.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2845_68x1715_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 649 patterns found. (out of a total of 1715 sites) . 1119 sites without polymorphism (65.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -11816.7722] [GTR parameters ] . ( 5 sec) [ -11662.0849] [Alpha ][ 0.500960] . ( 5 sec) [ -11660.9342] [ 1610] [depth= 1] . ( 6 sec) [ -11660.7720] [ 1610] [depth= 1] . ( 6 sec) [ -11660.6848] [ 1610] [depth= 1] . ( 6 sec) [ -11660.5983] [ 1610] [depth= 1] . ( 6 sec) [ -11660.4280] [ 1610] [depth= 1] . ( 6 sec) [ -11659.1195] [ 1610] [depth= 1] . ( 6 sec) [ -11655.5792] [ 1610] [depth= 1] . ( 7 sec) [ -11653.6958] [ 1610] [depth= 1] . ( 7 sec) [ -11653.5560] [ 1617] [depth= 1] . ( 8 sec) [ -11647.5359] [ 1616] [depth= 1] . ( 8 sec) [ -11646.9829] [ 1618] [depth= 1] . ( 8 sec) [ -11645.8122] [ 1616] [depth= 1] . ( 8 sec) [ -11645.5713] [ 1616] [depth= 3] . ( 8 sec) [ -11642.9865] [ 1615] [depth= 2] . ( 8 sec) [ -11639.1255] [ 1615] [depth= 2] . ( 8 sec) [ -11631.4518] [ 1613] [depth= 1] . ( 9 sec) [ -11630.4177] [ 1613] [depth= 1] . ( 9 sec) [ -11621.7662] [ 1612] [depth= 1] . ( 9 sec) [ -11617.0257] [ 1607] [depth= 1] . ( 9 sec) [ -11615.0970] [ 1606] [depth= 1] . ( 9 sec) [ -11612.2758] [ 1605] [depth= 1] . ( 10 sec) [ -11609.8670] [ 1605] [depth= 2] . ( 10 sec) [ -11605.6313] [ 1604] [depth= 1] . ( 10 sec) [ -11604.3468] [ 1603] [depth= 2] . ( 10 sec) [ -11602.5685] [ 1604] [depth= 1] . ( 10 sec) [ -11600.5629] [ 1603] [depth= 1] . ( 10 sec) [ -11595.1057] [ 1602] [depth= 1] . ( 11 sec) [ -11594.8873] [ 1603] [depth= 1] . ( 11 sec) [ -11593.8198] [ 1602] [depth= 1] . ( 11 sec) [ -11592.1471] [ 1603] [depth= 1] . ( 11 sec) [ -11589.6156] [ 1602] [depth= 1] . ( 11 sec) [ -11586.2409] [ 1603] [depth= 1] . ( 12 sec) [ -11586.0212] [ 1605] [depth= 2] . ( 12 sec) [ -11582.1253] [ 1604] [depth= 1] . ( 12 sec) [ -11578.8038] [ 1602] [depth= 1] . ( 12 sec) [ -11577.8583] [ 1604] [depth= 1] . ( 12 sec) [ -11570.4243] [ 1602] [depth= 1] . ( 13 sec) [ -11559.2670] [ 1602] [depth= 1] . ( 13 sec) [ -11558.1915] [ 1603] [depth= 1] . ( 13 sec) [ -11555.6192] [ 1602] [depth= 1] . ( 14 sec) [ -11554.3525] [ 1602] [depth= 1] . ( 14 sec) [ -11550.5849] [ 1606] [depth= 1] . ( 14 sec) [ -11549.4963] [ 1605] [depth= 2] . ( 14 sec) [ -11548.6928] [ 1604] [depth= 2] . ( 15 sec) [ -11546.5204] [ 1601] [depth= 1] . ( 15 sec) [ -11546.2226] [ 1602] [depth= 1] . ( 15 sec) [ -11545.8769] [ 1602] [depth= 1] . ( 15 sec) [ -11543.6012] [ 1600] [depth= 1] . ( 15 sec) [ -11540.9511] [ 1600] [depth= 1] . ( 15 sec) [ -11540.4619] [ 1600] [depth= 1] . ( 15 sec) [ -11540.4046] [ 1599] [depth= 1] . ( 16 sec) [ -11540.1801] [ 1601] [depth= 1] . ( 16 sec) [ -11533.4535] [ 1599] [depth= 1] . ( 16 sec) [ -11532.8096] [ 1600] [depth= 1] . ( 17 sec) [ -11470.8386] [Branch lengths ] . ( 20 sec) [ -11470.0610] [GTR parameters ] . ( 20 sec) [ -11393.5809] [Alpha ][ 0.251119] . ( 20 sec) [ -11392.2186] [ 1600] [depth= 1] . ( 21 sec) [ -11386.4919] [ 1593] [depth= 1] . ( 21 sec) [ -11386.2054] [ 1594] [depth= 2] . ( 22 sec) [ -11386.1759] [ 1594] [depth= 1] . ( 22 sec) [ -11386.0715] [ 1594] [depth= 1] . ( 22 sec) [ -11383.4349] [ 1594] [depth= 3] . ( 23 sec) [ -11382.9589] [ 1595] [depth= 1] . ( 24 sec) [ -11380.7271] [ 1594] [depth= 1] . ( 24 sec) [ -11380.5226] [ 1594] [depth= 2] . ( 25 sec) [ -11377.2304] [ 1590] [depth= 1] . ( 25 sec) [ -11377.1393] [ 1591] [depth= 1] . ( 30 sec) [ -11365.9002] [Branch lengths ] . ( 33 sec) [ -11365.5105] [GTR parameters ] . ( 33 sec) [ -11365.4895] [Alpha ][ 0.253724] . ( 34 sec) [ -11365.4572] [ 1591] [depth= 1] . ( 34 sec) [ -11364.7356] [ 1591] [depth= 1] . ( 43 sec) [ -11362.8779] [Branch lengths ] . ( 45 sec) [ -11362.8671] [GTR parameters ] . ( 45 sec) [ -11362.8669] [Alpha ][ 0.253977] . ( 55 sec) [ -11362.4787] [Branch lengths ] . ( 138 sec) [ -11362.3970] [Branch lengths ] . ( 138 sec) [ -11362.3970] [Topology ] . ( 140 sec) [ -11362.3246] [Topology ] . ( 142 sec) [ -11362.2365] [Topology ] . ( 144 sec) [ -11362.2242] [Topology ] . ( 146 sec) [ -11362.2201] [Topology ] . ( 148 sec) [ -11362.2181] [Topology ] . ( 150 sec) [ -11362.2170] [Topology ] . ( 152 sec) [ -11362.2164] [Topology ] . ( 154 sec) [ -11362.2101] [GTR parameters ] . ( 154 sec) [ -11362.2101] [Alpha ][ 0.253977] . ( 154 sec) [ -11362.2101] [Topology ] . ( 156 sec) [ -11362.2096] [Topology ] . ( 157 sec) [ -11362.2096] [GTR parameters ] . ( 157 sec) [ -11362.2096] [Alpha ][ 0.253977] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11362.209555. . Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'... . Time used 0h2m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 168.89user 0.00system 2:51.79elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps