.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2662_60x1348_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 664 patterns found. (out of a total of 1348 sites) . 794 sites without polymorphism (58.90%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -12871.6129] [GTR parameters ] . ( 4 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 14 sec) [ -12665.5249] [ 2217] [depth= 1] . ( 15 sec) [ -12664.1456] [ 2216] [depth= 1] . ( 19 sec) [ -12663.3354] [ 2216] [depth= 1] . ( 39 sec) [ -12661.6311] [ 2218] [depth= 2] . ( 39 sec) [ -12661.0790] [ 2219] [depth= 1] . ( 39 sec) [ -12653.9924] [ 2215] [depth= 1] . ( 40 sec) [ -12652.7357] [ 2219] [depth= 1] . ( 40 sec) [ -12650.1454] [ 2220] [depth= 1] . ( 42 sec) [ -12650.0086] [ 2219] [depth= 1] . ( 43 sec) [ -12648.4386] [ 2216] [depth= 2] . ( 43 sec) [ -12634.9783] [ 2220] [depth= 1] . ( 43 sec) [ -12633.2061] [ 2217] [depth= 1] . ( 43 sec) [ -12632.7527] [ 2218] [depth= 1] . ( 44 sec) [ -12620.6039] [ 2214] [depth= 1] . ( 48 sec) [ -12617.7329] [ 2214] [depth= 1] . ( 63 sec) [ -12615.3923] [ 2220] [depth= 3] . ( 63 sec) [ -12614.8796] [ 2224] [depth= 3] . ( 63 sec) [ -12613.4600] [ 2222] [depth= 4] . ( 69 sec) [ -12607.2825] [ 2225] [depth= 1] . ( 70 sec) [ -12607.1929] [ 2225] [depth= 1] . ( 70 sec) [ -12605.1808] [ 2222] [depth= 1] . ( 71 sec) [ -12603.8621] [ 2219] [depth= 3] . ( 71 sec) [ -12598.5731] [ 2223] [depth= 1] . ( 71 sec) [ -12598.4871] [ 2229] [depth= 1] . ( 77 sec) [ -12596.4592] [ 2231] [depth= 1] . ( 77 sec) [ -12594.1456] [ 2229] [depth= 1] . ( 81 sec) [ -12590.5600] [ 2227] [depth= 1] . ( 81 sec) [ -12588.6634] [ 2227] [depth= 1] . ( 81 sec) [ -12585.4610] [ 2220] [depth= 7] . ( 84 sec) [ -12572.4147] [ 2218] [depth= 1] . ( 85 sec) [ -12566.9567] [ 2217] [depth= 1] . ( 87 sec) [ -12562.4070] [ 2215] [depth= 1] . ( 87 sec) [ -12560.4637] [ 2217] [depth= 1] . ( 90 sec) [ -12558.9958] [ 2214] [depth= 1] . ( 90 sec) [ -12556.1670] [ 2215] [depth= 1] . ( 90 sec) [ -12552.0885] [ 2217] [depth= 2] . ( 90 sec) [ -12545.3087] [ 2215] [depth= 1] . ( 91 sec) [ -12544.6967] [ 2218] [depth= 1] . ( 92 sec) [ -12543.7033] [ 2220] [depth= 1] . ( 92 sec) [ -12542.1686] [ 2218] [depth= 1] . ( 92 sec) [ -12541.8196] [ 2220] [depth= 1] . ( 93 sec) [ -12538.0549] [ 2218] [depth= 1] . ( 93 sec) [ -12536.4165] [ 2218] [depth= 1] . ( 94 sec) [ -12536.1697] [ 2218] [depth= 2] . ( 95 sec) [ -12533.4257] [ 2217] [depth= 3] . ( 95 sec) [ -12532.8277] [ 2220] [depth= 2] . ( 97 sec) [ -12529.4534] [ 2217] [depth= 1] . ( 102 sec) [ -12527.3529] [ 2212] [depth= 2] . ( 105 sec) [ -12525.4196] [ 2212] [depth= 1] . ( 106 sec) [ -12440.0601] [Branch lengths ] . ( 109 sec) [ -12437.8136] [GTR parameters ] . ( 109 sec) [ -12376.1831] [Alpha ][ 0.289307] . ( 136 sec) [ -12375.3077] [ 2216] [depth= 2] . ( 143 sec) [ -12374.7325] [ 2217] [depth= 1] . ( 143 sec) [ -12374.2844] [ 2216] [depth= 1] . ( 143 sec) [ -12373.7396] [ 2216] [depth= 1] . ( 147 sec) [ -12373.3135] [ 2216] [depth= 1] . ( 149 sec) [ -12372.9661] [ 2217] [depth= 1] . ( 176 sec) [ -12371.2296] [ 2215] [depth= 2] . ( 177 sec) [ -12369.3831] [ 2214] [depth= 1] . ( 179 sec) [ -12369.3352] [ 2214] [depth= 1] . ( 186 sec) [ -12369.2709] [ 2218] [depth= 1] . ( 206 sec) [ -12365.2508] [ 2216] [depth= 5] . ( 211 sec) [ -12364.2169] [ 2211] [depth= 1] . ( 219 sec) [ -12363.9469] [ 2211] [depth= 1] . ( 227 sec) [ -12361.2841] [ 2208] [depth= 1] . ( 248 sec) [ -12350.1111] [Branch lengths ] . ( 251 sec) [ -12349.2836] [GTR parameters ] . ( 251 sec) [ -12349.2745] [Alpha ][ 0.291095] . ( 277 sec) [ -12349.2552] [ 2206] [depth= 1] . ( 293 sec) [ -12349.1990] [ 2202] [depth= 1] . ( 408 sec) [ -12347.3728] [Branch lengths ] . ( 409 sec) [ -12347.3271] [GTR parameters ] . ( 409 sec) [ -12347.3230] [Alpha ][ 0.292289] . ( 564 sec) [ -12347.0523] [Branch lengths ] . ( 630 sec) [ -12347.0089] [Branch lengths ] . ( 630 sec) [ -12347.0089] [Topology ] . ( 632 sec) [ -12347.0029] [Topology ] . ( 634 sec) [ -12346.9955] [Topology ] . ( 636 sec) [ -12346.9561] [Topology ] . ( 637 sec) [ -12346.7849] [Topology ] . ( 639 sec) [ -12346.7333] [Topology ] . ( 641 sec) [ -12346.7240] [Topology ] . ( 643 sec) [ -12346.7116] [GTR parameters ] . ( 643 sec) [ -12346.7093] [Alpha ][ 0.293167] . ( 643 sec) [ -12346.7093] [Topology ] . ( 645 sec) [ -12346.7067] [Topology ] . ( 647 sec) [ -12346.7058] [Topology ] . ( 648 sec) [ -12346.7057] [GTR parameters ] . ( 648 sec) [ -12346.7057] [Alpha ][ 0.293167] . ( 648 sec) [ -12346.7057] [Topology ] . ( 650 sec) [ -12346.7053] [Topology ] . ( 650 sec) [ -12346.7053] [GTR parameters ] . ( 650 sec) [ -12346.7053] [Alpha ][ 0.293167] . Checking for NNIs, optimizing five branches... . ( 663 sec) [ -12346.2905] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.290481. . Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'... . Time used 0h11m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 675.31user 0.00system 11:16.99elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps