.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -18030.1538] [GTR parameters ] . ( 7 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 7 sec) [ -17732.2284] [ 3534] [depth= 1] . ( 7 sec) [ -17727.9520] [ 3536] [depth= 1] . ( 12 sec) [ -17720.9232] [ 3536] [depth= 2] . ( 12 sec) [ -17710.1407] [ 3534] [depth= 2] . ( 12 sec) [ -17687.4237] [ 3532] [depth= 1] . ( 12 sec) [ -17673.6169] [ 3523] [depth= 2] . ( 14 sec) [ -17672.1004] [ 3522] [depth= 1] . ( 23 sec) [ -17670.5307] [ 3529] [depth= 1] . ( 23 sec) [ -17664.5235] [ 3522] [depth= 1] . ( 23 sec) [ -17662.9041] [ 3530] [depth= 2] . ( 23 sec) [ -17643.5574] [ 3527] [depth= 2] . ( 44 sec) [ -17643.3124] [ 3527] [depth= 1] . ( 45 sec) [ -17639.8189] [ 3526] [depth= 1] . ( 47 sec) [ -17639.2725] [ 3526] [depth= 1] . ( 48 sec) [ -17636.5010] [ 3526] [depth= 1] . ( 48 sec) [ -17636.3167] [ 3526] [depth= 1] . ( 51 sec) [ -17632.5779] [ 3533] [depth= 1] . ( 74 sec) [ -17632.0626] [ 3537] [depth= 1] . ( 74 sec) [ -17630.4664] [ 3528] [depth= 2] . ( 75 sec) [ -17629.2855] [ 3528] [depth= 1] . ( 77 sec) [ -17628.9925] [ 3528] [depth= 1] . ( 79 sec) [ -17624.8340] [ 3525] [depth= 1] . ( 101 sec) [ -17624.1505] [ 3523] [depth= 1] . ( 101 sec) [ -17623.7673] [ 3523] [depth= 1] . ( 102 sec) [ -17621.6607] [ 3523] [depth= 1] . ( 109 sec) [ -17621.1926] [ 3523] [depth= 1] . ( 109 sec) [ -17610.7327] [ 3521] [depth= 2] . ( 109 sec) [ -17610.6275] [ 3521] [depth= 1] . ( 135 sec) [ -17609.9897] [ 3523] [depth= 1] . ( 144 sec) [ -17601.2708] [ 3524] [depth= 1] . ( 145 sec) [ -17600.8338] [ 3523] [depth= 1] . ( 155 sec) [ -17597.6005] [ 3522] [depth= 1] . ( 155 sec) [ -17590.6391] [ 3523] [depth= 1] . ( 164 sec) [ -17585.6450] [ 3524] [depth= 1] . ( 164 sec) [ -17567.3487] [ 3523] [depth= 1] . ( 169 sec) [ -17565.7661] [ 3524] [depth= 1] . ( 178 sec) [ -17563.0590] [ 3521] [depth= 3] . ( 178 sec) [ -17557.5473] [ 3516] [depth= 2] . ( 178 sec) [ -17555.6545] [ 3515] [depth= 1] . ( 178 sec) [ -17553.3334] [ 3516] [depth= 2] . ( 187 sec) [ -17552.8137] [ 3516] [depth= 1] . ( 190 sec) [ -17543.6657] [ 3514] [depth= 1] . ( 193 sec) [ -17534.8214] [ 3510] [depth= 2] . ( 193 sec) [ -17533.7863] [ 3510] [depth= 1] . ( 198 sec) [ -17528.9104] [ 3510] [depth= 2] . ( 198 sec) [ -17516.5120] [ 3507] [depth= 1] . ( 211 sec) [ -17514.9696] [ 3510] [depth= 1] . ( 211 sec) [ -17514.8354] [ 3510] [depth= 1] . ( 214 sec) [ -17514.2106] [ 3516] [depth= 1] . ( 214 sec) [ -17509.9160] [ 3510] [depth= 1] . ( 214 sec) [ -17509.5800] [ 3507] [depth= 1] . ( 214 sec) [ -17507.9645] [ 3508] [depth= 1] . ( 215 sec) [ -17503.3081] [ 3511] [depth= 1] . ( 220 sec) [ -17499.1653] [ 3511] [depth= 1] . ( 220 sec) [ -17495.2044] [ 3510] [depth= 1] . ( 220 sec) [ -17489.1335] [ 3511] [depth= 2] . ( 221 sec) [ -17483.0521] [ 3513] [depth= 1] . ( 226 sec) [ -17481.4846] [ 3513] [depth= 1] . ( 226 sec) [ -17481.4311] [ 3519] [depth= 5] . ( 227 sec) [ -17453.2828] [ 3512] [depth= 2] . ( 227 sec) [ -17451.1739] [ 3510] [depth= 2] . ( 231 sec) [ -17450.2313] [ 3510] [depth= 1] . ( 231 sec) [ -17446.5869] [ 3507] [depth= 1] . ( 234 sec) [ -17444.1669] [ 3507] [depth= 1] . ( 235 sec) [ -17438.1269] [ 3507] [depth= 1] . ( 235 sec) [ -17416.5038] [ 3505] [depth= 7] . ( 241 sec) [ -17409.5108] [ 3503] [depth= 1] . ( 252 sec) [ -17406.2833] [ 3511] [depth= 6] . ( 262 sec) [ -17389.2503] [ 3510] [depth= 3] . ( 269 sec) [ -17385.9604] [ 3508] [depth= 1] . ( 270 sec) [ -17379.7373] [ 3500] [depth= 6] . ( 270 sec) [ -17374.2442] [ 3503] [depth= 1] . ( 270 sec) [ -17373.9989] [ 3504] [depth= 1] . ( 270 sec) [ -17371.0337] [ 3507] [depth= 1] . ( 271 sec) [ -17367.5737] [ 3507] [depth= 3] . ( 288 sec) [ -17367.2033] [ 3501] [depth= 4] . ( 288 sec) [ -17364.0937] [ 3502] [depth= 1] . ( 293 sec) [ -17346.5496] [ 3497] [depth= 2] . ( 305 sec) [ -17345.2333] [ 3497] [depth= 1] . ( 314 sec) [ -17343.6538] [ 3497] [depth= 1] . ( 314 sec) [ -17334.6339] [ 3497] [depth= 1] . ( 327 sec) [ -17327.7016] [ 3497] [depth= 1] . ( 327 sec) [ -17321.0371] [ 3493] [depth= 2] . ( 335 sec) [ -17319.2001] [ 3497] [depth= 1] . ( 340 sec) [ -17318.6395] [ 3499] [depth= 1] . ( 340 sec) [ -17317.9885] [ 3498] [depth= 1] . ( 340 sec) [ -17313.2336] [ 3499] [depth= 1] . ( 344 sec) [ -17310.8878] [ 3499] [depth= 1] . ( 344 sec) [ -17310.3464] [ 3496] [depth= 2] . ( 345 sec) [ -17308.8492] [ 3497] [depth= 1] . ( 345 sec) [ -17307.9739] [ 3494] [depth= 1] . ( 345 sec) [ -17305.9222] [ 3494] [depth= 1] . ( 345 sec) [ -17303.2957] [ 3495] [depth= 1] . ( 346 sec) [ -17301.8789] [ 3494] [depth= 1] . ( 346 sec) [ -17296.4772] [ 3493] [depth= 1] . ( 359 sec) [ -17290.6569] [ 3490] [depth= 3] . ( 368 sec) [ -17290.3810] [ 3492] [depth= 1] . ( 384 sec) [ -17288.9459] [ 3493] [depth= 1] . ( 384 sec) [ -17286.8118] [ 3492] [depth= 1] . ( 389 sec) [ -17286.5465] [ 3490] [depth= 1] . ( 403 sec) [ -17152.3230] [Branch lengths ] . ( 410 sec) [ -17141.5283] [GTR parameters ] . ( 411 sec) [ -17107.3770] [Alpha ][ 0.354565] . ( 466 sec) [ -17104.0273] [ 3490] [depth= 1] . ( 472 sec) [ -17096.4386] [ 3485] [depth= 1] . ( 529 sec) [ -17092.6035] [ 3483] [depth= 1] . ( 551 sec) [ -17080.9091] [ 3480] [depth= 5] . ( 572 sec) [ -17080.6448] [ 3482] [depth= 1] . ( 618 sec) [ -17080.0966] [ 3481] [depth= 1] . ( 770 sec) [ -17080.0400] [ 3485] [depth= 1] . ( 785 sec) [ -17079.6896] [ 3484] [depth= 1] . ( 819 sec) [ -17077.2588] [ 3482] [depth= 1] . ( 820 sec) [ -17076.6456] [ 3485] [depth= 1] . ( 836 sec) [ -17074.7429] [ 3486] [depth= 1] . ( 847 sec) [ -17074.6404] [ 3484] [depth= 1] . ( 859 sec) [ -17074.0603] [ 3485] [depth= 1] . ( 885 sec) [ -17073.9210] [ 3484] [depth= 1] . ( 902 sec) [ -17066.2285] [ 3481] [depth= 2] . ( 923 sec) [ -17063.4283] [ 3478] [depth= 3] . ( 970 sec) [ -17062.8510] [ 3482] [depth= 1] . ( 990 sec) [ -17062.0212] [ 3482] [depth= 1] . ( 994 sec) [ -17061.9789] [ 3483] [depth= 5] . ( 1019 sec) [ -17061.3122] [ 3483] [depth= 1] . ( 1028 sec) [ -17061.0481] [ 3482] [depth= 1] . ( 1049 sec) [ -17060.5557] [ 3482] [depth= 1] . ( 1110 sec) [ -17029.3625] [Branch lengths ] . ( 1116 sec) [ -17027.5403] [GTR parameters ] . ( 1116 sec) [ -17027.5086] [Alpha ][ 0.358160] . ( 1233 sec) [ -17026.3115] [ 3483] [depth= 1] . ( 1292 sec) [ -17026.2209] [ 3481] [depth= 1] . ( 1417 sec) [ -17026.1919] [ 3485] [depth= 2] . ( 1483 sec) [ -17025.5352] [ 3482] [depth= 1] . ( 1483 sec) [ -17023.3014] [ 3486] [depth= 3] . ( 1483 sec) [ -17022.2870] [ 3486] [depth= 1] . ( 1486 sec) [ -17021.8765] [ 3481] [depth= 1] . ( 1488 sec) [ -17021.7809] [ 3480] [depth= 1] . ( 1488 sec) [ -17021.7689] [ 3480] [depth= 1] . ( 1600 sec) [ -17021.3889] [ 3481] [depth= 2] . ( 1684 sec) [ -17009.3940] [Branch lengths ] . ( 1687 sec) [ -17009.2784] [GTR parameters ] . ( 1687 sec) [ -17009.2719] [Alpha ][ 0.359747] . ( 1944 sec) [ -17008.9297] [ 3482] [depth= 1] . ( 1945 sec) [ -17008.5314] [ 3482] [depth= 1] . ( 2044 sec) [ -17008.4466] [ 3484] [depth= 1] . ( 2057 sec) [ -17008.0160] [ 3483] [depth= 1] . ( 2074 sec) [ -17007.8911] [ 3483] [depth= 1] . ( 2099 sec) [ -17006.4640] [ 3486] [depth= 2] . ( 2208 sec) [ -16999.2136] [Branch lengths ] . ( 2213 sec) [ -16999.1640] [GTR parameters ] . ( 2214 sec) [ -16999.1623] [Alpha ][ 0.360527] . ( 2315 sec) [ -16998.1695] [ 3483] [depth= 1] . ( 2602 sec) [ -16995.8126] [ 3487] [depth= 1] . ( 2626 sec) [ -16995.7231] [ 3484] [depth= 1] . ( 2735 sec) [ -16993.7267] [Branch lengths ] . ( 2738 sec) [ -16993.6724] [GTR parameters ] . ( 2738 sec) [ -16993.6687] [Alpha ][ 0.361715] . ( 3005 sec) [ -16993.6356] [ 3485] [depth= 1] . ( 3265 sec) [ -16993.1392] [Branch lengths ] . ( 3268 sec) [ -16993.1307] [GTR parameters ] . ( 3268 sec) [ -16993.1298] [Alpha ][ 0.362278] . ( 3409 sec) [ -16993.0304] [Branch lengths ] . ( 3409 sec) [ -16993.0304] [Topology ] . ( 3412 sec) [ -16993.0113] [Topology ] . ( 3415 sec) [ -16993.0019] [Topology ] . ( 3419 sec) [ -16992.9957] [Topology ] . ( 3422 sec) [ -16992.9916] [Topology ] . ( 3425 sec) [ -16992.9887] [Topology ] . ( 3428 sec) [ -16992.9868] [Topology ] . ( 3431 sec) [ -16992.9815] [GTR parameters ] . ( 3431 sec) [ -16992.9804] [Alpha ][ 0.362912] . ( 3431 sec) [ -16992.9804] [Topology ] . ( 3434 sec) [ -16992.9779] [Topology ] . ( 3437 sec) [ -16992.9762] [Topology ] . ( 3440 sec) [ -16992.9751] [Topology ] . ( 3444 sec) [ -16992.9743] [Topology ] . ( 3445 sec) [ -16992.9741] [GTR parameters ] . ( 3446 sec) [ -16992.9741] [Alpha ][ 0.362912] . ( 3446 sec) [ -16992.9741] [Topology ] . ( 3449 sec) [ -16992.9735] [Topology ] . ( 3450 sec) [ -16992.9735] [GTR parameters ] . ( 3450 sec) [ -16992.9735] [Alpha ][ 0.362912] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -16992.973523. . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Time used 0h57m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3145.25user 0.00system 57:54.22elapsed 90%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps