.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2792_166x812_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 812 sites) . 322 sites without polymorphism (39.66%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 54Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 15 sec) [ -10920.5693] [GTR parameters ] . ( 16 sec) [ -10843.4467] [Alpha ][ 0.500960] . ( 27 sec) [ -10833.0450] [ 1899] [depth= 1] . ( 27 sec) [ -10824.3371] [ 1899] [depth= 1] . ( 48 sec) [ -10822.9897] [ 1899] [depth= 1] . ( 48 sec) [ -10791.3332] [ 1894] [depth= 4] . ( 92 sec) [ -10787.7700] [ 1900] [depth= 4] . ( 92 sec) [ -10786.7343] [ 1898] [depth= 2] . ( 93 sec) [ -10784.6686] [ 1897] [depth= 1] . ( 93 sec) [ -10782.8597] [ 1898] [depth= 1] . ( 98 sec) [ -10779.8119] [ 1897] [depth= 1] . ( 98 sec) [ -10777.0225] [ 1897] [depth= 5] . ( 110 sec) [ -10772.7606] [ 1896] [depth= 1] . ( 119 sec) [ -10772.7197] [ 1897] [depth= 1] . ( 149 sec) [ -10771.2569] [ 1898] [depth= 1] . ( 153 sec) [ -10771.2290] [ 1898] [depth= 1] . ( 177 sec) [ -10769.5962] [ 1898] [depth= 2] . ( 214 sec) [ -10768.6024] [ 1900] [depth= 1] . ( 220 sec) [ -10768.2622] [ 1900] [depth= 1] . ( 221 sec) [ -10767.9443] [ 1900] [depth= 1] . ( 221 sec) [ -10767.9018] [ 1900] [depth= 1] . ( 221 sec) [ -10767.8867] [ 1900] [depth= 2] . ( 266 sec) [ -10758.4171] [ 1899] [depth= 1] . ( 267 sec) [ -10757.1714] [ 1899] [depth= 1] . ( 295 sec) [ -10754.2624] [ 1898] [depth= 1] . ( 314 sec) [ -10754.1209] [ 1898] [depth= 1] . ( 314 sec) [ -10753.8373] [ 1898] [depth= 1] . ( 321 sec) [ -10752.6431] [ 1898] [depth= 2] . ( 336 sec) [ -10751.9580] [ 1899] [depth= 1] . ( 336 sec) [ -10751.5930] [ 1898] [depth= 2] . ( 337 sec) [ -10751.4808] [ 1898] [depth= 1] . ( 343 sec) [ -10749.7042] [ 1898] [depth= 2] . ( 343 sec) [ -10749.6720] [ 1898] [depth= 1] . ( 344 sec) [ -10749.2312] [ 1898] [depth= 4] . ( 344 sec) [ -10742.6917] [ 1897] [depth= 2] . ( 345 sec) [ -10742.6019] [ 1897] [depth= 2] . ( 345 sec) [ -10742.3033] [ 1897] [depth= 1] . ( 345 sec) [ -10742.1551] [ 1897] [depth= 1] . ( 359 sec) [ -10742.1126] [ 1897] [depth= 2] . ( 385 sec) [ -10740.0600] [ 1896] [depth= 3] . ( 385 sec) [ -10739.2581] [ 1898] [depth= 1] . ( 391 sec) [ -10735.2835] [ 1898] [depth= 1] . ( 397 sec) [ -10735.2683] [ 1898] [depth= 3] . ( 417 sec) [ -10735.2365] [ 1898] [depth= 2] . ( 423 sec) [ -10733.1754] [ 1896] [depth= 1] . ( 423 sec) [ -10732.1094] [ 1900] [depth= 1] . ( 446 sec) [ -10727.1094] [ 1898] [depth= 1] . ( 478 sec) [ -10724.9491] [ 1900] [depth= 1] . ( 498 sec) [ -10723.8601] [ 1900] [depth= 1] . ( 498 sec) [ -10723.3855] [ 1900] [depth= 1] . ( 505 sec) [ -10720.9137] [ 1899] [depth= 1] . ( 582 sec) [ -10720.8166] [ 1899] [depth= 1] . ( 583 sec) [ -10720.2273] [ 1899] [depth= 1] . ( 590 sec) [ -10719.4032] [ 1899] [depth= 1] . ( 591 sec) [ -10719.0059] [ 1899] [depth= 1] . ( 605 sec) [ -10718.9548] [ 1899] [depth= 1] . ( 627 sec) [ -10718.5547] [ 1900] [depth= 1] . ( 667 sec) [ -10717.7592] [ 1900] [depth= 1] . ( 668 sec) [ -10717.2338] [ 1900] [depth= 1] . ( 697 sec) [ -10717.1979] [ 1900] [depth= 1] . ( 697 sec) [ -10717.1702] [ 1900] [depth= 1] . ( 709 sec) [ -10717.0811] [ 1900] [depth= 1] . ( 716 sec) [ -10717.0563] [ 1900] [depth= 1] . ( 716 sec) [ -10716.5525] [ 1900] [depth= 1] . ( 717 sec) [ -10716.2026] [ 1900] [depth= 1] . ( 760 sec) [ -10716.1909] [ 1900] [depth= 1] . ( 761 sec) [ -10716.0771] [ 1900] [depth= 1] . ( 761 sec) [ -10716.0419] [ 1900] [depth= 1] . ( 762 sec) [ -10716.0317] [ 1900] [depth= 1] . ( 783 sec) [ -10714.4824] [ 1900] [depth= 1] . ( 811 sec) [ -10713.6162] [ 1900] [depth= 1] . ( 811 sec) [ -10713.1598] [ 1900] [depth= 1] . ( 823 sec) [ -10713.0941] [ 1900] [depth= 1] . ( 829 sec) [ -10712.9287] [ 1900] [depth= 2] . ( 829 sec) [ -10711.6145] [ 1900] [depth= 1] . ( 830 sec) [ -10710.9986] [ 1899] [depth= 2] . ( 831 sec) [ -10710.8121] [ 1899] [depth= 1] . ( 831 sec) [ -10710.7972] [ 1900] [depth= 2] . ( 838 sec) [ -10710.7448] [ 1900] [depth= 1] . ( 838 sec) [ -10710.5032] [ 1900] [depth= 1] . ( 839 sec) [ -10710.3816] [ 1900] [depth= 2] . ( 839 sec) [ -10710.1893] [ 1900] [depth= 2] . ( 840 sec) [ -10709.8904] [ 1900] [depth= 2] . ( 841 sec) [ -10709.8647] [ 1900] [depth= 2] . ( 842 sec) [ -10709.4140] [ 1899] [depth= 2] . ( 849 sec) [ -10709.2789] [ 1899] [depth= 2] . ( 855 sec) [ -10709.2422] [ 1899] [depth= 3] . ( 862 sec) [ -10709.0230] [ 1899] [depth= 4] . ( 876 sec) [ -10708.1173] [ 1901] [depth= 1] . ( 901 sec) [ -10707.6263] [ 1903] [depth= 1] . ( 901 sec) [ -10694.0966] [ 1901] [depth= 1] . ( 922 sec) [ -10692.7690] [ 1904] [depth= 1] . ( 945 sec) [ -10691.8148] [ 1902] [depth= 2] . ( 946 sec) [ -10690.2160] [ 1901] [depth= 1] . ( 947 sec) [ -10689.6307] [ 1902] [depth= 1] . ( 951 sec) [ -10688.4438] [ 1900] [depth= 1] . ( 951 sec) [ -10684.5397] [ 1900] [depth= 2] . ( 951 sec) [ -10678.7605] [ 1897] [depth= 1] . ( 970 sec) [ -10675.4691] [ 1895] [depth= 1] . ( 997 sec) [ -10675.1889] [ 1896] [depth= 3] . ( 1002 sec) [ -10675.0112] [ 1901] [depth= 1] . ( 1009 sec) [ -10669.1219] [ 1899] [depth= 1] . ( 1015 sec) [ -10668.8527] [ 1900] [depth= 1] . ( 1021 sec) [ -10668.7705] [ 1900] [depth= 1] . ( 1021 sec) [ -10668.5349] [ 1900] [depth= 1] . ( 1022 sec) [ -10668.0237] [ 1900] [depth= 1] . ( 1028 sec) [ -10668.0069] [ 1900] [depth= 2] . ( 1043 sec) [ -10667.6890] [ 1900] [depth= 1] . ( 1043 sec) [ -10667.5822] [ 1900] [depth= 1] . ( 1044 sec) [ -10667.5545] [ 1900] [depth= 2] . ( 1044 sec) [ -10667.5300] [ 1900] [depth= 1] . ( 1088 sec) [ -10667.1652] [ 1899] [depth= 2] . ( 1089 sec) [ -10666.9005] [ 1899] [depth= 1] . ( 1096 sec) [ -10666.7841] [ 1899] [depth= 1] . ( 1096 sec) [ -10666.7325] [ 1899] [depth= 2] . ( 1115 sec) [ -10666.5745] [ 1900] [depth= 1] . ( 1116 sec) [ -10665.5487] [ 1899] [depth= 1] . ( 1121 sec) [ -10665.1068] [ 1899] [depth= 1] . ( 1159 sec) [ -10664.8612] [ 1900] [depth= 1] . ( 1185 sec) [ -10664.6817] [ 1899] [depth= 1] . ( 1186 sec) [ -10664.2561] [ 1899] [depth= 1] . ( 1186 sec) [ -10664.2373] [ 1899] [depth= 1] . ( 1215 sec) [ -10664.0278] [ 1901] [depth= 1] . ( 1215 sec) [ -10663.4971] [ 1901] [depth= 2] . ( 1216 sec) [ -10661.3781] [ 1899] [depth= 1] . ( 1217 sec) [ -10658.9406] [ 1899] [depth= 1] . ( 1250 sec) [ -10658.5083] [ 1899] [depth= 2] . ( 1251 sec) [ -10658.0784] [ 1899] [depth= 3] . ( 1258 sec) [ -10658.0681] [ 1899] [depth= 1] . ( 1267 sec) [ -10656.8775] [ 1899] [depth= 2] . ( 1267 sec) [ -10656.5449] [ 1899] [depth= 1] . ( 1268 sec) [ -10655.9821] [ 1898] [depth= 2] . ( 1268 sec) [ -10655.8121] [ 1897] [depth= 1] . ( 1268 sec) [ -10655.5944] [ 1897] [depth= 1] . ( 1277 sec) [ -10655.3865] [ 1897] [depth= 1] . ( 1278 sec) [ -10654.9839] [ 1897] [depth= 1] . ( 1279 sec) [ -10654.4772] [ 1897] [depth= 2] . ( 1302 sec) [ -10653.6470] [ 1897] [depth= 1] . ( 1332 sec) [ -10649.4404] [ 1896] [depth= 2] . ( 1393 sec) [ -10649.3439] [ 1896] [depth= 2] . ( 1393 sec) [ -10648.7012] [ 1896] [depth= 2] . ( 1394 sec) [ -10648.6827] [ 1896] [depth= 1] . ( 1394 sec) [ -10648.5212] [ 1896] [depth= 3] . ( 1395 sec) [ -10648.4433] [ 1896] [depth= 1] . ( 1395 sec) [ -10648.3984] [ 1896] [depth= 3] . ( 1396 sec) [ -10648.3849] [ 1896] [depth= 1] . ( 1397 sec) [ -10648.2173] [ 1896] [depth= 1] . ( 1397 sec) [ -10648.1882] [ 1896] [depth= 2] . ( 1439 sec) [ -10600.0419] [Branch lengths ] . ( 1453 sec) [ -10598.7086] [GTR parameters ] . ( 1454 sec) [ -10598.5154] [Alpha ][ 0.482455] . ( 1567 sec) [ -10598.1319] [ 1894] [depth= 1] . ( 1568 sec) [ -10597.5458] [ 1892] [depth= 1] . ( 1581 sec) [ -10596.6204] [ 1894] [depth= 1] . ( 1600 sec) [ -10596.5657] [ 1893] [depth= 1] . ( 1962 sec) [ -10595.3529] [ 1893] [depth= 5] . ( 1968 sec) [ -10595.2660] [ 1893] [depth= 1] . ( 1968 sec) [ -10595.2435] [ 1893] [depth= 4] . ( 2005 sec) [ -10583.2998] [ 1890] [depth= 8] . ( 2032 sec) [ -10583.2870] [ 1890] [depth= 3] . ( 2118 sec) [ -10583.2260] [ 1889] [depth= 1] . ( 2656 sec) [ -10582.8420] [ 1894] [depth= 1] . ( 2658 sec) [ -10582.6851] [ 1889] [depth= 1] . ( 3024 sec) [ -10582.4294] [ 1889] [depth= 1] . ( 3052 sec) [ -10582.3599] [ 1889] [depth= 1] . ( 3175 sec) [ -10582.3411] [ 1889] [depth= 1] . ( 3380 sec) [ -10573.7131] [Branch lengths ] . ( 3388 sec) [ -10573.6086] [GTR parameters ] . ( 3389 sec) [ -10573.5560] [Alpha ][ 0.492030] . ( 3425 sec) [ -10572.9751] [ 1889] [depth= 4] . ( 3466 sec) [ -10572.8779] [ 1891] [depth= 1] . ( 3796 sec) [ -10572.8165] [ 1891] [depth= 2] . ( 5050 sec) [ -10570.6196] [Branch lengths ] . ( 5054 sec) [ -10570.6137] [GTR parameters ] . ( 5054 sec) [ -10570.6012] [Alpha ][ 0.496701] . ( 5133 sec) [ -10570.5765] [ 1889] [depth= 1] . ( 6650 sec) [ -10569.1346] [Branch lengths ] . ( 6657 sec) [ -10569.1304] [GTR parameters ] . ( 6658 sec) [ -10569.1301] [Alpha ][ 0.497339] . ( 7942 sec) [ -10569.0015] [Branch lengths ] . ( 7971 sec) [ -10568.9593] [ 1891] [depth= 1] . ( 8189 sec) [ -10567.8606] [Branch lengths ] . ( 8193 sec) [ -10567.8533] [GTR parameters ] . ( 8194 sec) [ -10567.8532] [Alpha ][ 0.496842] . ( 8221 sec) [ -10567.7427] [ 1897] [depth= 3] . ( 8224 sec) [ -10567.5220] [ 1899] [depth= 1] . ( 8265 sec) [ -10566.8164] [ 1900] [depth= 3] . ( 8356 sec) [ -10561.8174] [ 1895] [depth= 1] . ( 8446 sec) [ -10557.5869] [Branch lengths ] . ( 8452 sec) [ -10557.3847] [GTR parameters ] . ( 8452 sec) [ -10557.3841] [Alpha ][ 0.495731] . ( 8457 sec) [ -10557.0466] [ 1892] [depth= 1] . ( 8708 sec) [ -10555.1663] [Branch lengths ] . ( 8711 sec) [ -10555.1658] [GTR parameters ] . ( 8712 sec) [ -10555.1656] [Alpha ][ 0.494975] . ( 8960 sec) [ -10555.1317] [Branch lengths ] . ( 8961 sec) [ -10555.1317] [Topology ] . ( 8965 sec) [ -10555.1297] [Topology ] . ( 8970 sec) [ -10555.1290] [Topology ] . ( 8972 sec) [ -10555.1288] [GTR parameters ] . ( 8972 sec) [ -10555.1288] [Alpha ][ 0.494975] . ( 8972 sec) [ -10555.1288] [Topology ] . ( 8977 sec) [ -10555.1283] [Topology ] . ( 8978 sec) [ -10555.1283] [GTR parameters ] . ( 8978 sec) [ -10555.1283] [Alpha ][ 0.494975] . Checking for NNIs, optimizing five branches... . ( 9010 sec) [ -10555.1070] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10555.107001. . Printing the most likely tree in file 'nucleic_M2792_166x812_2006.phy_phyml_tree.txt'... . Time used 2h30m42s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 6876.37user 0.00system 2:30:44elapsed 76%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps