.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2879_70x800_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_M2879_70x800_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 466 patterns found. (out of a total of 800 sites) . 405 sites without polymorphism (50.62%). . Reading tree... . This analysis requires at least 17Mo of memory space. . ( 0 sec) [ -5986.5039] [Branch lengths ] . ( 4 sec) [ -5799.0060] [GTR parameters ] . ( 4 sec) [ -5784.0216] [Alpha ][ 0.574724] . ( 4 sec) [ -5783.1456] [Branch lengths ] . ( 6 sec) [ -5783.0649] [GTR parameters ] . ( 6 sec) [ -5783.0593] [Alpha ][ 0.568794] . ( 6 sec) [ -5782.8963] [Branch lengths ] . ( 7 sec) [ -5782.8953] [GTR parameters ] . ( 7 sec) [ -5782.8953] [Alpha ][ 0.568794] . ( 8 sec) [ -5782.4947] [Branch lengths ] . ( 9 sec) [ -5782.4929] [GTR parameters ] . ( 9 sec) [ -5782.4929] [Alpha ][ 0.568794] . ( 9 sec) [ -5782.4181] [Branch lengths ] . ( 10 sec) [ -5782.4179] [GTR parameters ] . ( 10 sec) [ -5782.4179] [Alpha ][ 0.568794] . ( 11 sec) [ -5782.4166] [Branch lengths ] . ( 11 sec) [ -5782.4166] [GTR parameters ] . ( 11 sec) [ -5782.4166] [Alpha ][ 0.568794] . ( 12 sec) [ -5782.4166] [Branch lengths ] . ( 12 sec) [ -5782.4166] [GTR parameters ] . ( 12 sec) [ -5782.4166] [Alpha ][ 0.568794] . ( 12 sec) [ -5782.4166] [GTR parameters ] . ( 13 sec) [ -5782.4166] [Alpha ][ 0.568794] . Log likelihood of the current tree: -5782.416607. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2879_70x800_2006.phy_phyml_tree.txt'... . Time used 0h0m25s 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)