.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2770_86x1628_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_M2770_86x1628_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 571 patterns found. (out of a total of 1628 sites) . 1267 sites without polymorphism (77.83%). . Reading tree... . This analysis requires at least 26Mo of memory space. . ( 1 sec) [ -5878.4160] [Branch lengths ] . ( 7 sec) [ -5816.1013] [GTR parameters ] . ( 7 sec) [ -5815.7518] [Alpha ][ 1.185708] . ( 8 sec) [ -5815.7321] [Branch lengths ] . ( 9 sec) [ -5815.7317] [GTR parameters ] . ( 9 sec) [ -5815.7317] [Alpha ][ 1.185708] . ( 10 sec) [ -5815.7316] [Branch lengths ] . ( 11 sec) [ -5815.7316] [GTR parameters ] . ( 11 sec) [ -5815.7316] [Alpha ][ 1.185708] . ( 12 sec) [ -5815.7316] [GTR parameters ] . ( 12 sec) [ -5815.7316] [Alpha ][ 1.185708] . Log likelihood of the current tree: -5815.731591. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2770_86x1628_2006.phy_phyml_tree.txt'... . Time used 0h0m31s 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)