CIPRES_THREADSPP=24 CIPRES_NP=1 NOTICE : Your input file may have been altered to activate multi-threading. running: beast2 -threads 24 -instances 1 -beagle_SSE -beagle_scaling dynamic infile_altered.xml BEAST v2.6.1, 2002-2019 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 Random number seed: 1590598720916 AccretaA_P5_4P_Ssagehen_FaccretaA: 5907 3 AccretaA_PSW15985_1Pmale_BCL_FaccretaA: 5907 3 AccretaA_Pol499_1P_Sagehen_FaccretaA: 5907 3 AccretaA_RWG001_2P_JuneLake: 5907 3 AccretaB_NDT736_2P_nearBloomfieldCamp: 5907 3 AccretaB_PSW06720_P_CampSpaulding: 5907 3 AccretaB_Pol550c_Sagehen_FaccretaB: 5907 3 AccretaB_Pol782_1P_Sagehen_FaccretaB: 5907 3 Argentea_NDT718_P_nearRedbridgeCamp: 5907 3 Argentea_P2_6P_Sagehen_Fargente: 5907 3 Argentea_P4_12P_Sagehen_Fargentea: 5907 3 Argentea_P7_5P_Sagehen_Fargentea: 5907 3 Sub_P10_8P_Sagehen_Fsubaenescens: 5907 3 Sub_P6_11P_Sagehen_Fsubaenescens: 5907 3 Sub_P6_14P_Sagehen_Fsubaenescens: 5907 3 Sub_Pol549_1P_Sagehen_Fsubaenescens: 5907 3 Alignment(TestForSNAPP) 16 taxa 5907 sites 4609 patterns Sub: 5907 9 Argentea: 5907 9 AccretaB: 5907 9 AccretaA: 5907 9 Data(snap.TestForSNAPP) 4 taxa 5907 sites 1112 patterns Seq: seq_Sub_P6_11P_Sagehen_Fsubaenescens Seq: seq_Sub_P6_14P_Sagehen_Fsubaenescens Seq: seq_Sub_P10_8P_Sagehen_Fsubaenescens Seq: seq_Sub_Pol549_1P_Sagehen_Fsubaenescens Seq: seq_Argentea_NDT718_P_nearRedbridgeCamp Seq: seq_Argentea_P2_6P_Sagehen_Fargente Seq: seq_Argentea_P4_12P_Sagehen_Fargentea Seq: seq_Argentea_P7_5P_Sagehen_Fargentea Seq: seq_AccretaB_NDT736_2P_nearBloomfieldCamp Seq: seq_AccretaB_Pol550c_Sagehen_FaccretaB Seq: seq_AccretaB_Pol782_1P_Sagehen_FaccretaB Seq: seq_AccretaB_PSW06720_P_CampSpaulding Seq: seq_AccretaA_P5_4P_Ssagehen_FaccretaA Seq: seq_AccretaA_Pol499_1P_Sagehen_FaccretaA Seq: seq_AccretaA_PSW15985_1Pmale_BCL_FaccretaA Seq: seq_AccretaA_RWG001_2P_JuneLake WARNING: removed 46 patterns (46 sites) because they have one or more branches without data. 4 taxa 5861 sites 3372 patterns =============================================================================== Citations for this model: Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology 15, no. 4 (2019): e1006650. David Bryant, Remco Bouckaert, Joseph Felsenstein, Noah Rosenberg, Arindam RoyChoudhury. Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis. Mol. Biol. Evol. 29(8):1917-1932, 2012 =============================================================================== Start likelihood: -89858.77115908563 Writing file RUN2.log Writing file RUN2.trees Sample posterior ESS(posterior) likelihood prior 0 -89858.7705 N -88521.6981 -1337.0723 -- 100 -86699.0109 2.0 -85812.0520 -886.9588 -- 200 -86115.2454 3.0 -85237.1894 -878.0560 -- 300 -86054.1194 4.0 -85236.9574 -817.1619 -- 400 -86028.8785 5.0 -85201.9109 -826.9676 -- 500 -85902.7584 5.5 -85072.8502 -829.9082 -- 600 -80652.3581 5.8 -79828.2312 -824.1268 -- 700 -73101.3670 4.7 -72267.1883 -834.1786 -- 800 -72652.6941 3.3 -71758.6647 -894.0294 -- 900 -72615.1635 2.6 -71720.9106 -894.2528 -- 1000 -72610.3419 2.6 -71666.8707 -943.4711 -- 1100 -72610.7279 2.5 -71671.5423 -939.1856 -- 1200 -72600.8597 2.4 -71665.0437 -935.8160 -- 1300 -72597.6209 2.5 -71664.2729 -933.3479 -- 1400 -72598.1227 2.5 -71665.8872 -932.2355 -- 1500 -72597.5128 2.6 -71675.4060 -922.1067 -- 1600 -72597.3313 2.8 -71675.1829 -922.1484 -- 1700 -72595.6327 2.9 -71676.1114 -919.5212 -- 1800 -72594.4831 3.1 -71708.3409 -886.1421 -- 1900 -72589.0921 3.6 -71684.7294 -904.3627 -- 2000 -72583.0703 3.7 -71683.5007 -899.5696 -- 2100 -72581.7598 3.9 -71683.9171 -897.8427 -- 2200 -72580.4718 4.1 -71668.6097 -911.8621 -- 2300 -72581.9683 4.3 -71688.6327 -893.3355 -- 2400 -72580.2636 4.5 -71687.1341 -893.1295 -- 2500 -72578.0913 4.7 -71686.8795 -891.2117 -- 2600 -72576.3311 4.9 -71666.2168 -910.1143 -- 2700 -72580.8603 5.1 -71671.0063 -909.8539 -- 2800 -72578.2715 5.2 -71668.1007 -910.1707 -- 2900 -72579.8942 6.6 -71669.5088 -910.3854 -- 3000 -72579.5832 6.9 -71668.8073 -910.7759 -- 3100 -72581.7122 7.1 -71699.8834 -881.8287 -- 3200 -72580.2654 7.4 -71684.1891 -896.0762 -- 3300 -72579.2439 7.6 -71672.3664 -906.8775 -- 3400 -72579.8046 7.9 -71672.0590 -907.7456 -- 3500 -72578.0122 8.1 -71659.4538 -918.5583 -- 3600 -72580.0265 8.4 -71699.8867 -880.1398 -- 3700 -72580.6736 8.6 -71690.1510 -890.5225 -- 3800 -72581.4281 8.9 -71689.6004 -891.8277 -- 3900 -72578.9849 11.9 -71688.6021 -890.3828 -- 4000 -72578.0697 12.3 -71673.0026 -905.0671 -- 4100 -72579.7151 12.6 -71689.8903 -889.8248 -- 4200 -72579.4512 12.9 -71672.5501 -906.9011 -- 4300 -72580.4063 13.3 -71676.5951 -903.8112 -- 4400 -72577.4549 13.6 -71673.7221 -903.7327 -- 4500 -72575.4287 13.9 -71682.4408 -892.9878 -- 4600 -72575.3292 14.3 -71682.3883 -892.9408 -- 4700 -72575.3524 14.6 -71687.0503 -888.3021 -- 4800 -72577.1080 14.9 -71700.1537 -876.9543 -- 4900 -72575.3256 22.4 -71692.2072 -883.1183 -- 5000 -72577.3075 22.9 -71693.2887 -884.0187 -- 5100 -72577.0029 23.4 -71692.9048 -884.0981 -- 5200 -72575.4726 23.9 -71691.9485 -883.5241 -- 5300 -72574.9581 24.4 -71691.3775 -883.5806 -- 5400 -72577.2876 24.9 -71663.8661 -913.4214 -- 5500 -72576.8558 25.4 -71685.8826 -890.9732 -- 5600 -72576.1184 25.8 -71701.0939 -875.0244 -- 5700 -72574.3814 26.3 -71687.6523 -886.7290 -- 5800 -72576.7308 26.8 -71689.5249 -887.2059 -- 5900 -72576.5523 46.4 -71689.6093 -886.9430 -- 6000 -72577.6311 47.2 -71690.2462 -887.3849 -- 6100 -72574.0638 48.1 -71682.7650 -891.2988 -- 6200 -72575.0263 48.9 -71692.9210 -882.1052 -- 6300 -72574.0721 49.7 -71664.7138 -909.3582 -- 6400 -72574.9835 50.5 -71669.5814 -905.4020 -- 6500 -72578.5113 51.4 -71645.3262 -933.1851 14h50m15s/Msamples 6600 -72574.9993 52.2 -71694.7061 -880.2931 14h48m48s/Msamples 6700 -72577.7456 53.0 -71661.7531 -915.9925 14h44m16s/Msamples 6800 -72574.7464 53.8 -71658.3667 -916.3796 14h50m21s/Msamples 6900 -72578.8302 25.5 -71703.5407 -875.2894 14h52m14s/Msamples 7000 -72579.0330 25.9 -71702.4698 -876.5632 14h58m53s/Msamples 7100 -72578.1791 26.2 -71686.8222 -891.3569 14h52m50s/Msamples 7200 -72578.6510 26.5 -71687.2490 -891.4020 14h48m40s/Msamples 7300 -72578.0919 26.9 -71696.7028 -881.3890 14h49m11s/Msamples 7400 -72577.0634 27.2 -71658.9118 -918.1515 14h46m1s/Msamples 7500 -72576.1918 27.5 -71658.1893 -918.0024 14h44m19s/Msamples 7600 -72576.2175 27.8 -71658.5310 -917.6865 14h43m34s/Msamples 7700 -72576.1374 28.2 -71658.8656 -917.2717 14h41m46s/Msamples 7800 -72576.5328 28.5 -71658.5420 -917.9907 14h38m49s/Msamples 7900 -72577.1252 6.7 -71659.7698 -917.3554 14h42m9s/Msamples 8000 -72576.4340 6.7 -71659.8289 -916.6051 14h45m36s/Msamples 8100 -72575.4246 6.8 -71658.4162 -917.0083 14h46m49s/Msamples 8200 -72575.5325 6.8 -71658.3943 -917.1382 14h44m3s/Msamples 8300 -72576.3924 6.9 -71705.5644 -870.8279 14h46m49s/Msamples 8400 -72579.9357 6.9 -71705.8666 -874.0691 14h44m9s/Msamples 8500 -72579.7423 7.0 -71705.3308 -874.4115 14h43m59s/Msamples 8600 -72578.6375 7.1 -71705.1855 -873.4519 14h45m30s/Msamples 8700 -72579.6860 7.2 -71704.7497 -874.9363 14h48m56s/Msamples 8800 -72579.0354 7.2 -71706.1732 -872.8621 14h47m41s/Msamples 8900 -72579.2175 5.9 -71706.1771 -873.0403 14h47m54s/Msamples 9000 -72578.2503 5.9 -71689.1741 -889.0761 14h50m7s/Msamples 9100 -72577.5629 6.0 -71685.8293 -891.7335 14h53m13s/Msamples 9200 -72577.3317 6.1 -71684.4477 -892.8839 14h54m5s/Msamples 9300 -72575.6847 6.1 -71683.4309 -892.2537 14h57m15s/Msamples 9400 -72576.8301 6.2 -71684.8265 -892.0035 14h58m10s/Msamples 9500 -72578.6280 6.2 -71687.4748 -891.1531 14h59m36s/Msamples 9600 -72574.3006 6.3 -71683.1605 -891.1401 15h0m7s/Msamples 9700 -72577.6890 6.4 -71662.6280 -915.0609 14h59m30s/Msamples 9800 -72576.0443 6.4 -71652.6844 -923.3599 14h59m15s/Msamples 9900 -72576.8659 6.5 -71707.1722 -869.6936 14h57m59s/Msamples 10000 -72576.1427 6.6 -71664.8311 -911.3115 14h58m55s/Msamples 10100 -72576.9833 6.7 -71666.4005 -910.5827 14h58m30s/Msamples 10200 -72577.5524 6.7 -71699.8163 -877.7361 14h57m22s/Msamples 10300 -72575.6316 6.8 -71689.2885 -886.3431 14h58m21s/Msamples 10400 -72574.8211 6.9 -71687.9061 -886.9149 14h56m15s/Msamples 10500 -72576.6966 6.9 -71702.3584 -874.3382 14h53m44s/Msamples 10600 -72573.7225 7.0 -71690.5736 -883.1488 14h53m11s/Msamples 10700 -72574.2642 7.1 -71691.5051 -882.7590 14h55m37s/Msamples 10800 -72575.6847 7.1 -71692.8860 -882.7987 14h54m44s/Msamples 10900 -72579.4649 7.3 -71696.4586 -883.0062 14h54m38s/Msamples 11000 -72574.3981 7.4 -71676.9490 -897.4490 14h54m36s/Msamples 11100 -72577.4816 7.5 -71672.7720 -904.7095 14h53m12s/Msamples 11200 -72574.0112 7.6 -71673.8739 -900.1373 14h53m25s/Msamples 11300 -72575.8633 7.6 -71674.4653 -901.3979 14h53m53s/Msamples 11400 -72575.7727 7.7 -71674.7644 -901.0082 14h54m10s/Msamples 11500 -72574.0871 7.7 -71679.9728 -894.1143 14h53m56s/Msamples 11600 -72575.5120 7.8 -71680.6973 -894.8147 14h56m9s/Msamples 11700 -72575.8690 7.8 -71680.7518 -895.1172 14h56m1s/Msamples 11800 -72578.3865 7.9 -71682.8044 -895.5820 14h56m12s/Msamples 11900 -72578.7012 7.9 -71683.5987 -895.1025 14h56m30s/Msamples 12000 -72576.5127 8.0 -71687.2640 -889.2487 14h56m59s/Msamples 12100 -72575.8938 8.0 -71686.0068 -889.8869 14h58m57s/Msamples 12200 -72576.0078 8.0 -71687.0926 -888.9152 14h58m39s/Msamples 12300 -72575.8530 8.1 -71686.4536 -889.3994 14h58m56s/Msamples 12400 -72575.0717 8.1 -71678.6538 -896.4179 15h0m19s/Msamples 12500 -72574.2713 8.2 -71679.5964 -894.6749 15h1m42s/Msamples 12600 -72573.6678 8.2 -71691.7048 -881.9629 15h1m28s/Msamples 12700 -72576.6985 8.2 -71693.4381 -883.2604 15h1m16s/Msamples 12800 -72576.2978 8.3 -71693.8352 -882.4626 15h1m7s/Msamples 12900 -72576.1025 8.6 -71671.7537 -904.3488 15h1m45s/Msamples 13000 -72574.6043 8.7 -71669.7993 -904.8050 15h1m36s/Msamples 13100 -72579.9457 8.8 -71675.9512 -903.9945 15h1m5s/Msamples 13200 -72577.5787 8.9 -71700.9592 -876.6195 15h1m15s/Msamples 13300 -72579.0909 9.0 -71690.6016 -888.4893 15h1m29s/Msamples 13400 -72577.6633 9.0 -71690.4440 -887.2193 15h0m58s/Msamples 13500 -72577.5243 9.1 -71687.2602 -890.2640 15h0m56s/Msamples 13600 -72578.9525 9.2 -71687.0581 -891.8944 14h59m53s/Msamples 13700 -72576.6472 9.2 -71701.7478 -874.8994 14h59m7s/Msamples 13800 -72580.0113 9.4 -71705.4596 -874.5516 14h58m56s/Msamples 13900 -72579.7763 10.0 -71658.3705 -921.4058 14h59m1s/Msamples 14000 -72579.6508 10.1 -71687.1075 -892.5433 14h58m49s/Msamples 14100 -72578.2397 10.2 -71698.9932 -879.2464 14h58m57s/Msamples 14200 -72579.0188 10.3 -71670.0573 -908.9615 14h59m1s/Msamples 14300 -72579.6169 10.4 -71671.4533 -908.1636 14h59m52s/Msamples 14400 -72579.5194 10.5 -71671.2757 -908.2437 14h59m6s/Msamples 14500 -72579.3020 10.6 -71671.1544 -908.1475 14h58m58s/Msamples 14600 -72579.0164 10.7 -71685.3603 -893.6561 14h58m53s/Msamples 14700 -72577.5886 10.8 -71683.8713 -893.7172 14h59m2s/Msamples 14800 -72580.0306 10.9 -71685.9298 -894.1007 14h59m17s/Msamples 14900 -72579.6579 11.5 -71687.0905 -892.5673 14h59m28s/Msamples 15000 -72578.3990 11.6 -71697.9269 -880.4720 15h0m6s/Msamples 15100 -72576.3493 11.8 -71663.0192 -913.3301 15h0m25s/Msamples 15200 -72579.3898 11.8 -71665.8881 -913.5016 15h0m31s/Msamples 15300 -72577.6421 11.9 -71662.9268 -914.7153 15h0m45s/Msamples 15400 -72579.7735 12.0 -71706.2498 -873.5236 15h0m22s/Msamples 15500 -72579.8923 12.0 -71706.2672 -873.6250 15h0m52s/Msamples 15600 -72578.2058 12.1 -71704.7709 -873.4348 15h0m35s/Msamples 15700 -72577.7392 12.2 -71704.7761 -872.9630 15h1m0s/Msamples 15800 -72580.4037 12.3 -71706.0252 -874.3785 15h1m19s/Msamples 15900 -72579.0911 12.9 -71694.4845 -884.6066 15h1m37s/Msamples 16000 -72576.5615 13.1 -71670.1554 -906.4061 15h2m17s/Msamples 16100 -72578.0177 13.2 -71663.2622 -914.7554 15h1m25s/Msamples 16200 -72577.7640 13.3 -71662.3612 -915.4028 15h1m19s/Msamples 16300 -72579.7631 13.3 -71663.2174 -916.5457 15h2m0s/Msamples 16400 -72579.3809 13.4 -71663.6195 -915.7613 15h2m21s/Msamples 16500 -72576.7686 13.5 -71661.9083 -914.8602 15h2m40s/Msamples 16600 -72575.8259 13.8 -71684.0991 -891.7267 15h2m30s/Msamples 16700 -72576.9240 13.9 -71686.5138 -890.4101 15h2m14s/Msamples 16800 -72575.5521 14.2 -71684.5258 -891.0262 15h2m11s/Msamples 16900 -72579.5589 14.5 -71688.3817 -891.1772 15h2m3s/Msamples 17000 -72575.7470 14.8 -71686.3420 -889.4050 15h1m38s/Msamples 17100 -72576.7840 14.9 -71687.4356 -889.3484 15h1m2s/Msamples 17200 -72576.2605 15.1 -71686.5741 -889.6863 15h0m31s/Msamples 17300 -72577.2132 15.3 -71674.6682 -902.5449 15h0m17s/Msamples 17400 -72579.1452 15.3 -71687.7650 -891.3802 14h59m59s/Msamples 17500 -72574.3521 15.7 -71682.1583 -892.1937 15h0m6s/Msamples 17600 -72575.7922 15.8 -71697.7038 -878.0883 15h0m18s/Msamples 17700 -72574.1840 16.1 -71696.2709 -877.9130 14h59m57s/Msamples 17800 -72578.2555 16.2 -71659.0026 -919.2529 14h59m26s/Msamples 17900 -72574.6787 16.5 -71657.9611 -916.7176 14h58m40s/Msamples 18000 -72574.2837 16.7 -71678.8742 -895.4095 14h58m56s/Msamples 18100 -72578.9594 16.8 -71682.1210 -896.8383 14h59m8s/Msamples 18200 -72572.7980 17.1 -71677.8709 -894.9271 14h58m50s/Msamples 18300 -72572.1076 17.3 -71677.0781 -895.0295 14h58m6s/Msamples 18400 -72571.7208 17.5 -71676.6979 -895.0229 14h58m11s/Msamples 18500 -72572.8937 17.4 -71676.8221 -896.0715 14h57m59s/Msamples 18600 -72573.7428 17.3 -71677.5512 -896.1915 14h59m25s/Msamples 18700 -72574.0619 17.2 -71678.7889 -895.2730 15h0m57s/Msamples 18800 -72573.0453 17.0 -71678.0518 -894.9935 15h3m41s/Msamples 18900 -72574.3575 16.2 -71667.0140 -907.3435 15h6m31s/Msamples 19000 -72573.7481 16.0 -71696.8386 -876.9095 15h8m46s/Msamples 19100 -72575.7179 15.9 -71699.5750 -876.1428 15h10m19s/Msamples 19200 -72575.3970 15.7 -71698.4677 -876.9293 15h12m26s/Msamples 19300 -72574.0667 15.5 -71680.4381 -893.6286 15h14m32s/Msamples 19400 -72576.0316 15.4 -71687.6752 -888.3563 15h17m10s/Msamples 19500 -72575.3068 15.3 -71689.8726 -885.4341 15h19m38s/Msamples 19600 -72574.9206 15.1 -71689.4475 -885.4730 15h22m11s/Msamples 19700 -72575.4930 15.0 -71689.8840 -885.6090 15h24m36s/Msamples 19800 -72574.2618 14.8 -71699.3575 -874.9042 15h27m20s/Msamples 19900 -72573.5979 14.3 -71700.0402 -873.5576 15h29m33s/Msamples 20000 -72573.8825 14.0 -71700.2942 -873.5882 15h31m33s/Msamples 20100 -72579.8616 14.6 -71705.2695 -874.5920 15h33m57s/Msamples 20200 -72576.6662 14.6 -71681.3313 -895.3348 15h36m11s/Msamples 20300 -72577.9560 14.8 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21900 -72571.6542 15.7 -71694.8754 -876.7787 15h49m30s/Msamples 22000 -72570.2147 15.6 -71673.9767 -896.2380 15h49m22s/Msamples 22100 -72577.3172 15.8 -71680.6348 -896.6823 15h49m6s/Msamples 22200 -72572.0777 15.7 -71672.3766 -899.7011 15h48m35s/Msamples 22300 -72574.0394 15.6 -71672.5772 -901.4621 15h48m30s/Msamples 22400 -72574.1735 15.4 -71672.1318 -902.0416 15h48m9s/Msamples 22500 -72572.8915 15.3 -71672.5616 -900.3298 15h47m45s/Msamples 22600 -72572.0111 15.0 -71685.0359 -886.9751 15h47m37s/Msamples 22700 -72574.6647 14.9 -71687.6372 -887.0274 15h47m33s/Msamples 22800 -72574.0039 14.8 -71661.2493 -912.7546 15h47m54s/Msamples 22900 -72576.2800 15.0 -71700.2248 -876.0551 15h47m50s/Msamples 23000 -72574.2254 14.9 -71661.3039 -912.9214 15h47m38s/Msamples 23100 -72574.3001 14.8 -71661.9245 -912.3755 15h46m57s/Msamples 23200 -72572.8615 14.5 -71660.5040 -912.3575 15h46m50s/Msamples 23300 -72577.0130 14.7 -71664.9528 -912.0601 15h46m40s/Msamples 23400 -72572.4526 14.4 -71659.6433 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