.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2752_106x1292_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_M2752_106x1292_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 11 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 427 patterns found. (out of a total of 1292 sites) . 807 sites without polymorphism (62.46%). . Reading tree... . This analysis requires at least 24Mo of memory space. . ( 1 sec) [ -8015.9572] [Branch lengths ] . ( 3 sec) [ -7900.6966] [GTR parameters ] . ( 3 sec) [ -7870.6293] [Alpha ][ 0.500960] . ( 4 sec) [ -7870.1005] [Branch lengths ] . ( 6 sec) [ -7869.8098] [GTR parameters ] . ( 6 sec) [ -7869.5684] [Alpha ][ 0.472443] . ( 6 sec) [ -7869.5500] [Branch lengths ] . ( 8 sec) [ -7869.5468] [GTR parameters ] . ( 8 sec) [ -7869.5468] [Alpha ][ 0.471948] . ( 8 sec) [ -7869.5110] [Branch lengths ] . ( 9 sec) [ -7869.5107] [GTR parameters ] . ( 9 sec) [ -7869.5107] [Alpha ][ 0.471948] . ( 10 sec) [ -7869.5087] [Branch lengths ] . ( 10 sec) [ -7869.5087] [GTR parameters ] . ( 10 sec) [ -7869.5087] [Alpha ][ 0.471948] . ( 11 sec) [ -7869.5086] [Branch lengths ] . ( 11 sec) [ -7869.5086] [GTR parameters ] . ( 11 sec) [ -7869.5086] [Alpha ][ 0.471948] . ( 12 sec) [ -7869.5086] [GTR parameters ] . ( 12 sec) [ -7869.5086] [Alpha ][ 0.471948] . Log likelihood of the current tree: -7869.508583. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2752_106x1292_2006.phy_phyml_tree.txt'... . Time used 0h0m29s 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)