..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename : 				 nucleic_M2786_104x1051_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_M2786_104x1051_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')...

. Compressing sequences...

. 717 patterns found. (out of a total of 1051 sites) 

. 402 sites without polymorphism (38.25%).

. Reading tree...

. This analysis requires at least 39Mo of memory space.

. (    2 sec) [    -16331.3349] [Branch lengths     ]
. (   10 sec) [    -15750.5212] [GTR parameters     ]
. (   10 sec) [    -15683.8879] [Alpha              ][  0.558980]
. (   12 sec) [    -15671.2097] [Branch lengths     ]
. (   18 sec) [    -15668.6277] [GTR parameters     ]
. (   19 sec) [    -15668.3823] [Alpha              ][  0.540492]
. (   20 sec) [    -15666.3646] [Branch lengths     ]
. (   25 sec) [    -15666.3087] [GTR parameters     ]
. (   25 sec) [    -15666.3024] [Alpha              ][  0.543396]
. (   26 sec) [    -15665.7169] [Branch lengths     ]
. (   30 sec) [    -15665.7126] [GTR parameters     ]
. (   31 sec) [    -15665.7106] [Alpha              ][  0.545024]
. (   32 sec) [    -15665.4625] [Branch lengths     ]
. (   34 sec) [    -15665.4608] [GTR parameters     ]
. (   35 sec) [    -15665.4600] [Alpha              ][  0.545983]
. (   36 sec) [    -15665.3491] [Branch lengths     ]
. (   38 sec) [    -15665.3483] [GTR parameters     ]
. (   39 sec) [    -15665.3481] [Alpha              ][  0.546529]
. (   40 sec) [    -15665.2918] [Branch lengths     ]
. (   42 sec) [    -15665.2915] [GTR parameters     ]
. (   42 sec) [    -15665.2915] [Alpha              ][  0.546529]
. (   43 sec) [    -15665.2634] [Branch lengths     ]
. (   45 sec) [    -15665.2630] [GTR parameters     ]
. (   45 sec) [    -15665.2630] [Alpha              ][  0.547076]
. (   46 sec) [    -15665.2463] [Branch lengths     ]
. (   48 sec) [    -15665.2462] [GTR parameters     ]
. (   48 sec) [    -15665.2462] [Alpha              ][  0.547076]
. (   49 sec) [    -15665.2360] [Branch lengths     ]
. (   51 sec) [    -15665.2360] [GTR parameters     ]
. (   51 sec) [    -15665.2360] [Alpha              ][  0.547076]
. (   52 sec) [    -15665.2286] [Branch lengths     ]
. (   53 sec) [    -15665.2286] [GTR parameters     ]
. (   53 sec) [    -15665.2286] [Alpha              ][  0.547076]
. (   55 sec) [    -15665.2229] [Branch lengths     ]
. (   56 sec) [    -15665.2229] [GTR parameters     ]
. (   56 sec) [    -15665.2229] [Alpha              ][  0.547076]
. (   57 sec) [    -15665.2178] [Branch lengths     ]
. (   58 sec) [    -15665.2178] [GTR parameters     ]
. (   59 sec) [    -15665.2178] [Alpha              ][  0.547076]
. (   60 sec) [    -15665.2131] [Branch lengths     ]
. (   61 sec) [    -15665.2131] [GTR parameters     ]
. (   61 sec) [    -15665.2131] [Alpha              ][  0.547076]
. (   62 sec) [    -15665.2088] [Branch lengths     ]
. (   63 sec) [    -15665.2088] [GTR parameters     ]
. (   63 sec) [    -15665.2088] [Alpha              ][  0.547076]
. (   64 sec) [    -15665.2045] [Branch lengths     ]
. (   65 sec) [    -15665.2045] [GTR parameters     ]
. (   65 sec) [    -15665.2045] [Alpha              ][  0.547076]
. (   66 sec) [    -15665.2002] [Branch lengths     ]
. (   67 sec) [    -15665.2002] [GTR parameters     ]
. (   67 sec) [    -15665.2002] [Alpha              ][  0.547076]
. (   69 sec) [    -15665.1959] [Branch lengths     ]
. (   69 sec) [    -15665.1959] [GTR parameters     ]
. (   70 sec) [    -15665.1959] [Alpha              ][  0.547076]
. (   71 sec) [    -15665.1945] [Branch lengths     ]
. (   71 sec) [    -15665.1945] [GTR parameters     ]
. (   72 sec) [    -15665.1945] [Alpha              ][  0.547076]
. (   73 sec) [    -15665.1944] [Branch lengths     ]
. (   74 sec) [    -15665.1943] [GTR parameters     ]
. (   74 sec) [    -15665.1943] [Alpha              ][  0.547076]
. (   75 sec) [    -15665.1943] [GTR parameters     ]
. (   75 sec) [    -15665.1943] [Alpha              ][  0.547076]
. Log likelihood of the current tree: -15665.194341.

. Compute aLRT branch supports on the most likely tree...

. Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'...


. Time used 0h1m45s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
java.lang.NullPointerException
	at java.io.FileInputStream.<init>(FileInputStream.java:103)
	at java.io.FileReader.<init>(FileReader.java:55)
	at Recomp.<init>(Recomp.java:114)
	at Recomp.main(Recomp.java:52)