.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2711_123x1181_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1181 sites) . 633 sites without polymorphism (53.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 40Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -11331.0777] [GTR parameters ] . ( 8 sec) [ -11137.6083] [Alpha ][ 0.500960] . ( 9 sec) [ -11136.4430] [ 2014] [depth= 1] . ( 9 sec) [ -11133.4793] [ 2014] [depth= 1] . ( 10 sec) [ -11116.3234] [ 2007] [depth= 1] . ( 12 sec) [ -11116.1090] [ 2007] [depth= 1] . ( 13 sec) [ -11115.0846] [ 2007] [depth= 1] . ( 13 sec) [ -11114.5969] [ 2006] [depth= 1] . ( 13 sec) [ -11113.9350] [ 2005] [depth= 1] . ( 14 sec) [ -11113.7647] [ 2006] [depth= 2] . ( 14 sec) [ -11108.3844] [ 2003] [depth= 1] . ( 14 sec) [ -11107.2501] [ 2003] [depth= 2] . ( 16 sec) [ -11106.0105] [ 2003] [depth= 1] . ( 16 sec) [ -11105.1080] [ 2003] [depth= 1] . ( 16 sec) [ -11105.0588] [ 2003] [depth= 1] . ( 17 sec) [ -11104.8599] [ 2003] [depth= 1] . ( 17 sec) [ -11104.6092] [ 2003] [depth= 1] . ( 18 sec) [ -11104.5901] [ 2003] [depth= 1] . ( 18 sec) [ -11103.6079] [ 2003] [depth= 1] . ( 18 sec) [ -11103.5268] [ 2003] [depth= 1] . ( 19 sec) [ -11102.3631] [ 2003] [depth= 1] . ( 19 sec) [ -11102.2977] [ 2003] [depth= 2] . ( 19 sec) [ -11102.1355] [ 2003] [depth= 1] . ( 19 sec) [ -11101.3620] [ 2003] [depth= 1] . ( 20 sec) [ -11101.2542] [ 2003] [depth= 1] . ( 20 sec) [ -11101.2409] [ 2003] [depth= 1] . ( 21 sec) [ -11101.2252] [ 2003] [depth= 1] . ( 21 sec) [ -11101.1937] [ 2003] [depth= 1] . ( 22 sec) [ -11101.1179] [ 2003] [depth= 3] . ( 23 sec) [ -11101.0912] [ 2003] [depth= 1] . ( 23 sec) [ -11098.1667] [ 2004] [depth= 1] . ( 24 sec) [ -11091.1431] [ 2009] [depth= 1] . ( 24 sec) [ -11086.4029] [ 2011] [depth= 1] . ( 25 sec) [ -11086.2805] [ 2011] [depth= 1] . ( 25 sec) [ -11081.6850] [ 2011] [depth= 1] . ( 26 sec) [ -11068.4600] [ 2007] [depth= 4] . ( 26 sec) [ -11068.3726] [ 2007] [depth= 1] . ( 26 sec) [ -11068.1988] [ 2007] [depth= 1] . ( 27 sec) [ -11067.9164] [ 2007] [depth= 1] . ( 27 sec) [ -11066.2698] [ 2006] [depth= 1] . ( 27 sec) [ -11066.2105] [ 2006] [depth= 1] . ( 29 sec) [ -11062.0386] [ 2005] [depth= 1] . ( 29 sec) [ -11061.9709] [ 2005] [depth= 2] . ( 30 sec) [ -11055.5825] [ 2005] [depth= 1] . ( 30 sec) [ -11046.7908] [ 2003] [depth= 1] . ( 31 sec) [ -11046.6927] [ 2005] [depth= 1] . ( 31 sec) [ -11046.6762] [ 2005] [depth= 1] . ( 31 sec) [ -11045.1825] [ 2005] [depth= 1] . ( 32 sec) [ -11029.3523] [ 2004] [depth= 3] . ( 32 sec) [ -11021.6239] [ 2006] [depth= 3] . ( 33 sec) [ -11016.3588] [ 2006] [depth= 1] . ( 33 sec) [ -11015.4897] [ 2006] [depth= 1] . ( 33 sec) [ -11015.0997] [ 2006] [depth= 1] . ( 34 sec) [ -11013.1812] [ 2006] [depth= 1] . ( 34 sec) [ -11012.6655] [ 2005] [depth= 1] . ( 35 sec) [ -11004.6198] [ 2001] [depth= 1] . ( 35 sec) [ -10980.8007] [ 1996] [depth= 1] . ( 35 sec) [ -10948.7523] [ 1997] [depth= 4] . ( 36 sec) [ -10947.6247] [ 1997] [depth= 1] . ( 36 sec) [ -10947.0358] [ 1997] [depth= 1] . ( 36 sec) [ -10947.0142] [ 1997] [depth= 2] . ( 37 sec) [ -10946.9515] [ 1997] [depth= 1] . ( 38 sec) [ -10941.0651] [ 1997] [depth= 2] . ( 38 sec) [ -10939.5879] [ 1997] [depth= 1] . ( 38 sec) [ -10939.5623] [ 1997] [depth= 1] . ( 39 sec) [ -10939.5352] [ 1997] [depth= 1] . ( 39 sec) [ -10938.6967] [ 1997] [depth= 1] . ( 40 sec) [ -10937.7584] [ 1997] [depth= 1] . ( 40 sec) [ -10937.6826] [ 1997] [depth= 1] . ( 41 sec) [ -10937.6565] [ 1997] [depth= 2] . ( 42 sec) [ -10934.3676] [ 1997] [depth= 1] . ( 42 sec) [ -10928.0465] [ 1998] [depth= 2] . ( 42 sec) [ -10923.2728] [ 1997] [depth= 4] . ( 44 sec) [ -10923.1128] [ 1997] [depth= 1] . ( 44 sec) [ -10912.5587] [ 1996] [depth= 1] . ( 45 sec) [ -10912.3779] [ 1997] [depth= 1] . ( 45 sec) [ -10912.2735] [ 1996] [depth= 1] . ( 46 sec) [ -10910.2132] [ 2004] [depth= 7] . ( 46 sec) [ -10909.9006] [ 2003] [depth= 1] . ( 46 sec) [ -10897.4833] [ 2003] [depth= 1] . ( 47 sec) [ -10869.0274] [ 2006] [depth= 1] . ( 47 sec) [ -10868.9114] [ 2006] [depth= 3] . ( 48 sec) [ -10867.2055] [ 2005] [depth= 1] . ( 49 sec) [ -10867.1063] [ 2005] [depth= 1] . ( 49 sec) [ -10853.5178] [ 2004] [depth= 1] . ( 50 sec) [ -10849.1641] [ 2005] [depth= 1] . ( 50 sec) [ -10848.9629] [ 2005] [depth= 1] . ( 50 sec) [ -10848.9317] [ 2005] [depth= 1] . ( 51 sec) [ -10848.8979] [ 2005] [depth= 1] . ( 51 sec) [ -10848.8878] [ 2005] [depth= 3] . ( 51 sec) [ -10848.8703] [ 2005] [depth= 1] . ( 52 sec) [ -10848.6873] [ 2005] [depth= 4] . ( 53 sec) [ -10848.6750] [ 2005] [depth= 2] . ( 54 sec) [ -10848.4053] [ 2005] [depth= 1] . ( 54 sec) [ -10847.8555] [ 2005] [depth= 1] . ( 55 sec) [ -10846.6526] [ 2004] [depth= 1] . ( 55 sec) [ -10846.6373] [ 2004] [depth= 1] . ( 56 sec) [ -10841.3342] [ 2005] [depth= 1] . ( 56 sec) [ -10840.5525] [ 2004] [depth= 1] . ( 57 sec) [ -10836.7146] [ 2004] [depth= 1] . ( 58 sec) [ -10833.8636] [ 2004] [depth= 1] . ( 58 sec) [ -10833.6875] [ 2004] [depth= 1] . ( 60 sec) [ -10833.6219] [ 2004] [depth= 2] . ( 60 sec) [ -10833.4578] [ 2004] [depth= 2] . ( 60 sec) [ -10833.3842] [ 2004] [depth= 2] . ( 61 sec) [ -10833.1536] [ 2004] [depth= 2] . ( 62 sec) [ -10833.0859] [ 2004] [depth= 2] . ( 62 sec) [ -10832.2564] [ 2004] [depth= 2] . ( 62 sec) [ -10832.1316] [ 2004] [depth= 1] . ( 62 sec) [ -10832.0793] [ 2004] [depth= 1] . ( 63 sec) [ -10832.0648] [ 2004] [depth= 1] . ( 64 sec) [ -10832.0348] [ 2004] [depth= 1] . ( 71 sec) [ -10754.9769] [Branch lengths ] . ( 79 sec) [ -10749.8149] [GTR parameters ] . ( 80 sec) [ -10689.9365] [Alpha ][ 0.284078] . ( 81 sec) [ -10689.9213] [ 2004] [depth= 1] . ( 88 sec) [ -10689.9087] [ 2004] [depth= 2] . ( 94 sec) [ -10689.8507] [ 2004] [depth= 1] . ( 94 sec) [ -10688.4188] [ 2003] [depth= 1] . ( 97 sec) [ -10686.7971] [ 2000] [depth= 5] . ( 100 sec) [ -10686.7854] [ 1998] [depth= 1] . ( 101 sec) [ -10686.7092] [ 1998] [depth= 1] . ( 101 sec) [ -10684.2252] [ 1998] [depth= 2] . ( 101 sec) [ -10684.0389] [ 1998] [depth= 2] . ( 102 sec) [ -10683.9966] [ 1998] [depth= 1] . ( 102 sec) [ -10682.9988] [ 1998] [depth= 1] . ( 106 sec) [ -10681.5364] [ 1995] [depth= 2] . ( 108 sec) [ -10680.1920] [ 1995] [depth= 1] . ( 113 sec) [ -10679.2696] [ 1995] [depth= 1] . ( 116 sec) [ -10679.2534] [ 1995] [depth= 2] . ( 128 sec) [ -10671.2131] [Branch lengths ] . ( 139 sec) [ -10669.8855] [GTR parameters ] . ( 139 sec) [ -10669.6571] [Alpha ][ 0.274951] . ( 142 sec) [ -10669.6415] [ 1995] [depth= 2] . ( 151 sec) [ -10669.6248] [ 1995] [depth= 1] . ( 153 sec) [ -10669.6053] [ 1995] [depth= 1] . ( 204 sec) [ -10667.8099] [Branch lengths ] . ( 216 sec) [ -10667.7774] [GTR parameters ] . ( 216 sec) [ -10667.7772] [Alpha ][ 0.274676] . ( 287 sec) [ -10667.4344] [Branch lengths ] . ( 406 sec) [ -10667.1599] [ 2018] [depth= 8] . ( 436 sec) [ -10667.1489] [ 2006] [depth= 1] . ( 604 sec) [ -10666.5853] [Branch lengths ] . ( 615 sec) [ -10666.5429] [GTR parameters ] . ( 616 sec) [ -10666.5423] [Alpha ][ 0.274145] . ( 616 sec) [ -10666.5423] [Topology ] . ( 622 sec) [ -10665.1400] [Topology ] . ( 628 sec) [ -10661.9734] [Topology ] . ( 635 sec) [ -10658.7183] [Topology ] . ( 641 sec) [ -10657.0702] [Topology ] . ( 647 sec) [ -10656.9021] [Topology ] . ( 653 sec) [ -10656.8613] [Topology ] . ( 659 sec) [ -10656.8494] [Topology ] . ( 666 sec) [ -10656.8454] [Topology ] . ( 672 sec) [ -10656.8437] [Topology ] . ( 676 sec) [ -10656.8414] [GTR parameters ] . ( 676 sec) [ -10656.8360] [Alpha ][ 0.275477] . ( 676 sec) [ -10656.8360] [Topology ] . ( 683 sec) [ -10656.8347] [Topology ] . ( 689 sec) [ -10656.8342] [Topology ] . ( 690 sec) [ -10656.8341] [GTR parameters ] . ( 691 sec) [ -10656.8341] [Alpha ][ 0.275477] . ( 691 sec) [ -10656.8341] [Topology ] . ( 697 sec) [ -10656.8339] [Topology ] . ( 698 sec) [ -10656.8339] [GTR parameters ] . ( 699 sec) [ -10656.8339] [Alpha ][ 0.275477] . Checking for NNIs, optimizing five branches... . ( 742 sec) [ -10656.3011] [Topology ] . Checking for NNIs, optimizing five branches... . ( 782 sec) [ -10656.2730] [Topology ] . Checking for NNIs, optimizing five branches... . ( 821 sec) [ -10656.2658] [Topology ] . Checking for NNIs, optimizing five branches... . ( 858 sec) [ -10656.2644] [Topology ] . Checking for NNIs, optimizing five branches... . ( 896 sec) [ -10656.2642] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10656.264216. . Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'... . Time used 0h15m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 505.09user 0.00system 15:36.97elapsed 53%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps