.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2696_50x1472_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_M2696_50x1472_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1472 sites) . 982 sites without polymorphism (66.71%). . Reading tree... . This analysis requires at least 16Mo of memory space. . ( 1 sec) [ -6247.3654] [Branch lengths ] . ( 3 sec) [ -6166.4097] [GTR parameters ] . ( 3 sec) [ -6166.3113] [Alpha ][ 0.928376] . ( 4 sec) [ -6166.2797] [Branch lengths ] . ( 5 sec) [ -6166.2792] [GTR parameters ] . ( 5 sec) [ -6166.2792] [Alpha ][ 0.926594] . ( 5 sec) [ -6166.2788] [Branch lengths ] . ( 6 sec) [ -6166.2788] [GTR parameters ] . ( 6 sec) [ -6166.2788] [Alpha ][ 0.926594] . ( 6 sec) [ -6166.2788] [GTR parameters ] . ( 6 sec) [ -6166.2788] [Alpha ][ 0.926594] . Log likelihood of the current tree: -6166.278761. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2696_50x1472_2006.phy_phyml_tree.txt'... . Time used 0h0m19s 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)