.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2716_79x1252_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_M2716_79x1252_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 280 patterns found. (out of a total of 1252 sites) . 984 sites without polymorphism (78.59%). . Reading tree... . This analysis requires at least 12Mo of memory space. . ( 1 sec) [ -3403.3999] [Branch lengths ] . ( 2 sec) [ -3366.5842] [GTR parameters ] . ( 2 sec) [ -3353.6872] [Alpha ][ 0.500960] . ( 3 sec) [ -3352.7459] [Branch lengths ] . ( 3 sec) [ -3352.6803] [GTR parameters ] . ( 3 sec) [ -3346.6695] [Alpha ][ 0.258524] . ( 4 sec) [ -3345.8188] [Branch lengths ] . ( 4 sec) [ -3345.7129] [GTR parameters ] . ( 4 sec) [ -3345.6422] [Alpha ][ 0.242169] . ( 5 sec) [ -3345.5841] [Branch lengths ] . ( 5 sec) [ -3345.5805] [GTR parameters ] . ( 5 sec) [ -3345.5788] [Alpha ][ 0.239688] . ( 6 sec) [ -3345.5731] [Branch lengths ] . ( 6 sec) [ -3345.5730] [GTR parameters ] . ( 6 sec) [ -3345.5729] [Alpha ][ 0.239059] . ( 6 sec) [ -3345.5717] [Branch lengths ] . ( 7 sec) [ -3345.5717] [GTR parameters ] . ( 7 sec) [ -3345.5717] [Alpha ][ 0.238820] . ( 7 sec) [ -3345.5715] [Branch lengths ] . ( 7 sec) [ -3345.5714] [GTR parameters ] . ( 7 sec) [ -3345.5714] [Alpha ][ 0.238820] . ( 8 sec) [ -3345.5714] [GTR parameters ] . ( 8 sec) [ -3345.5714] [Alpha ][ 0.238820] . Log likelihood of the current tree: -3345.571446. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2716_79x1252_2006.phy_phyml_tree.txt'... . Time used 0h0m15s 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)