.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M4058_406x6016_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 . 71 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 5231 patterns found. (out of a total of 6016 sites) . 919 sites without polymorphism (15.28%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1133Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 136 sec) [ -490006.6934] [GTR parameters ] . ( 147 sec) [ -489279.9174] [Alpha ][ 0.667175] . ( 150 sec) [ -489279.9174] [Topology ] . ( 244 sec) [ -482058.4797] [Topology ] . ( 346 sec) [ -479736.1167] [Topology ] . ( 442 sec) [ -478655.7271] [Topology ] . ( 539 sec) [ -477748.8078] [Topology ] . ( 636 sec) [ -476979.7854] [Topology ] . ( 733 sec) [ -476335.7714] [Topology ] . ( 829 sec) [ -475739.6358] [Topology ] . ( 924 sec) [ -475342.1795] [Topology ] . ( 1019 sec) [ -474957.4772] [Topology ] . ( 1204 sec) [ -474373.9413] [GTR parameters ] . ( 1215 sec) [ -473904.1221] [Alpha ][ 0.890055] . ( 1218 sec) [ -473904.1221] [Topology ] . ( 1311 sec) [ -473650.7684] [Topology ] . ( 1405 sec) [ -473481.9639] [Topology ] . ( 1499 sec) [ -473308.0175] [Topology ] . ( 1594 sec) [ -473205.1028] [Topology ] . ( 1688 sec) [ -473158.6893] [Topology ] . ( 1783 sec) [ -473125.5489] [Topology ] . ( 1878 sec) [ -473107.9565] [Topology ] . ( 1972 sec) [ -473097.8676] [Topology ] . ( 2067 sec) [ -473091.5365] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2993 sec) [ -473083.5395] [Topology ] . ( 3076 sec) [ -473082.7319] [GTR parameters ] . ( 3085 sec) [ -473082.5257] [Alpha ][ 0.895380] . ( 3089 sec) [ -473082.5257] [Topology ] . ( 3184 sec) [ -473077.8926] [Topology ] . ( 3280 sec) [ -473071.2826] [Topology ] . ( 3376 sec) [ -473064.7157] [Topology ] . ( 3472 sec) [ -473049.0304] [Topology ] . ( 3568 sec) [ -473036.9758] [Topology ] . ( 3664 sec) [ -473033.4922] [Topology ] . ( 3760 sec) [ -473032.2029] [Topology ] . ( 3856 sec) [ -473031.5394] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4686 sec) [ -473028.1007] [Topology ] . ( 4737 sec) [ -473028.0367] [GTR parameters ] . ( 4748 sec) [ -473027.9890] [Alpha ][ 0.892761] . ( 4751 sec) [ -473027.9890] [Topology ] . ( 4846 sec) [ -473027.3115] [Topology ] . ( 4941 sec) [ -473026.8438] [Topology ] . ( 5036 sec) [ -473026.4383] [Topology ] . ( 5131 sec) [ -473026.0573] [Topology ] . ( 5226 sec) [ -473025.6863] [Topology ] . ( 5321 sec) [ -473025.3173] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6146 sec) [ -473022.6621] [Topology ] . ( 6212 sec) [ -473022.6452] [GTR parameters ] . ( 6221 sec) [ -473022.6183] [Alpha ][ 0.890809] . ( 6224 sec) [ -473022.6183] [Topology ] . ( 6320 sec) [ -473019.0334] [Topology ] . ( 6416 sec) [ -473016.5739] [Topology ] . ( 6512 sec) [ -473015.8176] [Topology ] . ( 6609 sec) [ -473015.2896] [Topology ] . ( 6705 sec) [ -473014.8109] [Topology ] . ( 6801 sec) [ -473014.3319] [Topology ] . ( 6897 sec) [ -473013.8349] [Topology ] . Checking for NNIs, optimizing five branches... . ( 7726 sec) [ -473011.9842] [Topology ] . ( 7778 sec) [ -473011.9745] [GTR parameters ] . ( 7788 sec) [ -473011.8908] [Alpha ][ 0.887470] . ( 7791 sec) [ -473011.8908] [Topology ] . ( 7887 sec) [ -473003.6427] [Topology ] . ( 7983 sec) [ -473000.4554] [Topology ] . ( 8079 sec) [ -472995.3340] [Topology ] . ( 8175 sec) [ -472993.6675] [Topology ] . ( 8271 sec) [ -472992.3550] [Topology ] . ( 8368 sec) [ -472991.1375] [Topology ] . ( 8463 sec) [ -472989.9880] [Topology ] . ( 8559 sec) [ -472988.9190] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9393 sec) [ -472987.1176] [Topology ] . ( 9436 sec) [ -472987.0958] [GTR parameters ] . ( 9445 sec) [ -472986.7001] [Alpha ][ 0.880509] . ( 9449 sec) [ -472986.7001] [Topology ] . ( 9544 sec) [ -472971.2477] [Topology ] . ( 9639 sec) [ -472964.7012] [Topology ] . ( 9736 sec) [ -472962.8734] [Topology ] . ( 9832 sec) [ -472961.8405] [Topology ] . ( 9928 sec) [ -472960.9986] [Topology ] . (10024 sec) [ -472955.6456] [Topology ] . (10120 sec) [ -472955.1902] [Topology ] . (10217 sec) [ -472953.3951] [Topology ] . (10313 sec) [ -472951.9459] [Topology ] . Checking for NNIs, optimizing five branches... . (11233 sec) [ -472951.1468] [Topology ] . (11294 sec) [ -472951.0040] [GTR parameters ] . (11304 sec) [ -472950.1369] [Alpha ][ 0.870597] . (11307 sec) [ -472950.1369] [Topology ] . (11402 sec) [ -472948.2147] [Topology ] . (11497 sec) [ -472941.1432] [Topology ] . (11593 sec) [ -472939.8588] [Topology ] . (11688 sec) [ -472939.5300] [Topology ] . (11783 sec) [ -472939.3335] [Topology ] . (11879 sec) [ -472939.1880] [Topology ] . (11974 sec) [ -472939.0730] [Topology ] . (12070 sec) [ -472938.9796] [Topology ] . Checking for NNIs, optimizing five branches... . (12900 sec) [ -472938.7372] [Topology ] . (12934 sec) [ -472938.7133] [GTR parameters ] . (12944 sec) [ -472938.4621] [Alpha ][ 0.865344] . (12947 sec) [ -472938.4621] [Topology ] . (13042 sec) [ -472938.1674] [Topology ] . (13137 sec) [ -472938.0006] [Topology ] . (13232 sec) [ -472937.8740] [Topology ] . (13327 sec) [ -472937.7707] [Topology ] . (13421 sec) [ -472937.6846] [Topology ] . (13517 sec) [ -472937.6119] [Topology ] . Checking for NNIs, optimizing five branches... . (14346 sec) [ -472937.3885] [Topology ] . (14400 sec) [ -472937.3808] [GTR parameters ] . (14411 sec) [ -472937.3202] [Alpha ][ 0.862752] . (14414 sec) [ -472937.3202] [Topology ] . (14509 sec) [ -472930.9291] [Topology ] . (14604 sec) [ -472916.2162] [Topology ] . (14699 sec) [ -472906.3919] [Topology ] . (14794 sec) [ -472896.0319] [Topology ] . (14890 sec) [ -472892.9586] [Topology ] . (14985 sec) [ -472892.4216] [Topology ] . (15082 sec) [ -472892.2562] [Topology ] . (15178 sec) [ -472892.1887] [Topology ] . (15274 sec) [ -472892.1551] [Topology ] . Checking for NNIs, optimizing five branches... . (16200 sec) [ -472892.0948] [Topology ] . (16218 sec) [ -472892.0903] [GTR parameters ] . (16229 sec) [ -472892.0461] [Alpha ][ 0.860560] . (16232 sec) [ -472892.0461] [Topology ] . (16328 sec) [ -472891.9522] [Topology ] . (16425 sec) [ -472891.9117] [Topology ] . (16521 sec) [ -472891.8839] [Topology ] . (16617 sec) [ -472891.8620] [Topology ] . (16714 sec) [ -472891.8441] [Topology ] . (16810 sec) [ -472891.8293] [Topology ] . Checking for NNIs, optimizing five branches... . (17637 sec) [ -472891.7798] [Topology ] . (17673 sec) [ -472891.7778] [GTR parameters ] . (17681 sec) [ -472891.7627] [Alpha ][ 0.859277] . (17684 sec) [ -472891.7627] [Topology ] . (17781 sec) [ -472891.6423] [Topology ] . (17876 sec) [ -472891.5984] [Topology ] . (17971 sec) [ -472891.5682] [Topology ] . (18067 sec) [ -472891.5445] [Topology ] . (18162 sec) [ -472891.5253] [Topology ] . (18258 sec) [ -472891.5096] [Topology ] . Checking for NNIs, optimizing five branches... . (19082 sec) [ -472891.5086] [Topology ] . (19100 sec) [ -472891.5080] [GTR parameters ] . (19109 sec) [ -472891.4916] [Alpha ][ 0.857942] . (19112 sec) [ -472891.4916] [Topology ] . (19207 sec) [ -472891.4630] [Topology ] . (19303 sec) [ -472891.3997] [Topology ] . (19398 sec) [ -472891.1422] [Topology ] . (19494 sec) [ -472891.0156] [Topology ] . (19589 sec) [ -472890.9683] [Topology ] . (19685 sec) [ -472890.9463] [Topology ] . Checking for NNIs, optimizing five branches... . (20571 sec) [ -472890.9438] [GTR parameters ] . (20580 sec) [ -472890.9344] [Alpha ][ 0.856925] . (20583 sec) [ -472890.9344] [Topology ] . (20678 sec) [ -472890.9164] [Topology ] . (20775 sec) [ -472890.9040] [Topology ] . (20872 sec) [ -472890.8950] [Topology ] . (20967 sec) [ -472890.8881] [Topology ] . (21063 sec) [ -472890.8827] [Topology ] . (21158 sec) [ -472890.8784] [Topology ] . Checking for NNIs, optimizing five branches... . (22011 sec) [ -472890.8784] [GTR parameters ] . (22020 sec) [ -472890.8742] [Alpha ][ 0.856068] . (22023 sec) [ -472890.8742] [Topology ] . (22119 sec) [ -472890.8675] [Topology ] . (22214 sec) [ -472890.8622] [Topology ] . (22310 sec) [ -472890.8580] [Topology ] . (22406 sec) [ -472890.8547] [Topology ] . (22502 sec) [ -472890.8520] [Topology ] . (22597 sec) [ -472890.8498] [Topology ] . Checking for NNIs, optimizing five branches... . (23445 sec) [ -472890.8498] [GTR parameters ] . (23454 sec) [ -472890.8498] [Alpha ][ 0.856068] . (23457 sec) [ -472890.8498] [Topology ] . (23553 sec) [ -472890.8481] [Topology ] . (23648 sec) [ -472890.8467] [Topology ] . (23745 sec) [ -472890.8457] [Topology ] . (23841 sec) [ -472890.8448] [Topology ] . Checking for NNIs, optimizing five branches... . (24669 sec) [ -472890.8431] [Topology ] . (24696 sec) [ -472890.8422] [GTR parameters ] . (24705 sec) [ -472890.8422] [Alpha ][ 0.856068] . (24708 sec) [ -472890.8422] [Topology ] . (24803 sec) [ -472890.7489] [Topology ] . (24899 sec) [ -472890.7264] [Topology ] . (24994 sec) [ -472890.7170] [Topology ] . (25090 sec) [ -472890.7115] [Topology ] . (25185 sec) [ -472890.7076] [Topology ] . (25282 sec) [ -472890.7047] [Topology ] . Checking for NNIs, optimizing five branches... . (26148 sec) [ -472890.7045] [GTR parameters ] . (26156 sec) [ -472890.6939] [Alpha ][ 0.854996] . (26159 sec) [ -472890.6939] [Topology ] . (26254 sec) [ -472890.6880] [Topology ] . (26349 sec) [ -472890.6835] [Topology ] . (26444 sec) [ -472890.6801] [Topology ] . (26540 sec) [ -472890.6774] [Topology ] . (26635 sec) [ -472890.6753] [Topology ] . (26730 sec) [ -472890.6737] [Topology ] . Checking for NNIs, optimizing five branches... . (27573 sec) [ -472890.6737] [GTR parameters ] . (27581 sec) [ -472890.6737] [Alpha ][ 0.854996] . (27584 sec) [ -472890.6737] [Topology ] . (27679 sec) [ -472890.6725] [Topology ] . (27775 sec) [ -472890.6715] [Topology ] . Checking for NNIs, optimizing five branches... . (28609 sec) [ -472890.6710] [GTR parameters ] . (28618 sec) [ -472890.6695] [Alpha ][ 0.854141] . (28621 sec) [ -472890.6695] [Topology ] . (28716 sec) [ -472890.6668] [Topology ] . (28811 sec) [ -472890.6647] [Topology ] . (28906 sec) [ -472890.6632] [Topology ] . (29001 sec) [ -472890.6620] [Topology ] . (29096 sec) [ -472890.6611] [Topology ] . Checking for NNIs, optimizing five branches... . (29931 sec) [ -472890.6610] [GTR parameters ] . (29939 sec) [ -472890.6610] [Alpha ][ 0.854141] . (29942 sec) [ -472890.6610] [Topology ] . (30037 sec) [ -472890.6603] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -472890.660258. . Printing the most likely tree in file 'nucleic_M4058_406x6016_2008.phy_phyml_tree.txt'... . Time used 8h47m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 31510.59user 0.00system 8:49:14elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps