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

                . Sequence filename : 				 nucleic_M2702_54x886_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_M2702_54x886_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 382 patterns found. (out of a total of 886 sites) 

. 582 sites without polymorphism (65.69%).

. Reading tree...

. This analysis requires at least 11Mo of memory space.

. (    1 sec) [     -5791.1253] [Branch lengths     ]
. (    2 sec) [     -5525.4147] [GTR parameters     ]
. (    3 sec) [     -5440.7272] [Alpha              ][  0.500960]
. (    3 sec) [     -5434.6627] [Branch lengths     ]
. (    5 sec) [     -5434.1953] [GTR parameters     ]
. (    5 sec) [     -5393.6691] [Alpha              ][  0.250961]
. (    5 sec) [     -5391.6753] [Branch lengths     ]
. (    6 sec) [     -5390.9330] [GTR parameters     ]
. (    6 sec) [     -5390.7857] [Alpha              ][  0.241460]
. (    7 sec) [     -5390.3223] [Branch lengths     ]
. (    7 sec) [     -5390.3019] [GTR parameters     ]
. (    7 sec) [     -5390.3018] [Alpha              ][  0.241701]
. (    7 sec) [     -5390.1994] [Branch lengths     ]
. (    8 sec) [     -5390.1971] [GTR parameters     ]
. (    8 sec) [     -5390.1971] [Alpha              ][  0.241701]
. (    9 sec) [     -5390.1775] [Branch lengths     ]
. (    9 sec) [     -5390.1770] [GTR parameters     ]
. (    9 sec) [     -5390.1769] [Alpha              ][  0.241943]
. (    9 sec) [     -5390.1731] [Branch lengths     ]
. (   10 sec) [     -5390.1730] [GTR parameters     ]
. (   10 sec) [     -5390.1730] [Alpha              ][  0.241943]
. (   10 sec) [     -5390.1723] [Branch lengths     ]
. (   10 sec) [     -5390.1723] [GTR parameters     ]
. (   11 sec) [     -5390.1723] [Alpha              ][  0.241943]
. (   11 sec) [     -5390.1723] [GTR parameters     ]
. (   11 sec) [     -5390.1723] [Alpha              ][  0.241943]
. Log likelihood of the current tree: -5390.172282.

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

. Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'...


. Time used 0h0m19s

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)