.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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_M2901_56x1802_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . Reading tree... . This analysis requires at least 19Mo of memory space. . ( 1 sec) [ -8133.6491] [Branch lengths ] . ( 4 sec) [ -7958.8492] [GTR parameters ] . ( 4 sec) [ -7877.9218] [Alpha ][ 0.500960] . ( 4 sec) [ -7876.4276] [Branch lengths ] . ( 6 sec) [ -7876.3714] [GTR parameters ] . ( 6 sec) [ -7829.2134] [Alpha ][ 0.250961] . ( 7 sec) [ -7828.7406] [Branch lengths ] . ( 8 sec) [ -7828.6560] [GTR parameters ] . ( 9 sec) [ -7826.5573] [Alpha ][ 0.213173] . ( 9 sec) [ -7826.5260] [Branch lengths ] . ( 11 sec) [ -7826.5204] [GTR parameters ] . ( 11 sec) [ -7826.5201] [Alpha ][ 0.212732] . ( 11 sec) [ -7826.5185] [Branch lengths ] . ( 12 sec) [ -7826.5185] [GTR parameters ] . ( 12 sec) [ -7826.5185] [Alpha ][ 0.212732] . ( 12 sec) [ -7826.5183] [Branch lengths ] . ( 13 sec) [ -7826.5183] [GTR parameters ] . ( 13 sec) [ -7826.5183] [Alpha ][ 0.212732] . ( 13 sec) [ -7826.5183] [GTR parameters ] . ( 13 sec) [ -7826.5183] [Alpha ][ 0.212732] . Log likelihood of the current tree: -7826.518304. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Time used 0h0m30s 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)