.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2975_93x982_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... . 725 patterns found. (out of a total of 982 sites) . 454 sites without polymorphism (46.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12806.7417] [GTR parameters ] . ( 2 sec) [ -12644.1413] [Alpha ][ 0.500960] . ( 2 sec) [ -12640.5693] [ 2378] [depth= 1] . ( 2 sec) [ -12635.2836] [ 2377] [depth= 1] . ( 3 sec) [ -12633.3264] [ 2376] [depth= 1] . ( 4 sec) [ -12632.1744] [ 2375] [depth= 1] . ( 4 sec) [ -12631.1947] [ 2375] [depth= 1] . ( 4 sec) [ -12621.3535] [ 2371] [depth= 1] . ( 5 sec) [ -12619.0053] [ 2371] [depth= 1] . ( 6 sec) [ -12618.9888] [ 2371] [depth= 1] . ( 7 sec) [ -12615.6155] [ 2371] [depth= 1] . ( 7 sec) [ -12610.0772] [ 2371] [depth= 1] . ( 7 sec) [ -12606.6864] [ 2373] [depth= 1] . ( 8 sec) [ -12606.2007] [ 2373] [depth= 1] . ( 8 sec) [ -12603.2752] [ 2373] [depth= 1] . ( 9 sec) [ -12602.6902] [ 2373] [depth= 1] . ( 9 sec) [ -12599.8897] [ 2373] [depth= 1] . ( 9 sec) [ -12599.1654] [ 2373] [depth= 1] . ( 10 sec) [ -12595.6730] [ 2373] [depth= 1] . ( 10 sec) [ -12595.4015] [ 2373] [depth= 1] . ( 10 sec) [ -12595.0611] [ 2378] [depth= 1] . ( 11 sec) [ -12587.3877] [ 2373] [depth= 1] . ( 11 sec) [ -12574.3400] [ 2376] [depth= 1] . ( 11 sec) [ -12567.7437] [ 2373] [depth= 1] . ( 11 sec) [ -12567.3661] [ 2373] [depth= 1] . ( 12 sec) [ -12565.0608] [ 2373] [depth= 1] . ( 13 sec) [ -12564.3577] [ 2376] [depth= 1] . ( 13 sec) [ -12563.9763] [ 2376] [depth= 1] . ( 13 sec) [ -12563.8626] [ 2376] [depth= 1] . ( 14 sec) [ -12556.2000] [ 2381] [depth= 2] . ( 15 sec) [ -12551.7691] [ 2379] [depth= 1] . ( 15 sec) [ -12546.8419] [ 2376] [depth= 1] . ( 15 sec) [ -12542.3763] [ 2375] [depth= 1] . ( 15 sec) [ -12524.4351] [ 2376] [depth= 2] . ( 16 sec) [ -12524.2539] [ 2376] [depth= 1] . ( 16 sec) [ -12521.8405] [ 2376] [depth= 4] . ( 17 sec) [ -12521.4048] [ 2377] [depth= 1] . ( 17 sec) [ -12517.7802] [ 2376] [depth= 2] . ( 17 sec) [ -12516.9892] [ 2373] [depth= 1] . ( 17 sec) [ -12513.4274] [ 2375] [depth= 1] . ( 18 sec) [ -12512.0353] [ 2374] [depth= 2] . ( 18 sec) [ -12508.1417] [ 2373] [depth= 1] . ( 19 sec) [ -12505.6687] [ 2371] [depth= 1] . ( 19 sec) [ -12505.6391] [ 2370] [depth= 1] . ( 19 sec) [ -12501.5659] [ 2369] [depth= 2] . ( 20 sec) [ -12501.4198] [ 2371] [depth= 1] . ( 20 sec) [ -12496.4143] [ 2370] [depth= 2] . ( 20 sec) [ -12491.4820] [ 2366] [depth= 2] . ( 21 sec) [ -12488.8510] [ 2366] [depth= 1] . ( 21 sec) [ -12488.6578] [ 2367] [depth= 1] . ( 22 sec) [ -12487.2116] [ 2366] [depth= 1] . ( 23 sec) [ -12487.0791] [ 2364] [depth= 3] . ( 23 sec) [ -12483.3047] [ 2364] [depth= 1] . ( 23 sec) [ -12483.0992] [ 2365] [depth= 1] . ( 24 sec) [ -12477.3303] [ 2365] [depth= 1] . ( 24 sec) [ -12477.2034] [ 2361] [depth= 6] . ( 24 sec) [ -12474.8144] [ 2360] [depth= 2] . ( 24 sec) [ -12462.2627] [ 2359] [depth= 6] . ( 25 sec) [ -12462.0863] [ 2359] [depth= 1] . ( 26 sec) [ -12461.7382] [ 2359] [depth= 1] . ( 26 sec) [ -12453.6225] [ 2360] [depth= 2] . ( 26 sec) [ -12450.4831] [ 2359] [depth= 1] . ( 26 sec) [ -12448.8703] [ 2350] [depth= 3] . ( 26 sec) [ -12446.7075] [ 2349] [depth= 1] . ( 27 sec) [ -12446.2220] [ 2350] [depth= 1] . ( 27 sec) [ -12444.4673] [ 2348] [depth= 1] . ( 27 sec) [ -12443.4579] [ 2347] [depth= 1] . ( 28 sec) [ -12442.7010] [ 2347] [depth= 1] . ( 28 sec) [ -12442.3207] [ 2345] [depth= 1] . ( 28 sec) [ -12436.7729] [ 2351] [depth= 5] . ( 29 sec) [ -12436.5471] [ 2351] [depth= 1] . ( 30 sec) [ -12436.1268] [ 2351] [depth= 1] . ( 30 sec) [ -12433.8147] [ 2355] [depth= 1] . ( 31 sec) [ -12430.9646] [ 2355] [depth= 1] . ( 31 sec) [ -12429.6626] [ 2354] [depth= 1] . ( 32 sec) [ -12427.4547] [ 2351] [depth= 2] . ( 32 sec) [ -12425.6497] [ 2350] [depth= 1] . ( 32 sec) [ -12423.6891] [ 2350] [depth= 4] . ( 32 sec) [ -12422.8982] [ 2350] [depth= 1] . ( 33 sec) [ -12422.3809] [ 2349] [depth= 2] . ( 33 sec) [ -12420.9558] [ 2347] [depth= 1] . ( 33 sec) [ -12420.7926] [ 2344] [depth= 1] . ( 35 sec) [ -12346.5166] [Branch lengths ] . ( 40 sec) [ -12331.0900] [GTR parameters ] . ( 41 sec) [ -12319.3813] [Alpha ][ 0.387015] . ( 42 sec) [ -12318.9076] [ 2344] [depth= 1] . ( 44 sec) [ -12318.8972] [ 2344] [depth= 1] . ( 51 sec) [ -12315.4305] [ 2343] [depth= 1] . ( 52 sec) [ -12313.8979] [ 2343] [depth= 1] . ( 53 sec) [ -12311.7541] [ 2344] [depth= 1] . ( 57 sec) [ -12309.5234] [ 2341] [depth= 1] . ( 57 sec) [ -12309.2825] [ 2340] [depth= 1] . ( 61 sec) [ -12309.0810] [ 2340] [depth= 1] . ( 63 sec) [ -12308.9995] [ 2344] [depth= 1] . ( 65 sec) [ -12305.1054] [ 2344] [depth= 4] . ( 65 sec) [ -12304.9192] [ 2346] [depth= 1] . ( 68 sec) [ -12296.8738] [Branch lengths ] . ( 73 sec) [ -12296.3992] [GTR parameters ] . ( 73 sec) [ -12296.3811] [Alpha ][ 0.390910] . ( 92 sec) [ -12295.8139] [Branch lengths ] . ( 187 sec) [ -12295.5309] [ 2348] [depth= 3] . ( 189 sec) [ -12293.1784] [ 2352] [depth= 2] . ( 202 sec) [ -12293.0742] [ 2351] [depth= 1] . ( 202 sec) [ -12292.4973] [ 2352] [depth= 1] . ( 210 sec) [ -12292.4610] [ 2353] [depth= 1] . ( 212 sec) [ -12292.4335] [ 2354] [depth= 2] . ( 212 sec) [ -12292.1302] [ 2354] [depth= 3] . ( 217 sec) [ -12291.4277] [ 2354] [depth= 3] . ( 219 sec) [ -12290.9313] [ 2354] [depth= 1] . ( 220 sec) [ -12290.2792] [ 2354] [depth= 1] . ( 223 sec) [ -12289.3336] [ 2354] [depth= 1] . ( 227 sec) [ -12287.6952] [Branch lengths ] . ( 230 sec) [ -12287.6666] [GTR parameters ] . ( 231 sec) [ -12287.6615] [Alpha ][ 0.392964] . ( 335 sec) [ -12286.5446] [ 2351] [depth= 1] . ( 384 sec) [ -12286.4407] [Branch lengths ] . ( 387 sec) [ -12286.4391] [GTR parameters ] . ( 388 sec) [ -12286.4373] [Alpha ][ 0.394168] . ( 534 sec) [ -12286.4183] [Branch lengths ] . ( 534 sec) [ -12286.4183] [Topology ] . ( 537 sec) [ -12286.3242] [Topology ] . ( 540 sec) [ -12285.7810] [Topology ] . ( 543 sec) [ -12285.6735] [Topology ] . ( 546 sec) [ -12285.6259] [Topology ] . ( 549 sec) [ -12285.6029] [Topology ] . ( 552 sec) [ -12285.5915] [Topology ] . ( 556 sec) [ -12285.5857] [Topology ] . ( 560 sec) [ -12285.5831] [GTR parameters ] . ( 560 sec) [ -12285.5821] [Alpha ][ 0.395057] . ( 560 sec) [ -12285.5821] [Topology ] . ( 563 sec) [ -12285.5796] [Topology ] . ( 566 sec) [ -12285.5786] [Topology ] . ( 566 sec) [ -12285.5786] [GTR parameters ] . ( 567 sec) [ -12285.5786] [Alpha ][ 0.395057] . ( 567 sec) [ -12285.5786] [Topology ] . ( 570 sec) [ -12285.5782] [Topology ] . ( 570 sec) [ -12285.5782] [GTR parameters ] . ( 571 sec) [ -12285.5782] [Alpha ][ 0.395057] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12285.578193. . Printing the most likely tree in file 'nucleic_M2975_93x982_2006.phy_phyml_tree.txt'... . Time used 0h9m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 582.40user 0.00system 9:52.89elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps