),KR348916_2008-08-18_USA_CA_ContraCosta_-121.679_37.9986),W657_2008-07-24_USA_CA_Sacramento_-121.53_38.707),((W007_2013-07-23_USA_CA_SanDiego_-117.247_33.081,W705_2015-07-07_USA_CA_Sacramento_-121.481_38.418),KR349021_2011-01-09_USA_CA_Sacramento_-121.4389_38.4318)),KR349013_2007-09-25_USA_CA_Sacramento_-121.219_38.3849),((((W055_2013-08-01_USA_CA_SanDiego_-116.958_32.792,W233_2016-06-29_USA_CA_Fresno_-119.895_36.839),W656_2008-07-08_USA_CA_Sacramento_-121.381_38.444),W812_2008-07-06_USA_CA_Sacramento_-121.362_38.72),(((W170_2017-07-31_USA_CA_Butte_-121.586_39.505,W770_2016-06-15_USA_CA_Sacramento_-121.324_38.644),W494_2017-06-28_USA_CA_Kern_-119.478_35.501),W150_2012-07-20_USA_CA_LosAngeles_-118.402_34.061))),W684_2012-06-07_USA_CA_Sacramento_-121.261_38.487),((W679_2011-08-18_USA_CA_Sacramento_-121.421_38.455,W730_2010-08-02_USA_CA_Sacramento_-121.336_38.631),KR348998_2008-06-27_USA_CA_Sacramento_-121.499_38.5035)),((((((W470_2014-07-18_USA_CA_Kern_-119.143_35.411,W756_2014-07-10_USA_CA_Sacramento_-121.329_38.431),KR349002_2011-01-09_USA_CA_Sacramento_-121.3575_38.4598),W672_2010-07-20_USA_CA_Yolo_-121.856_38.548),W138_2010-07-30_USA_CA_Stanislaus_-120.952_37.585),((((W712_2016-06-14_USA_CA_Sacramento_-121.241_38.675,W782_2017-09-17_USA_CA_Yolo_-121.79_38.557),W772_2016-06-22_USA_CA_Sacramento_-121.218_38.653),W757_2014-08-12_USA_CA_Sacramento_-121.293_38.438),((W059_2013-11-07_USA_CA_SanDiego_-116.998_32.84,W753_2013-08-19_USA_CA_Yolo_-121.702_38.547),W687_2012-07-03_USA_CA_Yolo_-121.583_38.445))),W630_2004-08-06_USA_CA_Sacramento_-121.247_38.388)),((((((W151_2012-08-08_USA_CA_Merced_-120.6_37.302,W651_2007-07-28_USA_CA_Sacramento_-121.447_38.661),W653_2007-07-31_USA_CA_Yolo_-121.882_38.797),W641_2005-09-09_USA_CA_Yolo_-121.73_38.556),((W654_2007-08-01_USA_CA_Sacramento_-121.36_38.606,W798_2006-09-14_USA_CA_Yolo_-121.956_38.73),W369_2006-07-11_USA_CA_Kern_-119.129_35.32)),W342_2017-07-04_USA_CA_Kern_-119.097_35.389),(((((W157_2013-08-12_USA_CA_Shasta_-122.277_40.468,W763_2015-07-12_USA_CA_Yolo_-121.797_38.544),W704_2014-07-31_USA_CA_Sacramento_-121.321_38.568),W755_2014-06-15_USA_CA_Sacramento_-121.354_38.592),(W006_2013-07-10_USA_CA_SanDiego_-116.946_32.885,W321_2011-06-17_USA_CA_Kern_-118.938_35.378)),W130_2008-08-18_USA_CA_ContraCosta_-121.814_38.015))),(((((((((((((W232_2016-07-05_USA_CA_Sutter_-121.503_38.824,W746_2012-06-28_USA_CA_Sacramento_-121.377_38.436),W159_2013-08-25_USA_CA_Merced_-120.636_37.338),((W692_2013-07-16_USA_CA_Sacramento_-121.279_38.417,W765_2015-08-06_USA_CA_Sacramento_-121.369_38.442),W204_2013-09-11_USA_CA_Lake_-122.938_39.077)),((W096_2017-10-16_USA_CA_SanDiego_-116.692_33.214,W493_2017-06-28_USA_CA_Kern_-119.009_35.377),KR349005_2011-01-09_USA_CA_Sacramento_-121.3948_38.4601)),(W689_2012-07-31_USA_CA_Sacramento_-121.325_38.431,W743_2012-06-13_USA_CA_Sacramento_-121.377_38.407)),KR349000_2008-07-25_USA_CA_Sacramento_-121.587_38.2861),W693_2013-07-16_USA_CA_Yolo_-121.877_38.795),(W631_2004-08-11_USA_CA_Sacramento_-121.5_38.44,W792_2005-08-03_USA_CA_Yolo_-121.714_38.539)),(((W124_2007-06-21_USA_CA_Butte_-121.66_39.362,W649_2007-07-06_USA_CA_Sacramento_-121.198_38.448),W800_2006-07-11_USA_CA_Sacramento_-121.373_38.705),W707_2015-07-28_USA_CA_Yolo_-121.764_38.664)),((W144_2012-06-12_USA_CA_Stanislaus_-120.981_37.674,W695_2013-07-23_USA_CA_Yolo_-121.868_38.681),W268_2005-08-15_USA_CA_Kern_-118.931_35.398)),(((((((((W206_2013-08-28_USA_CA_Kern_-119.276_35.093,W207_2013-08-26_USA_CA_Sutter_-121.641_39.16),W244_2017-07-04_USA_CA_Tulare_-119.297_35.971),W699_2014-07-01_USA_CA_Sacramento_-121.384_38.478),KR349006_2011-01-09_USA_CA_Sacramento_-121.4389_38.4318),W694_2013-07-19_USA_CA_Sacramento_-121.412_38.276),((W202_2013-08-14_USA_CA_Butte_-121.642_39.65,W752_2013-07-30_USA_CA_Sacramento_-121.495_38.561),W205_2013-08-28_USA_CA_Kern_-119.276_35.093)),W803_2007-07-13_USA_CA_Sacramento_-121.197_38.442),KR348917_2008-08-18_USA_CA_ContraCosta_-121.797_38.0108),W660_2008-08-13_USA_CA_Sacramento_-121.452_38.562)),(((W299_2008-06-27_USA_CA_Kern_-119.051_35.344,W728_2010-07-09_USA_CA_Sacramento_-121.341_38.702),KJ501341_2005-08-01_USA_CA_Glenn_-122.3915_39.599),(W661_2008-08-19_USA_CA_Sacramento_-121.373_38.714,W735_2011-08-20_USA_CA_Sacramento_-121.326_38.426))),((((((W462_2013-08-21_USA_CA_Kern_-119.478_35.501,W762_2015-06-11_USA_CA_Yolo_-121.769_38.563),W481_2015-08-28_USA_CA_Kern_-119.196_35.53),W680_2011-08-25_USA_CA_Sacramento_-121.499_38.427),W136_2010-07-21_USA_CA_Stanislaus_-120.948_37.547),(((KR349018_2007-07-26_USA_CA_Shasta_-122.3479_40.4815,W801_2006-07-04_USA_CA_Sacramento_-121.406_38.718),W122_2006-08-14_USA_CA_Butte_-121.53_39.642),((W729_2010-07-09_USA_CA_Sacramento_-121.358_38.535,W807_2007-07-24_USA_CA_Sacramento_-121.258_38.652),W738_2011-08-29_USA_CA_Sacramento_-121.498_38.571))),(W802_2007-07-09_USA_CA_Yolo_-121.703_38.56,W815_2008-09-08_USA_CA_Sacramento_-121.302_38.607)))),(((((((((((((W087_2015-08-28_USA_CA_SanDiego_-117.254_32.961,W222_2015-06-09_USA_CA_Fresno_-119.842_36.409),(W698_2014-06-24_USA_CA_Sacramento_-121.425_38.441,W700_2014-07-03_USA_CA_Sacramento_-121.421_38.455)),W697_2013-08-23_USA_CA_Sacramento_-121.22_38.288),W727_2010-07-02_USA_CA_Sacramento_-121.313_38.43),W137_2010-07-29_USA_CA_Placer_-121.357_38.731),W126_2007-06-24_USA_CA_Fresno_-119.763_36.821),W650_2007-07-13_USA_CA_Sacramento_-121.208_38.423),(((W213_2014-06-23_USA_CA_Yuba_-121.564_39.165,W737_2011-08-23_USA_CA_Sacramento_-121.292_38.284),W135_2009-09-04_USA_CA_Stanislaus_-120.852_37.51),W799_2006-06-21_USA_CA_Sacramento_-121.45_38.723)),W125_2007-06-24_USA_CA_Stanislaus_-120.979_37.641),(((((W131_2008-08-21_USA_CA_Stanislaus_-120.861_37.537,W742_2012-06-07_USA_CA_Sacramento_-121.32_38.459),W153_2013-08-08_USA_CA_Shasta_-122.316_40.57),W662_2008-08-20_USA_CA_Sacramento_-121.354_38.51),(KR349001_2011-01-09_USA_CA_Sacramento_-121.3665_38.4491,W685_2012-06-14_USA_CA_Sacramento_-121.325_38.46)),W791_2005-08-01_USA_CA_Sacramento_-121.496_38.37)),(((KR349015_2004-11-08_USA_CA_Sacramento_-121.4998_38.4432,W637_2005-07-30_USA_CA_Sacramento_-121.175_38.455),KR348994_2005-08-24_USA_CA_Sacramento_-121.3948_38.4891),(KR349003_2011-01-09_USA_CA_Sacramento_-121.4528_38.4672,KR349026_2011-09-13_USA_CA_Sutter_-121.7567_39.1172))),((((((((W212_2014-06-20_USA_CA_Fresno_-119.79_36.866,W486_2016-07-28_USA_CA_Kern_-119.213_35.598),W749_2013-07-02_USA_CA_Sacramento_-121.51_38.501),(W734_2011-08-18_USA_CA_Sacramento_-121.375_38.42,W754_2013-09-18_USA_CA_Sacramento_-121.36_38.606)),(W057_2013-09-09_USA_CA_SanDiego_-116.998_32.84,W478_2015-07-28_USA_CA_Kern_-118.825_35.166)),((KR349004_2011-01-09_USA_CA_Sacramento_-121.4528_38.4672,W744_2012-06-15_USA_CA_Sacramento_-121.357_38.544),KR349025_2007-07-25_USA_CA_Shasta_-122.3158_40.5033)),((W166_2017-07-03_USA_CA_Riverside_-117.469_33.756,W169_2017-07-26_USA_CA_ContraCosta_-122.024_37.921),(W235_2016-07-01_USA_CA_Fresno_-119.891_36.839,W750_2013-07-16_USA_CA_Yolo_-121.769_38.674))),W784_2004-08-30_USA_CA_Sacramento_-121.299_38.577),(((W201_2013-08-21_USA_CA_Lake_-122.875_38.993,W696_2013-08-16_USA_CA_Yolo_-121.882_38.797),W688_2012-07-12_USA_CA_Sacramento_-121.38_38.466),(W071_2014-11-10_USA_CA_SanDiego_-117.244_32.932,W148_2012-07-17_USA_CA_Merced_-120.591_37.347)))),((KR349020_2011-02-09_USA_CA_Shasta_-122.239_40.4162,W485_2016-07-26_USA_CA_Kern_-119.406_35.428),KR349017_2007-07-25_USA_CA_Shasta_-122.3158_40.5034)))
tree height = 392.3375022796296
Creating the tree model, 'Clade_3_CA_sampled_1.treeModel'
initial tree topology = ((((((((((((((((((((W544_2014-11-13_USA_CA_SanDiego_-116.813_33.011,W592_2017-08-04_USA_CA_SanDiego_-116.936_32.552),W158_2013-08-20_USA_CA_Butte_-121.841_39.732),W005_2012-10-29_USA_CA_SanDiego_-117.258_32.828),KR348964_2011-10-25_USA_CA_LosAngeles_-118.6339_34.1633),(((W097_2017-10-19_USA_CA_SanDiego_-117.125_32.575,W162_2017-06-23_USA_CA_Lake_-122.618_38.95),W168_2017-07-13_USA_CA_LosAngeles_-118.847_34.205),KR348954_2010-11-08_USA_CA_LosAngeles_-118.475_34.4)),(W147_2012-07-17_USA_CA_LosAngeles_-118.513_34.249,W195_2012-08-23_USA_CA_Riverside_-116.061_33.462)),KR348969_2011-06-24_USA_CA_LosAngeles_-118.148_33.9533),W042_2009-01-20_USA_CA_SanDiego_-117.042_33.005),W051_2009-09-30_USA_CA_SanDiego_-117.072_33.26),((((((W155_2013-08-08_USA_CA_LosAngeles_-118.391_33.859,W221_2015-05-14_USA_CA_LosAngeles_-118.197_33.945),KR348960_2011-02-09_USA_CA_LosAngeles_-118.4925_34.1856),W034_2008-08-07_USA_CA_SanDiego_-117.07_33.091),W522_2009-09-26_USA_CA_SanDiego_-117.053_32.751),W506_2008-06-02_USA_CA_SanDiego_-117.229_32.953),W002_2007-10-02_USA_CA_SanDiego_-116.95_32.786)),W508_2008-06-18_USA_CA_SanDiego_-117.236_32.792),KR348952_2007-10-18_USA_CA_LosAngeles_-118.4944_34.19),(((((((W542_2014-10-02_USA_CA_SanDiego_-117.2_32.763,W586_2016-03-16_USA_CA_SanDiego_-117.054_33.147),W058_2013-11-01_USA_CA_SanDiego_-117.149_32.736),W196_2012-08-07_USA_CA_LosAngeles_-118.039_33.937),W209_2013-08-22_USA_CA_LosAngeles_-118.494_34.19),KR348973_2011-06-07_USA_CA_LosAngeles_-118.0339_33.8686),((W048_2008-12-22_USA_CA_SanDiego_-116.924_32.78,W049_2009-06-18_USA_CA_SanDiego_-116.983_33.256),W511_2008-08-06_USA_CA_SanDiego_-117.167_32.773)),W017_2007-03-19_USA_CA_SanDiego_-117.072_32.757)),DQ080056_2003-08-01_USA_CA_Imperial_-114.9009_32.9392),GQ507475_2005-06-27_USA_CA_SanBernardino_-117.0172_34.036),((((((KR348970_2008-07-22_USA_CA_LosAngeles_-117.8633_33.98,W032_2008-06-25_USA_CA_SanDiego_-117.251_32.763),W529_2008-12-22_USA_CA_SanDiego_-116.924_32.78),W515_2008-09-10_USA_CA_SanDiego_-117.242_32.897),((GQ507477_2005-08-01_USA_CA_LosAngeles_-118.1468_33.8491,KR348956_2010-12-08_USA_CA_LosAngeles_-118.4925_34.1856),(KR349023_2004-08-13_USA_CA_Yolo_-121.9761_38.6428,W177_2005-06-13_USA_CA_LosAngeles_-118.098_33.842))),(((JF703161_2004-07-02_USA_CA_Imperial_-114.9633_32.7475,W786_2004-08-26_USA_CA_Sacramento_-121.312_38.459),KR348939_2005-06-19_USA_CA_Riverside_-116.0615_33.5691),JF703162_2003-07-15_USA_CA_Imperial_-114.9633_32.7475)),KR348949_2004-08-24_USA_CA_Riverside_-116.372_33.7025)),((((((((((KR348936_2008-09-25_USA_CA_Riverside_-116.4984_33.8055,W509_2008-06-18_USA_CA_SanDiego_-117.236_32.792),KR348950_2008-05-22_USA_CA_LosAngeles_-118.0964_33.9497),(W513_2008-08-25_USA_CA_SanDiego_-117.228_32.796,W519_2008-09-24_USA_CA_SanDiego_-117.06_33.028)),KR348968_2008-07-22_USA_CA_LosAngeles_-117.8125_34.005),KR348951_2004-05-17_USA_CA_LosAngeles_-118.0186_33.8989),(((W072_2014-11-17_USA_CA_SanDiego_-117.084_33.029,W197_2012-08-29_USA_CA_LosAngeles_-118.469_34.189),W505_2008-05-22_USA_CA_SanDiego_-117.101_32.827),(KR348947_2007-09-18_USA_CA_LosAngeles_-118.493_34.1856,W026_2008-05-14_USA_CA_SanDiego_-117.158_32.901))),((((((W028_2008-06-11_USA_CA_SanDiego_-117.241_32.958,W516_2008-09-12_USA_CA_SanDiego_-117.198_32.788),W031_2008-09-15_USA_CA_SanDiego_-117.14_32.958),KR349008_2005-07-15_USA_CA_Yolo_-121.7308_38.5717),KR349010_2005-07-26_USA_CA_Sacramento_-121.5053_38.3428),(((W036_2008-09-18_USA_CA_SanDiego_-116.886_33.03,W046_2009-04-08_USA_CA_SanDiego_-116.958_32.754),W018_2007-03-19_USA_CA_SanDiego_-117.335_33.239),(DQ431700_2004-08-01_USA_CA_SanFransisco_-122.4615_37.7817,KR348943_2004-04-14_USA_CA_Riverside_-115.9255_33.5112))),(W255_2004-08-23_USA_CA_Kern_-119.123_35.406,W364_2005-07-07_USA_CA_Kern_-119.265_35.507))),((KR349024_2003-08-19_USA_CA_Imperial_-115.5786_33.2819,W114_2004-05-28_USA_CA_SanBernardino_-117.322_34.111),KR348923_2003-08-19_USA_CA_Imperial_-115.5786_33.2819)),W116_2004-07-23_USA_CA_Butte_-121.569_39.526),((((((KJ501342_2005-09-15_USA_CA_SanDiego_-116.732_33.0358,W254_2004-08-17_USA_CA_Kern_-119.053_35.389),(KR348924_2003-08-19_USA_CA_Imperial_-115.6144_33.1781,W253_2004-08-11_USA_CA_Kern_-119.121_35.385)),((W129_2008-08-15_USA_CA_LosAngeles_-117.769_34.107,W517_2008-09-19_USA_CA_SanDiego_-117.228_32.796),W044_2008-12-01_USA_CA_SanDiego_-117.227_33.33)),KR348945_2004-04-28_USA_CA_Riverside_-115.9393_33.5211),((((W512_2008-08-11_USA_CA_SanDiego_-117.223_32.948,W521_2008-09-25_USA_CA_SanDiego_-117.226_32.861),KR348957_2010-12-08_USA_CA_LosAngeles_-118.5681_34.1931),(W004_2009-05-13_USA_CA_SanDiego_-117.243_32.904,W530_2009-01-16_USA_CA_SanDiego_-117.23_32.906)),KR348927_2003-09-16_USA_CA_Imperial_-115.5786_33.2819)),(((W003_2008-08-18_USA_CA_SanDiego_-116.97_32.784,W047_2009-05-21_USA_CA_SanDiego_-117.261_32.972),W787_2005-06-21_USA_CA_Yolo_-121.762_38.538),KR349016_2004-08-13_USA_CA_Yolo_-122.0458_38.6944)))),((((((((W210_2013-08-15_USA_CA_SanBernardino_-117.673_34.071,W216_2014-07-08_USA_CA_SanBernardino_-117.664_34.082),W208_2013-08-22_USA_CA_LosAngeles_-118.515_34.222),W022_2008-02-06_USA_CA_SanDiego_-117.004_32.855),W510_2008-07-28_USA_CA_SanDiego_-117.24_32.895),W132_2008-08-25_USA_CA_LosAngeles_-118.752_34.168),(DQ080054_2003-08-01_USA_CA_LosAngeles_-118.0804_34.4834,GQ507473_2004-07-24_USA_CA_LosAngeles_-118.4446_34.2243)),(W503_2008-03-12_USA_CA_SanDiego_-117.067_33.105,W524_2008-11-10_USA_CA_SanDiego_-117.236_32.783)),(KR348925_2003-08-19_USA_CA_Imperial_-115.6144_33.1781,W640_2005-09-07_USA_CA_Solano_-121.757_38.52))),((((((((KR348959_2011-02-09_USA_CA_LosAngeles_-118.4892_34.1728,W534_2009-06-23_USA_CA_SanDiego_-116.983_33.256),(W081_2015-07-28_USA_CA_SanDiego_-116.86_32.849,W110_2016-01-27_USA_CA_SanDiego_-117.003_33.099)),(W102_2015-08-31_USA_CA_SanDiego_-117.324_33.155,W145_2012-06-14_USA_CA_Riverside_-117.48_34.002)),((W041_2008-09-18_USA_CA_SanDiego_-116.766_32.837,W050_2009-09-15_USA_CA_SanDiego_-116.518_32.828),W526_2008-12-01_USA_CA_SanDiego_-117.139_32.928)),W029_2008-06-11_USA_CA_SanDiego_-117.255_32.999),(W019_2007-10-02_USA_CA_SanDiego_-116.95_32.786,W035_2008-09-18_USA_CA_SanDiego_-117.289_33.032)),W531_2009-01-26_USA_CA_SanDiego_-117.23_32.905),((((((KR348962_2011-02-09_USA_CA_LosAngeles_-118.4944_34.19,W164_2017-06-23_USA_CA_LosAngeles_-118.623_34.197),W141_2011-08-22_USA_CA_SanBernardino_-117.567_34.135),KR348963_2011-02-09_USA_CA_LosAngeles_-118.493_34.1856),((KR348967_2011-11-17_USA_CA_LosAngeles_-118.1114_34.1167,W043_2008-12-08_USA_CA_SanDiego_-116.802_33.016),GQ507483_2007-08-02_USA_CA_LosAngeles_-117.9068_34.0976)),((KR349009_2005-07-15_USA_CA_Solano_-121.7567_38.5197,W356_2004-09-21_USA_CA_Kern_-119.115_35.428),W176_2004-09-02_USA_CA_LosAngeles_-118.13_34.015)),(W038_2008-12-01_USA_CA_SanDiego_-117.139_32.928,W638_2005-08-05_USA_CA_Sacramento_-121.5_38.44)))),(((((((((((W156_2013-07-31_USA_CA_LosAngeles_-117.805_34.098,W203_2013-09-10_USA_CA_LosAngeles_-118.436_34.293),W523_2008-11-05_USA_CA_SanDiego_-117.223_32.913),W089_2015-09-29_USA_CA_SanDiego_-117.121_33.193),(W127_2008-08-11_USA_CA_SanBernardino_-117.152_34.033,W535_2009-09-08_USA_CA_SanDiego_-117.222_32.913)),W793_2005-08-03_USA_CA_Yolo_-121.777_38.531),W634_2004-10-08_USA_CA_Sacramento_-121.5_38.44),((KR348971_2011-06-30_USA_CA_LosAngeles_-117.817_34.0313,W190_2011-08-11_USA_CA_LosAngeles_-118.529_34.258),W533_2009-06-18_USA_CA_SanDiego_-117.153_32.904)),GQ507478_2005-08-26_USA_CA_LosAngeles_-118.0797_33.8404),(((((((KR348961_2011-02-09_USA_CA_LosAngeles_-118.4925_34.186,W143_2012-06-06_USA_CA_LosAngeles_-118.043_34.158),W187_2011-08-11_USA_CA_LosAngeles_-118.568_34.193),KR348965_2011-10-26_USA_CA_LosAngeles_-118.6272_34.2392),W030_2008-06-25_USA_CA_SanDiego_-117.032_32.73),KR348958_2011-02-09_USA_CA_LosAngeles_-118.4975_34.1742),W180_2006-08-05_USA_CA_LosAngeles_-118.485_34.183),(DQ431708_2004-07-16_USA_CA_SanDiego_-117.1721_32.7253,W632_2004-08-13_USA_CA_Yolo_-122.046_38.694))),(((((DQ431709_2004-07-16_USA_CA_LosAngeles_-117.6703_34.0578,GQ507474_2004-08-27_USA_CA_SanBernardino_-117.1532_34.1353),W528_2008-12-08_USA_CA_SanDiego_-117.058_32.951),W179_2006-08-07_USA_CA_LosAngeles_-118.481_34.181),(((KR348935_2005-05-29_USA_CA_Riverside_-115.9255_33.5112,W001_2007-10-02_USA_CA_SanDiego_-116.93_32.846),W502_2008-02-06_USA_CA_SanDiego_-117.004_32.855),W011_2008-12-08_USA_CA_SanDiego_-116.802_33.016)),((((KR348972_2011-06-07_USA_CA_LosAngeles_-118.0611_33.8417,W037_2008-09-18_USA_CA_SanDiego_-117.01_33.228),(W040_2008-09-15_USA_CA_SanDiego_-116.649_32.81,W536_2009-09-30_USA_CA_SanDiego_-117.224_32.913)),W021_2007-10-25_USA_CA_SanDiego_0.0_0.0),W020_2007-10-02_USA_CA_SanDiego_-117.328_33.246))),(((((((KR348953_2008-09-25_USA_CA_LosAngeles_-118.276_34.1375,W816_2008-09-02_USA_CA_Yolo_-121.714_38.562),W514_2008-09-04_USA_CA_SanDiego_-117.143_32.925),((KR349022_2011-02-09_USA_CA_LosAngeles_-118.493_34.1856,W525_2008-11-17_USA_CA_SanDiego_-117.196_32.886),W532_2009-02-05_USA_CA_SanDiego_-117.051_32.751)),W115_2004-07-09_USA_CA_LosAngeles_-118.506_34.21),GQ507476_2005-07-27_USA_CA_SanBernardino_-117.7322_33.9508),(((((W033_2008-08-07_USA_CA_SanDiego_-116.969_32.844,W518_2008-09-23_USA_CA_SanDiego_-117.228_32.796),W520_2008-09-24_USA_CA_SanDiego_-117.078_32.733),((W219_2014-07-22_USA_CA_LosAngeles_-118.065_34.679,W545_2014-11-17_USA_CA_SanDiego_-117.084_33.029),W507_2008-06-18_USA_CA_SanDiego_-117.236_32.792)),(DQ080055_2003-08-01_USA_CA_Imperial_-114.9009_32.9392,JF703164_2003-08-01_USA_CA_Imperial_-114.9633_32.7475)),(W039_2008-12-08_USA_CA_SanDiego_-117.058_32.951,W537_2009-10-22_USA_CA_SanDiego_-117.179_32.805))),(DQ431710_2004-07-31_USA_CA_LosAngeles_-117.9517_33.9421,KR348996_2004-08-10_USA_CA_Sacramento_-121.4998_38.4432))))
tree height = 157.16592220538666
Creating the tree model, 'Clade_2_CA_sampled_1.treeModel'
initial tree topology = ((((((((((((((((W307_2009-06-15_USA_CA_Kern_-119.026_35.36,W409_2009-07-30_USA_CA_Kern_-118.833_35.21),W339_2013-06-10_USA_CA_Kern_-119.032_35.406),W430_2011-07-13_USA_CA_Kern_-119.181_35.333),W280_2006-08-15_USA_CA_Kern_-119.069_35.42),(W271_2005-09-01_USA_CA_Kern_-119.041_35.36,W305_2009-06-08_USA_CA_Kern_-119.085_35.402)),(((((W401_2009-07-01_USA_CA_Kern_-118.932_35.283,W417_2010-07-08_USA_CA_Kern_-119.021_35.36),W403_2009-07-14_USA_CA_Kern_-119.125_35.342),(W320_2010-07-28_USA_CA_Kern_-118.965_35.372,W406_2009-07-22_USA_CA_Kern_-119.143_35.411)),W399_2009-06-17_USA_CA_Kern_-119.111_35.38),(KR348988_2008-12-09_USA_CA_Kern_-119.0206_35.3597,W273_2006-07-21_USA_CA_Kern_-118.941_35.381))),W288_2007-06-22_USA_CA_Kern_-119.064_35.346),W360_2005-07-01_USA_CA_Kern_-119.06_35.317),((W281_2006-08-17_USA_CA_Kern_-119.016_35.398,W388_2007-06-22_USA_CA_Kern_-119.075_35.326),(W361_2005-07-01_USA_CA_Kern_-119.075_35.326,W389_2007-08-03_USA_CA_Kern_-119.06_35.317))),((((W330_2012-06-12_USA_CA_Kern_-119.016_35.267,W433_2011-07-13_USA_CA_Kern_-119.172_35.346),W325_2011-08-08_USA_CA_Kern_-119.142_35.37),W306_2009-06-16_USA_CA_Kern_-119.066_35.406),W182_2007-07-20_USA_CA_Kings_-119.624_36.342)),((W310_2009-07-13_USA_CA_Kern_-119.092_35.395,W386_2007-06-08_USA_CA_Kern_-119.06_35.317),W298_2007-07-13_USA_CA_Kern_-119.064_35.346)),((KR348978_2008-06-27_USA_CA_Kern_-119.0403_35.3486,W421_2010-07-28_USA_CA_Kern_-119.021_35.36),W258_2005-06-24_USA_CA_Kern_-119.046_35.36)),((((((W312_2010-07-06_USA_CA_Kern_-119.083_35.327,W426_2010-10-05_USA_CA_Kern_-119.406_35.436),KR348955_2007-05-12_USA_CA_LosAngeles_-118.4653_34.1572),KR348985_2007-08-14_USA_CA_Kern_-118.9431_35.2939),(((W362_2005-07-06_USA_CA_Kern_-119.162_35.351,W370_2006-07-11_USA_CA_Kern_-119.099_35.276),W347_2004-08-10_USA_CA_Kern_-119.099_35.276),W133_2009-06-18_USA_CA_Kern_-119.073_35.417)),((W400_2009-06-30_USA_CA_Kern_-119.1_35.346,W402_2009-07-14_USA_CA_Kern_-119.099_35.276),W394_2007-08-15_USA_CA_Kern_-119.06_35.317)),((((W422_2010-08-18_USA_CA_Kern_-118.815_35.158,W440_2011-08-18_USA_CA_Kern_-118.825_35.166),W333_2012-06-24_USA_CA_Kern_-119.031_35.386),W398_2009-06-17_USA_CA_Kern_-119.115_35.392),W264_2005-07-26_USA_CA_Kern_-118.957_35.403))),((((((((W309_2009-07-07_USA_CA_Kern_-119.189_35.457,W414_2010-06-29_USA_CA_Kern_-118.928_35.399),W285_2007-06-13_USA_CA_Kern_-118.966_35.362),(W327_2011-11-17_USA_CA_Kern_-119.114_35.414,W408_2009-07-29_USA_CA_Kern_-119.115_35.392)),W304_2009-06-14_USA_CA_Kern_-119.055_35.282),((KR348991_2007-09-14_USA_CA_Kern_-119.036_35.3783,W390_2007-08-03_USA_CA_Kern_-119.06_35.317),(W387_2007-06-15_USA_CA_Kern_-119.06_35.317,W412_2010-06-15_USA_CA_Kern_-118.928_35.399))),W358_2005-06-21_USA_CA_Kern_-119.162_35.351),W354_2004-08-13_USA_CA_Kern_-119.075_35.326),W365_2005-07-14_USA_CA_Kern_-119.004_35.299)),(((((((((W311_2009-07-23_USA_CA_Kern_-119.124_35.31,W419_2010-07-09_USA_CA_Kern_-119.06_35.317),W413_2010-06-25_USA_CA_Kern_-119.06_35.317),((W317_2010-07-23_USA_CA_Kern_-119.103_35.412,W420_2010-07-09_USA_CA_Kern_-119.075_35.326),W301_2008-07-07_USA_CA_Kern_-119.065_35.364)),(W326_2011-11-15_USA_CA_Kern_-119.033_35.403,W407_2009-07-28_USA_CA_Kern_-118.956_35.391)),(((W261_2005-07-10_USA_CA_Kern_-119.061_35.33,W434_2011-07-13_USA_CA_Kern_-119.172_35.346),GQ507484_2007-08-16_USA_CA_LosAngeles_-118.5185_34.2368),W294_2007-07-09_USA_CA_Kern_-119.067_35.35)),((KR348931_2009-01-09_USA_CA_Riverside_-116.0789_33.54,W368_2005-07-19_USA_CA_Kern_-119.236_35.245),W418_2010-07-08_USA_CA_Kern_-119.021_35.36)),W308_2009-06-24_USA_CA_Kern_-119.122_35.424),((((KR348946_2008-07-24_USA_CA_LosAngeles_-118.469_34.1894,W314_2010-07-19_USA_CA_Kern_-119.067_35.347),W373_2006-07-14_USA_CA_Kern_-119.036_35.378),W357_2004-09-23_USA_CA_Kern_-118.998_35.365),(KR348987_2008-10-09_USA_CA_Kern_-118.9431_35.2939,W367_2005-07-14_USA_CA_Kern_-119.036_35.378))),((((((((W318_2010-07-26_USA_CA_Kern_-118.92_35.407,W427_2011-06-08_USA_CA_Kern_-119.164_35.346),W410_2009-09-04_USA_CA_Kern_-119.254_35.502),W416_2010-07-01_USA_CA_Kern_-119.025_35.336),((W385_2007-06-06_USA_CA_Kern_-118.979_35.29,W396_2007-08-15_USA_CA_Kern_-119.075_35.326),KR348930_2009-01-09_USA_CA_Riverside_-116.0789_33.526)),(W302_2008-07-23_USA_CA_Kern_-119.164_35.372,W404_2009-07-15_USA_CA_Kern_-119.021_35.36)),(W284_2007-06-07_USA_CA_Kern_-119.065_35.341,W295_2007-07-09_USA_CA_Kern_-119.119_35.346)),(((W252_2004-08-05_USA_CA_Kern_-119.053_35.302,W256_2004-09-08_USA_CA_Kern_-119.052_35.265),(W329_2012-06-10_USA_CA_Kern_-119.151_35.396,W428_2011-07-07_USA_CA_Kern_-119.181_35.333)),W265_2005-07-28_USA_CA_Kern_-119.19_35.374)),((W384_2007-06-05_USA_CA_Kern_-119.236_35.252,W436_2011-07-27_USA_CA_Kern_-119.125_35.342),W415_2010-07-01_USA_CA_Kern_-119.026_35.313)))),(KR348981_2011-01-09_USA_CA_Kern_-119.0986_35.2758,W313_2010-07-12_USA_CA_Kern_-119.067_35.347))
tree height = 234.9517659772
Creating the tree model, 'Clade_1_CA_sampled_1.treeModel'
initial tree topology = (((((((((((W411_2009-09-04_USA_CA_Kern_-119.477_35.532,W764_2015-07-26_USA_CA_Yolo_-121.721_38.557),W283_2006-08-30_USA_CA_Kern_-119.166_35.371),W290_2007-06-25_USA_CA_Kern_-119.126_35.34),(W293_2007-07-05_USA_CA_Kern_-119.028_35.35,W391_2007-08-15_USA_CA_Kern_-118.833_35.198)),((KR348992_2006-09-22_USA_CA_Kern_-119.1117_35.3797,W378_2006-07-21_USA_CA_Kern_-119.021_35.36),(W186_2009-07-28_USA_CA_Fresno_-119.535_36.66,W269_2005-08-19_USA_CA_Kern_-119.076_35.423))),((((W012_2014-10-28_USA_CA_SanDiego_-117.07_33.016,W667_2009-08-20_USA_CA_Sacramento_-121.276_38.251),W376_2006-07-21_USA_CA_Kern_-119.06_35.317),W366_2005-07-14_USA_CA_Kern_-119.036_35.378),(((W379_2006-07-21_USA_CA_Kern_-119.075_35.326,W382_2006-08-04_USA_CA_Kern_-119.149_35.352),W392_2007-08-15_USA_CA_Kern_-119.149_35.352),W267_2005-08-09_USA_CA_Kern_-119.385_35.602))),((((KR348976_2011-07-18_USA_CA_Inyo_-118.3681_37.3494,W381_2006-08-04_USA_CA_Kern_-119.149_35.352),W375_2006-07-21_USA_CA_Kern_-119.04_35.349),((W374_2006-07-21_USA_CA_Kern_-119.149_35.352,W397_2007-08-17_USA_CA_Kern_-119.149_35.352),W184_2008-09-09_USA_CA_Stanislaus_-120.786_37.522)),(W279_2006-08-14_USA_CA_Kern_-119.095_35.4,W666_2009-08-18_USA_CA_Yolo_-121.712_38.61))),(((W820_2009-09-04_USA_CA_Sacramento_-121.391_38.723,W821_2009-09-27_USA_CA_Sacramento_-121.224_38.436),W291_2007-06-29_USA_CA_Kern_-119.15_35.389),KR348986_2007-08-14_USA_CA_Kern_-118.8247_35.1664)),(((W117_2005-06-13_USA_CA_Tulare_-119.33_36.316,W277_2006-08-03_USA_CA_Kern_-118.967_35.39),W383_2006-08-04_USA_CA_Kern_-119.06_35.317),(W276_2006-08-02_USA_CA_Kern_-119.144_35.373,W371_2006-07-11_USA_CA_Kern_-119.236_35.245))),(((((((KR348990_2007-09-13_USA_CA_Kern_-119.2539_35.502,W183_2008-09-09_USA_CA_Tulare_-119.35_36.567),W363_2005-07-06_USA_CA_Kern_-119.115_35.428),W278_2006-08-09_USA_CA_Kern_-119.019_35.328),W270_2005-08-29_USA_CA_Kern_-119.065_35.352),((KR348989_2007-11-09_USA_CA_Kern_-119.2375_35.2525,W377_2006-07-21_USA_CA_Kern_-119.004_35.299),W286_2007-06-14_USA_CA_Kern_-118.94_35.354)),((KR348977_2011-08-15_USA_CA_Inyo_-118.3681_37.3494,W272_2006-07-13_USA_CA_Kern_-119.072_35.323),W297_2007-07-12_USA_CA_Kern_-119.158_35.373)),(((((W068_2014-10-28_USA_CA_SanDiego_-117.07_33.016,W191_2012-09-18_USA_CA_Tulare_-119.195_36.094),W134_2009-06-23_USA_CA_Kings_-119.622_36.354),((W266_2005-08-01_USA_CA_Kern_-119.016_35.408,W395_2007-08-15_USA_CA_Kern_-119.021_35.36),W289_2007-06-25_USA_CA_Kern_-119.041_35.288)),(W275_2006-08-01_USA_CA_Kern_-119.122_35.377,W296_2007-07-09_USA_CA_Kern_-119.147_35.358)),W359_2005-07-01_USA_CA_Kern_-119.109_35.317))),(((((W262_2005-07-13_USA_CA_Kern_-119.11_35.338,W274_2006-07-31_USA_CA_Kern_-119.203_35.386),W380_2006-08-04_USA_CA_Kern_-119.149_35.352),W287_2007-06-20_USA_CA_Kern_-119.116_35.377),(W263_2005-07-15_USA_CA_Kern_-119.006_35.405,W393_2007-08-15_USA_CA_Kern_-119.111_35.38)),((W181_2007-07-20_USA_CA_Fresno_-119.616_36.751,W292_2007-06-29_USA_CA_Kern_-119.15_35.389),(W194_2012-08-28_USA_CA_Tulare_-119.217_36.144,W300_2008-03-13_USA_CA_Kern_-119.01_35.347))))
tree height = 234.6088159462914
Creating the tree model, 'Clade_0_CA_sampled_1.treeModel'
initial tree topology = (((((((((((((W016_2016-05-16_USA_CA_SanDiego_0.0_0.0,W557_2015-07-28_USA_CA_SanDiego_-117.247_32.728),W108_2015-11-10_USA_CA_SanDiego_-117.141_33.013),((W550_2015-04-28_USA_CA_SanDiego_-117.229_32.84,W587_2016-04-11_USA_CA_SanDiego_-117.2_32.809),W556_2015-07-21_USA_CA_SanDiego_-117.136_32.927)),((W090_2015-10-02_USA_CA_SanDiego_-116.996_32.812,W554_2015-07-02_USA_CA_SanDiego_-117.096_32.729),(W555_2015-07-09_USA_CA_SanDiego_-117.094_32.983,W589_2016-04-21_USA_CA_SanDiego_-117.073_32.772))),((((W173_2017-08-28_USA_CA_Ventura_-118.668_34.273,W559_2015-08-04_USA_CA_SanDiego_-117.097_32.828),W569_2015-09-22_USA_CA_SanDiego_-117.064_32.756),(W564_2015-09-01_USA_CA_SanDiego_-117.225_32.796,W566_2015-09-08_USA_CA_SanDiego_-117.092_32.904)),W082_2015-08-14_USA_CA_SanDiego_-117.332_33.18)),((W010_2016-08-15_USA_CA_SanDiego_-117.073_32.631,W107_2015-11-10_USA_CA_SanDiego_-117.34_33.167),(W101_2015-08-31_USA_CA_SanDiego_-117.073_32.643,W571_2015-09-22_USA_CA_SanDiego_-117.194_32.766))),(W076_2015-04-16_USA_CA_SanDiego_-117.153_32.835,W572_2015-09-28_USA_CA_SanDiego_-117.116_33.014)),((((W111_2016-02-03_USA_CA_SanDiego_-117.228_32.748,W574_2015-10-02_USA_CA_SanDiego_-117.165_32.795),W008_2014-10-07_USA_CA_SanDiego_-117.071_32.677),W075_2014-12-18_USA_CA_SanDiego_-117.081_32.736),W073_2014-11-17_USA_CA_SanDiego_-116.884_33.018)),(((W070_2014-11-07_USA_CA_SanDiego_-116.966_32.629,W546_2014-12-18_USA_CA_SanDiego_-117.101_32.84),(W583_2015-12-28_USA_CA_SanDiego_-117.065_33.044,W584_2016-02-27_USA_CA_SanDiego_-117.245_32.946)),(W064_2014-08-13_USA_CA_SanDiego_-116.996_32.776,W080_2015-07-10_USA_CA_SanDiego_-117.029_32.737))),(((((W567_2015-09-10_USA_CA_SanDiego_-117.242_32.897,W581_2015-11-17_USA_CA_SanDiego_-117.085_33.029),W539_2014-08-13_USA_CA_SanDiego_-117.02_32.797),(W014_2014-10-31_USA_CA_SanDiego_-117.129_32.839,W074_2014-12-18_USA_CA_SanDiego_-117.018_32.797)),W585_2016-02-28_USA_CA_SanDiego_-117.245_32.946),((W063_2014-08-13_USA_CA_SanDiego_-117.02_32.797,W570_2015-09-22_USA_CA_SanDiego_-117.226_32.729),W551_2015-05-11_USA_CA_SanDiego_-117.036_32.721))),(((((W109_2015-11-10_USA_CA_SanDiego_-116.981_32.837,W560_2015-08-17_USA_CA_SanDiego_-117.083_32.795),W077_2015-05-13_USA_CA_SanDiego_-117.004_32.852),(W543_2014-11-10_USA_CA_SanDiego_-117.031_32.795,W595_2017-09-11_USA_CA_SanDiego_-116.999_33.091)),W527_2008-12-08_USA_CA_SanDiego_-116.802_33.016),((W066_2014-10-03_USA_CA_SanDiego_-116.997_32.84,W575_2015-10-06_USA_CA_SanDiego_-117.058_32.668),W541_2014-09-29_USA_CA_SanDiego_-117.205_32.775))),(((((((W015_2015-08-21_USA_CA_SanDiego_-117.107_32.652,W562_2015-08-24_USA_CA_SanDiego_-117.135_32.701),W549_2015-04-16_USA_CA_SanDiego_-117.153_32.835),(W078_2015-07-10_USA_CA_SanDiego_-117.045_32.727,W084_2015-08-18_USA_CA_SanDiego_-117.053_32.673)),((W104_2015-10-02_USA_CA_SanDiego_-116.879_33.025,W573_2015-10-01_USA_CA_SanDiego_-117.086_32.837),W576_2015-10-07_USA_CA_SanDiego_-117.123_32.757)),((W079_2015-07-10_USA_CA_SanDiego_-117.034_32.733,W540_2014-09-23_USA_CA_SanDiego_-117.008_32.803),W565_2015-09-03_USA_CA_SanDiego_-117.159_32.749)),((W065_2014-09-25_USA_CA_SanDiego_-116.937_32.852,W552_2015-06-05_USA_CA_SanDiego_-117.149_32.736),W085_2015-08-21_USA_CA_SanDiego_-117.107_32.652)),((((W547_2014-12-18_USA_CA_SanDiego_-117.018_32.797,W568_2015-09-10_USA_CA_SanDiego_-117.031_32.8),(W548_2014-12-16_USA_CA_SanDiego_-117.081_32.736,W577_2015-10-10_USA_CA_SanDiego_-117.059_33.023)),W061_2014-08-06_USA_CA_SanDiego_-116.894_32.838),(W009_2015-10-02_USA_CA_SanDiego_-117.142_32.827,W112_2016-02-18_USA_CA_SanDiego_-117.024_32.63)))),(((W086_2015-08-28_USA_CA_SanDiego_-117.227_32.984,W563_2015-08-25_USA_CA_SanDiego_-117.186_32.824),(W561_2015-08-19_USA_CA_SanDiego_-117.187_32.908,W582_2015-12-11_USA_CA_SanDiego_-117.052_32.767)),W067_2014-10-03_USA_CA_SanDiego_-117.205_32.775))
tree height = 116.47423437605924
The gmrfSkyrideLikelihood has time aware smoothing
Creating a GMRF smoothed skyride model for multiple loci (SkyGrid)
Population sizes: 50
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 1
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Using strict molecular clock model.
Creating state frequencies model 'CP1+2.frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25}
Creating HKY substitution model. Initial kappa = 2.0
Creating state frequencies model 'CP3.frequencies': Initial frequencies = {0.25, 0.25, 0.25, 0.25}
Creating HKY substitution model. Initial kappa = 2.0
Creating site model:
with initial relative rate = 1.0
4 category discrete gamma with initial shape = 0.5
Creating site model:
with initial relative rate = 1.0
4 category discrete gamma with initial shape = 0.5
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 6 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 5 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Using BEAGLE resource 0: CPU
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.
With 4 unique site patterns.
Using rescaling scheme : dynamic (rescaling every 100 evaluations, delay rescaling until first overflow)
Creating state frequencies model 'Location0.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
General Substitution Model (stateCount=29)
Using BSSVS Complex Substitution Model
Creating site model.
Creating state frequencies model 'Location1.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
General Substitution Model (stateCount=29)
Using BSSVS Complex Substitution Model
Creating site model.
Creating state frequencies model 'Location2.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
General Substitution Model (stateCount=29)
Using BSSVS Complex Substitution Model
Creating site model.
Creating state frequencies model 'Location3.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
General Substitution Model (stateCount=29)
Using BSSVS Complex Substitution Model
Creating site model.
Creating state frequencies model 'Location4.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
General Substitution Model (stateCount=29)
Using BSSVS Complex Substitution Model
Creating site model.
Creating state frequencies model 'Location5.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
General Substitution Model (stateCount=29)
Using BSSVS Complex Substitution Model
Creating site model.
Creating state frequencies model 'Location0.root.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 1 unique site patterns.
Using rescaling scheme : delayed (delay rescaling until first overflow)
Creating state frequencies model 'Location1.root.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 1 unique site patterns.
Using rescaling scheme : delayed (delay rescaling until first overflow)
Creating state frequencies model 'Location2.root.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 1 unique site patterns.
Using rescaling scheme : delayed (delay rescaling until first overflow)
Creating state frequencies model 'Location3.root.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 1 unique site patterns.
Using rescaling scheme : delayed (delay rescaling until first overflow)
Creating state frequencies model 'Location4.root.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 1 unique site patterns.
Using rescaling scheme : delayed (delay rescaling until first overflow)
Creating state frequencies model 'Location5.root.frequencies': Initial frequencies = {0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448, 0.03448}
Using BEAGLE TreeLikelihood
Branch rate model used: strictClockBranchRates
Using BEAGLE resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
Ignoring ambiguities in tree likelihood.
With 1 unique site patterns.
Using rescaling scheme : delayed (delay rescaling until first overflow)
Parameter weights for delta exchange are: 41208 20604
Creating swap operator for parameter Clade_5_CA_sampled_1.branchRates.categories (weight=10.0)
Creating swap operator for parameter Clade_5_CA_sampled_1.Clade_4_CA_sampled_1.branchRates.categories (weight=10.0)
Creating swap operator for parameter Clade_5_CA_sampled_1.Clade_3_CA_sampled_1.branchRates.categories (weight=10.0)
Creating swap operator for parameter Clade_5_CA_sampled_1.Clade_2_CA_sampled_1.branchRates.categories (weight=10.0)
Creating swap operator for parameter Clade_5_CA_sampled_1.Clade_1_CA_sampled_1.branchRates.categories (weight=10.0)
Creating swap operator for parameter Clade_5_CA_sampled_1.Clade_0_CA_sampled_1.branchRates.categories (weight=10.0)
Optimization Schedule: log
Creating CTMC Scale Reference Prior model.
Creating CTMC Scale Reference Prior model.
Creating CTMC Scale Reference Prior model.
Creating CTMC Scale Reference Prior model.
Creating CTMC Scale Reference Prior model.
Creating CTMC Scale Reference Prior model.
Creating CTMC Scale Reference Prior model.
Constructing a cache around likelihood 'null', signal = Location0.rates
Constructing a cache around likelihood 'null', signal = Location1.rates
Constructing a cache around likelihood 'null', signal = Location2.rates
Constructing a cache around likelihood 'null', signal = Location3.rates
Constructing a cache around likelihood 'null', signal = Location4.rates
Constructing a cache around likelihood 'null', signal = Location5.rates
Likelihood computation is using an auto sizing thread pool.
Creating the MCMC chain:
chainLength=100000000
autoOptimize=true
autoOptimize delayed for 1000000 steps
WARNING: Likelihood component, null, created but not used in the MCMC
WARNING: Likelihood component, null, created but not used in the MCMC
WARNING: Likelihood component, Clade_5_CA_sampled_1.Clade_0_CA_sampled_1.branchRates, created but not used in the MCMC
WARNING: Likelihood component, Clade_5_CA_sampled_1.Clade_2_CA_sampled_1.branchRates, created but not used in the MCMC
WARNING: Likelihood component, null, created but not used in the MCMC
WARNING: Likelihood component, null, created but not used in the MCMC
WARNING: Likelihood component, Clade_5_CA_sampled_1.Clade_1_CA_sampled_1.branchRates, created but not used in the MCMC
WARNING: Likelihood component, null, created but not used in the MCMC
WARNING: Likelihood component, Clade_5_CA_sampled_1.Clade_3_CA_sampled_1.branchRates, created but not used in the MCMC
WARNING: Likelihood component, null, created but not used in the MCMC
WARNING: Likelihood component, Clade_5_CA_sampled_1.Clade_4_CA_sampled_1.branchRates, created but not used in the MCMC
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 368
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood.evaluateLikelihoods(Unknown Source)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.markovchain.MarkovChain.evaluate(Unknown Source)
at dr.inference.markovchain.MarkovChain.<init>(Unknown Source)
at dr.inference.mcmc.MCMC.init(Unknown Source)
at dr.inference.mcmc.MCMC.init(Unknown Source)
at dr.inferencexml.MCMCParser.parseXMLObject(Unknown Source)
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 368
at dr.inference.model.Parameter$Default.getParameterValue(Unknown Source)
at dr.evomodel.tree.TreeParameterModel.getNodeValue(Unknown Source)
at dr.evomodel.branchratemodel.DiscretizedBranchRates.getBranchRate(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Citations for this analysis:
FRAMEWORK
BEAST primary citation:
Drummond AJ, Suchard MA, Xie Dong, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29, 1969-1973. DOI:10.1093/molbev/mss075
Using BEAGLE likelihood calculation library:
Ayres et al (2012) BEAGLE: a common application programming inferface and high-performance computing library for statistical phylogenetics. Syst Biol. 61, 170-173. DOI:10.1093/sysbio/syr100
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
MOLECULAR CLOCK MODELS
Uncorrelated relaxed clock:
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biology. 4: e88. DOI:10.1371/journal.pbio.0040088
SUBSTITUTION MODELS
HKY nucleotide substitution model:
Hasegowa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol.. 22, 160-174
Discrete gamma-distributed rate heterogeneity model:
Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol.. 39, 306-314
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 v1.8.4
# Generated Sun Aug 19 15:32:46 PDT 2018 [seed=1534717956964]
# ../2018-08-18_Clade_CA_sampled_1.xml
state Posterior Prior Likelihood Clade_5_CA_sampled_1.rootHeight Clade_4_CA_sampled_1.rootHeight Clade_3_CA_sampled_1.rootHeight Clade_2_CA_sampled_1.rootHeight Clade_1_CA_sampled_1.rootHeight Clade_0_CA_sampled_1.rootHeight Clade_5_CA_sampled_1.ucld.mean Location0.clock.rate Location0.nonZeroRates Location1.nonZeroRates Location2.nonZeroRates Location3.nonZeroRates Location4.nonZeroRates Location5.nonZeroRates
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 368
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood.evaluateLikelihoods(Unknown Source)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.markovchain.MarkovChain.evaluate(Unknown Source)
at dr.inference.markovchain.MarkovChain.runChain(Unknown Source)
at dr.inference.mcmc.MCMC.chain(Unknown Source)
at dr.inference.mcmc.MCMC.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 368
at dr.inference.model.Parameter$Default.getParameterValue(Unknown Source)
at dr.evomodel.tree.TreeParameterModel.getNodeValue(Unknown Source)
at dr.evomodel.branchratemodel.DiscretizedBranchRates.getBranchRate(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 368
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood.evaluateLikelihoods(Unknown Source)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodColumn.getDoubleValue(Unknown Source)
at dr.inference.loggers.NumberColumn.getFormattedValue(Unknown Source)
at dr.inference.loggers.LogColumn$Abstract.getFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.getColumnFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.log(Unknown Source)
at dr.inference.mcmc.MCMC$2.currentState(Unknown Source)
at dr.inference.markovchain.MarkovChain.fireCurrentModel(Unknown Source)
at dr.inference.markovchain.MarkovChain.runChain(Unknown Source)
at dr.inference.mcmc.MCMC.chain(Unknown Source)
at dr.inference.mcmc.MCMC.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 368
at dr.inference.model.Parameter$Default.getParameterValue(Unknown Source)
at dr.evomodel.tree.TreeParameterModel.getNodeValue(Unknown Source)
at dr.evomodel.branchratemodel.DiscretizedBranchRates.getBranchRate(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 368
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodColumn.getDoubleValue(Unknown Source)
at dr.inference.loggers.NumberColumn.getFormattedValue(Unknown Source)
at dr.inference.loggers.LogColumn$Abstract.getFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.getColumnFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.log(Unknown Source)
at dr.inference.mcmc.MCMC$2.currentState(Unknown Source)
at dr.inference.markovchain.MarkovChain.fireCurrentModel(Unknown Source)
at dr.inference.markovchain.MarkovChain.runChain(Unknown Source)
at dr.inference.mcmc.MCMC.chain(Unknown Source)
at dr.inference.mcmc.MCMC.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 368
at dr.inference.model.Parameter$Default.getParameterValue(Unknown Source)
at dr.evomodel.tree.TreeParameterModel.getNodeValue(Unknown Source)
at dr.evomodel.branchratemodel.DiscretizedBranchRates.getBranchRate(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
0 -666636.9731 -55334.1784 -611302.7946 172.133 392.338 157.166 234.952 234.609 116.474 1.00000 1.00000 812.000 812.000 812.000 812.000 812.000 812.000 -
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 368
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood.evaluateLikelihoods(Unknown Source)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodColumn.getDoubleValue(Unknown Source)
at dr.inference.loggers.NumberColumn.getFormattedValue(Unknown Source)
at dr.inference.loggers.LogColumn$Abstract.getFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.getColumnFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.log(Unknown Source)
at dr.inference.mcmc.MCMC$2.currentState(Unknown Source)
at dr.inference.markovchain.MarkovChain.fireCurrentModel(Unknown Source)
at dr.inference.markovchain.MarkovChain.runChain(Unknown Source)
at dr.inference.mcmc.MCMC.chain(Unknown Source)
at dr.inference.mcmc.MCMC.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 368
at dr.inference.model.Parameter$Default.getParameterValue(Unknown Source)
at dr.evomodel.tree.TreeParameterModel.getNodeValue(Unknown Source)
at dr.evomodel.branchratemodel.DiscretizedBranchRates.getBranchRate(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.traverse(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood(Unknown Source)
at dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodCaller.call(Unknown Source)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at dr.inference.model.CompoundLikelihood.getLogLikelihood(Unknown Source)
at dr.inference.model.CompoundLikelihood$LikelihoodColumn.getDoubleValue(Unknown Source)
at dr.inference.loggers.NumberColumn.getFormattedValue(Unknown Source)
at dr.inference.loggers.LogColumn$Abstract.getFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.getColumnFormatted(Unknown Source)
at dr.inference.loggers.MCLogger.log(Unknown Source)
at dr.inference.mcmc.MCMC$2.currentState(Unknown Source)
at dr.inference.markovchain.MarkovChain.fireCurrentModel(Unknown Source)
at dr.inference.markovchain.MarkovChain.runChain(Unknown Source)
at dr.inference.mcmc.MCMC.chain(Unknown Source)
at dr.inference.mcmc.MCMC.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException
Exception in thread "Thread-1" java.lang.ArrayIndexOutOfBoundsException
0.703 seconds
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