.......................... 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 ] . ( 3 sec) [ -28718.2078] [Alpha ][ 0.500960] . ( 20 sec) [ -28715.8595] [ 5819] [depth= 1] . ( 39 sec) [ -28709.8159] [ 5824] [depth= 1] . ( 40 sec) [ -28697.5201] [ 5819] [depth= 1] . ( 65 sec) [ -28696.6045] [ 5823] [depth= 1] . ( 65 sec) [ -28683.6351] [ 5819] [depth= 1] . ( 65 sec) [ -28681.3289] [ 5822] [depth= 1] . ( 65 sec) [ -28679.2730] [ 5819] [depth= 1] . ( 74 sec) [ -28672.1645] [ 5820] [depth= 1] . ( 99 sec) [ -28670.8541] [ 5822] [depth= 1] . ( 99 sec) [ -28669.3735] [ 5824] [depth= 1] . ( 99 sec) [ -28667.7191] [ 5823] [depth= 1] . ( 102 sec) [ -28664.6733] [ 5818] [depth= 1] . ( 107 sec) [ -28658.0320] [ 5822] [depth= 1] . ( 107 sec) [ -28635.3083] [ 5811] [depth= 4] . ( 114 sec) [ -28627.6068] [ 5812] [depth= 1] . ( 115 sec) [ -28627.4745] [ 5811] [depth= 1] . ( 115 sec) [ -28624.7292] [ 5812] [depth= 1] . ( 124 sec) [ -28617.2890] [ 5818] [depth= 2] . ( 124 sec) [ -28611.4844] [ 5815] [depth= 1] . ( 125 sec) [ -28610.8862] [ 5818] [depth= 1] . ( 127 sec) [ -28608.7460] [ 5815] [depth= 1] . ( 127 sec) [ -28600.3927] [ 5806] [depth= 1] . ( 127 sec) [ -28596.8627] [ 5807] [depth= 1] . ( 132 sec) [ -28593.0794] [ 5801] [depth= 1] . ( 137 sec) [ -28589.2988] [ 5802] [depth= 1] . ( 140 sec) [ -28585.9063] [ 5810] [depth= 3] . ( 142 sec) [ -28584.4371] [ 5815] [depth= 1] . ( 145 sec) [ -28579.5392] [ 5821] [depth= 1] . ( 145 sec) [ -28578.2007] [ 5833] [depth= 1] . ( 145 sec) [ -28555.1827] [ 5821] [depth= 1] . ( 150 sec) [ -28544.2047] [ 5832] [depth= 1] . ( 150 sec) [ -28526.4792] [ 5821] [depth= 1] . ( 150 sec) [ -28526.0146] [ 5821] [depth= 1] . ( 153 sec) [ -28523.9562] [ 5816] [depth= 1] . ( 156 sec) [ -28522.8229] [ 5823] [depth= 1] . ( 156 sec) [ -28521.8381] [ 5821] [depth= 1] . ( 173 sec) [ -28505.0474] [ 5828] [depth= 1] . ( 173 sec) [ -28487.4604] [ 5820] [depth= 2] . ( 174 sec) [ -28480.1618] [ 5821] [depth= 2] . ( 174 sec) [ -28469.5684] [ 5820] [depth= 1] . ( 174 sec) [ -28465.1020] [ 5827] [depth= 2] . ( 175 sec) [ -28445.1146] [ 5822] [depth= 1] . ( 177 sec) [ -28444.7033] [ 5822] [depth= 1] . ( 177 sec) [ -28443.8089] [ 5823] [depth= 2] . ( 178 sec) [ -28434.1164] [ 5822] [depth= 2] . ( 180 sec) [ -28423.5977] [ 5819] [depth= 2] . ( 191 sec) [ -28422.3841] [ 5821] [depth= 1] . ( 197 sec) [ -28418.1484] [ 5812] [depth= 6] . ( 203 sec) [ -28415.2506] [ 5814] [depth= 2] . ( 203 sec) [ -28414.3676] [ 5814] [depth= 1] . ( 203 sec) [ -28412.6625] [ 5814] [depth= 1] . ( 206 sec) [ -28411.6587] [ 5814] [depth= 1] . ( 237 sec) [ -28409.2515] [ 5812] [depth= 1] . ( 237 sec) [ -28405.4419] [ 5814] [depth= 1] . ( 237 sec) [ -28391.1220] [ 5805] [depth= 3] . ( 244 sec) [ -28387.1281] [ 5808] [depth= 1] . ( 244 sec) [ -28384.2632] [ 5805] [depth= 1] . ( 247 sec) [ -28382.8108] [ 5806] [depth= 1] . ( 247 sec) [ -28379.7361] [ 5805] [depth= 1] . ( 252 sec) [ -28377.0259] [ 5802] [depth= 2] . ( 253 sec) [ -28376.2183] [ 5804] [depth= 1] . ( 253 sec) [ -28373.2119] [ 5805] [depth= 1] . ( 253 sec) [ -28370.0239] [ 5806] [depth= 1] . ( 256 sec) [ -28369.9733] [ 5805] [depth= 1] . ( 302 sec) [ -28368.0581] [ 5802] [depth= 1] . ( 321 sec) [ -28364.9641] [ 5801] [depth= 1] . ( 326 sec) [ -28364.4841] [ 5802] [depth= 2] . ( 335 sec) [ -28361.8855] [ 5801] [depth= 1] . ( 338 sec) [ -28360.2909] [ 5801] [depth= 1] . ( 347 sec) [ -28359.4233] [ 5802] [depth= 5] . ( 352 sec) [ -28358.4387] [ 5802] [depth= 2] . ( 355 sec) [ -28357.5406] [ 5802] [depth= 1] . ( 356 sec) [ -28356.8526] [ 5800] [depth= 1] . ( 383 sec) [ -28356.8370] [ 5800] [depth= 1] . ( 387 sec) [ -28283.2096] [Branch lengths ] . ( 394 sec) [ -27061.1011] [GTR parameters ] . ( 394 sec) [ -26998.0913] [Alpha ][ 0.341278] . ( 469 sec) [ -26996.9451] [ 5803] [depth= 1] . ( 474 sec) [ -26992.5705] [ 5806] [depth= 1] . ( 514 sec) [ -26991.7017] [ 5804] [depth= 1] . ( 517 sec) [ -26991.4354] [ 5804] [depth= 1] . ( 551 sec) [ -26988.2474] [ 5792] [depth= 1] . ( 606 sec) [ -26987.9471] [ 5796] [depth= 2] . ( 606 sec) [ -26986.0891] [ 5795] [depth= 1] . ( 651 sec) [ -26982.3979] [ 5795] [depth= 1] . ( 655 sec) [ -26982.3680] [ 5798] [depth= 1] . ( 658 sec) [ -26972.7933] [ 5802] [depth= 2] . ( 824 sec) [ -26972.2903] [ 5803] [depth= 2] . ( 827 sec) [ -26972.2768] [ 5802] [depth= 1] . ( 938 sec) [ -26969.6256] [ 5801] [depth= 2] . ( 960 sec) [ -26969.6137] [ 5801] [depth= 1] . ( 1050 sec) [ -26952.7956] [Branch lengths ] . ( 1059 sec) [ -26949.9750] [GTR parameters ] . ( 1059 sec) [ -26948.6041] [Alpha ][ 0.322410] . ( 1304 sec) [ -26948.5346] [ 5805] [depth= 1] . ( 1432 sec) [ -26948.5151] [ 5803] [depth= 1] . ( 1447 sec) [ -26948.4721] [ 5805] [depth= 1] . ( 1564 sec) [ -26948.4013] [ 5803] [depth= 1] . ( 1787 sec) [ -26946.7526] [Branch lengths ] . ( 1793 sec) [ -26946.7211] [GTR parameters ] . ( 1793 sec) [ -26946.4605] [Alpha ][ 0.314587] . ( 2474 sec) [ -26946.0366] [Branch lengths ] . ( 2634 sec) [ -26945.9845] [Branch lengths ] . ( 2634 sec) [ -26945.9845] [Topology ] . ( 2637 sec) [ -26945.9812] [Topology ] . ( 2641 sec) [ -26945.9804] [Topology ] . ( 2645 sec) [ -26945.9731] [GTR parameters ] . ( 2645 sec) [ -26945.7690] [Alpha ][ 0.307788] . ( 2645 sec) [ -26945.7690] [Topology ] . ( 2648 sec) [ -26945.6931] [Topology ] . ( 2652 sec) [ -26945.6687] [Topology ] . ( 2655 sec) [ -26945.6600] [Topology ] . ( 2659 sec) [ -26945.6567] [Topology ] . ( 2663 sec) [ -26945.6555] [Topology ] . ( 2667 sec) [ -26945.6550] [Topology ] . ( 2668 sec) [ -26945.6542] [GTR parameters ] . ( 2669 sec) [ -26945.5937] [Alpha ][ 0.303955] . ( 2669 sec) [ -26945.5937] [Topology ] . ( 2674 sec) [ -26945.5682] [Topology ] . ( 2678 sec) [ -26945.5602] [Topology ] . ( 2682 sec) [ -26945.5574] [Topology ] . ( 2686 sec) [ -26945.5564] [Topology ] . ( 2691 sec) [ -26945.5560] [Topology ] . ( 2692 sec) [ -26945.5559] [GTR parameters ] . ( 2692 sec) [ -26945.5401] [Alpha ][ 0.302000] . ( 2692 sec) [ -26945.5401] [Topology ] . ( 2695 sec) [ -26945.5324] [Topology ] . ( 2699 sec) [ -26945.5299] [Topology ] . ( 2702 sec) [ -26945.5291] [Topology ] . ( 2705 sec) [ -26945.5197] [GTR parameters ] . ( 2706 sec) [ -26945.5143] [Alpha ][ 0.300860] . ( 2706 sec) [ -26945.5143] [Topology ] . ( 2709 sec) [ -26945.4897] [Topology ] . ( 2712 sec) [ -26945.3613] [Topology ] . ( 2716 sec) [ -26945.3405] [Topology ] . ( 2719 sec) [ -26945.3332] [Topology ] . ( 2722 sec) [ -26945.3304] [Topology ] . ( 2725 sec) [ -26945.3293] [Topology ] . ( 2729 sec) [ -26945.3288] [Topology ] . ( 2732 sec) [ -26945.3268] [GTR parameters ] . ( 2732 sec) [ -26945.3163] [Alpha ][ 0.299272] . ( 2732 sec) [ -26945.3163] [Topology ] . ( 2736 sec) [ -26945.3115] [Topology ] . ( 2741 sec) [ -26945.3100] [Topology ] . ( 2744 sec) [ -26945.3094] [Topology ] . ( 2748 sec) [ -26945.3092] [GTR parameters ] . ( 2749 sec) [ -26945.3069] [Alpha ][ 0.298519] . ( 2749 sec) [ -26945.3069] [Topology ] . ( 2752 sec) [ -26945.3051] [Topology ] . ( 2756 sec) [ -26945.3045] [Topology ] . ( 2758 sec) [ -26945.3043] [GTR parameters ] . ( 2758 sec) [ -26945.3036] [Alpha ][ 0.298119] . ( 2759 sec) [ -26945.3036] [Topology ] . ( 2763 sec) [ -26945.3028] [Topology ] . ( 2763 sec) [ -26945.3028] [GTR parameters ] . ( 2764 sec) [ -26945.3028] [Alpha ][ 0.298119] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -26945.302796. . Printing the most likely tree in file 'nucleic_M2606_110x1206_2006.phy_phyml_tree.txt'... . Time used 0h46m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2255.07user 0.00system 46:35.81elapsed 80%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps