.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2564_142x1130_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 . Compressing sequences... . 780 patterns found. (out of a total of 1130 sites) . 486 sites without polymorphism (43.01%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 8 sec) [ -21575.3354] [GTR parameters ] . ( 9 sec) [ -21206.7214] [Alpha ][ 0.500960] . ( 9 sec) [ -21206.1411] [ 4073] [depth= 1] . ( 10 sec) [ -21199.5150] [ 4077] [depth= 1] . ( 11 sec) [ -21185.9218] [ 4073] [depth= 1] . ( 11 sec) [ -21171.3223] [ 4059] [depth= 1] . ( 11 sec) [ -21169.7149] [ 4065] [depth= 1] . ( 13 sec) [ -21169.1018] [ 4076] [depth= 1] . ( 14 sec) [ -21148.9782] [ 4065] [depth= 1] . ( 15 sec) [ -21148.1301] [ 4070] [depth= 1] . ( 15 sec) [ -21138.2511] [ 4065] [depth= 1] . ( 16 sec) [ -21132.9040] [ 4069] [depth= 1] . ( 16 sec) [ -21118.3850] [ 4065] [depth= 1] . ( 17 sec) [ -21116.7828] [ 4067] [depth= 1] . ( 17 sec) [ -21107.9046] [ 4065] [depth= 1] . ( 19 sec) [ -21102.4914] [ 4078] [depth= 1] . ( 19 sec) [ -21073.9168] [ 4065] [depth= 1] . ( 20 sec) [ -21072.3112] [ 4069] [depth= 1] . ( 21 sec) [ -21045.5814] [ 4078] [depth= 4] . ( 22 sec) [ -21040.0925] [ 4074] [depth= 1] . ( 22 sec) [ -21039.7956] [ 4069] [depth= 1] . ( 25 sec) [ -21032.6965] [ 4072] [depth= 1] . ( 25 sec) [ -21030.1875] [ 4071] [depth= 1] . ( 26 sec) [ -21025.5930] [ 4072] [depth= 1] . ( 26 sec) [ -21016.9708] [ 4070] [depth= 2] . ( 28 sec) [ -21016.2407] [ 4071] [depth= 1] . ( 28 sec) [ -21015.4072] [ 4070] [depth= 1] . ( 28 sec) [ -21010.3359] [ 4069] [depth= 1] . ( 29 sec) [ -21005.1078] [ 4070] [depth= 1] . ( 30 sec) [ -21000.9905] [ 4071] [depth= 1] . ( 31 sec) [ -20972.4034] [ 4067] [depth= 4] . ( 32 sec) [ -20962.7287] [ 4062] [depth= 1] . ( 34 sec) [ -20962.0933] [ 4062] [depth= 1] . ( 35 sec) [ -20955.2444] [ 4059] [depth= 12] . ( 37 sec) [ -20946.9932] [ 4058] [depth= 6] . ( 37 sec) [ -20938.7663] [ 4057] [depth= 2] . ( 38 sec) [ -20938.5902] [ 4058] [depth= 1] . ( 39 sec) [ -20919.3426] [ 4053] [depth= 4] . ( 39 sec) [ -20917.4903] [ 4053] [depth= 2] . ( 40 sec) [ -20917.1720] [ 4053] [depth= 1] . ( 40 sec) [ -20916.9943] [ 4053] [depth= 1] . ( 41 sec) [ -20906.7166] [ 4051] [depth= 2] . ( 41 sec) [ -20900.3946] [ 4050] [depth= 1] . ( 42 sec) [ -20894.7657] [ 4052] [depth= 1] . ( 43 sec) [ -20892.1549] [ 4052] [depth= 2] . ( 43 sec) [ -20891.4766] [ 4052] [depth= 1] . ( 44 sec) [ -20890.8791] [ 4052] [depth= 1] . ( 44 sec) [ -20883.4743] [ 4050] [depth= 6] . ( 45 sec) [ -20883.4294] [ 4050] [depth= 1] . ( 45 sec) [ -20882.2483] [ 4049] [depth= 1] . ( 49 sec) [ -20881.6852] [ 4049] [depth= 1] . ( 49 sec) [ -20881.6560] [ 4050] [depth= 2] . ( 50 sec) [ -20879.8979] [ 4050] [depth= 2] . ( 51 sec) [ -20879.1862] [ 4050] [depth= 1] . ( 52 sec) [ -20878.2773] [ 4050] [depth= 1] . ( 52 sec) [ -20878.0937] [ 4050] [depth= 1] . ( 54 sec) [ -20877.9801] [ 4050] [depth= 1] . ( 54 sec) [ -20877.6356] [ 4050] [depth= 1] . ( 55 sec) [ -20876.7066] [ 4050] [depth= 1] . ( 55 sec) [ -20874.4786] [ 4050] [depth= 1] . ( 56 sec) [ -20873.0381] [ 4052] [depth= 1] . ( 57 sec) [ -20866.1171] [ 4050] [depth= 1] . ( 58 sec) [ -20866.0287] [ 4050] [depth= 1] . ( 58 sec) [ -20861.8383] [ 4049] [depth= 1] . ( 59 sec) [ -20861.6021] [ 4049] [depth= 1] . ( 59 sec) [ -20861.3241] [ 4049] [depth= 2] . ( 59 sec) [ -20855.9549] [ 4048] [depth= 1] . ( 60 sec) [ -20851.7567] [ 4047] [depth= 1] . ( 61 sec) [ -20848.8063] [ 4047] [depth= 1] . ( 63 sec) [ -20842.9537] [ 4046] [depth= 1] . ( 63 sec) [ -20841.4747] [ 4047] [depth= 1] . ( 64 sec) [ -20838.1945] [ 4046] [depth= 1] . ( 65 sec) [ -20834.6172] [ 4046] [depth= 1] . ( 67 sec) [ -20830.0067] [ 4046] [depth= 1] . ( 67 sec) [ -20829.8379] [ 4046] [depth= 1] . ( 68 sec) [ -20828.0566] [ 4046] [depth= 1] . ( 69 sec) [ -20827.9767] [ 4045] [depth= 1] . ( 69 sec) [ -20825.2898] [ 4048] [depth= 1] . ( 69 sec) [ -20822.7316] [ 4045] [depth= 1] . ( 70 sec) [ -20810.8250] [ 4042] [depth= 8] . ( 70 sec) [ -20806.7549] [ 4041] [depth= 1] . ( 71 sec) [ -20804.8078] [ 4040] [depth= 1] . ( 72 sec) [ -20803.7398] [ 4041] [depth= 3] . ( 72 sec) [ -20791.0381] [ 4038] [depth= 3] . ( 74 sec) [ -20790.4114] [ 4040] [depth= 1] . ( 76 sec) [ -20784.4915] [ 4036] [depth= 5] . ( 77 sec) [ -20779.2143] [ 4037] [depth= 4] . ( 77 sec) [ -20777.2141] [ 4039] [depth= 1] . ( 78 sec) [ -20777.1425] [ 4035] [depth= 3] . ( 78 sec) [ -20775.7280] [ 4037] [depth= 1] . ( 79 sec) [ -20775.6264] [ 4036] [depth= 3] . ( 79 sec) [ -20769.1635] [ 4034] [depth= 5] . ( 80 sec) [ -20761.7539] [ 4031] [depth= 6] . ( 80 sec) [ -20760.3252] [ 4031] [depth= 3] . ( 81 sec) [ -20752.3416] [ 4030] [depth= 4] . ( 81 sec) [ -20750.6503] [ 4032] [depth= 1] . ( 82 sec) [ -20742.1223] [ 4030] [depth= 1] . ( 82 sec) [ -20741.7763] [ 4028] [depth= 1] . ( 83 sec) [ -20741.7330] [ 4029] [depth= 1] . ( 84 sec) [ -20741.2096] [ 4029] [depth= 1] . ( 84 sec) [ -20740.8980] [ 4028] [depth= 4] . ( 85 sec) [ -20740.6994] [ 4028] [depth= 1] . ( 85 sec) [ -20740.4934] [ 4030] [depth= 1] . ( 85 sec) [ -20739.6446] [ 4030] [depth= 1] . ( 86 sec) [ -20739.0956] [ 4030] [depth= 1] . ( 87 sec) [ -20738.8787] [ 4028] [depth= 1] . ( 87 sec) [ -20738.3044] [ 4027] [depth= 1] . ( 88 sec) [ -20737.3994] [ 4027] [depth= 1] . ( 88 sec) [ -20737.2987] [ 4027] [depth= 1] . ( 91 sec) [ -20541.9224] [Branch lengths ] . ( 99 sec) [ -20533.5018] [GTR parameters ] . ( 99 sec) [ -20475.2607] [Alpha ][ 0.336881] . ( 100 sec) [ -20472.5052] [ 4027] [depth= 1] . ( 102 sec) [ -20471.9945] [ 4032] [depth= 1] . ( 108 sec) [ -20469.1135] [ 4033] [depth= 1] . ( 109 sec) [ -20468.9828] [ 4032] [depth= 1] . ( 110 sec) [ -20466.3896] [ 4032] [depth= 1] . ( 119 sec) [ -20466.2460] [ 4032] [depth= 1] . ( 121 sec) [ -20464.6569] [ 4030] [depth= 1] . ( 122 sec) [ -20464.4577] [ 4030] [depth= 1] . ( 128 sec) [ -20464.4441] [ 4030] [depth= 1] . ( 132 sec) [ -20464.0890] [ 4033] [depth= 1] . ( 136 sec) [ -20463.9793] [ 4033] [depth= 1] . ( 138 sec) [ -20463.9510] [ 4033] [depth= 1] . ( 145 sec) [ -20463.9374] [ 4033] [depth= 1] . ( 146 sec) [ -20463.2237] [ 4032] [depth= 1] . ( 147 sec) [ -20463.1286] [ 4032] [depth= 1] . ( 147 sec) [ -20463.0920] [ 4032] [depth= 1] . ( 149 sec) [ -20462.7025] [ 4033] [depth= 1] . ( 150 sec) [ -20462.0152] [ 4033] [depth= 1] . ( 152 sec) [ -20461.9299] [ 4034] [depth= 1] . ( 157 sec) [ -20461.7296] [ 4033] [depth= 5] . ( 157 sec) [ -20460.8713] [ 4032] [depth= 2] . ( 160 sec) [ -20459.5836] [ 4032] [depth= 1] . ( 162 sec) [ -20459.5430] [ 4032] [depth= 1] . ( 163 sec) [ -20459.4775] [ 4032] [depth= 1] . ( 164 sec) [ -20459.4616] [ 4032] [depth= 1] . ( 166 sec) [ -20434.3834] [Branch lengths ] . ( 172 sec) [ -20433.3674] [GTR parameters ] . ( 172 sec) [ -20433.3633] [Alpha ][ 0.337891] . ( 180 sec) [ -20433.0602] [ 4031] [depth= 2] . ( 181 sec) [ -20431.1159] [ 4031] [depth= 2] . ( 214 sec) [ -20431.1031] [ 4031] [depth= 1] . ( 224 sec) [ -20430.9182] [ 4029] [depth= 1] . ( 245 sec) [ -20427.7920] [Branch lengths ] . ( 251 sec) [ -20427.7775] [GTR parameters ] . ( 252 sec) [ -20427.7488] [Alpha ][ 0.340666] . ( 320 sec) [ -20427.2875] [Branch lengths ] . ( 360 sec) [ -20426.2673] [ 4033] [depth= 1] . ( 382 sec) [ -20426.1048] [ 4042] [depth= 2] . ( 383 sec) [ -20424.5998] [ 4044] [depth= 1] . ( 783 sec) [ -20423.1779] [Branch lengths ] . ( 789 sec) [ -20423.1504] [GTR parameters ] . ( 790 sec) [ -20423.1500] [Alpha ][ 0.341007] . ( 799 sec) [ -20421.9087] [ 4047] [depth= 1] . ( 846 sec) [ -20421.4377] [ 4048] [depth= 3] . ( 847 sec) [ -20420.7576] [ 4047] [depth= 1] . ( 854 sec) [ -20420.7024] [ 4048] [depth= 1] . ( 856 sec) [ -20420.5906] [ 4047] [depth= 1] . ( 1213 sec) [ -20417.1974] [Branch lengths ] . ( 1215 sec) [ -20417.1871] [GTR parameters ] . ( 1216 sec) [ -20417.1860] [Alpha ][ 0.341490] . ( 1287 sec) [ -20417.1497] [ 4041] [depth= 1] . ( 1657 sec) [ -20414.6953] [Branch lengths ] . ( 1658 sec) [ -20414.6950] [GTR parameters ] . ( 1659 sec) [ -20414.6949] [Alpha ][ 0.341832] . ( 2097 sec) [ -20411.3437] [Branch lengths ] . ( 2097 sec) [ -20411.3437] [Topology ] . ( 2107 sec) [ -20407.0676] [Topology ] . ( 2115 sec) [ -20406.3143] [Topology ] . ( 2125 sec) [ -20406.2207] [Topology ] . ( 2134 sec) [ -20406.2066] [Topology ] . ( 2144 sec) [ -20406.2031] [Topology ] . ( 2153 sec) [ -20406.2018] [Topology ] . ( 2162 sec) [ -20406.2012] [Topology ] . ( 2167 sec) [ -20406.1975] [GTR parameters ] . ( 2168 sec) [ -20406.1960] [Alpha ][ 0.342408] . ( 2169 sec) [ -20406.1960] [Topology ] . ( 2177 sec) [ -20406.1955] [Topology ] . ( 2179 sec) [ -20406.1955] [GTR parameters ] . ( 2180 sec) [ -20406.1955] [Alpha ][ 0.342408] . Checking for NNIs, optimizing five branches... . ( 2241 sec) [ -20406.1954] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -20406.195359. . Printing the most likely tree in file 'nucleic_M2564_142x1130_2006.phy_phyml_tree.txt'... . Time used 0h38m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1326.61user 0.00system 38:24.53elapsed 57%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps