.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_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... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -18030.1538] [GTR parameters ] . ( 7 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 7 sec) [ -17732.2284] [ 3534] [depth= 1] . ( 7 sec) [ -17727.9520] [ 3536] [depth= 1] . ( 7 sec) [ -17720.9232] [ 3536] [depth= 2] . ( 8 sec) [ -17710.1407] [ 3534] [depth= 2] . ( 8 sec) [ -17687.4237] [ 3532] [depth= 1] . ( 8 sec) [ -17673.6169] [ 3523] [depth= 2] . ( 8 sec) [ -17672.1004] [ 3522] [depth= 1] . ( 10 sec) [ -17671.8543] [ 3522] [depth= 1] . ( 10 sec) [ -17668.2870] [ 3521] [depth= 1] . ( 10 sec) [ -17667.7826] [ 3521] [depth= 1] . ( 11 sec) [ -17665.2764] [ 3521] [depth= 1] . ( 11 sec) [ -17665.0808] [ 3521] [depth= 1] . ( 11 sec) [ -17662.2901] [ 3528] [depth= 1] . ( 12 sec) [ -17649.7618] [ 3529] [depth= 1] . ( 12 sec) [ -17647.0321] [ 3528] [depth= 2] . ( 13 sec) [ -17645.8889] [ 3528] [depth= 1] . ( 13 sec) [ -17645.5956] [ 3528] [depth= 1] . ( 13 sec) [ -17641.4722] [ 3525] [depth= 1] . ( 14 sec) [ -17641.0441] [ 3523] [depth= 1] . ( 14 sec) [ -17640.6873] [ 3523] [depth= 1] . ( 15 sec) [ -17638.6764] [ 3523] [depth= 1] . ( 15 sec) [ -17625.5744] [ 3522] [depth= 3] . ( 15 sec) [ -17625.1000] [ 3522] [depth= 1] . ( 15 sec) [ -17614.7584] [ 3520] [depth= 2] . ( 16 sec) [ -17614.6570] [ 3520] [depth= 1] . ( 17 sec) [ -17614.0769] [ 3522] [depth= 1] . ( 17 sec) [ -17606.7578] [ 3525] [depth= 1] . ( 18 sec) [ -17605.8674] [ 3522] [depth= 1] . ( 18 sec) [ -17603.1185] [ 3521] [depth= 1] . ( 18 sec) [ -17595.5106] [ 3522] [depth= 1] . ( 19 sec) [ -17591.3249] [ 3525] [depth= 1] . ( 19 sec) [ -17582.7946] [ 3523] [depth= 2] . ( 19 sec) [ -17581.4385] [ 3524] [depth= 1] . ( 20 sec) [ -17576.5902] [ 3521] [depth= 3] . ( 20 sec) [ -17570.1001] [ 3515] [depth= 2] . ( 20 sec) [ -17568.1545] [ 3514] [depth= 1] . ( 20 sec) [ -17565.9700] [ 3515] [depth= 2] . ( 21 sec) [ -17565.5582] [ 3515] [depth= 1] . ( 22 sec) [ -17556.2693] [ 3513] [depth= 1] . ( 22 sec) [ -17547.3723] [ 3509] [depth= 2] . ( 22 sec) [ -17546.3350] [ 3509] [depth= 1] . ( 23 sec) [ -17541.5026] [ 3509] [depth= 2] . ( 23 sec) [ -17528.9614] [ 3505] [depth= 1] . ( 24 sec) [ -17527.4592] [ 3508] [depth= 1] . ( 24 sec) [ -17527.3316] [ 3508] [depth= 1] . ( 24 sec) [ -17527.3063] [ 3512] [depth= 1] . ( 24 sec) [ -17527.2528] [ 3509] [depth= 1] . ( 24 sec) [ -17525.5769] [ 3510] [depth= 1] . ( 25 sec) [ -17522.0796] [ 3513] [depth= 1] . ( 26 sec) [ -17515.7045] [ 3513] [depth= 1] . ( 26 sec) [ -17512.0364] [ 3512] [depth= 1] . ( 26 sec) [ -17506.2200] [ 3513] [depth= 2] . ( 26 sec) [ -17502.5205] [ 3515] [depth= 1] . ( 27 sec) [ -17501.0224] [ 3515] [depth= 1] . ( 27 sec) [ -17498.9748] [ 3513] [depth= 1] . ( 27 sec) [ -17498.6457] [ 3515] [depth= 1] . ( 28 sec) [ -17497.8277] [ 3518] [depth= 2] . ( 28 sec) [ -17494.5538] [ 3516] [depth= 1] . ( 28 sec) [ -17493.8148] [ 3517] [depth= 1] . ( 28 sec) [ -17487.7673] [ 3516] [depth= 1] . ( 29 sec) [ -17477.0588] [ 3517] [depth= 2] . ( 29 sec) [ -17472.5607] [ 3513] [depth= 1] . ( 30 sec) [ -17447.2737] [ 3509] [depth= 2] . ( 30 sec) [ -17438.2099] [ 3509] [depth= 1] . ( 31 sec) [ -17432.9037] [ 3513] [depth= 1] . ( 31 sec) [ -17430.8153] [ 3509] [depth= 1] . ( 31 sec) [ -17428.4813] [ 3511] [depth= 1] . ( 31 sec) [ -17385.6114] [ 3509] [depth= 6] . ( 31 sec) [ -17383.2046] [ 3510] [depth= 1] . ( 31 sec) [ -17383.0598] [ 3509] [depth= 1] . ( 33 sec) [ -17362.7768] [ 3504] [depth= 1] . ( 34 sec) [ -17360.6969] [ 3508] [depth= 1] . ( 34 sec) [ -17353.4635] [ 3501] [depth= 1] . ( 34 sec) [ -17347.5013] [ 3497] [depth= 2] . ( 35 sec) [ -17344.2898] [ 3500] [depth= 2] . ( 35 sec) [ -17341.7376] [ 3505] [depth= 1] . ( 35 sec) [ -17332.8490] [ 3503] [depth= 1] . ( 35 sec) [ -17327.3566] [ 3499] [depth= 1] . ( 36 sec) [ -17320.9950] [ 3499] [depth= 1] . ( 36 sec) [ -17314.6835] [ 3495] [depth= 2] . ( 37 sec) [ -17314.4520] [ 3494] [depth= 1] . ( 37 sec) [ -17309.5389] [ 3495] [depth= 1] . ( 38 sec) [ -17307.8887] [ 3495] [depth= 1] . ( 38 sec) [ -17303.2636] [ 3494] [depth= 1] . ( 38 sec) [ -17302.2737] [ 3495] [depth= 4] . ( 38 sec) [ -17299.9575] [ 3495] [depth= 1] . ( 38 sec) [ -17297.3650] [ 3495] [depth= 1] . ( 38 sec) [ -17296.1814] [ 3494] [depth= 1] . ( 39 sec) [ -17291.1740] [ 3493] [depth= 1] . ( 40 sec) [ -17290.7274] [ 3494] [depth= 1] . ( 40 sec) [ -17289.4688] [ 3493] [depth= 1] . ( 40 sec) [ -17288.4265] [ 3492] [depth= 1] . ( 41 sec) [ -17288.1997] [ 3494] [depth= 1] . ( 41 sec) [ -17287.8339] [ 3496] [depth= 1] . ( 41 sec) [ -17285.6605] [ 3494] [depth= 1] . ( 42 sec) [ -17284.9520] [ 3496] [depth= 1] . ( 42 sec) [ -17283.8794] [ 3494] [depth= 1] . ( 44 sec) [ -17118.6287] [Branch lengths ] . ( 49 sec) [ -17106.5366] [GTR parameters ] . ( 49 sec) [ -17069.3882] [Alpha ][ 0.348580] . ( 52 sec) [ -17067.7315] [ 3496] [depth= 1] . ( 52 sec) [ -17060.2362] [ 3487] [depth= 1] . ( 54 sec) [ -17058.0829] [ 3483] [depth= 2] . ( 54 sec) [ -17055.7461] [ 3484] [depth= 1] . ( 56 sec) [ -17055.0689] [ 3486] [depth= 1] . ( 57 sec) [ -17052.7666] [ 3484] [depth= 1] . ( 58 sec) [ -17052.2562] [ 3483] [depth= 1] . ( 59 sec) [ -17050.8560] [ 3483] [depth= 1] . ( 67 sec) [ -17050.1894] [ 3486] [depth= 1] . ( 68 sec) [ -17050.0303] [ 3485] [depth= 1] . ( 73 sec) [ -17047.8575] [ 3484] [depth= 1] . ( 75 sec) [ -17047.7667] [ 3483] [depth= 1] . ( 76 sec) [ -17047.5997] [ 3484] [depth= 1] . ( 76 sec) [ -17045.3743] [ 3487] [depth= 1] . ( 78 sec) [ -17044.5819] [ 3487] [depth= 1] . ( 79 sec) [ -17043.8421] [ 3487] [depth= 5] . ( 80 sec) [ -17042.9538] [ 3487] [depth= 1] . ( 82 sec) [ -17042.4450] [ 3487] [depth= 1] . ( 88 sec) [ -17007.0987] [Branch lengths ] . ( 92 sec) [ -17005.3774] [GTR parameters ] . ( 92 sec) [ -17005.2591] [Alpha ][ 0.355080] . ( 100 sec) [ -17005.1982] [ 3485] [depth= 1] . ( 101 sec) [ -17005.1710] [ 3487] [depth= 1] . ( 123 sec) [ -17005.0176] [ 3489] [depth= 2] . ( 133 sec) [ -16996.3325] [Branch lengths ] . ( 136 sec) [ -16996.2585] [GTR parameters ] . ( 137 sec) [ -16996.2221] [Alpha ][ 0.358898] . ( 144 sec) [ -16996.2027] [ 3487] [depth= 1] . ( 176 sec) [ -16994.3391] [Branch lengths ] . ( 180 sec) [ -16994.3141] [GTR parameters ] . ( 180 sec) [ -16994.3061] [Alpha ][ 0.360657] . ( 222 sec) [ -16993.7035] [Branch lengths ] . ( 368 sec) [ -16993.5115] [Branch lengths ] . ( 368 sec) [ -16993.5115] [Topology ] . ( 371 sec) [ -16993.2548] [Topology ] . ( 374 sec) [ -16993.1930] [Topology ] . ( 378 sec) [ -16993.1147] [Topology ] . ( 381 sec) [ -16993.0677] [Topology ] . ( 384 sec) [ -16993.0509] [Topology ] . ( 388 sec) [ -16993.0441] [Topology ] . ( 391 sec) [ -16993.0410] [Topology ] . ( 394 sec) [ -16993.0012] [GTR parameters ] . ( 394 sec) [ -16992.9885] [Alpha ][ 0.362902] . ( 394 sec) [ -16992.9885] [Topology ] . ( 397 sec) [ -16992.9828] [Topology ] . ( 401 sec) [ -16992.9796] [Topology ] . ( 404 sec) [ -16992.9774] [Topology ] . ( 407 sec) [ -16992.9760] [Topology ] . ( 410 sec) [ -16992.9751] [Topology ] . ( 412 sec) [ -16992.9747] [GTR parameters ] . ( 412 sec) [ -16992.9747] [Alpha ][ 0.362902] . ( 412 sec) [ -16992.9747] [Topology ] . ( 415 sec) [ -16992.9739] [Topology ] . ( 416 sec) [ -16992.9739] [GTR parameters ] . ( 416 sec) [ -16992.9739] [Alpha ][ 0.362902] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16992.973865. . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Time used 0h7m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 435.36user 0.00system 7:20.85elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps