.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2708_78x1107_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Compute approximate likelihood ratio test : yes (SH-like branch supports) . 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 : no . Evaluted tree : file "user tree (nucleic_M2708_78x1107_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 1107 sites) . 505 sites without polymorphism (45.62%). . Reading tree... . This analysis requires at least 25Mo of memory space. . ( 1 sec) [ -6734.9333] [Branch lengths ] . ( 4 sec) [ -6607.7852] [GTR parameters ] . ( 4 sec) [ -6567.8470] [Alpha ][ 0.500960] . ( 5 sec) [ -6549.5961] [Branch lengths ] . ( 7 sec) [ -6548.5786] [GTR parameters ] . ( 7 sec) [ -6543.7422] [Alpha ][ 0.404323] . ( 8 sec) [ -6537.6487] [Branch lengths ] . ( 9 sec) [ -6537.4730] [GTR parameters ] . ( 10 sec) [ -6536.5788] [Alpha ][ 0.370709] . ( 10 sec) [ -6534.6315] [Branch lengths ] . ( 12 sec) [ -6534.5894] [GTR parameters ] . ( 12 sec) [ -6534.3824] [Alpha ][ 0.355966] . ( 13 sec) [ -6533.6534] [Branch lengths ] . ( 14 sec) [ -6533.6429] [GTR parameters ] . ( 15 sec) [ -6533.5898] [Alpha ][ 0.348967] . ( 15 sec) [ -6533.2702] [Branch lengths ] . ( 17 sec) [ -6533.2672] [GTR parameters ] . ( 17 sec) [ -6533.2482] [Alpha ][ 0.344665] . ( 18 sec) [ -6533.0985] [Branch lengths ] . ( 20 sec) [ -6533.0975] [GTR parameters ] . ( 20 sec) [ -6533.0914] [Alpha ][ 0.342238] . ( 20 sec) [ -6533.0195] [Branch lengths ] . ( 22 sec) [ -6533.0192] [GTR parameters ] . ( 22 sec) [ -6533.0169] [Alpha ][ 0.340751] . ( 23 sec) [ -6532.9826] [Branch lengths ] . ( 25 sec) [ -6532.9825] [GTR parameters ] . ( 25 sec) [ -6532.9815] [Alpha ][ 0.339783] . ( 26 sec) [ -6532.9645] [Branch lengths ] . ( 27 sec) [ -6532.9644] [GTR parameters ] . ( 27 sec) [ -6532.9640] [Alpha ][ 0.339121] . ( 28 sec) [ -6532.9553] [Branch lengths ] . ( 28 sec) [ -6532.9553] [GTR parameters ] . ( 28 sec) [ -6532.9551] [Alpha ][ 0.338646] . ( 29 sec) [ -6532.9507] [Branch lengths ] . ( 29 sec) [ -6532.9507] [GTR parameters ] . ( 30 sec) [ -6532.9506] [Alpha ][ 0.338307] . ( 30 sec) [ -6532.9483] [Branch lengths ] . ( 31 sec) [ -6532.9483] [GTR parameters ] . ( 31 sec) [ -6532.9482] [Alpha ][ 0.337969] . ( 32 sec) [ -6532.9470] [Branch lengths ] . ( 32 sec) [ -6532.9470] [GTR parameters ] . ( 32 sec) [ -6532.9470] [Alpha ][ 0.337969] . ( 33 sec) [ -6532.9466] [Branch lengths ] . ( 33 sec) [ -6532.9466] [GTR parameters ] . ( 33 sec) [ -6532.9466] [Alpha ][ 0.337969] . ( 34 sec) [ -6532.9466] [GTR parameters ] . ( 34 sec) [ -6532.9466] [Alpha ][ 0.337969] . Log likelihood of the current tree: -6532.946645. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 0h0m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo java.lang.NullPointerException at java.io.FileInputStream.(FileInputStream.java:103) at java.io.FileReader.(FileReader.java:55) at Recomp.(Recomp.java:114) at Recomp.main(Recomp.java:52)