.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2862_54x1011_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_M2862_54x1011_2006.phy_RAXML_CAT)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 587 patterns found. (out of a total of 1011 sites) . 443 sites without polymorphism (43.82%). . Reading tree... . This analysis requires at least 16Mo of memory space. . ( 0 sec) [ -17658.6467] [Branch lengths ] . ( 1 sec) [ -17155.5118] [GTR parameters ] . ( 1 sec) [ -16901.3198] [Alpha ][ 0.500960] . ( 2 sec) [ -16879.2902] [Branch lengths ] . ( 5 sec) [ -16370.3816] [GTR parameters ] . ( 5 sec) [ -16305.9862] [Alpha ][ 0.317290] . ( 6 sec) [ -16284.9903] [Branch lengths ] . ( 9 sec) [ -16272.3358] [GTR parameters ] . ( 9 sec) [ -16270.5734] [Alpha ][ 0.295551] . ( 10 sec) [ -16263.8428] [Branch lengths ] . ( 13 sec) [ -16262.0305] [GTR parameters ] . ( 13 sec) [ -16262.0207] [Alpha ][ 0.293917] . ( 13 sec) [ -16258.1724] [Branch lengths ] . ( 17 sec) [ -16257.5940] [GTR parameters ] . ( 17 sec) [ -16257.5892] [Alpha ][ 0.292768] . ( 17 sec) [ -16255.9729] [Branch lengths ] . ( 18 sec) [ -16255.7315] [GTR parameters ] . ( 19 sec) [ -16255.7303] [Alpha ][ 0.292154] . ( 19 sec) [ -16255.0070] [Branch lengths ] . ( 21 sec) [ -16254.9020] [GTR parameters ] . ( 22 sec) [ -16254.8972] [Alpha ][ 0.291006] . ( 22 sec) [ -16254.6283] [Branch lengths ] . ( 25 sec) [ -16254.5840] [GTR parameters ] . ( 26 sec) [ -16254.5833] [Alpha ][ 0.290494] . ( 26 sec) [ -16254.4642] [Branch lengths ] . ( 27 sec) [ -16254.4463] [GTR parameters ] . ( 27 sec) [ -16254.4455] [Alpha ][ 0.289959] . ( 28 sec) [ -16254.4012] [Branch lengths ] . ( 31 sec) [ -16254.3926] [GTR parameters ] . ( 31 sec) [ -16254.3926] [Alpha ][ 0.289959] . ( 32 sec) [ -16254.3720] [Branch lengths ] . ( 32 sec) [ -16254.3693] [GTR parameters ] . ( 33 sec) [ -16254.3688] [Alpha ][ 0.289530] . ( 33 sec) [ -16254.3608] [Branch lengths ] . ( 34 sec) [ -16254.3594] [GTR parameters ] . ( 34 sec) [ -16254.3594] [Alpha ][ 0.289530] . ( 34 sec) [ -16254.3557] [Branch lengths ] . ( 37 sec) [ -16254.3550] [GTR parameters ] . ( 37 sec) [ -16254.3550] [Alpha ][ 0.289530] . ( 37 sec) [ -16254.3534] [Branch lengths ] . ( 38 sec) [ -16254.3533] [GTR parameters ] . ( 38 sec) [ -16254.3533] [Alpha ][ 0.289530] . ( 39 sec) [ -16254.3526] [Branch lengths ] . ( 39 sec) [ -16254.3525] [GTR parameters ] . ( 39 sec) [ -16254.3525] [Alpha ][ 0.289241] . ( 40 sec) [ -16254.3525] [GTR parameters ] . ( 40 sec) [ -16254.3525] [Alpha ][ 0.289241] . Log likelihood of the current tree: -16254.352497. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'... . Time used 0h0m54s 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)