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

                . Sequence filename : 				 nucleic_M2792_166x812_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_M2792_166x812_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 616 patterns found. (out of a total of 812 sites) 

. 322 sites without polymorphism (39.66%).

. Reading tree...

. This analysis requires at least 54Mo of memory space.

. (    3 sec) [    -10988.6447] [Branch lengths     ]
. (   13 sec) [    -10630.1289] [GTR parameters     ]
. (   14 sec) [    -10576.4177] [Alpha              ][  0.515861]
. (   16 sec) [    -10570.2598] [Branch lengths     ]
. (   23 sec) [    -10569.8517] [GTR parameters     ]
. (   23 sec) [    -10569.7157] [Alpha              ][  0.500067]
. (   25 sec) [    -10569.0347] [Branch lengths     ]
. (   26 sec) [    -10569.0307] [GTR parameters     ]
. (   27 sec) [    -10569.0299] [Alpha              ][  0.501233]
. (   28 sec) [    -10568.9536] [Branch lengths     ]
. (   29 sec) [    -10568.9535] [GTR parameters     ]
. (   30 sec) [    -10568.9534] [Alpha              ][  0.501765]
. (   31 sec) [    -10568.9366] [Branch lengths     ]
. (   34 sec) [    -10568.9360] [GTR parameters     ]
. (   34 sec) [    -10568.9360] [Alpha              ][  0.501765]
. (   36 sec) [    -10568.9303] [Branch lengths     ]
. (   37 sec) [    -10568.9303] [GTR parameters     ]
. (   37 sec) [    -10568.9303] [Alpha              ][  0.502267]
. (   38 sec) [    -10568.9280] [Branch lengths     ]
. (   42 sec) [    -10568.9279] [GTR parameters     ]
. (   42 sec) [    -10568.9279] [Alpha              ][  0.502267]
. (   44 sec) [    -10568.9267] [Branch lengths     ]
. (   46 sec) [    -10568.9267] [GTR parameters     ]
. (   46 sec) [    -10568.9267] [Alpha              ][  0.502267]
. (   48 sec) [    -10568.9259] [Branch lengths     ]
. (   49 sec) [    -10568.9259] [GTR parameters     ]
. (   49 sec) [    -10568.9259] [Alpha              ][  0.502267]
. (   50 sec) [    -10568.9259] [GTR parameters     ]
. (   50 sec) [    -10568.9259] [Alpha              ][  0.502267]
. Log likelihood of the current tree: -10568.925851.

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

. Printing the most likely tree in file 'nucleic_M2792_166x812_2006.phy_phyml_tree.txt'...


. Time used 0h1m26s

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)