.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2606_110x1206_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... . 662 patterns found. (out of a total of 1206 sites) . 540 sites without polymorphism (44.78%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -29176.8561] [GTR parameters ] . ( 2 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 3 sec) [ -28715.8595] [ 5819] [depth= 1] . ( 4 sec) [ -28709.8159] [ 5824] [depth= 1] . ( 4 sec) [ -28697.5201] [ 5819] [depth= 1] . ( 5 sec) [ -28696.6045] [ 5823] [depth= 1] . ( 6 sec) [ -28683.6351] [ 5819] [depth= 1] . ( 6 sec) [ -28681.3289] [ 5822] [depth= 1] . ( 6 sec) [ -28679.2730] [ 5819] [depth= 1] . ( 6 sec) [ -28672.1645] [ 5820] [depth= 1] . ( 8 sec) [ -28670.8541] [ 5822] [depth= 1] . ( 9 sec) [ -28669.3735] [ 5824] [depth= 1] . ( 9 sec) [ -28667.7191] [ 5823] [depth= 1] . ( 9 sec) [ -28664.6733] [ 5818] [depth= 1] . ( 10 sec) [ -28658.0320] [ 5822] [depth= 1] . ( 10 sec) [ -28635.3083] [ 5811] [depth= 4] . ( 10 sec) [ -28627.6068] [ 5812] [depth= 1] . ( 10 sec) [ -28627.4745] [ 5811] [depth= 1] . ( 11 sec) [ -28624.7292] [ 5812] [depth= 1] . ( 11 sec) [ -28618.7177] [ 5809] [depth= 1] . ( 12 sec) [ -28618.1073] [ 5811] [depth= 1] . ( 12 sec) [ -28616.9607] [ 5809] [depth= 1] . ( 12 sec) [ -28608.6871] [ 5800] [depth= 1] . ( 13 sec) [ -28605.2953] [ 5801] [depth= 1] . ( 13 sec) [ -28603.7189] [ 5806] [depth= 1] . ( 14 sec) [ -28603.2967] [ 5805] [depth= 1] . ( 14 sec) [ -28596.6809] [ 5802] [depth= 1] . ( 15 sec) [ -28581.8849] [ 5812] [depth= 1] . ( 15 sec) [ -28556.9955] [ 5802] [depth= 1] . ( 15 sec) [ -28553.6707] [ 5805] [depth= 1] . ( 15 sec) [ -28550.7503] [ 5805] [depth= 1] . ( 16 sec) [ -28532.9785] [ 5811] [depth= 2] . ( 16 sec) [ -28505.2161] [ 5801] [depth= 2] . ( 17 sec) [ -28494.7125] [ 5801] [depth= 1] . ( 17 sec) [ -28493.8834] [ 5801] [depth= 1] . ( 17 sec) [ -28484.6717] [ 5800] [depth= 1] . ( 17 sec) [ -28481.3638] [ 5802] [depth= 1] . ( 17 sec) [ -28479.5954] [ 5800] [depth= 1] . ( 18 sec) [ -28475.0670] [ 5797] [depth= 2] . ( 18 sec) [ -28471.8349] [ 5798] [depth= 1] . ( 18 sec) [ -28471.0611] [ 5799] [depth= 2] . ( 19 sec) [ -28470.1203] [ 5801] [depth= 1] . ( 19 sec) [ -28465.6616] [ 5796] [depth= 1] . ( 19 sec) [ -28456.6326] [ 5803] [depth= 1] . ( 19 sec) [ -28454.4766] [ 5803] [depth= 1] . ( 20 sec) [ -28452.0039] [ 5805] [depth= 2] . ( 20 sec) [ -28450.9616] [ 5805] [depth= 1] . ( 20 sec) [ -28449.4810] [ 5805] [depth= 1] . ( 20 sec) [ -28448.4225] [ 5805] [depth= 1] . ( 21 sec) [ -28442.1678] [ 5798] [depth= 1] . ( 21 sec) [ -28441.6328] [ 5799] [depth= 1] . ( 22 sec) [ -28439.7610] [ 5797] [depth= 1] . ( 23 sec) [ -28436.0051] [ 5799] [depth= 1] . ( 23 sec) [ -28421.7718] [ 5791] [depth= 3] . ( 23 sec) [ -28418.4526] [ 5794] [depth= 1] . ( 23 sec) [ -28415.5810] [ 5791] [depth= 1] . ( 24 sec) [ -28414.3279] [ 5792] [depth= 1] . ( 24 sec) [ -28411.2934] [ 5791] [depth= 1] . ( 24 sec) [ -28408.9258] [ 5788] [depth= 2] . ( 25 sec) [ -28408.0051] [ 5790] [depth= 1] . ( 25 sec) [ -28405.2591] [ 5791] [depth= 1] . ( 25 sec) [ -28404.9784] [ 5791] [depth= 1] . ( 25 sec) [ -28404.3581] [ 5790] [depth= 2] . ( 26 sec) [ -28401.9181] [ 5788] [depth= 1] . ( 27 sec) [ -28401.4738] [ 5788] [depth= 1] . ( 27 sec) [ -28398.8514] [ 5786] [depth= 1] . ( 30 sec) [ -28395.7868] [ 5785] [depth= 1] . ( 32 sec) [ -28393.1605] [ 5784] [depth= 1] . ( 33 sec) [ -28391.5912] [ 5784] [depth= 1] . ( 35 sec) [ -28389.0516] [ 5784] [depth= 4] . ( 37 sec) [ -28385.4871] [ 5783] [depth= 1] . ( 48 sec) [ -28286.9092] [Branch lengths ] . ( 55 sec) [ -27076.2807] [GTR parameters ] . ( 55 sec) [ -27006.2899] [Alpha ][ 0.332427] . ( 58 sec) [ -27005.0990] [ 5785] [depth= 1] . ( 59 sec) [ -27004.5914] [ 5790] [depth= 1] . ( 61 sec) [ -27004.3819] [ 5788] [depth= 1] . ( 62 sec) [ -27003.5448] [ 5785] [depth= 1] . ( 63 sec) [ -26996.9663] [ 5784] [depth= 2] . ( 63 sec) [ -26996.4399] [ 5787] [depth= 1] . ( 64 sec) [ -26994.6504] [ 5788] [depth= 1] . ( 65 sec) [ -26992.4700] [ 5788] [depth= 1] . ( 67 sec) [ -26981.6455] [ 5790] [depth= 1] . ( 68 sec) [ -26981.0775] [ 5792] [depth= 1] . ( 69 sec) [ -26981.0141] [ 5790] [depth= 1] . ( 69 sec) [ -26980.5630] [ 5791] [depth= 1] . ( 69 sec) [ -26977.0447] [ 5793] [depth= 1] . ( 70 sec) [ -26976.5660] [ 5795] [depth= 1] . ( 72 sec) [ -26974.1025] [ 5798] [depth= 1] . ( 101 sec) [ -26954.7785] [Branch lengths ] . ( 106 sec) [ -26952.1491] [GTR parameters ] . ( 106 sec) [ -26951.4636] [Alpha ][ 0.319341] . ( 116 sec) [ -26948.4777] [ 5802] [depth= 3] . ( 152 sec) [ -26946.4044] [Branch lengths ] . ( 156 sec) [ -26946.3229] [GTR parameters ] . ( 156 sec) [ -26946.1128] [Alpha ][ 0.312384] . ( 202 sec) [ -26945.7659] [Branch lengths ] . ( 338 sec) [ -26945.7305] [Branch lengths ] . ( 338 sec) [ -26945.7305] [Topology ] . ( 341 sec) [ -26945.7283] [Topology ] . ( 344 sec) [ -26945.7277] [Topology ] . ( 348 sec) [ -26945.7225] [GTR parameters ] . ( 348 sec) [ -26945.5805] [Alpha ][ 0.306476] . ( 348 sec) [ -26945.5805] [Topology ] . ( 352 sec) [ -26945.5235] [Topology ] . ( 355 sec) [ -26945.5055] [Topology ] . ( 358 sec) [ -26945.4991] [Topology ] . ( 361 sec) [ -26945.4967] [Topology ] . ( 365 sec) [ -26945.4959] [Topology ] . ( 368 sec) [ -26945.4921] [GTR parameters ] . ( 368 sec) [ -26945.4538] [Alpha ][ 0.303429] . ( 368 sec) [ -26945.4538] [Topology ] . ( 372 sec) [ -26945.4361] [Topology ] . ( 375 sec) [ -26945.4305] [Topology ] . ( 378 sec) [ -26945.4285] [Topology ] . ( 381 sec) [ -26945.4277] [Topology ] . ( 385 sec) [ -26945.4266] [GTR parameters ] . ( 385 sec) [ -26945.4159] [Alpha ][ 0.301819] . ( 386 sec) [ -26945.4159] [Topology ] . ( 389 sec) [ -26945.4099] [Topology ] . ( 392 sec) [ -26945.4079] [Topology ] . ( 395 sec) [ -26945.4072] [Topology ] . ( 402 sec) [ -26945.4070] [GTR parameters ] . ( 402 sec) [ -26945.4041] [Alpha ][ 0.300970] . ( 402 sec) [ -26945.4041] [Topology ] . ( 406 sec) [ -26945.4018] [Topology ] . ( 409 sec) [ -26945.4011] [Topology ] . ( 410 sec) [ -26945.4010] [GTR parameters ] . ( 410 sec) [ -26945.4003] [Alpha ][ 0.300543] . ( 410 sec) [ -26945.4003] [Topology ] . ( 413 sec) [ -26945.3992] [Topology ] . ( 417 sec) [ -26945.3989] [Topology ] . ( 420 sec) [ -26945.3988] [GTR parameters ] . ( 421 sec) [ -26945.3985] [Alpha ][ 0.300242] . ( 421 sec) [ -26945.3985] [Topology ] . ( 424 sec) [ -26945.3980] [Topology ] . ( 426 sec) [ -26945.3978] [GTR parameters ] . ( 426 sec) [ -26945.3978] [Alpha ][ 0.300242] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26945.397843. . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Time used 0h7m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 449.13user 0.00system 7:31.52elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps