.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2623_139x1044_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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 959 patterns found. (out of a total of 1044 sites) . 202 sites without polymorphism (19.35%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 71Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 12 sec) [ -48412.0933] [GTR parameters ] . ( 13 sec) [ -47896.6604] [Alpha ][ 0.500960] . ( 13 sec) [ -47896.6604] [Topology ] . ( 19 sec) [ -46842.0254] [Topology ] . ( 25 sec) [ -46574.5707] [Topology ] . ( 30 sec) [ -46466.2556] [Topology ] . ( 36 sec) [ -46392.6354] [Topology ] . ( 42 sec) [ -46362.0933] [Topology ] . ( 47 sec) [ -46342.1045] [Topology ] . ( 53 sec) [ -46333.8995] [Topology ] . ( 58 sec) [ -46304.5516] [Topology ] . ( 64 sec) [ -46279.5135] [Topology ] . ( 79 sec) [ -46184.8533] [GTR parameters ] . ( 79 sec) [ -46184.4821] [Alpha ][ 0.511611] . ( 80 sec) [ -46184.4821] [Topology ] . ( 85 sec) [ -46167.1499] [Topology ] . ( 91 sec) [ -46151.3147] [Topology ] . ( 96 sec) [ -46138.3074] [Topology ] . ( 102 sec) [ -46135.8864] [Topology ] . ( 107 sec) [ -46120.4211] [Topology ] . ( 113 sec) [ -46110.9562] [Topology ] . ( 118 sec) [ -46106.1377] [Topology ] . ( 124 sec) [ -46091.5607] [Topology ] . ( 130 sec) [ -46085.7800] [Topology ] . ( 143 sec) [ -46071.4695] [GTR parameters ] . ( 144 sec) [ -46071.0192] [Alpha ][ 0.522934] . ( 144 sec) [ -46071.0192] [Topology ] . ( 149 sec) [ -46059.5651] [Topology ] . ( 155 sec) [ -46049.7743] [Topology ] . ( 160 sec) [ -46047.5282] [Topology ] . ( 166 sec) [ -46045.6369] [Topology ] . ( 171 sec) [ -46045.0146] [Topology ] . ( 177 sec) [ -46044.6647] [Topology ] . ( 183 sec) [ -46044.4817] [Topology ] . ( 188 sec) [ -46044.4043] [Topology ] . ( 194 sec) [ -46044.3553] [Topology ] . Checking for NNIs, optimizing five branches... . ( 256 sec) [ -46042.9471] [Topology ] . ( 262 sec) [ -46042.8071] [GTR parameters ] . ( 262 sec) [ -46042.8071] [Alpha ][ 0.522934] . ( 262 sec) [ -46042.8071] [Topology ] . ( 268 sec) [ -46042.7034] [Topology ] . ( 273 sec) [ -46042.6692] [Topology ] . ( 279 sec) [ -46042.6479] [Topology ] . ( 284 sec) [ -46042.6315] [Topology ] . ( 290 sec) [ -46042.6181] [Topology ] . ( 295 sec) [ -46042.6066] [Topology ] . Checking for NNIs, optimizing five branches... . ( 352 sec) [ -46041.5640] [Topology ] . ( 357 sec) [ -46041.5547] [GTR parameters ] . ( 358 sec) [ -46041.5547] [Alpha ][ 0.522934] . ( 358 sec) [ -46041.5547] [Topology ] . ( 363 sec) [ -46041.3916] [Topology ] . ( 369 sec) [ -46041.3637] [Topology ] . ( 375 sec) [ -46041.3520] [Topology ] . ( 380 sec) [ -46041.3438] [Topology ] . ( 386 sec) [ -46041.3421] [Topology ] . ( 391 sec) [ -46039.7492] [Topology ] . ( 397 sec) [ -46037.2589] [Topology ] . ( 402 sec) [ -46035.7809] [Topology ] . ( 408 sec) [ -46035.4547] [Topology ] . Checking for NNIs, optimizing five branches... . ( 470 sec) [ -46032.5470] [Topology ] . ( 475 sec) [ -46032.5264] [GTR parameters ] . ( 475 sec) [ -46032.5248] [Alpha ][ 0.523649] . ( 476 sec) [ -46032.5248] [Topology ] . ( 481 sec) [ -46032.3831] [Topology ] . ( 487 sec) [ -46032.3489] [Topology ] . ( 492 sec) [ -46032.3367] [Topology ] . ( 498 sec) [ -46032.3308] [Topology ] . ( 503 sec) [ -46032.3270] [Topology ] . ( 509 sec) [ -46032.3240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 566 sec) [ -46027.1343] [Topology ] . ( 571 sec) [ -46027.1327] [GTR parameters ] . ( 572 sec) [ -46027.1327] [Alpha ][ 0.523649] . ( 572 sec) [ -46027.1327] [Topology ] . ( 577 sec) [ -46027.0998] [Topology ] . ( 583 sec) [ -46026.0971] [Topology ] . ( 589 sec) [ -46025.9513] [Topology ] . ( 594 sec) [ -46024.7626] [Topology ] . ( 600 sec) [ -46024.4995] [Topology ] . ( 605 sec) [ -46024.2885] [Topology ] . ( 611 sec) [ -46024.1962] [Topology ] . ( 616 sec) [ -46024.1417] [Topology ] . ( 622 sec) [ -46024.1067] [Topology ] . Checking for NNIs, optimizing five branches... . ( 684 sec) [ -46023.6154] [Topology ] . ( 689 sec) [ -46023.5871] [GTR parameters ] . ( 690 sec) [ -46023.5856] [Alpha ][ 0.523125] . ( 690 sec) [ -46023.5856] [Topology ] . ( 696 sec) [ -46016.3974] [Topology ] . ( 701 sec) [ -46015.1162] [Topology ] . ( 707 sec) [ -46014.8537] [Topology ] . ( 712 sec) [ -46014.7646] [Topology ] . ( 718 sec) [ -46014.7284] [Topology ] . ( 724 sec) [ -46014.7106] [Topology ] . ( 729 sec) [ -46014.7000] [Topology ] . Checking for NNIs, optimizing five branches... . ( 787 sec) [ -46009.7342] [Topology ] . ( 792 sec) [ -46009.7240] [GTR parameters ] . ( 792 sec) [ -46009.7215] [Alpha ][ 0.523919] . ( 792 sec) [ -46009.7215] [Topology ] . ( 798 sec) [ -46009.4455] [Topology ] . ( 804 sec) [ -46008.8597] [Topology ] . ( 809 sec) [ -46008.5137] [Topology ] . ( 815 sec) [ -46007.3799] [Topology ] . ( 820 sec) [ -46007.1656] [Topology ] . ( 826 sec) [ -46007.0637] [Topology ] . ( 831 sec) [ -46007.0035] [Topology ] . ( 837 sec) [ -46006.9556] [Topology ] . ( 843 sec) [ -46006.9179] [Topology ] . Checking for NNIs, optimizing five branches... . ( 899 sec) [ -46006.5112] [Topology ] . ( 904 sec) [ -46006.5086] [GTR parameters ] . ( 904 sec) [ -46006.5064] [Alpha ][ 0.524665] . ( 904 sec) [ -46006.5064] [Topology ] . ( 910 sec) [ -46005.6454] [Topology ] . ( 915 sec) [ -46005.2060] [Topology ] . ( 921 sec) [ -46004.9538] [Topology ] . ( 927 sec) [ -46004.7773] [Topology ] . ( 932 sec) [ -46004.6535] [Topology ] . ( 938 sec) [ -46004.5431] [Topology ] . ( 943 sec) [ -46003.9570] [Topology ] . ( 949 sec) [ -46002.9752] [Topology ] . ( 955 sec) [ -46002.9684] [Topology ] . ( 965 sec) [ -46003.4267] [GTR parameters ] . ( 966 sec) [ -46003.4267] [Alpha ][ 0.524665] . ( 966 sec) [ -46003.4267] [Topology ] . ( 971 sec) [ -46003.3818] [Topology ] . ( 977 sec) [ -46004.0080] [Topology ] . Moving backward . ( 977 sec) [ -46002.2125] [Topology ] . ( 983 sec) [ -46002.0682] [Topology ] . ( 988 sec) [ -46002.1911] [Topology ] . Moving backward . ( 989 sec) [ -46001.7457] [Topology ] . ( 994 sec) [ -46001.5749] [Topology ] . ( 1000 sec) [ -46001.5162] [Topology ] . ( 1006 sec) [ -46001.4795] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1067 sec) [ -45999.3953] [Topology ] . ( 1072 sec) [ -45999.3861] [GTR parameters ] . ( 1073 sec) [ -45999.3861] [Alpha ][ 0.524665] . ( 1073 sec) [ -45999.3861] [Topology ] . ( 1078 sec) [ -45999.3173] [Topology ] . ( 1084 sec) [ -45999.2910] [Topology ] . ( 1090 sec) [ -45999.2735] [Topology ] . ( 1095 sec) [ -45999.2597] [Topology ] . ( 1101 sec) [ -45999.2479] [Topology ] . ( 1106 sec) [ -45999.2374] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1161 sec) [ -45999.1785] [Topology ] . ( 1164 sec) [ -45999.1776] [GTR parameters ] . ( 1165 sec) [ -45999.1776] [Alpha ][ 0.524665] . ( 1165 sec) [ -45999.1776] [Topology ] . ( 1171 sec) [ -45999.0388] [Topology ] . ( 1176 sec) [ -45998.9517] [Topology ] . ( 1182 sec) [ -45998.9217] [Topology ] . ( 1187 sec) [ -45998.9030] [Topology ] . ( 1193 sec) [ -45998.8894] [Topology ] . ( 1198 sec) [ -45998.8784] [Topology ] . ( 1204 sec) [ -45998.8691] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1259 sec) [ -45998.8086] [Topology ] . ( 1266 sec) [ -45998.8068] [GTR parameters ] . ( 1266 sec) [ -45998.8068] [Alpha ][ 0.524665] . ( 1267 sec) [ -45998.8068] [Topology ] . ( 1272 sec) [ -45998.8028] [Topology ] . ( 1278 sec) [ -45998.8008] [Topology ] . ( 1283 sec) [ -45998.7997] [Topology ] . ( 1289 sec) [ -45998.7991] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1344 sec) [ -45998.3504] [Topology ] . ( 1348 sec) [ -45998.3498] [GTR parameters ] . ( 1348 sec) [ -45998.3498] [Alpha ][ 0.524665] . ( 1348 sec) [ -45998.3498] [Topology ] . ( 1354 sec) [ -45998.2875] [Topology ] . ( 1359 sec) [ -45998.2766] [Topology ] . ( 1365 sec) [ -45998.2728] [Topology ] . ( 1371 sec) [ -45998.2712] [Topology ] . ( 1376 sec) [ -45998.2705] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1431 sec) [ -45998.2696] [Topology ] . ( 1434 sec) [ -45998.2692] [GTR parameters ] . ( 1434 sec) [ -45998.2692] [Alpha ][ 0.524665] . ( 1434 sec) [ -45998.2692] [Topology ] . ( 1440 sec) [ -45998.2635] [Topology ] . ( 1445 sec) [ -45998.2258] [Topology ] . ( 1451 sec) [ -45998.1315] [Topology ] . ( 1456 sec) [ -45998.0538] [Topology ] . ( 1462 sec) [ -45997.9915] [Topology ] . ( 1468 sec) [ -45997.9382] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1523 sec) [ -45997.6111] [Topology ] . ( 1525 sec) [ -45997.6104] [GTR parameters ] . ( 1525 sec) [ -45997.6083] [Alpha ][ 0.525380] . ( 1526 sec) [ -45997.6083] [Topology ] . ( 1531 sec) [ -45997.5720] [Topology ] . ( 1537 sec) [ -45997.5656] [Topology ] . ( 1542 sec) [ -45997.5635] [Topology ] . ( 1548 sec) [ -45997.5626] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1603 sec) [ -45996.2886] [Topology ] . ( 1604 sec) [ -45996.2857] [GTR parameters ] . ( 1605 sec) [ -45996.2857] [Alpha ][ 0.525380] . ( 1605 sec) [ -45996.2857] [Topology ] . ( 1610 sec) [ -45996.2439] [Topology ] . ( 1616 sec) [ -45996.2361] [Topology ] . ( 1621 sec) [ -45996.2333] [Topology ] . ( 1627 sec) [ -45996.2320] [Topology ] . ( 1632 sec) [ -45996.2314] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1687 sec) [ -45996.2249] [Topology ] . ( 1689 sec) [ -45996.2246] [GTR parameters ] . ( 1689 sec) [ -45996.2246] [Alpha ][ 0.525380] . ( 1689 sec) [ -45996.2246] [Topology ] . ( 1695 sec) [ -45996.2058] [Topology ] . ( 1700 sec) [ -45996.1996] [Topology ] . ( 1706 sec) [ -45996.1962] [Topology ] . ( 1712 sec) [ -45996.1938] [Topology ] . ( 1717 sec) [ -45996.1919] [Topology ] . ( 1723 sec) [ -45996.1904] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1778 sec) [ -45996.1902] [Topology ] . ( 1779 sec) [ -45996.1901] [GTR parameters ] . ( 1779 sec) [ -45996.1901] [Alpha ][ 0.525380] . ( 1779 sec) [ -45996.1901] [Topology ] . ( 1785 sec) [ -45996.1888] [Topology ] . ( 1790 sec) [ -45996.1876] [Topology ] . ( 1796 sec) [ -45996.1867] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1852 sec) [ -45996.1864] [GTR parameters ] . ( 1852 sec) [ -45996.1864] [Alpha ][ 0.525380] . ( 1852 sec) [ -45996.1864] [Topology ] . ( 1858 sec) [ -45996.1855] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1913 sec) [ -45996.1855] [GTR parameters ] . ( 1914 sec) [ -45996.1855] [Alpha ][ 0.525380] . ( 1914 sec) [ -45996.1855] [Topology ] . ( 1919 sec) [ -45996.1849] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -45996.184860. . Printing the most likely tree in file 'nucleic_M2623_139x1044_2006.phy_phyml_tree.txt'... . Time used 0h33m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2029.78user 0.00system 33:53.80elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps