.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2573_346x897_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... . 649 patterns found. (out of a total of 897 sites) . 315 sites without polymorphism (35.12%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 120Mo of memory space... . Maximizing likelihood (using SPR moves)... . ( 21 sec) [ -10190.7400] [GTR parameters ] . ( 22 sec) [ -10163.7051] [Alpha ][ 0.559325] . ( 24 sec) [ -10163.6036] [ 1580] [depth= 1] . ( 24 sec) [ -10163.5661] [ 1580] [depth= 1] . ( 25 sec) [ -10163.2283] [ 1580] [depth= 1] . ( 25 sec) [ -10163.2145] [ 1580] [depth= 3] . ( 26 sec) [ -10162.7447] [ 1580] [depth= 1] . ( 27 sec) [ -10161.3711] [ 1580] [depth= 3] . ( 27 sec) [ -10161.0068] [ 1580] [depth= 1] . ( 28 sec) [ -10160.9933] [ 1580] [depth= 2] . ( 30 sec) [ -10145.4998] [ 1578] [depth= 1] . ( 30 sec) [ -10141.8201] [ 1574] [depth= 1] . ( 31 sec) [ -10141.6590] [ 1574] [depth= 1] . ( 32 sec) [ -10141.5681] [ 1574] [depth= 1] . ( 32 sec) [ -10141.5106] [ 1574] [depth= 8] . ( 33 sec) [ -10140.3354] [ 1574] [depth= 1] . ( 34 sec) [ -10140.3220] [ 1574] [depth= 8] . ( 34 sec) [ -10136.9963] [ 1573] [depth= 4] . ( 34 sec) [ -10122.7103] [ 1570] [depth= 3] . ( 35 sec) [ -10122.6420] [ 1570] [depth= 1] . ( 35 sec) [ -10122.6305] [ 1570] [depth= 1] . ( 36 sec) [ -10122.6114] [ 1570] [depth= 3] . ( 37 sec) [ -10122.5329] [ 1570] [depth= 2] . ( 38 sec) [ -10122.4951] [ 1570] [depth= 3] . ( 39 sec) [ -10122.4827] [ 1570] [depth= 1] . ( 45 sec) [ -10122.4525] [ 1570] [depth= 1] . ( 46 sec) [ -10122.3161] [ 1570] [depth= 1] . ( 46 sec) [ -10121.5260] [ 1570] [depth= 2] . ( 47 sec) [ -10120.2417] [ 1570] [depth= 1] . ( 48 sec) [ -10118.0917] [ 1570] [depth= 6] . ( 48 sec) [ -10105.9515] [ 1569] [depth= 4] . ( 49 sec) [ -10105.8551] [ 1569] [depth= 2] . ( 49 sec) [ -10105.7597] [ 1569] [depth= 2] . ( 50 sec) [ -10105.6266] [ 1569] [depth= 2] . ( 50 sec) [ -10105.6145] [ 1569] [depth= 2] . ( 51 sec) [ -10101.4015] [ 1568] [depth= 8] . ( 51 sec) [ -10082.5556] [ 1565] [depth= 5] . ( 52 sec) [ -10082.5452] [ 1565] [depth= 1] . ( 53 sec) [ -10081.3075] [ 1564] [depth= 2] . 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( 79 sec) [ -10042.3773] [ 1561] [depth= 1] . ( 82 sec) [ -10042.3664] [ 1561] [depth= 1] . ( 82 sec) [ -10041.8972] [ 1561] [depth= 1] . ( 84 sec) [ -10041.8511] [ 1561] [depth= 1] . ( 85 sec) [ -10041.5724] [ 1561] [depth= 1] . ( 86 sec) [ -10041.5555] [ 1561] [depth= 1] . ( 87 sec) [ -10040.1672] [ 1561] [depth= 1] . ( 87 sec) [ -10037.1993] [ 1561] [depth= 1] . ( 89 sec) [ -10036.4456] [ 1561] [depth= 1] . ( 89 sec) [ -10036.3434] [ 1561] [depth= 2] . ( 90 sec) [ -10036.0601] [ 1561] [depth= 1] . ( 91 sec) [ -10028.6379] [ 1563] [depth= 1] . ( 92 sec) [ -10025.3944] [ 1562] [depth= 2] . ( 92 sec) [ -10023.4440] [ 1562] [depth= 3] . ( 93 sec) [ -10023.4020] [ 1562] [depth= 1] . ( 93 sec) [ -10023.0446] [ 1562] [depth= 1] . ( 94 sec) [ -10022.6112] [ 1562] [depth= 1] . ( 95 sec) [ -10022.5567] [ 1562] [depth= 2] . ( 95 sec) [ -10018.2660] [ 1564] [depth= 1] . ( 96 sec) [ -9999.6801] [ 1558] [depth= 1] . ( 97 sec) [ -9999.5438] [ 1558] [depth= 1] . 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( 375 sec) [ -9783.3669] [ 1531] [depth= 1] . ( 381 sec) [ -9782.8603] [ 1531] [depth= 1] . ( 382 sec) [ -9782.6292] [ 1531] [depth= 1] . ( 386 sec) [ -9782.5393] [ 1531] [depth= 1] . ( 386 sec) [ -9781.6902] [ 1531] [depth= 1] . ( 388 sec) [ -9781.5528] [ 1531] [depth= 1] . ( 391 sec) [ -9781.5264] [ 1531] [depth= 1] . ( 392 sec) [ -9781.4966] [ 1531] [depth= 1] . ( 397 sec) [ -9781.4613] [ 1531] [depth= 1] . ( 400 sec) [ -9773.7118] [ 1529] [depth= 1] . ( 401 sec) [ -9773.6857] [ 1529] [depth= 1] . ( 401 sec) [ -9773.6742] [ 1529] [depth= 2] . ( 407 sec) [ -9773.2246] [ 1529] [depth= 1] . ( 408 sec) [ -9773.1815] [ 1529] [depth= 1] . ( 408 sec) [ -9771.2505] [ 1529] [depth= 3] . ( 410 sec) [ -9770.6958] [ 1529] [depth= 1] . ( 412 sec) [ -9770.5408] [ 1529] [depth= 1] . ( 413 sec) [ -9770.5176] [ 1529] [depth= 1] . ( 413 sec) [ -9767.5786] [ 1528] [depth= 2] . ( 414 sec) [ -9767.3244] [ 1528] [depth= 4] . ( 421 sec) [ -9767.3135] [ 1528] [depth= 1] . 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( 491 sec) [ -9751.3951] [ 1527] [depth= 3] . ( 491 sec) [ -9751.3548] [ 1527] [depth= 4] . ( 492 sec) [ -9751.2790] [ 1527] [depth= 2] . ( 492 sec) [ -9751.2105] [ 1527] [depth= 1] . ( 504 sec) [ -9750.7336] [ 1527] [depth= 1] . ( 505 sec) [ -9749.7558] [ 1527] [depth= 4] . ( 505 sec) [ -9749.4101] [ 1527] [depth= 2] . ( 506 sec) [ -9742.8364] [ 1526] [depth= 6] . ( 509 sec) [ -9742.7680] [ 1526] [depth= 7] . ( 510 sec) [ -9742.7578] [ 1526] [depth= 1] . ( 511 sec) [ -9742.6573] [ 1526] [depth= 5] . ( 511 sec) [ -9742.6164] [ 1526] [depth= 4] . ( 512 sec) [ -9742.2674] [ 1526] [depth= 3] . ( 513 sec) [ -9741.9761] [ 1526] [depth= 6] . ( 513 sec) [ -9741.3670] [ 1526] [depth= 1] . ( 514 sec) [ -9741.3385] [ 1526] [depth= 6] . ( 514 sec) [ -9741.3106] [ 1526] [depth= 7] . ( 515 sec) [ -9741.2127] [ 1526] [depth= 6] . ( 516 sec) [ -9741.1511] [ 1526] [depth= 6] . ( 518 sec) [ -9740.5098] [ 1526] [depth= 1] . ( 519 sec) [ -9740.4989] [ 1526] [depth= 2] . ( 519 sec) [ -9735.4741] [ 1525] [depth= 10] . ( 520 sec) [ -9735.4018] [ 1525] [depth= 1] . ( 520 sec) [ -9735.2065] [ 1525] [depth= 1] . ( 521 sec) [ -9735.1944] [ 1525] [depth= 5] . ( 522 sec) [ -9735.0436] [ 1525] [depth= 6] . ( 522 sec) [ -9734.8952] [ 1525] [depth= 1] . ( 524 sec) [ -9734.8706] [ 1525] [depth= 3] . ( 525 sec) [ -9734.5008] [ 1525] [depth= 1] . ( 525 sec) [ -9734.4835] [ 1525] [depth= 1] . ( 526 sec) [ -9734.4044] [ 1525] [depth= 2] . ( 527 sec) [ -9734.3710] [ 1525] [depth= 1] . ( 527 sec) [ -9734.3328] [ 1525] [depth= 6] . ( 538 sec) [ -9734.1720] [ 1525] [depth= 2] . ( 538 sec) [ -9734.0449] [ 1525] [depth= 1] . ( 539 sec) [ -9734.0179] [ 1525] [depth= 3] . ( 539 sec) [ -9733.9476] [ 1525] [depth= 3] . ( 542 sec) [ -9733.9325] [ 1525] [depth= 1] . ( 545 sec) [ -9723.9597] [ 1524] [depth= 11] . ( 565 sec) [ -9722.5297] [ 1524] [depth= 1] . ( 582 sec) [ -9722.4489] [ 1524] [depth= 2] . ( 583 sec) [ -9722.3132] [ 1524] [depth= 2] . ( 585 sec) [ -9722.1334] [ 1524] [depth= 2] . ( 587 sec) [ -9722.1145] [ 1524] [depth= 2] . ( 594 sec) [ -9722.0787] [ 1524] [depth= 5] . ( 595 sec) [ -9721.8453] [ 1524] [depth= 1] . ( 596 sec) [ -9721.8091] [ 1524] [depth= 2] . ( 596 sec) [ -9721.5141] [ 1524] [depth= 4] . ( 597 sec) [ -9721.3711] [ 1524] [depth= 2] . ( 597 sec) [ -9721.2354] [ 1524] [depth= 5] . ( 598 sec) [ -9721.2189] [ 1524] [depth= 4] . ( 598 sec) [ -9721.0830] [ 1524] [depth= 2] . ( 599 sec) [ -9720.6444] [ 1524] [depth= 4] . ( 599 sec) [ -9719.2511] [ 1523] [depth= 1] . ( 600 sec) [ -9718.9872] [ 1523] [depth= 2] . ( 600 sec) [ -9713.5884] [ 1523] [depth= 5] . ( 601 sec) [ -9712.5624] [ 1523] [depth= 5] . ( 601 sec) [ -9712.5379] [ 1523] [depth= 1] . ( 603 sec) [ -9712.4932] [ 1523] [depth= 1] . ( 604 sec) [ -9712.4761] [ 1523] [depth= 4] . ( 605 sec) [ -9712.4609] [ 1523] [depth= 1] . ( 605 sec) [ -9712.2340] [ 1523] [depth= 4] . ( 607 sec) [ -9709.7196] [ 1523] [depth= 3] . ( 608 sec) [ -9709.4003] [ 1523] [depth= 1] . ( 611 sec) [ -9709.3586] [ 1523] [depth= 1] . ( 617 sec) [ -9709.2427] [ 1523] [depth= 8] . ( 620 sec) [ -9708.5771] [ 1523] [depth= 2] . ( 621 sec) [ -9708.3934] [ 1523] [depth= 1] . ( 621 sec) [ -9708.2240] [ 1523] [depth= 2] . ( 622 sec) [ -9708.1402] [ 1523] [depth= 3] . ( 622 sec) [ -9708.1121] [ 1523] [depth= 2] . ( 626 sec) [ -9708.0671] [ 1523] [depth= 2] . ( 626 sec) [ -9707.7447] [ 1523] [depth= 2] . ( 627 sec) [ -9707.6039] [ 1523] [depth= 1] . ( 627 sec) [ -9707.5369] [ 1523] [depth= 2] . ( 628 sec) [ -9707.3391] [ 1523] [depth= 1] . ( 628 sec) [ -9707.2291] [ 1523] [depth= 1] . ( 629 sec) [ -9707.1212] [ 1523] [depth= 3] . ( 632 sec) [ -9707.0776] [ 1523] [depth= 3] . ( 633 sec) [ -9707.0660] [ 1523] [depth= 3] . ( 637 sec) [ -9707.0557] [ 1523] [depth= 1] . ( 651 sec) [ -9658.4778] [Branch lengths ] . ( 660 sec) [ -9653.8987] [GTR parameters ] . ( 661 sec) [ -9653.3139] [Alpha ][ 0.603107] . ( 662 sec) [ -9653.1178] [ 1523] [depth= 3] . ( 663 sec) [ -9653.1014] [ 1523] [depth= 4] . ( 667 sec) [ -9653.0069] [ 1525] [depth= 1] . ( 667 sec) [ -9652.3606] [ 1522] [depth= 2] . ( 668 sec) [ -9652.3439] [ 1522] [depth= 1] . ( 684 sec) [ -9652.2954] [ 1522] [depth= 1] . ( 697 sec) [ -9651.1740] [ 1522] [depth= 6] . ( 698 sec) [ -9650.9732] [ 1522] [depth= 1] . ( 699 sec) [ -9650.9625] [ 1522] [depth= 3] . ( 700 sec) [ -9650.9425] [ 1522] [depth= 1] . ( 700 sec) [ -9650.9286] [ 1522] [depth= 1] . ( 701 sec) [ -9650.8850] [ 1522] [depth= 1] . ( 711 sec) [ -9650.6854] [ 1522] [depth= 1] . ( 711 sec) [ -9650.6728] [ 1522] [depth= 1] . ( 722 sec) [ -9650.6179] [ 1522] [depth= 1] . ( 722 sec) [ -9650.5564] [ 1522] [depth= 2] . ( 723 sec) [ -9650.5437] [ 1522] [depth= 2] . ( 728 sec) [ -9650.4933] [ 1522] [depth= 1] . ( 728 sec) [ -9650.4720] [ 1522] [depth= 1] . ( 731 sec) [ -9650.4511] [ 1522] [depth= 2] . ( 738 sec) [ -9650.2997] [ 1523] [depth= 1] . ( 739 sec) [ -9650.1275] [ 1523] [depth= 4] . ( 745 sec) [ -9650.0368] [ 1523] [depth= 4] . ( 746 sec) [ -9650.0258] [ 1523] [depth= 1] . ( 764 sec) [ -9650.0144] [ 1523] [depth= 3] . ( 779 sec) [ -9644.0509] [ 1522] [depth= 6] . ( 779 sec) [ -9643.9132] [ 1522] [depth= 1] . ( 781 sec) [ -9643.8835] [ 1522] [depth= 1] . ( 857 sec) [ -9643.8388] [ 1522] [depth= 4] . ( 858 sec) [ -9643.8258] [ 1522] [depth= 1] . ( 862 sec) [ -9643.8139] [ 1522] [depth= 1] . ( 862 sec) [ -9643.7838] [ 1522] [depth= 2] . ( 922 sec) [ -9641.1347] [ 1523] [depth= 2] . ( 930 sec) [ -9638.4376] [ 1522] [depth= 11] . ( 937 sec) [ -9638.4208] [ 1522] [depth= 1] . ( 999 sec) [ -9638.4092] [ 1522] [depth= 1] . ( 1013 sec) [ -9638.3641] [ 1522] [depth= 2] . ( 1021 sec) [ -9638.3540] [ 1522] [depth= 1] . ( 1056 sec) [ -9638.3399] [ 1522] [depth= 3] . ( 1063 sec) [ -9638.2272] [ 1522] [depth= 1] . ( 1125 sec) [ -9638.1948] [ 1522] [depth= 4] . ( 1125 sec) [ -9638.1560] [ 1522] [depth= 1] . ( 1126 sec) [ -9638.1284] [ 1522] [depth= 1] . ( 1129 sec) [ -9638.0967] [ 1522] [depth= 10] . ( 1157 sec) [ -9638.0030] [ 1522] [depth= 1] . ( 1159 sec) [ -9637.9901] [ 1522] [depth= 2] . ( 1183 sec) [ -9637.5826] [ 1519] [depth= 1] . ( 1253 sec) [ -9637.4053] [ 1519] [depth= 4] . ( 1259 sec) [ -9636.9496] [ 1519] [depth= 1] . ( 1266 sec) [ -9636.8662] [ 1519] [depth= 1] . ( 1268 sec) [ -9636.8501] [ 1519] [depth= 1] . ( 1329 sec) [ -9636.8319] [ 1519] [depth= 4] . ( 1403 sec) [ -9632.7758] [ 1518] [depth= 1] . ( 1538 sec) [ -9631.8298] [ 1518] [depth= 6] . ( 1630 sec) [ -9625.1411] [Branch lengths ] . ( 1637 sec) [ -9625.0479] [GTR parameters ] . ( 1637 sec) [ -9625.0442] [Alpha ][ 0.599427] . ( 1639 sec) [ -9625.0283] [ 1518] [depth= 5] . ( 1688 sec) [ -9625.0103] [ 1518] [depth= 1] . ( 2034 sec) [ -9624.9493] [ 1518] [depth= 4] . ( 2035 sec) [ -9624.8750] [ 1518] [depth= 17] . ( 2040 sec) [ -9624.6570] [ 1518] [depth= 2] . ( 2043 sec) [ -9624.5438] [ 1518] [depth= 3] . ( 2055 sec) [ -9624.3823] [ 1518] [depth= 5] . ( 2056 sec) [ -9624.3144] [ 1518] [depth= 2] . ( 2115 sec) [ -9624.2951] [ 1518] [depth= 6] . ( 2475 sec) [ -9624.2834] [ 1518] [depth= 13] . ( 2585 sec) [ -9623.8006] [Branch lengths ] . ( 2592 sec) [ -9623.7760] [GTR parameters ] . ( 2593 sec) [ -9623.7758] [Alpha ][ 0.598492] . ( 3575 sec) [ -9623.7024] [Branch lengths ] . ( 4091 sec) [ -9623.6300] [ 1518] [depth= 10] . ( 4236 sec) [ -9623.6130] [Branch lengths ] . ( 4241 sec) [ -9623.6054] [GTR parameters ] . ( 4242 sec) [ -9623.6039] [Alpha ][ 0.596145] . ( 4242 sec) [ -9623.6039] [Topology ] . ( 4257 sec) [ -9623.6015] [Topology ] . ( 4271 sec) [ -9623.6007] [Topology ] . ( 4275 sec) [ -9623.6006] [GTR parameters ] . ( 4276 sec) [ -9623.6006] [Alpha ][ 0.596145] . ( 4276 sec) [ -9623.6006] [Topology ] . ( 4291 sec) [ -9623.6004] [Topology ] . ( 4293 sec) [ -9623.6004] [GTR parameters ] . ( 4294 sec) [ -9623.6004] [Alpha ][ 0.595549] . Checking for NNIs, optimizing five branches... . ( 4348 sec) [ -9623.5986] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4402 sec) [ -9623.5955] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4456 sec) [ -9623.5954] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4511 sec) [ -9623.5953] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4565 sec) [ -9623.5952] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4620 sec) [ -9623.5951] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4675 sec) [ -9623.5928] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4729 sec) [ -9623.5904] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4784 sec) [ -9623.5903] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4838 sec) [ -9623.5902] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4893 sec) [ -9623.5900] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9623.590045. . Printing the most likely tree in file 'nucleic_M2573_346x897_2006.phy_phyml_tree.txt'... . Time used 1h22m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 4955.22user 0.00system 1:22:37elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps