.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_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_M2826_60x1398_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . Reading tree... . This analysis requires at least 20Mo of memory space. . ( 0 sec) [ -15274.3149] [Branch lengths ] . ( 4 sec) [ -14709.8461] [GTR parameters ] . ( 4 sec) [ -14431.0710] [Alpha ][ 0.500960] . ( 5 sec) [ -14426.3567] [Branch lengths ] . ( 7 sec) [ -14425.9721] [GTR parameters ] . ( 7 sec) [ -14335.8248] [Alpha ][ 0.278108] . ( 8 sec) [ -14334.7708] [Branch lengths ] . ( 10 sec) [ -14334.4208] [GTR parameters ] . ( 10 sec) [ -14334.4059] [Alpha ][ 0.276031] . ( 11 sec) [ -14334.3231] [Branch lengths ] . ( 12 sec) [ -14334.3229] [GTR parameters ] . ( 12 sec) [ -14334.3216] [Alpha ][ 0.275398] . ( 13 sec) [ -14334.2994] [Branch lengths ] . ( 14 sec) [ -14334.2993] [GTR parameters ] . ( 14 sec) [ -14334.2988] [Alpha ][ 0.275002] . ( 14 sec) [ -14334.2917] [Branch lengths ] . ( 15 sec) [ -14334.2916] [GTR parameters ] . ( 15 sec) [ -14334.2915] [Alpha ][ 0.274727] . ( 16 sec) [ -14334.2893] [Branch lengths ] . ( 16 sec) [ -14334.2892] [GTR parameters ] . ( 16 sec) [ -14334.2892] [Alpha ][ 0.274727] . ( 17 sec) [ -14334.2886] [Branch lengths ] . ( 18 sec) [ -14334.2886] [GTR parameters ] . ( 18 sec) [ -14334.2886] [Alpha ][ 0.274727] . ( 18 sec) [ -14334.2886] [GTR parameters ] . ( 18 sec) [ -14334.2886] [Alpha ][ 0.274727] . Log likelihood of the current tree: -14334.288624. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Time used 0h0m33s 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)