.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -12703.7048] [GTR parameters ] . ( 5 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 6 sec) [ -12504.9636] [ 2715] [depth= 1] . ( 6 sec) [ -12504.7654] [ 2715] [depth= 1] . ( 9 sec) [ -12497.1136] [ 2715] [depth= 1] . ( 9 sec) [ -12493.5302] [ 2715] [depth= 1] . ( 9 sec) [ -12491.3616] [ 2715] [depth= 1] . ( 10 sec) [ -12483.4602] [ 2713] [depth= 2] . ( 10 sec) [ -12482.5118] [ 2713] [depth= 1] . ( 11 sec) [ -12482.4575] [ 2713] [depth= 1] . ( 11 sec) [ -12470.4830] [ 2713] [depth= 1] . ( 12 sec) [ -12466.0686] [ 2713] [depth= 1] . ( 12 sec) [ -12465.9179] [ 2713] [depth= 1] . ( 12 sec) [ -12449.2031] [ 2705] [depth= 1] . ( 12 sec) [ -12449.1587] [ 2705] [depth= 1] . ( 21 sec) [ -12437.2290] [ 2704] [depth= 1] . ( 21 sec) [ -12432.0204] [ 2705] [depth= 1] . ( 21 sec) [ -12431.2264] [ 2705] [depth= 1] . ( 21 sec) [ -12431.1803] [ 2705] [depth= 1] . ( 21 sec) [ -12414.3902] [ 2705] [depth= 1] . ( 29 sec) [ -12409.0498] [ 2715] [depth= 1] . ( 29 sec) [ -12380.3592] [ 2705] [depth= 1] . ( 38 sec) [ -12361.1851] [ 2704] [depth= 1] . ( 38 sec) [ -12360.6730] [ 2702] [depth= 1] . ( 41 sec) [ -12346.2915] [ 2689] [depth= 3] . ( 41 sec) [ -12344.0157] [ 2692] [depth= 1] . ( 41 sec) [ -12306.0855] [ 2697] [depth= 1] . ( 41 sec) [ -12294.8897] [ 2700] [depth= 1] . ( 41 sec) [ -12293.1638] [ 2702] [depth= 1] . ( 41 sec) [ -12292.6061] [ 2713] [depth= 2] . ( 43 sec) [ -12291.1069] [ 2703] [depth= 2] . ( 43 sec) [ -12289.7156] [ 2701] [depth= 1] . ( 44 sec) [ -12283.8015] [ 2692] [depth= 2] . ( 44 sec) [ -12271.8307] [ 2689] [depth= 2] . ( 44 sec) [ -12269.1053] [ 2694] [depth= 2] . ( 47 sec) [ -12267.0084] [ 2700] [depth= 2] . ( 47 sec) [ -12266.6919] [ 2700] [depth= 1] . ( 48 sec) [ -12258.4166] [ 2687] [depth= 3] . ( 48 sec) [ -12257.0286] [ 2692] [depth= 2] . ( 51 sec) [ -12253.0691] [ 2691] [depth= 1] . ( 51 sec) [ -12248.6148] [ 2692] [depth= 1] . ( 51 sec) [ -12242.3094] [ 2694] [depth= 1] . ( 52 sec) [ -12233.9417] [ 2703] [depth= 1] . ( 55 sec) [ -12233.8385] [ 2703] [depth= 1] . ( 55 sec) [ -12228.4471] [ 2707] [depth= 1] . ( 55 sec) [ -12227.8161] [ 2707] [depth= 1] . ( 56 sec) [ -12225.0158] [ 2702] [depth= 1] . ( 58 sec) [ -12210.7785] [ 2700] [depth= 1] . ( 59 sec) [ -12209.4467] [ 2707] [depth= 1] . ( 61 sec) [ -12198.3702] [ 2701] [depth= 1] . ( 69 sec) [ -12190.1944] [ 2701] [depth= 1] . ( 69 sec) [ -12188.4121] [ 2701] [depth= 1] . ( 72 sec) [ -12188.3875] [ 2701] [depth= 2] . ( 72 sec) [ -12187.8355] [ 2701] [depth= 1] . ( 73 sec) [ -12187.7112] [ 2701] [depth= 1] . ( 73 sec) [ -12187.4897] [ 2701] [depth= 1] . ( 91 sec) [ -12186.6214] [ 2701] [depth= 1] . ( 91 sec) [ -12184.5553] [ 2701] [depth= 1] . ( 92 sec) [ -12184.2747] [ 2701] [depth= 4] . ( 93 sec) [ -12184.2613] [ 2701] [depth= 7] . ( 103 sec) [ -12179.7037] [ 2702] [depth= 9] . ( 104 sec) [ -12175.5428] [ 2701] [depth= 9] . ( 104 sec) [ -12173.8047] [ 2700] [depth= 3] . ( 104 sec) [ -12172.5265] [ 2700] [depth= 3] . ( 106 sec) [ -12172.0806] [ 2700] [depth= 1] . ( 106 sec) [ -12171.8989] [ 2700] [depth= 1] . ( 107 sec) [ -12171.8570] [ 2700] [depth= 2] . ( 108 sec) [ -12171.8345] [ 2700] [depth= 6] . ( 108 sec) [ -12171.7958] [ 2700] [depth= 6] . ( 108 sec) [ -12171.7736] [ 2700] [depth= 3] . ( 140 sec) [ -12123.8193] [Branch lengths ] . ( 143 sec) [ -12103.9258] [GTR parameters ] . ( 144 sec) [ -12063.8899] [Alpha ][ 0.322361] . ( 148 sec) [ -12063.8635] [ 2700] [depth= 1] . ( 183 sec) [ -12059.7203] [ 2690] [depth= 1] . ( 208 sec) [ -12057.7186] [ 2705] [depth= 2] . ( 239 sec) [ -12050.8504] [ 2700] [depth= 5] . ( 239 sec) [ -12050.6990] [ 2678] [depth= 2] . ( 254 sec) [ -12050.0554] [ 2678] [depth= 1] . ( 254 sec) [ -12049.4188] [ 2678] [depth= 1] . ( 256 sec) [ -12049.3499] [ 2678] [depth= 1] . ( 270 sec) [ -12049.3131] [ 2678] [depth= 1] . ( 318 sec) [ -12049.2999] [ 2678] [depth= 1] . ( 318 sec) [ -12049.2880] [ 2678] [depth= 1] . ( 366 sec) [ -12039.0918] [Branch lengths ] . ( 368 sec) [ -12035.5188] [GTR parameters ] . ( 368 sec) [ -12035.1172] [Alpha ][ 0.309333] . ( 370 sec) [ -12035.0998] [ 2678] [depth= 1] . ( 383 sec) [ -12035.0667] [ 2678] [depth= 1] . ( 404 sec) [ -12035.0014] [ 2678] [depth= 1] . ( 462 sec) [ -12034.9882] [ 2678] [depth= 1] . ( 466 sec) [ -12033.9858] [ 2683] [depth= 2] . ( 599 sec) [ -12030.8814] [Branch lengths ] . ( 602 sec) [ -12030.4214] [GTR parameters ] . ( 602 sec) [ -12030.3996] [Alpha ][ 0.306292] . ( 622 sec) [ -12030.3747] [ 2683] [depth= 1] . ( 701 sec) [ -12028.6569] [ 2694] [depth= 6] . ( 833 sec) [ -12026.9520] [Branch lengths ] . ( 834 sec) [ -12026.7883] [GTR parameters ] . ( 835 sec) [ -12026.7391] [Alpha ][ 0.302129] . ( 852 sec) [ -12026.7279] [ 2694] [depth= 1] . ( 860 sec) [ -12026.6966] [ 2694] [depth= 1] . ( 935 sec) [ -12024.7466] [ 2678] [depth= 7] . ( 1067 sec) [ -12024.2303] [Branch lengths ] . ( 1069 sec) [ -12024.1940] [GTR parameters ] . ( 1069 sec) [ -12024.1927] [Alpha ][ 0.302804] . ( 1173 sec) [ -12023.8600] [ 2683] [depth= 2] . ( 1305 sec) [ -12023.5300] [Branch lengths ] . ( 1306 sec) [ -12023.5181] [GTR parameters ] . ( 1307 sec) [ -12023.5180] [Alpha ][ 0.302501] . ( 1383 sec) [ -12023.3241] [Branch lengths ] . ( 1383 sec) [ -12023.3241] [Topology ] . ( 1385 sec) [ -12023.2445] [Topology ] . ( 1387 sec) [ -12023.1054] [Topology ] . ( 1388 sec) [ -12022.8848] [Topology ] . ( 1390 sec) [ -12022.7802] [Topology ] . ( 1392 sec) [ -12022.7347] [Topology ] . ( 1394 sec) [ -12022.7149] [Topology ] . ( 1395 sec) [ -12022.7062] [GTR parameters ] . ( 1395 sec) [ -12022.7054] [Alpha ][ 0.301906] . ( 1395 sec) [ -12022.7054] [Topology ] . ( 1397 sec) [ -12022.6959] [Topology ] . ( 1399 sec) [ -12022.6918] [Topology ] . ( 1401 sec) [ -12022.6898] [Topology ] . ( 1403 sec) [ -12022.6889] [Topology ] . ( 1403 sec) [ -12022.6883] [GTR parameters ] . ( 1404 sec) [ -12022.6883] [Alpha ][ 0.301906] . ( 1404 sec) [ -12022.6883] [Topology ] . ( 1405 sec) [ -12022.6876] [Topology ] . ( 1406 sec) [ -12022.6876] [GTR parameters ] . ( 1406 sec) [ -12022.6876] [Alpha ][ 0.301906] . Checking for NNIs, optimizing five branches... . ( 1420 sec) [ -12022.6875] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1434 sec) [ -12022.6873] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12022.687348. . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 0h24m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1447.70user 0.00system 24:09.77elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps