stdout.txt

Public content shared with everyone by Mark Miller

stdout.txt (34530 bytes)

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

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