.......................... 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 ] . ( 6 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 6 sec) [ -12504.9636] [ 2715] [depth= 1] . ( 6 sec) [ -12504.7654] [ 2715] [depth= 1] . ( 6 sec) [ -12497.1136] [ 2715] [depth= 1] . ( 6 sec) [ -12493.5302] [ 2715] [depth= 1] . ( 6 sec) [ -12491.3616] [ 2715] [depth= 1] . ( 7 sec) [ -12483.4602] [ 2713] [depth= 2] . ( 7 sec) [ -12482.5118] [ 2713] [depth= 1] . ( 7 sec) [ -12482.4575] [ 2713] [depth= 1] . ( 7 sec) [ -12470.4830] [ 2713] [depth= 1] . ( 7 sec) [ -12466.0686] [ 2713] [depth= 1] . ( 7 sec) [ -12465.9179] [ 2713] [depth= 1] . ( 7 sec) [ -12449.2031] [ 2705] [depth= 1] . ( 7 sec) [ -12449.1587] [ 2705] [depth= 1] . ( 8 sec) [ -12437.2290] [ 2704] [depth= 1] . ( 8 sec) [ -12432.0204] [ 2705] [depth= 1] . ( 8 sec) [ -12431.2264] [ 2705] [depth= 1] . ( 8 sec) [ -12431.1803] [ 2705] [depth= 1] . ( 9 sec) [ -12414.3902] [ 2705] [depth= 1] . ( 9 sec) [ -12397.8831] [ 2704] [depth= 1] . ( 10 sec) [ -12388.4419] [ 2704] [depth= 1] . ( 10 sec) [ -12357.7085] [ 2703] [depth= 4] . ( 10 sec) [ -12340.0539] [ 2692] [depth= 4] . ( 10 sec) [ -12337.3933] [ 2693] [depth= 1] . ( 10 sec) [ -12290.3349] [ 2697] [depth= 1] . ( 10 sec) [ -12276.7111] [ 2700] [depth= 1] . ( 10 sec) [ -12275.6885] [ 2702] [depth= 2] . ( 11 sec) [ -12275.1313] [ 2706] [depth= 1] . ( 11 sec) [ -12274.3385] [ 2703] [depth= 1] . ( 11 sec) [ -12272.9383] [ 2701] [depth= 1] . ( 11 sec) [ -12266.5292] [ 2692] [depth= 2] . ( 11 sec) [ -12256.4860] [ 2690] [depth= 2] . ( 12 sec) [ -12252.4458] [ 2688] [depth= 1] . ( 12 sec) [ -12248.8610] [ 2682] [depth= 2] . ( 12 sec) [ -12248.1344] [ 2687] [depth= 2] . ( 12 sec) [ -12246.6557] [ 2687] [depth= 1] . ( 13 sec) [ -12246.3006] [ 2689] [depth= 1] . ( 13 sec) [ -12217.8872] [ 2684] [depth= 1] . ( 14 sec) [ -12209.5068] [ 2684] [depth= 1] . ( 14 sec) [ -12207.6577] [ 2684] [depth= 1] . ( 15 sec) [ -12207.6325] [ 2684] [depth= 2] . ( 15 sec) [ -12207.0453] [ 2684] [depth= 1] . ( 15 sec) [ -12206.9176] [ 2684] [depth= 1] . ( 15 sec) [ -12206.6771] [ 2684] [depth= 1] . ( 20 sec) [ -12205.6860] [ 2684] [depth= 1] . ( 20 sec) [ -12203.4087] [ 2684] [depth= 1] . ( 21 sec) [ -12203.3920] [ 2684] [depth= 6] . ( 21 sec) [ -12203.3687] [ 2684] [depth= 7] . ( 22 sec) [ -12198.4249] [ 2685] [depth= 9] . ( 22 sec) [ -12194.4738] [ 2684] [depth= 9] . ( 22 sec) [ -12192.8649] [ 2683] [depth= 3] . ( 22 sec) [ -12191.5426] [ 2683] [depth= 3] . ( 23 sec) [ -12191.0843] [ 2683] [depth= 1] . ( 23 sec) [ -12190.8974] [ 2683] [depth= 1] . ( 24 sec) [ -12190.8719] [ 2683] [depth= 2] . ( 24 sec) [ -12190.8488] [ 2683] [depth= 6] . ( 24 sec) [ -12190.8090] [ 2683] [depth= 6] . ( 24 sec) [ -12190.7862] [ 2683] [depth= 3] . ( 35 sec) [ -12121.2317] [Branch lengths ] . ( 37 sec) [ -12102.7305] [GTR parameters ] . ( 37 sec) [ -12064.9048] [Alpha ][ 0.326790] . ( 39 sec) [ -12064.8902] [ 2683] [depth= 1] . ( 39 sec) [ -12064.7775] [ 2680] [depth= 2] . ( 39 sec) [ -12064.2603] [ 2684] [depth= 2] . ( 40 sec) [ -12064.2338] [ 2684] [depth= 1] . ( 40 sec) [ -12060.1695] [ 2683] [depth= 1] . ( 41 sec) [ -12057.9052] [ 2680] [depth= 2] . ( 41 sec) [ -12052.4725] [ 2683] [depth= 3] . ( 43 sec) [ -12050.5920] [ 2678] [depth= 1] . ( 53 sec) [ -12050.5800] [ 2678] [depth= 1] . ( 53 sec) [ -12050.5672] [ 2678] [depth= 1] . ( 69 sec) [ -12040.1040] [Branch lengths ] . ( 72 sec) [ -12035.8716] [GTR parameters ] . ( 72 sec) [ -12035.2488] [Alpha ][ 0.310434] . ( 74 sec) [ -12035.1353] [ 2678] [depth= 1] . ( 77 sec) [ -12035.0962] [ 2678] [depth= 1] . ( 77 sec) [ -12034.2176] [ 2683] [depth= 2] . ( 90 sec) [ -12034.2061] [ 2683] [depth= 9] . ( 104 sec) [ -12030.7991] [Branch lengths ] . ( 107 sec) [ -12030.3420] [GTR parameters ] . ( 107 sec) [ -12030.3032] [Alpha ][ 0.306697] . ( 109 sec) [ -12030.2795] [ 2683] [depth= 1] . ( 139 sec) [ -12029.0319] [Branch lengths ] . ( 142 sec) [ -12028.9324] [GTR parameters ] . ( 142 sec) [ -12028.9229] [Alpha ][ 0.304719] . ( 174 sec) [ -12028.3656] [Branch lengths ] . ( 250 sec) [ -12027.5935] [Branch lengths ] . ( 250 sec) [ -12027.5935] [Topology ] . ( 252 sec) [ -12026.0225] [Topology ] . ( 254 sec) [ -12023.9745] [Topology ] . ( 255 sec) [ -12023.2568] [Topology ] . ( 257 sec) [ -12023.0084] [Topology ] . ( 259 sec) [ -12022.9239] [Topology ] . ( 261 sec) [ -12022.8906] [Topology ] . ( 262 sec) [ -12022.7514] [GTR parameters ] . ( 262 sec) [ -12022.7392] [Alpha ][ 0.302503] . ( 262 sec) [ -12022.7392] [Topology ] . ( 264 sec) [ -12022.7114] [Topology ] . ( 266 sec) [ -12022.7006] [Topology ] . ( 267 sec) [ -12022.6955] [Topology ] . ( 269 sec) [ -12022.6929] [Topology ] . ( 271 sec) [ -12022.6916] [Topology ] . ( 273 sec) [ -12022.6909] [Topology ] . ( 274 sec) [ -12022.6850] [GTR parameters ] . ( 274 sec) [ -12022.6842] [Alpha ][ 0.301899] . ( 274 sec) [ -12022.6842] [Topology ] . ( 276 sec) [ -12022.6823] [Topology ] . ( 278 sec) [ -12022.6814] [Topology ] . ( 279 sec) [ -12022.6810] [GTR parameters ] . ( 279 sec) [ -12022.6810] [Alpha ][ 0.301899] . ( 279 sec) [ -12022.6810] [Topology ] . ( 281 sec) [ -12022.6803] [Topology ] . ( 281 sec) [ -12022.6802] [GTR parameters ] . ( 281 sec) [ -12022.6802] [Alpha ][ 0.301899] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12022.680231. . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 0h4m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 295.33user 0.00system 4:56.89elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps