.......................... 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 ] . ( 0 sec) [ -17215.2965] [Alpha ][ 0.500960] . ( 1 sec) [ -17215.2819] [ 3954] [depth= 1] . ( 1 sec) [ -17212.5717] [ 3953] [depth= 1] . ( 1 sec) [ -17211.0309] [ 3956] [depth= 1] . ( 1 sec) [ -17210.9694] [ 3957] [depth= 1] . ( 1 sec) [ -17209.0242] [ 3961] [depth= 2] . ( 1 sec) [ -17208.2432] [ 3961] [depth= 2] . ( 2 sec) [ -17196.5597] [ 3953] [depth= 1] . ( 2 sec) [ -17188.0683] [ 3957] [depth= 1] . ( 2 sec) [ -17187.7368] [ 3956] [depth= 3] . ( 3 sec) [ -17183.4824] [ 3957] [depth= 3] . ( 3 sec) [ -17182.6056] [ 3957] [depth= 1] . ( 3 sec) [ -17182.2647] [ 3957] [depth= 1] . ( 3 sec) [ -17182.0751] [ 3957] [depth= 1] . ( 3 sec) [ -17179.9553] [ 3956] [depth= 2] . ( 4 sec) [ -17171.8169] [ 3955] [depth= 2] . ( 4 sec) [ -17170.6583] [ 3954] [depth= 1] . ( 4 sec) [ -17170.3929] [ 3954] [depth= 1] . ( 4 sec) [ -17170.2910] [ 3954] [depth= 1] . ( 5 sec) [ -17170.1443] [ 3954] [depth= 1] . ( 5 sec) [ -17168.6264] [ 3957] [depth= 1] . ( 5 sec) [ -17161.6293] [ 3955] [depth= 1] . ( 5 sec) [ -17161.6041] [ 3955] [depth= 1] . ( 6 sec) [ -17159.9143] [ 3957] [depth= 1] . ( 6 sec) [ -17140.6645] [ 3974] [depth= 2] . ( 6 sec) [ -17103.7654] [ 3959] [depth= 2] . ( 6 sec) [ -17095.7780] [ 3972] [depth= 1] . ( 6 sec) [ -17081.8023] [ 3959] [depth= 1] . ( 6 sec) [ -17079.8526] [ 3952] [depth= 1] . ( 6 sec) [ -17070.9245] [ 3951] [depth= 1] . ( 6 sec) [ -17069.8324] [ 3952] [depth= 1] . ( 7 sec) [ -17066.5519] [ 3957] [depth= 1] . ( 7 sec) [ -17063.8078] [ 3954] [depth= 2] . ( 7 sec) [ -17055.2804] [ 3952] [depth= 2] . ( 7 sec) [ -17046.1616] [ 3956] [depth= 1] . ( 7 sec) [ -17044.4079] [ 3955] [depth= 1] . ( 7 sec) [ -17025.4110] [ 3953] [depth= 1] . ( 7 sec) [ -17015.1784] [ 3953] [depth= 1] . ( 7 sec) [ -16989.7343] [ 3948] [depth= 1] . ( 8 sec) [ -16988.5808] [ 3946] [depth= 1] . ( 8 sec) [ -16988.4308] [ 3948] [depth= 1] . ( 8 sec) [ -16985.2922] [ 3952] [depth= 1] . ( 8 sec) [ -16977.0947] [ 3954] [depth= 2] . ( 9 sec) [ -16913.0865] [Branch lengths ] . ( 13 sec) [ -16443.4134] [GTR parameters ] . ( 13 sec) [ -16372.1845] [Alpha ][ 0.306024] . ( 13 sec) [ -16371.6719] [ 3954] [depth= 1] . ( 13 sec) [ -16371.6338] [ 3956] [depth= 1] . ( 14 sec) [ -16371.3508] [ 3956] [depth= 2] . ( 14 sec) [ -16370.9277] [ 3959] [depth= 1] . ( 14 sec) [ -16370.5992] [ 3954] [depth= 1] . ( 14 sec) [ -16369.5120] [ 3948] [depth= 1] . ( 15 sec) [ -16369.4212] [ 3949] [depth= 1] . ( 15 sec) [ -16369.3971] [ 3949] [depth= 1] . ( 16 sec) [ -16369.3846] [ 3949] [depth= 1] . ( 16 sec) [ -16369.3197] [ 3949] [depth= 1] . ( 17 sec) [ -16361.3214] [ 3944] [depth= 1] . ( 19 sec) [ -16360.7520] [ 3947] [depth= 1] . ( 19 sec) [ -16358.8862] [ 3949] [depth= 1] . ( 20 sec) [ -16358.8613] [ 3955] [depth= 3] . ( 20 sec) [ -16346.7839] [ 3943] [depth= 2] . ( 20 sec) [ -16334.5016] [ 3944] [depth= 1] . ( 21 sec) [ -16300.4734] [Branch lengths ] . ( 25 sec) [ -16281.9168] [GTR parameters ] . ( 25 sec) [ -16281.2715] [Alpha ][ 0.292982] . ( 26 sec) [ -16280.6311] [ 3945] [depth= 1] . ( 34 sec) [ -16268.6402] [Branch lengths ] . ( 38 sec) [ -16266.1326] [GTR parameters ] . ( 38 sec) [ -16266.1321] [Alpha ][ 0.292554] . ( 47 sec) [ -16259.8282] [Branch lengths ] . ( 90 sec) [ -16258.3282] [Branch lengths ] . ( 90 sec) [ -16258.3282] [Topology ] . ( 92 sec) [ -16257.0357] [Topology ] . ( 93 sec) [ -16256.8731] [Topology ] . ( 94 sec) [ -16256.8272] [Topology ] . ( 96 sec) [ -16256.8093] [Topology ] . ( 97 sec) [ -16256.8012] [Topology ] . ( 98 sec) [ -16256.7973] [Topology ] . ( 100 sec) [ -16256.7954] [Topology ] . ( 103 sec) [ -16254.4858] [GTR parameters ] . ( 103 sec) [ -16254.4846] [Alpha ][ 0.291936] . ( 103 sec) [ -16254.4846] [Topology ] . ( 104 sec) [ -16253.9978] [Topology ] . ( 106 sec) [ -16253.8230] [Topology ] . ( 107 sec) [ -16253.7375] [Topology ] . ( 108 sec) [ -16253.6934] [Topology ] . ( 110 sec) [ -16253.6700] [Topology ] . ( 111 sec) [ -16253.6576] [Topology ] . ( 115 sec) [ -16253.4004] [GTR parameters ] . ( 115 sec) [ -16253.3884] [Alpha ][ 0.290462] . ( 115 sec) [ -16253.3884] [Topology ] . ( 116 sec) [ -16253.2950] [Topology ] . ( 118 sec) [ -16253.2583] [Topology ] . ( 119 sec) [ -16253.2394] [Topology ] . ( 120 sec) [ -16253.2294] [Topology ] . ( 122 sec) [ -16253.2240] [Topology ] . ( 123 sec) [ -16253.2211] [Topology ] . ( 126 sec) [ -16253.1616] [GTR parameters ] . ( 126 sec) [ -16253.1566] [Alpha ][ 0.289296] . ( 126 sec) [ -16253.1566] [Topology ] . ( 128 sec) [ -16253.1348] [Topology ] . ( 129 sec) [ -16253.1265] [Topology ] . ( 130 sec) [ -16253.1222] [Topology ] . ( 132 sec) [ -16253.1199] [Topology ] . ( 133 sec) [ -16253.1186] [Topology ] . ( 134 sec) [ -16253.1179] [Topology ] . ( 138 sec) [ -16253.1019] [GTR parameters ] . ( 138 sec) [ -16253.1013] [Alpha ][ 0.288818] . ( 138 sec) [ -16253.1013] [Topology ] . ( 139 sec) [ -16253.0958] [Topology ] . ( 141 sec) [ -16253.0937] [Topology ] . ( 142 sec) [ -16253.0926] [Topology ] . ( 143 sec) [ -16253.0920] [Topology ] . ( 144 sec) [ -16253.0887] [GTR parameters ] . ( 144 sec) [ -16253.0887] [Alpha ][ 0.288530] . ( 144 sec) [ -16253.0887] [Topology ] . ( 145 sec) [ -16253.0870] [Topology ] . ( 147 sec) [ -16253.0862] [Topology ] . ( 148 sec) [ -16253.0855] [GTR parameters ] . ( 148 sec) [ -16253.0855] [Alpha ][ 0.288530] . ( 148 sec) [ -16253.0855] [Topology ] . ( 149 sec) [ -16253.0846] [Topology ] . ( 150 sec) [ -16253.0845] [GTR parameters ] . ( 150 sec) [ -16253.0845] [Alpha ][ 0.288530] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16253.084546. . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 0h2m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 161.18user 0.00system 2:43.28elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps