.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M3703_1566x915_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 . Compressing sequences... . 896 patterns found. (out of a total of 915 sites) . 79 sites without polymorphism (8.63%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 753Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3188 sec) [ -83457.7105] [GTR parameters ] . ( 3197 sec) [ -82943.4363] [Alpha ][ 0.500960] . ( 3199 sec) [ -82943.4363] [Topology ] . ( 6369 sec) [ -81212.2926] [Topology ] . ( 9538 sec) [ -80722.5757] [Topology ] . (12706 sec) [ -80503.5702] [Topology ] . (15880 sec) [ -80376.7776] [Topology ] . (19053 sec) [ -80286.9604] [Topology ] . (22220 sec) [ -80223.7727] [Topology ] . (25392 sec) [ -80200.7172] [Topology ] . (28575 sec) [ -80182.2081] [Topology ] . (31739 sec) [ -80145.1081] [Topology ] . (34958 sec) [ -80073.7807] [GTR parameters ] . (34963 sec) [ -80004.6446] [Alpha ][ 0.660643] . (34965 sec) [ -80004.6446] [Topology ] . (38124 sec) [ -79944.2649] [Topology ] . (41285 sec) [ -79903.8103] [Topology ] . (44447 sec) [ -79869.2104] [Topology ] . (47607 sec) [ -79865.3932] [Topology ] . (50766 sec) [ -79863.7916] [Topology ] . (53925 sec) [ -79863.6087] [Topology ] . (57085 sec) [ -79863.0437] [Topology ] . (60246 sec) [ -79863.2670] [Topology ] . Moving backward . (60250 sec) [ -79862.3709] [Topology ] . Checking for NNIs, optimizing five branches... . (63840 sec) [ -79860.0356] [Topology ] . (63887 sec) [ -79858.6081] [GTR parameters ] . (63891 sec) [ -79858.1269] [Alpha ][ 0.674171] . (63893 sec) [ -79858.1269] [Topology ] . (67054 sec) [ -79858.0345] [Topology ] . (70215 sec) [ -79857.8947] [Topology ] . (73375 sec) [ -79857.8712] [Topology ] . (76536 sec) [ -79857.8631] [Topology ] . (79694 sec) [ -79857.8595] [Topology ] . (82853 sec) [ -79857.8578] [Topology ] . (86014 sec) [ -79857.8569] [Topology ] . Checking for NNIs, optimizing five branches... . (86446 sec) [ -79856.4994] [Topology ] . (86470 sec) [ -79856.4832] [GTR parameters ] . (86474 sec) [ -79856.4832] [Alpha ][ 0.674171] . (86476 sec) [ -79856.4832] [Topology ] . (89636 sec) [ -79856.4437] [Topology ] . (92796 sec) [ -79856.4370] [Topology ] . (95956 sec) [ -79856.4346] [Topology ] . (99115 sec) [ -79856.4336] [Topology ] . (102274 sec) [ -79856.4331] [Topology ] . Checking for NNIs, optimizing five branches... . (102707 sec) [ -79855.4337] [Topology ] . (102726 sec) [ -79855.4329] [GTR parameters ] . (102730 sec) [ -79855.4329] [Alpha ][ 0.674171] . (102731 sec) [ -79855.4329] [Topology ] . (105891 sec) [ -79855.0724] [Topology ] . (109050 sec) [ -79855.0538] [Topology ] . (112208 sec) [ -79855.0525] [Topology ] . (115367 sec) [ -79855.0524] [Topology ] . Checking for NNIs, optimizing five branches... . (115798 sec) [ -79853.5042] [Topology ] . (115810 sec) [ -79853.5041] [GTR parameters ] . (115814 sec) [ -79853.5041] [Alpha ][ 0.674171] . (115816 sec) [ -79853.5041] [Topology ] . (118975 sec) [ -79853.0472] [Topology ] . (122134 sec) [ -79853.0191] [Topology ] . (125292 sec) [ -79853.0158] [Topology ] . (128451 sec) [ -79853.0154] [Topology ] . Checking for NNIs, optimizing five branches... . (128882 sec) [ -79852.6286] [Topology ] . (128901 sec) [ -79852.6269] [GTR parameters ] . (128905 sec) [ -79852.6269] [Alpha ][ 0.674171] . (128907 sec) [ -79852.6269] [Topology ] . (132066 sec) [ -79852.6254] [Topology ] . (135227 sec) [ -79852.6206] [Topology ] . (138388 sec) [ -79852.5869] [Topology ] . (141546 sec) [ -79852.4036] [Topology ] . (144708 sec) [ -79852.1950] [Topology ] . (147868 sec) [ -79852.0943] [Topology ] . Checking for NNIs, optimizing five branches... . (148299 sec) [ -79848.2586] [Topology ] . (148311 sec) [ -79848.2585] [GTR parameters ] . (148315 sec) [ -79848.2585] [Alpha ][ 0.674171] . (148317 sec) [ -79848.2585] [Topology ] . (151477 sec) [ -79847.7705] [Topology ] . (154638 sec) [ -79847.6489] [Topology ] . (157798 sec) [ -79847.6190] [Topology ] . (160959 sec) [ -79847.6117] [Topology ] . (164119 sec) [ -79847.6099] [Topology ] . (167278 sec) [ -79847.6094] [Topology ] . Checking for NNIs, optimizing five branches... . (167708 sec) [ -79847.2430] [Topology ] . (167750 sec) [ -79847.2397] [GTR parameters ] . (167754 sec) [ -79847.2397] [Alpha ][ 0.674171] . (167756 sec) [ -79847.2397] [Topology ] . (170917 sec) [ -79847.1858] [Topology ] . (174077 sec) [ -79847.1765] [Topology ] . (177239 sec) [ -79847.1745] [Topology ] . (180397 sec) [ -79847.1739] [Topology ] . Checking for NNIs, optimizing five branches... . (180828 sec) [ -79846.8540] [Topology ] . (180853 sec) [ -79846.8515] [GTR parameters ] . (180859 sec) [ -79846.8511] [Alpha ][ 0.673497] . (180861 sec) [ -79846.8511] [Topology ] . (184021 sec) [ -79841.3705] [Topology ] . (187181 sec) [ -79838.7168] [Topology ] . (190341 sec) [ -79835.4281] [Topology ] . (193503 sec) [ -79834.9456] [Topology ] . (196663 sec) [ -79834.8959] [Topology ] . (199823 sec) [ -79834.8895] [Topology ] . (202985 sec) [ -79834.8883] [Topology ] . (206143 sec) [ -79834.8879] [Topology ] . Checking for NNIs, optimizing five branches... . (206575 sec) [ -79834.6310] [Topology ] . (206621 sec) [ -79834.6230] [GTR parameters ] . (206626 sec) [ -79834.6217] [Alpha ][ 0.674170] . (206628 sec) [ -79834.6217] [Topology ] . (209786 sec) [ -79834.6215] [Topology ] . Checking for NNIs, optimizing five branches... . (210218 sec) [ -79834.4072] [Topology ] . (210229 sec) [ -79834.4072] [GTR parameters ] . (210233 sec) [ -79834.4072] [Alpha ][ 0.674170] . (210235 sec) [ -79834.4072] [Topology ] . (213395 sec) [ -79833.7791] [Topology ] . (216557 sec) [ -79833.1719] [Topology ] . (219717 sec) [ -79832.9418] [Topology ] . (222875 sec) [ -79832.9139] [Topology ] . (226034 sec) [ -79832.9090] [Topology ] . (229193 sec) [ -79832.9079] [Topology ] . (232353 sec) [ -79832.9077] [Topology ] . Checking for NNIs, optimizing five branches... . (232785 sec) [ -79832.0128] [Topology ] . (232797 sec) [ -79832.0128] [GTR parameters ] . (232801 sec) [ -79832.0128] [Alpha ][ 0.674170] . (232803 sec) [ -79832.0128] [Topology ] . (235962 sec) [ -79832.0101] [Topology ] . (239120 sec) [ -79832.0096] [Topology ] . Checking for NNIs, optimizing five branches... . (239552 sec) [ -79831.8101] [Topology ] . (239570 sec) [ -79831.8099] [GTR parameters ] . (239574 sec) [ -79831.8099] [Alpha ][ 0.674170] . (239576 sec) [ -79831.8099] [Topology ] . (242735 sec) [ -79831.8098] [Topology ] . Checking for NNIs, optimizing five branches... . (243166 sec) [ -79831.6421] [Topology ] . (243178 sec) [ -79831.6420] [GTR parameters ] . (243182 sec) [ -79831.6420] [Alpha ][ 0.674170] . (243184 sec) [ -79831.6420] [Topology ] . (246345 sec) [ -79831.6050] [Topology ] . (249506 sec) [ -79831.6001] [Topology ] . (252666 sec) [ -79831.5987] [Topology ] . (255828 sec) [ -79831.5983] [Topology ] . Checking for NNIs, optimizing five branches... . (256258 sec) [ -79831.4432] [Topology ] . (256270 sec) [ -79831.4432] [GTR parameters ] . (256274 sec) [ -79831.4432] [Alpha ][ 0.674170] . (256276 sec) [ -79831.4432] [Topology ] . (259436 sec) [ -79831.0165] [Topology ] . (262596 sec) [ -79830.8322] [Topology ] . (265755 sec) [ -79830.8197] [Topology ] . (268914 sec) [ -79830.8175] [Topology ] . (272074 sec) [ -79830.8171] [Topology ] . Checking for NNIs, optimizing five branches... . (272505 sec) [ -79830.7768] [Topology ] . (272523 sec) [ -79830.7727] [GTR parameters ] . (272528 sec) [ -79830.7690] [Alpha ][ 0.672823] . (272530 sec) [ -79830.7690] [Topology ] . (275690 sec) [ -79830.7430] [Topology ] . (278852 sec) [ -79830.7388] [Topology ] . (282013 sec) [ -79830.7376] [Topology ] . (285172 sec) [ -79830.7372] [Topology ] . Checking for NNIs, optimizing five branches... . (285602 sec) [ -79830.7101] [Topology ] . (285615 sec) [ -79830.7099] [GTR parameters ] . (285619 sec) [ -79830.7099] [Alpha ][ 0.672823] . (285620 sec) [ -79830.7099] [Topology ] . (288782 sec) [ -79830.6960] [Topology ] . (291942 sec) [ -79830.6949] [Topology ] . (295101 sec) [ -79830.6947] [Topology ] . Checking for NNIs, optimizing five branches... . (295531 sec) [ -79830.6769] [Topology ] . (295543 sec) [ -79830.6768] [GTR parameters ] . (295547 sec) [ -79830.6768] [Alpha ][ 0.672823] . (295549 sec) [ -79830.6768] [Topology ] . (298708 sec) [ -79830.6709] [Topology ] . (301867 sec) [ -79830.6705] [Topology ] . Checking for NNIs, optimizing five branches... . (302298 sec) [ -79830.6612] [Topology ] . (302309 sec) [ -79830.6611] [GTR parameters ] . (302313 sec) [ -79830.6611] [Alpha ][ 0.672823] . (302315 sec) [ -79830.6611] [Topology ] . (305474 sec) [ -79830.6611] [Topology ] . Checking for NNIs, optimizing five branches... . (305903 sec) [ -79830.6602] [Topology ] . (305916 sec) [ -79830.6601] [GTR parameters ] . (305920 sec) [ -79830.6601] [Alpha ][ 0.672823] . (305922 sec) [ -79830.6601] [Topology ] . (309080 sec) [ -79830.6556] [Topology ] . (312239 sec) [ -79830.6500] [Topology ] . (315400 sec) [ -79830.6461] [Topology ] . (318559 sec) [ -79830.6433] [Topology ] . (321718 sec) [ -79830.6414] [Topology ] . (324878 sec) [ -79830.6401] [Topology ] . Checking for NNIs, optimizing five branches... . (325308 sec) [ -79830.6394] [Topology ] . (325319 sec) [ -79830.6394] [GTR parameters ] . (325323 sec) [ -79830.6394] [Alpha ][ 0.672823] . (325325 sec) [ -79830.6394] [Topology ] . (328486 sec) [ -79830.6385] [Topology ] . Checking for NNIs, optimizing five branches... . (328916 sec) [ -79830.6379] [Topology ] . (328928 sec) [ -79830.6379] [GTR parameters ] . (328932 sec) [ -79830.6379] [Alpha ][ 0.672823] . (328934 sec) [ -79830.6379] [Topology ] . (332094 sec) [ -79830.6344] [Topology ] . (335252 sec) [ -79830.6227] [Topology ] . (338412 sec) [ -79830.6032] [Topology ] . (341573 sec) [ -79830.5730] [Topology ] . (344734 sec) [ -79830.5218] [Topology ] . (347892 sec) [ -79830.4381] [Topology ] . Checking for NNIs, optimizing five branches... . (348322 sec) [ -79830.4379] [Topology ] . (348334 sec) [ -79830.4379] [GTR parameters ] . (348338 sec) [ -79830.4379] [Alpha ][ 0.672823] . (348339 sec) [ -79830.4379] [Topology ] . (351499 sec) [ -79830.2990] [Topology ] . (354658 sec) [ -79830.1529] [Topology ] . (357819 sec) [ -79830.0997] [Topology ] . (360978 sec) [ -79830.0891] [Topology ] . (364140 sec) [ -79830.0870] [Topology ] . (367301 sec) [ -79830.0865] [Topology ] . Checking for NNIs, optimizing five branches... . (367730 sec) [ -79830.0863] [Topology ] . (367743 sec) [ -79830.0863] [GTR parameters ] . (367747 sec) [ -79830.0863] [Alpha ][ 0.672823] . (367748 sec) [ -79830.0863] [Topology ] . (370909 sec) [ -79830.0857] [Topology ] . Checking for NNIs, optimizing five branches... . (371340 sec) [ -79830.0853] [Topology ] . (371352 sec) [ -79830.0853] [GTR parameters ] . (371356 sec) [ -79830.0853] [Alpha ][ 0.672823] . (371358 sec) [ -79830.0853] [Topology ] . (374518 sec) [ -79830.0840] [Topology ] . (377678 sec) [ -79830.0821] [Topology ] . (380839 sec) [ -79830.0793] [Topology ] . (383998 sec) [ -79830.0748] [Topology ] . (387157 sec) [ -79830.0679] [Topology ] . (390317 sec) [ -79830.0569] [Topology ] . Checking for NNIs, optimizing five branches... . (390748 sec) [ -79830.0566] [Topology ] . (390760 sec) [ -79830.0566] [GTR parameters ] . (390764 sec) [ -79830.0566] [Alpha ][ 0.672823] . (390766 sec) [ -79830.0566] [Topology ] . (393926 sec) [ -79830.0399] [Topology ] . (397085 sec) [ -79830.0141] [Topology ] . (400245 sec) [ -79829.9744] [Topology ] . (403406 sec) [ -79829.9140] [Topology ] . (406566 sec) [ -79829.8222] [Topology ] . (409725 sec) [ -79829.7321] [Topology ] . Checking for NNIs, optimizing five branches... . (410165 sec) [ -79829.7321] [GTR parameters ] . (410169 sec) [ -79829.7321] [Alpha ][ 0.672823] . (410171 sec) [ -79829.7321] [Topology ] . (413331 sec) [ -79829.6973] [Topology ] . (416492 sec) [ -79829.6905] [Topology ] . (419650 sec) [ -79829.6891] [Topology ] . (422810 sec) [ -79829.6887] [Topology ] . Checking for NNIs, optimizing five branches... . (423251 sec) [ -79829.6887] [GTR parameters ] . (423255 sec) [ -79829.6887] [Alpha ][ 0.672823] . (423257 sec) [ -79829.6887] [Topology ] . (426418 sec) [ -79829.6886] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -79829.688633. . Printing the most likely tree in file 'nucleic_M3703_1566x915_2008.phy_phyml_tree.txt'... . Time used 118h41m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 427203.31user 0.00system 118:45:10elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps