.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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 (nucleic_M2901_56x1802_2006.phy_FAST_TREE)" . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . Reading tree... . This analysis requires at least 19Mo of memory space. . ( 1 sec) [ -8170.2829] [Branch lengths ] . ( 4 sec) [ -7996.7961] [GTR parameters ] . ( 4 sec) [ -7915.6834] [Alpha ][ 0.500960] . ( 4 sec) [ -7913.3968] [Branch lengths ] . ( 6 sec) [ -7913.3389] [GTR parameters ] . ( 6 sec) [ -7865.1897] [Alpha ][ 0.250961] . ( 7 sec) [ -7864.5929] [Branch lengths ] . ( 9 sec) [ -7864.5030] [GTR parameters ] . ( 9 sec) [ -7862.1298] [Alpha ][ 0.210952] . ( 9 sec) [ -7862.0701] [Branch lengths ] . ( 10 sec) [ -7862.0631] [GTR parameters ] . ( 10 sec) [ -7862.0624] [Alpha ][ 0.210310] . ( 11 sec) [ -7862.0574] [Branch lengths ] . ( 12 sec) [ -7862.0563] [GTR parameters ] . ( 12 sec) [ -7862.0563] [Alpha ][ 0.210100] . ( 12 sec) [ -7862.0544] [Branch lengths ] . ( 13 sec) [ -7862.0541] [GTR parameters ] . ( 13 sec) [ -7862.0541] [Alpha ][ 0.210100] . ( 14 sec) [ -7862.0527] [Branch lengths ] . ( 14 sec) [ -7862.0527] [GTR parameters ] . ( 14 sec) [ -7862.0527] [Alpha ][ 0.210100] . ( 15 sec) [ -7862.0514] [Branch lengths ] . ( 15 sec) [ -7862.0514] [GTR parameters ] . ( 15 sec) [ -7862.0514] [Alpha ][ 0.210100] . ( 16 sec) [ -7862.0500] [Branch lengths ] . ( 16 sec) [ -7862.0500] [GTR parameters ] . ( 16 sec) [ -7862.0500] [Alpha ][ 0.210100] . ( 17 sec) [ -7862.0487] [Branch lengths ] . ( 17 sec) [ -7862.0487] [GTR parameters ] . ( 17 sec) [ -7862.0487] [Alpha ][ 0.210100] . ( 18 sec) [ -7862.0473] [Branch lengths ] . ( 18 sec) [ -7862.0473] [GTR parameters ] . ( 18 sec) [ -7862.0473] [Alpha ][ 0.210100] . ( 19 sec) [ -7862.0460] [Branch lengths ] . ( 19 sec) [ -7862.0460] [GTR parameters ] . ( 19 sec) [ -7862.0460] [Alpha ][ 0.210100] . ( 20 sec) [ -7862.0447] [Branch lengths ] . ( 20 sec) [ -7862.0447] [GTR parameters ] . ( 20 sec) [ -7862.0447] [Alpha ][ 0.210100] . ( 21 sec) [ -7862.0433] [Branch lengths ] . ( 21 sec) [ -7862.0433] [GTR parameters ] . ( 21 sec) [ -7862.0433] [Alpha ][ 0.210100] . ( 22 sec) [ -7862.0420] [Branch lengths ] . ( 22 sec) [ -7862.0420] [GTR parameters ] . ( 22 sec) [ -7862.0420] [Alpha ][ 0.210100] . ( 23 sec) [ -7862.0407] [Branch lengths ] . ( 23 sec) [ -7862.0407] [GTR parameters ] . ( 24 sec) [ -7862.0407] [Alpha ][ 0.210100] . ( 24 sec) [ -7862.0393] [Branch lengths ] . ( 24 sec) [ -7862.0393] [GTR parameters ] . ( 24 sec) [ -7862.0393] [Alpha ][ 0.210100] . ( 25 sec) [ -7862.0380] [Branch lengths ] . ( 25 sec) [ -7862.0380] [GTR parameters ] . ( 25 sec) [ -7862.0380] [Alpha ][ 0.210100] . ( 26 sec) [ -7862.0366] [Branch lengths ] . ( 26 sec) [ -7862.0366] [GTR parameters ] . ( 26 sec) [ -7862.0366] [Alpha ][ 0.210100] . ( 27 sec) [ -7862.0353] [Branch lengths ] . ( 27 sec) [ -7862.0353] [GTR parameters ] . ( 28 sec) [ -7862.0353] [Alpha ][ 0.210100] . ( 28 sec) [ -7862.0339] [Branch lengths ] . ( 28 sec) [ -7862.0339] [GTR parameters ] . ( 29 sec) [ -7862.0339] [Alpha ][ 0.210100] . ( 29 sec) [ -7862.0326] [Branch lengths ] . ( 29 sec) [ -7862.0326] [GTR parameters ] . ( 30 sec) [ -7862.0326] [Alpha ][ 0.210100] . ( 30 sec) [ -7862.0313] [Branch lengths ] . ( 30 sec) [ -7862.0313] [GTR parameters ] . ( 31 sec) [ -7862.0313] [Alpha ][ 0.210100] . ( 31 sec) [ -7862.0299] [Branch lengths ] . ( 31 sec) [ -7862.0299] [GTR parameters ] . ( 31 sec) [ -7862.0299] [Alpha ][ 0.210100] . ( 32 sec) [ -7862.0286] [Branch lengths ] . ( 32 sec) [ -7862.0286] [GTR parameters ] . ( 32 sec) [ -7862.0286] [Alpha ][ 0.210100] . ( 33 sec) [ -7862.0273] [Branch lengths ] . ( 33 sec) [ -7862.0273] [GTR parameters ] . ( 34 sec) [ -7862.0273] [Alpha ][ 0.210100] . ( 34 sec) [ -7862.0260] [Branch lengths ] . ( 34 sec) [ -7862.0260] [GTR parameters ] . ( 34 sec) [ -7862.0260] [Alpha ][ 0.210100] . ( 35 sec) [ -7862.0247] [Branch lengths ] . ( 35 sec) [ -7862.0247] [GTR parameters ] . ( 35 sec) [ -7862.0247] [Alpha ][ 0.210100] . ( 36 sec) [ -7862.0234] [Branch lengths ] . ( 36 sec) [ -7862.0234] [GTR parameters ] . ( 36 sec) [ -7862.0234] [Alpha ][ 0.210100] . ( 37 sec) [ -7862.0221] [Branch lengths ] . ( 37 sec) [ -7862.0221] [GTR parameters ] . ( 37 sec) [ -7862.0221] [Alpha ][ 0.210100] . ( 38 sec) [ -7862.0208] [Branch lengths ] . ( 38 sec) [ -7862.0208] [GTR parameters ] . ( 38 sec) [ -7862.0208] [Alpha ][ 0.210100] . ( 39 sec) [ -7862.0195] [Branch lengths ] . ( 39 sec) [ -7862.0195] [GTR parameters ] . ( 39 sec) [ -7862.0195] [Alpha ][ 0.210100] . ( 40 sec) [ -7862.0182] [Branch lengths ] . ( 40 sec) [ -7862.0182] [GTR parameters ] . ( 40 sec) [ -7862.0182] [Alpha ][ 0.210100] . ( 41 sec) [ -7862.0169] [Branch lengths ] . ( 41 sec) [ -7862.0169] [GTR parameters ] . ( 41 sec) [ -7862.0169] [Alpha ][ 0.210100] . ( 42 sec) [ -7862.0156] [Branch lengths ] . ( 42 sec) [ -7862.0156] [GTR parameters ] . ( 42 sec) [ -7862.0156] [Alpha ][ 0.210100] . ( 43 sec) [ -7862.0143] [Branch lengths ] . ( 43 sec) [ -7862.0143] [GTR parameters ] . ( 43 sec) [ -7862.0143] [Alpha ][ 0.210100] . ( 44 sec) [ -7862.0130] [Branch lengths ] . ( 44 sec) [ -7862.0130] [GTR parameters ] . ( 44 sec) [ -7862.0130] [Alpha ][ 0.210100] . ( 45 sec) [ -7862.0117] [Branch lengths ] . ( 45 sec) [ -7862.0117] [GTR parameters ] . ( 45 sec) [ -7862.0117] [Alpha ][ 0.210100] . ( 45 sec) [ -7862.0104] [Branch lengths ] . ( 46 sec) [ -7862.0104] [GTR parameters ] . ( 46 sec) [ -7862.0104] [Alpha ][ 0.210100] . ( 46 sec) [ -7862.0091] [Branch lengths ] . ( 47 sec) [ -7862.0091] [GTR parameters ] . ( 47 sec) [ -7862.0091] [Alpha ][ 0.210100] . ( 47 sec) [ -7862.0078] [Branch lengths ] . ( 48 sec) [ -7862.0078] [GTR parameters ] . ( 48 sec) [ -7862.0078] [Alpha ][ 0.210100] . ( 48 sec) [ -7862.0065] [Branch lengths ] . ( 49 sec) [ -7862.0065] [GTR parameters ] . ( 49 sec) [ -7862.0065] [Alpha ][ 0.210100] . ( 49 sec) [ -7862.0052] [Branch lengths ] . ( 50 sec) [ -7862.0052] [GTR parameters ] . ( 50 sec) [ -7862.0052] [Alpha ][ 0.210100] . ( 50 sec) [ -7862.0039] [Branch lengths ] . ( 51 sec) [ -7862.0039] [GTR parameters ] . ( 51 sec) [ -7862.0039] [Alpha ][ 0.210100] . ( 51 sec) [ -7862.0026] [Branch lengths ] . ( 52 sec) [ -7862.0026] [GTR parameters ] . ( 52 sec) [ -7862.0026] [Alpha ][ 0.210100] . ( 52 sec) [ -7862.0013] [Branch lengths ] . ( 53 sec) [ -7862.0013] [GTR parameters ] . ( 53 sec) [ -7862.0013] [Alpha ][ 0.210100] . ( 53 sec) [ -7862.0006] [Branch lengths ] . ( 53 sec) [ -7862.0006] [GTR parameters ] . ( 54 sec) [ -7862.0006] [Alpha ][ 0.210100] . ( 54 sec) [ -7862.0006] [GTR parameters ] . ( 54 sec) [ -7862.0006] [Alpha ][ 0.210100] . Log likelihood of the current tree: -7862.000626. . Compute aLRT branch supports on the most likely tree... . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Time used 0h1m10s 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)