.......................... 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 . 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 (RAxML_result.nucleic_M2845_68x1715_2006.phy_RAXML_CAT)" . 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%). . Reading tree... . This analysis requires at least 23Mo of memory space. . ( 1 sec) [ -11960.8895] [Branch lengths ] . ( 5 sec) [ -11625.5834] [GTR parameters ] . ( 5 sec) [ -11447.1412] [Alpha ][ 0.500960] . ( 6 sec) [ -11443.8831] [Branch lengths ] . ( 8 sec) [ -11443.7288] [GTR parameters ] . ( 8 sec) [ -11367.4447] [Alpha ][ 0.254269] . ( 9 sec) [ -11364.4702] [Branch lengths ] . ( 10 sec) [ -11364.2872] [GTR parameters ] . ( 11 sec) [ -11364.2872] [Alpha ][ 0.254269] . ( 11 sec) [ -11363.3482] [Branch lengths ] . ( 13 sec) [ -11363.3454] [GTR parameters ] . ( 13 sec) [ -11363.3453] [Alpha ][ 0.254523] . ( 14 sec) [ -11363.1173] [Branch lengths ] . ( 14 sec) [ -11363.1172] [GTR parameters ] . ( 15 sec) [ -11363.1172] [Alpha ][ 0.254523] . ( 15 sec) [ -11363.0687] [Branch lengths ] . ( 17 sec) [ -11363.0678] [GTR parameters ] . ( 17 sec) [ -11363.0678] [Alpha ][ 0.254523] . ( 17 sec) [ -11363.0571] [Branch lengths ] . ( 19 sec) [ -11363.0570] [GTR parameters ] . ( 19 sec) [ -11363.0570] [Alpha ][ 0.254523] . ( 19 sec) [ -11363.0546] [Branch lengths ] . ( 21 sec) [ -11363.0546] [GTR parameters ] . ( 21 sec) [ -11363.0546] [Alpha ][ 0.254523] . ( 22 sec) [ -11363.0541] [Branch lengths ] . ( 22 sec) [ -11363.0541] [GTR parameters ] . ( 23 sec) [ -11363.0541] [Alpha ][ 0.254523] . ( 23 sec) [ -11363.0541] [GTR parameters ] . ( 23 sec) [ -11363.0541] [Alpha ][ 0.254523] . Log likelihood of the current tree: -11363.054058. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'... . Time used 0h0m45s 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)