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

                . Sequence filename : 				 nucleic_M2772_77x900_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_M2772_77x900_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 575 patterns found. (out of a total of 900 sites) 

. 459 sites without polymorphism (51.00%).

. Reading tree...

. This analysis requires at least 23Mo of memory space.

. (    2 sec) [     -7370.4768] [Branch lengths     ]
. (    3 sec) [     -7318.6353] [GTR parameters     ]
. (    4 sec) [     -7227.0972] [Alpha              ][  0.500960]
. (    4 sec) [     -7224.4753] [Branch lengths     ]
. (    6 sec) [     -7224.3263] [GTR parameters     ]
. (    7 sec) [     -7206.3217] [Alpha              ][  0.328010]
. (    7 sec) [     -7205.8593] [Branch lengths     ]
. (    9 sec) [     -7205.7707] [GTR parameters     ]
. (    9 sec) [     -7205.7475] [Alpha              ][  0.323350]
. (   10 sec) [     -7205.7069] [Branch lengths     ]
. (   10 sec) [     -7205.7069] [GTR parameters     ]
. (   11 sec) [     -7205.7064] [Alpha              ][  0.322628]
. (   11 sec) [     -7205.7022] [Branch lengths     ]
. (   12 sec) [     -7205.7022] [GTR parameters     ]
. (   12 sec) [     -7205.7022] [Alpha              ][  0.322306]
. (   13 sec) [     -7205.7019] [Branch lengths     ]
. (   13 sec) [     -7205.7019] [GTR parameters     ]
. (   13 sec) [     -7205.7019] [Alpha              ][  0.322306]
. (   14 sec) [     -7205.7019] [GTR parameters     ]
. (   14 sec) [     -7205.7019] [Alpha              ][  0.322306]
. Log likelihood of the current tree: -7205.701859.

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

. Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'...


. Time used 0h0m29s

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)