.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_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... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17550.8937] [GTR parameters ] . ( 1 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 1 sec) [ -17212.6966] [ 3954] [depth= 1] . ( 2 sec) [ -17202.5775] [ 3950] [depth= 1] . ( 2 sec) [ -17196.9828] [ 3954] [depth= 1] . ( 2 sec) [ -17184.6052] [ 3953] [depth= 1] . ( 2 sec) [ -17182.2111] [ 3953] [depth= 1] . ( 3 sec) [ -17181.9176] [ 3952] [depth= 3] . ( 3 sec) [ -17177.6260] [ 3953] [depth= 3] . ( 3 sec) [ -17176.7432] [ 3953] [depth= 1] . ( 3 sec) [ -17176.4351] [ 3953] [depth= 1] . ( 4 sec) [ -17176.2334] [ 3953] [depth= 1] . ( 4 sec) [ -17174.1250] [ 3952] [depth= 2] . ( 4 sec) [ -17165.9874] [ 3951] [depth= 2] . ( 4 sec) [ -17164.8320] [ 3950] [depth= 1] . ( 4 sec) [ -17164.5557] [ 3950] [depth= 1] . ( 4 sec) [ -17164.4619] [ 3950] [depth= 1] . ( 4 sec) [ -17164.3253] [ 3950] [depth= 1] . ( 5 sec) [ -17162.5691] [ 3954] [depth= 1] . ( 5 sec) [ -17158.5562] [ 3950] [depth= 1] . ( 5 sec) [ -17146.3606] [ 3965] [depth= 1] . ( 5 sec) [ -17108.9466] [ 3950] [depth= 1] . ( 5 sec) [ -17100.6938] [ 3961] [depth= 1] . ( 5 sec) [ -17085.7730] [ 3950] [depth= 1] . ( 6 sec) [ -17080.5463] [ 3951] [depth= 2] . ( 6 sec) [ -17068.0887] [ 3954] [depth= 1] . ( 6 sec) [ -17036.3245] [ 3952] [depth= 1] . ( 6 sec) [ -17024.0452] [ 3948] [depth= 1] . ( 6 sec) [ -17023.2515] [ 3951] [depth= 1] . ( 6 sec) [ -17021.2880] [ 3951] [depth= 2] . ( 6 sec) [ -17017.4984] [ 3953] [depth= 1] . ( 6 sec) [ -17014.3243] [ 3952] [depth= 2] . ( 7 sec) [ -17005.5897] [ 3951] [depth= 2] . ( 7 sec) [ -16988.1985] [ 3949] [depth= 1] . ( 7 sec) [ -16986.2214] [ 3944] [depth= 1] . ( 7 sec) [ -16982.8376] [ 3947] [depth= 1] . ( 7 sec) [ -16966.1956] [ 3948] [depth= 1] . ( 8 sec) [ -16959.8932] [ 3945] [depth= 1] . ( 8 sec) [ -16892.9637] [Branch lengths ] . ( 12 sec) [ -16421.5483] [GTR parameters ] . ( 13 sec) [ -16349.6117] [Alpha ][ 0.304752] . ( 13 sec) [ -16349.2289] [ 3945] [depth= 1] . ( 13 sec) [ -16348.2347] [ 3947] [depth= 1] . ( 15 sec) [ -16348.2199] [ 3948] [depth= 1] . ( 15 sec) [ -16339.9788] [ 3945] [depth= 1] . ( 16 sec) [ -16336.8580] [ 3944] [depth= 1] . ( 17 sec) [ -16331.4915] [ 3941] [depth= 1] . ( 18 sec) [ -16300.4522] [Branch lengths ] . ( 22 sec) [ -16282.3264] [GTR parameters ] . ( 22 sec) [ -16281.5505] [Alpha ][ 0.290587] . ( 27 sec) [ -16269.1854] [Branch lengths ] . ( 57 sec) [ -16268.9957] [ 3943] [depth= 1] . ( 72 sec) [ -16265.5286] [Branch lengths ] . ( 75 sec) [ -16260.7138] [GTR parameters ] . ( 75 sec) [ -16260.7082] [Alpha ][ 0.291698] . ( 139 sec) [ -16257.7392] [Branch lengths ] . ( 140 sec) [ -16257.7392] [Topology ] . ( 142 sec) [ -16256.3604] [Topology ] . ( 144 sec) [ -16255.7075] [Topology ] . ( 146 sec) [ -16255.4809] [Topology ] . ( 149 sec) [ -16255.3803] [Topology ] . ( 151 sec) [ -16255.3323] [Topology ] . ( 154 sec) [ -16255.3082] [Topology ] . ( 156 sec) [ -16255.2953] [Topology ] . ( 163 sec) [ -16254.0329] [GTR parameters ] . ( 163 sec) [ -16254.0322] [Alpha ][ 0.291205] . ( 163 sec) [ -16254.0322] [Topology ] . ( 166 sec) [ -16253.7108] [Topology ] . ( 168 sec) [ -16253.5891] [Topology ] . ( 170 sec) [ -16253.5284] [Topology ] . ( 173 sec) [ -16253.4966] [Topology ] . ( 175 sec) [ -16253.4796] [Topology ] . ( 178 sec) [ -16253.4705] [Topology ] . ( 183 sec) [ -16253.2984] [GTR parameters ] . ( 183 sec) [ -16253.2917] [Alpha ][ 0.289869] . ( 183 sec) [ -16253.2917] [Topology ] . ( 186 sec) [ -16253.2285] [Topology ] . ( 188 sec) [ -16253.2035] [Topology ] . ( 190 sec) [ -16253.1907] [Topology ] . ( 192 sec) [ -16253.1839] [Topology ] . ( 195 sec) [ -16253.1801] [Topology ] . ( 197 sec) [ -16253.1781] [Topology ] . ( 201 sec) [ -16253.1355] [GTR parameters ] . ( 201 sec) [ -16253.1334] [Alpha ][ 0.289094] . ( 201 sec) [ -16253.1334] [Topology ] . ( 204 sec) [ -16253.1183] [Topology ] . ( 206 sec) [ -16253.1123] [Topology ] . ( 209 sec) [ -16253.1092] [Topology ] . ( 211 sec) [ -16253.1076] [Topology ] . ( 213 sec) [ -16253.1066] [Topology ] . ( 215 sec) [ -16253.0970] [GTR parameters ] . ( 216 sec) [ -16253.0967] [Alpha ][ 0.288711] . ( 216 sec) [ -16253.0967] [Topology ] . ( 218 sec) [ -16253.0926] [Topology ] . ( 220 sec) [ -16253.0909] [Topology ] . ( 223 sec) [ -16253.0900] [Topology ] . ( 224 sec) [ -16253.0882] [GTR parameters ] . ( 224 sec) [ -16253.0882] [Alpha ][ 0.288711] . ( 224 sec) [ -16253.0882] [Topology ] . ( 226 sec) [ -16253.0867] [Topology ] . ( 228 sec) [ -16253.0860] [Topology ] . ( 229 sec) [ -16253.0855] [GTR parameters ] . ( 230 sec) [ -16253.0855] [Alpha ][ 0.288711] . ( 230 sec) [ -16253.0855] [Topology ] . ( 232 sec) [ -16253.0849] [Topology ] . ( 233 sec) [ -16253.0847] [GTR parameters ] . ( 233 sec) [ -16253.0846] [Alpha ][ 0.288423] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084629. . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 0h4m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 182.15user 0.00system 4:13.45elapsed 71%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps