.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M4056_408x9563_2008.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 161 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 7664 patterns found. (out of a total of 9563 sites) . 1604 sites without polymorphism (16.77%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1669Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 202 sec) [ -220234.5143] [GTR parameters ] . ( 228 sec) [ -216982.4603] [Alpha ][ 0.500960] . ( 233 sec) [ -216982.4603] [Topology ] . ( 399 sec) [ -199461.1567] [Topology ] . ( 544 sec) [ -194196.7960] [Topology ] . ( 693 sec) [ -192918.7650] [Topology ] . ( 844 sec) [ -192754.3005] [Topology ] . ( 998 sec) [ -191948.5092] [Topology ] . ( 1150 sec) [ -191595.1693] [Topology ] . ( 1308 sec) [ -191154.8800] [Topology ] . ( 1463 sec) [ -190466.5703] [Topology ] . ( 1620 sec) [ -190020.7677] [Topology ] . ( 1988 sec) [ -189302.2475] [GTR parameters ] . ( 2001 sec) [ -189298.4979] [Alpha ][ 0.510629] . ( 2006 sec) [ -189298.4979] [Topology ] . ( 2164 sec) [ -189161.5132] [Topology ] . ( 2322 sec) [ -188876.6654] [Topology ] . ( 2482 sec) [ -188744.5330] [Topology ] . ( 2642 sec) [ -188630.2089] [Topology ] . ( 2802 sec) [ -188684.1300] [Topology ] . Moving backward . ( 2813 sec) [ -188283.5697] [Topology ] . ( 2978 sec) [ -188027.7238] [Topology ] . ( 3126 sec) [ -188275.9879] [Topology ] . Moving backward . ( 3137 sec) [ -187932.1074] [Topology ] . ( 3418 sec) [ -187821.8120] [GTR parameters ] . ( 3431 sec) [ -187820.6456] [Alpha ][ 0.505177] . ( 3436 sec) [ -187820.6456] [Topology ] . ( 3585 sec) [ -187996.0877] [Topology ] . Moving backward . ( 3596 sec) [ -187750.1644] [Topology ] . ( 3752 sec) [ -187645.3443] [Topology ] . ( 3904 sec) [ -187908.3115] [Topology ] . Moving backward . ( 3916 sec) [ -187602.8314] [Topology ] . ( 4071 sec) [ -187563.2385] [Topology ] . ( 4223 sec) [ -187730.8045] [Topology ] . Moving backward . ( 4235 sec) [ -187532.7577] [Topology ] . ( 4390 sec) [ -187512.3615] [Topology ] . ( 4695 sec) [ -187665.5298] [GTR parameters ] . ( 4709 sec) [ -187662.0266] [Alpha ][ 0.496096] . ( 4714 sec) [ -187662.0266] [Topology ] . ( 4867 sec) [ -187536.7482] [Topology ] . ( 5020 sec) [ -187706.5410] [Topology ] . Moving backward . ( 5031 sec) [ -187498.1746] [Topology ] . ( 5186 sec) [ -187449.1758] [Topology ] . ( 5338 sec) [ -187696.7487] [Topology ] . Moving backward . ( 5350 sec) [ -187436.1729] [Topology ] . ( 5503 sec) [ -187442.7657] [Topology ] . Moving backward . ( 5514 sec) [ -187404.9168] [Topology ] . ( 5664 sec) [ -187413.0774] [Topology ] . Moving backward . ( 5724 sec) [ -187402.0999] [GTR parameters ] . ( 5737 sec) [ -187402.0189] [Alpha ][ 0.497517] . ( 5742 sec) [ -187402.0189] [Topology ] . ( 5894 sec) [ -187409.9510] [Topology ] . Moving backward . ( 5905 sec) [ -187391.0222] [Topology ] . ( 6055 sec) [ -187390.2362] [Topology ] . ( 6211 sec) [ -187399.7671] [Topology ] . Moving backward . ( 6222 sec) [ -187371.4869] [Topology ] . ( 6376 sec) [ -187362.1953] [Topology ] . ( 6532 sec) [ -187345.8052] [Topology ] . ( 6688 sec) [ -187345.6566] [Topology ] . ( 6841 sec) [ -187382.1111] [Topology ] . Moving backward . ( 6884 sec) [ -187343.1568] [GTR parameters ] . ( 6897 sec) [ -187343.1001] [Alpha ][ 0.498698] . ( 6902 sec) [ -187343.1001] [Topology ] . ( 7058 sec) [ -187349.4180] [Topology ] . Moving backward . ( 7070 sec) [ -187339.5404] [Topology ] . ( 7226 sec) [ -187349.6159] [Topology ] . Moving backward . ( 7238 sec) [ -187337.5663] [Topology ] . ( 7393 sec) [ -187338.7749] [Topology ] . Moving backward . ( 7404 sec) [ -187336.8049] [Topology ] . ( 7558 sec) [ -187336.3179] [Topology ] . ( 7716 sec) [ -187336.4211] [Topology ] . Moving backward . ( 7727 sec) [ -187335.9632] [Topology ] . ( 7931 sec) [ -187335.3941] [GTR parameters ] . ( 7942 sec) [ -187335.3609] [Alpha ][ 0.499613] . ( 7947 sec) [ -187335.3609] [Topology ] . ( 8101 sec) [ -187335.1507] [Topology ] . ( 8256 sec) [ -187335.1596] [Topology ] . Moving backward . ( 8267 sec) [ -187335.0794] [Topology ] . ( 8421 sec) [ -187335.0522] [Topology ] . ( 8575 sec) [ -187335.0606] [Topology ] . Moving backward . ( 8586 sec) [ -187335.0306] [Topology ] . ( 8742 sec) [ -187335.0197] [Topology ] . ( 8894 sec) [ -187335.0201] [Topology ] . Checking for NNIs, optimizing five branches... . (10083 sec) [ -187330.5368] [Topology ] . (10118 sec) [ -187330.5363] [GTR parameters ] . (10129 sec) [ -187330.5336] [Alpha ][ 0.500113] . (10134 sec) [ -187330.5336] [Topology ] . (10286 sec) [ -187325.7629] [Topology ] . (10438 sec) [ -187323.0562] [Topology ] . (10589 sec) [ -187322.8076] [Topology ] . (10744 sec) [ -187322.8844] [Topology ] . Moving backward . (10755 sec) [ -187322.4687] [Topology ] . (10908 sec) [ -187322.4176] [Topology ] . (11060 sec) [ -187322.3978] [Topology ] . (11212 sec) [ -187322.4041] [Topology ] . Moving backward . (11223 sec) [ -187322.3669] [Topology ] . Checking for NNIs, optimizing five branches... . (12557 sec) [ -187321.5038] [Topology ] . (12591 sec) [ -187321.5007] [GTR parameters ] . (12603 sec) [ -187321.4971] [Alpha ][ 0.500613] . (12608 sec) [ -187321.4971] [Topology ] . (12762 sec) [ -187316.3649] [Topology ] . (12919 sec) [ -187312.9136] [Topology ] . (13075 sec) [ -187311.8934] [Topology ] . (13231 sec) [ -187306.8081] [Topology ] . (13388 sec) [ -187311.0753] [Topology ] . Moving backward . (13399 sec) [ -187304.1213] [Topology ] . (13557 sec) [ -187303.9545] [Topology ] . (13709 sec) [ -187305.8316] [Topology ] . Moving backward . (13721 sec) [ -187302.9393] [Topology ] . Checking for NNIs, optimizing five branches... . (15095 sec) [ -187302.6103] [Topology ] . (15130 sec) [ -187302.6076] [GTR parameters ] . (15142 sec) [ -187302.6068] [Alpha ][ 0.501114] . (15147 sec) [ -187302.6068] [Topology ] . (15302 sec) [ -187303.4820] [Topology ] . Moving backward . (15313 sec) [ -187301.9874] [Topology ] . (15468 sec) [ -187301.9312] [Topology ] . (15624 sec) [ -187302.3247] [Topology ] . Moving backward . (15635 sec) [ -187301.6166] [Topology ] . (15789 sec) [ -187301.5503] [Topology ] . (15941 sec) [ -187301.6700] [Topology ] . Moving backward . (15953 sec) [ -187301.3893] [Topology ] . (16105 sec) [ -187301.3158] [Topology ] . Checking for NNIs, optimizing five branches... . (17323 sec) [ -187300.1587] [Topology ] . (17358 sec) [ -187300.1561] [GTR parameters ] . (17370 sec) [ -187300.1561] [Alpha ][ 0.501114] . (17374 sec) [ -187300.1561] [Topology ] . (17528 sec) [ -187300.2390] [Topology ] . Moving backward . (17539 sec) [ -187300.0537] [Topology ] . (17696 sec) [ -187299.9701] [Topology ] . (17849 sec) [ -187299.9713] [Topology ] . Moving backward . (17860 sec) [ -187299.9246] [Topology ] . (18010 sec) [ -187299.7695] [Topology ] . (18161 sec) [ -187299.6609] [Topology ] . (18312 sec) [ -187299.6219] [Topology ] . (18462 sec) [ -187299.5971] [Topology ] . Checking for NNIs, optimizing five branches... . (19807 sec) [ -187299.1236] [Topology ] . (19841 sec) [ -187299.1233] [GTR parameters ] . (19853 sec) [ -187299.1233] [Alpha ][ 0.501114] . (19858 sec) [ -187299.1233] [Topology ] . (20006 sec) [ -187299.0728] [Topology ] . (20156 sec) [ -187299.0738] [Topology ] . Checking for NNIs, optimizing five branches... . (21325 sec) [ -187298.7201] [Topology ] . (21360 sec) [ -187298.7200] [GTR parameters ] . (21371 sec) [ -187298.7187] [Alpha ][ 0.500612] . (21376 sec) [ -187298.7187] [Topology ] . (21525 sec) [ -187298.5551] [Topology ] . (21673 sec) [ -187298.2500] [Topology ] . (21822 sec) [ -187298.3011] [Topology ] . Moving backward . (21833 sec) [ -187298.0182] [Topology ] . (21982 sec) [ -187297.9610] [Topology ] . (22131 sec) [ -187297.9785] [Topology ] . Moving backward . (22142 sec) [ -187297.9117] [Topology ] . (22291 sec) [ -187297.8858] [Topology ] . (22440 sec) [ -187297.8809] [Topology ] . Checking for NNIs, optimizing five branches... . (23803 sec) [ -187297.8960] [Topology ] . (23838 sec) [ -187297.8945] [GTR parameters ] . (23850 sec) [ -187297.8945] [Alpha ][ 0.500612] . (23855 sec) [ -187297.8945] [Topology ] . (24011 sec) [ -187297.9645] [Topology ] . Moving backward . (24023 sec) [ -187297.7850] [Topology ] . (24179 sec) [ -187297.7697] [Topology ] . (24334 sec) [ -187297.7999] [Topology ] . Moving backward . (24346 sec) [ -187297.7418] [Topology ] . (24499 sec) [ -187297.7368] [Topology ] . (24650 sec) [ -187297.7439] [Topology ] . Moving backward . (24661 sec) [ -187297.7267] [Topology ] . (24812 sec) [ -187297.7229] [Topology ] . Checking for NNIs, optimizing five branches... . (26010 sec) [ -187297.7216] [Topology ] . (26045 sec) [ -187297.7216] [GTR parameters ] . (26057 sec) [ -187297.7216] [Alpha ][ 0.500612] . (26061 sec) [ -187297.7216] [Topology ] . (26215 sec) [ -187297.7204] [Topology ] . (26366 sec) [ -187297.7260] [Topology ] . Moving backward . (26377 sec) [ -187297.7146] [Topology ] . (26528 sec) [ -187297.7132] [Topology ] . (26677 sec) [ -187297.7141] [Topology ] . Checking for NNIs, optimizing five branches... . (27868 sec) [ -187297.7141] [GTR parameters ] . (27879 sec) [ -187297.7141] [Alpha ][ 0.500612] . (27884 sec) [ -187297.7141] [Topology ] . (28033 sec) [ -187297.7201] [Topology ] . Moving backward . (28044 sec) [ -187297.7098] [Topology ] . (28193 sec) [ -187297.7095] [Topology ] . Checking for NNIs, optimizing five branches... . (29384 sec) [ -187297.7095] [GTR parameters ] . (29395 sec) [ -187297.7095] [Alpha ][ 0.500612] . (29400 sec) [ -187297.7095] [Topology ] . (29549 sec) [ -187297.7110] [Topology ] . Moving backward . (29560 sec) [ -187297.7079] [Topology ] . (29709 sec) [ -187297.7075] [Topology ] . Checking for NNIs, optimizing five branches... . (30900 sec) [ -187297.7075] [GTR parameters ] . (30911 sec) [ -187297.7075] [Alpha ][ 0.500612] . (30916 sec) [ -187297.7075] [Topology ] . (31065 sec) [ -187297.7077] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -187297.707698. . Printing the most likely tree in file 'nucleic_M4056_408x9563_2008.phy_phyml_tree.txt'... . Time used 9h16m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 33220.27user 0.00system 9:18:10elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps