.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M3459_407x1707_2007.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 1071 patterns found. (out of a total of 1707 sites) . 908 sites without polymorphism (53.19%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 233Mo of memory space... . Maximizing likelihood (using NNI moves)... . ( 23 sec) [ -21655.1675] [GTR parameters ] . ( 26 sec) [ -21419.0313] [Alpha ][ 0.500960] . ( 27 sec) [ -21419.0313] [Topology ] . ( 62 sec) [ -21013.4855] [Topology ] . ( 97 sec) [ -20953.9724] [Topology ] . ( 131 sec) [ -20938.5254] [Topology ] . ( 164 sec) [ -20931.3750] [Topology ] . ( 197 sec) [ -20916.6595] [Topology ] . ( 229 sec) [ -20896.9186] [Topology ] . ( 261 sec) [ -20866.5134] [Topology ] . ( 293 sec) [ -20831.9079] [Topology ] . ( 324 sec) [ -20810.0789] [Topology ] . ( 401 sec) [ -19523.2901] [GTR parameters ] . ( 403 sec) [ -19452.3617] [Alpha ][ 0.299467] . ( 404 sec) [ -19452.3617] [Topology ] . ( 436 sec) [ -19404.7066] [Topology ] . ( 468 sec) [ -19396.5130] [Topology ] . ( 499 sec) [ -19395.9596] [Topology ] . ( 531 sec) [ -19394.2181] [Topology ] . ( 562 sec) [ -19395.4235] [Topology ] . Moving backward . ( 563 sec) [ -19394.1066] [Topology ] . ( 595 sec) [ -19394.5245] [Topology ] . Moving backward . ( 596 sec) [ -19393.8652] [Topology ] . ( 627 sec) [ -19393.8447] [Topology ] . Checking for NNIs, optimizing five branches... . ( 777 sec) [ -19393.8564] [Topology ] . ( 789 sec) [ -19389.0139] [GTR parameters ] . ( 791 sec) [ -19388.0615] [Alpha ][ 0.283239] . ( 791 sec) [ -19388.0615] [Topology ] . ( 823 sec) [ -19388.4956] [Topology ] . Moving backward . ( 824 sec) [ -19386.7968] [Topology ] . ( 855 sec) [ -19387.2495] [Topology ] . Moving backward . ( 857 sec) [ -19386.5402] [Topology ] . ( 888 sec) [ -19386.5960] [Topology ] . Moving backward . ( 889 sec) [ -19386.4941] [Topology ] . ( 920 sec) [ -19386.9511] [Topology ] . Moving backward . ( 922 sec) [ -19386.4643] [Topology ] . ( 953 sec) [ -19386.5018] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 1072 sec) [ -19386.0047] [Topology ] . ( 1078 sec) [ -19386.0008] [GTR parameters ] . ( 1080 sec) [ -19385.9778] [Alpha ][ 0.280718] . ( 1080 sec) [ -19385.9778] [Topology ] . ( 1111 sec) [ -19386.1131] [Topology ] . Moving backward . ( 1113 sec) [ -19385.9748] [Topology ] . ( 1144 sec) [ -19386.0990] [Topology ] . Moving backward . ( 1145 sec) [ -19385.9745] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1264 sec) [ -19385.9741] [Topology ] . ( 1277 sec) [ -19385.7811] [GTR parameters ] . ( 1278 sec) [ -19385.7786] [Alpha ][ 0.279865] . ( 1279 sec) [ -19385.7786] [Topology ] . ( 1310 sec) [ -19386.2429] [Topology ] . Moving backward . ( 1312 sec) [ -19385.7780] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1430 sec) [ -19385.3008] [Topology ] . ( 1436 sec) [ -19385.2979] [GTR parameters ] . ( 1437 sec) [ -19385.2978] [Alpha ][ 0.279585] . ( 1438 sec) [ -19385.2978] [Topology ] . ( 1469 sec) [ -19385.7053] [Topology ] . Moving backward . ( 1470 sec) [ -19385.2527] [Topology ] . ( 1502 sec) [ -19386.0723] [Topology ] . Moving backward . ( 1503 sec) [ -19385.2263] [Topology ] . ( 1534 sec) [ -19385.8186] [Topology ] . Moving backward . ( 1536 sec) [ -19385.1853] [Topology ] . ( 1567 sec) [ -19385.4723] [Topology ] . Moving backward . ( 1568 sec) [ -19385.1640] [Topology ] . ( 1600 sec) [ -19385.1997] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 1719 sec) [ -19385.1516] [Topology ] . ( 1729 sec) [ -19384.9986] [GTR parameters ] . ( 1730 sec) [ -19384.9986] [Alpha ][ 0.279585] . ( 1730 sec) [ -19384.9986] [Topology ] . ( 1762 sec) [ -19384.9862] [Topology ] . ( 1793 sec) [ -19384.9814] [Topology ] . ( 1824 sec) [ -19384.9779] [Topology ] . ( 1856 sec) [ -19384.9768] [Topology ] . ( 1887 sec) [ -19384.9896] [Topology ] . Moving backward . ( 1888 sec) [ -19384.9742] [Topology ] . ( 1919 sec) [ -19384.9852] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2038 sec) [ -19384.9681] [Topology ] . ( 2059 sec) [ -19383.2807] [GTR parameters ] . ( 2061 sec) [ -19383.2561] [Alpha ][ 0.277008] . ( 2062 sec) [ -19383.2561] [Topology ] . ( 2093 sec) [ -19383.1999] [Topology ] . ( 2124 sec) [ -19383.1780] [Topology ] . ( 2155 sec) [ -19383.1663] [Topology ] . ( 2187 sec) [ -19383.1594] [Topology ] . ( 2218 sec) [ -19383.1565] [Topology ] . ( 2249 sec) [ -19383.1634] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2367 sec) [ -19383.0667] [Topology ] . ( 2381 sec) [ -19383.0440] [GTR parameters ] . ( 2383 sec) [ -19383.0409] [Alpha ][ 0.277882] . ( 2384 sec) [ -19383.0409] [Topology ] . ( 2415 sec) [ -19383.0625] [Topology ] . Moving backward . ( 2416 sec) [ -19383.0212] [Topology ] . ( 2447 sec) [ -19383.0242] [Topology ] . Moving backward . ( 2449 sec) [ -19383.0133] [Topology ] . ( 2480 sec) [ -19383.0091] [Topology ] . ( 2511 sec) [ -19383.0146] [Topology ] . Moving backward . ( 2512 sec) [ -19383.0043] [Topology ] . ( 2544 sec) [ -19383.0020] [Topology ] . ( 2575 sec) [ -19383.0071] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2693 sec) [ -19382.9481] [Topology ] . ( 2707 sec) [ -19382.9375] [GTR parameters ] . ( 2709 sec) [ -19382.9339] [Alpha ][ 0.276882] . ( 2709 sec) [ -19382.9339] [Topology ] . ( 2740 sec) [ -19382.8994] [Topology ] . ( 2772 sec) [ -19383.0746] [Topology ] . Moving backward . ( 2773 sec) [ -19382.8619] [Topology ] . ( 2804 sec) [ -19382.8788] [Topology ] . Moving backward . ( 2805 sec) [ -19382.8510] [Topology ] . ( 2837 sec) [ -19382.8533] [Topology ] . Moving backward . ( 2838 sec) [ -19382.8460] [Topology ] . ( 2869 sec) [ -19382.8429] [Topology ] . ( 2900 sec) [ -19382.8465] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3018 sec) [ -19382.8359] [Topology ] . ( 3028 sec) [ -19382.8337] [GTR parameters ] . ( 3029 sec) [ -19382.8337] [Alpha ][ 0.276882] . ( 3030 sec) [ -19382.8337] [Topology ] . ( 3061 sec) [ -19382.8298] [Topology ] . ( 3092 sec) [ -19382.8264] [Topology ] . ( 3123 sec) [ -19382.8245] [Topology ] . ( 3154 sec) [ -19382.8239] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3272 sec) [ -19382.8233] [Topology ] . ( 3281 sec) [ -19382.8221] [GTR parameters ] . ( 3282 sec) [ -19382.8221] [Alpha ][ 0.276882] . ( 3283 sec) [ -19382.8221] [Topology ] . ( 3314 sec) [ -19382.8219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3432 sec) [ -19382.8218] [Topology ] . ( 3439 sec) [ -19382.8216] [GTR parameters ] . ( 3440 sec) [ -19382.8216] [Alpha ][ 0.276882] . ( 3441 sec) [ -19382.8216] [Topology ] . ( 3472 sec) [ -19382.8215] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3589 sec) [ -19382.8214] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3707 sec) [ -19382.8146] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3825 sec) [ -19382.8145] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3943 sec) [ -19382.8144] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4060 sec) [ -19382.8138] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4178 sec) [ -19382.8056] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4295 sec) [ -19382.8055] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4412 sec) [ -19382.8052] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4529 sec) [ -19382.8046] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4646 sec) [ -19382.8014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4764 sec) [ -19377.6763] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4881 sec) [ -19377.6758] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4999 sec) [ -19377.6756] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -19377.675629. . Printing the most likely tree in file 'nucleic_M3459_407x1707_2007.phy_phyml_tree.txt'... . Time used 1h25m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 5135.30user 0.00system 1:25:38elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps