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

                . Sequence filename : 				 nucleic_M2916_143x897_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_M2916_143x897_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 303 patterns found. (out of a total of 897 sites) 

. 620 sites without polymorphism (69.12%).

. Reading tree...

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

. (    1 sec) [     -3604.5544] [Branch lengths     ]
. (    3 sec) [     -3519.4051] [GTR parameters     ]
. (    3 sec) [     -3498.5125] [Alpha              ][  0.500960]
. (    4 sec) [     -3496.9351] [Branch lengths     ]
. (    5 sec) [     -3496.6684] [GTR parameters     ]
. (    6 sec) [     -3488.1391] [Alpha              ][  0.270197]
. (    6 sec) [     -3487.6860] [Branch lengths     ]
. (    8 sec) [     -3487.4478] [GTR parameters     ]
. (    8 sec) [     -3487.4451] [Alpha              ][  0.267395]
. (    8 sec) [     -3486.8112] [Branch lengths     ]
. (   10 sec) [     -3486.7940] [GTR parameters     ]
. (   10 sec) [     -3486.7940] [Alpha              ][  0.267395]
. (   10 sec) [     -3486.4764] [Branch lengths     ]
. (   11 sec) [     -3486.4734] [GTR parameters     ]
. (   12 sec) [     -3486.4734] [Alpha              ][  0.267128]
. (   12 sec) [     -3486.4625] [Branch lengths     ]
. (   13 sec) [     -3486.4624] [GTR parameters     ]
. (   13 sec) [     -3486.4624] [Alpha              ][  0.267128]
. (   14 sec) [     -3486.4618] [Branch lengths     ]
. (   14 sec) [     -3486.4618] [GTR parameters     ]
. (   14 sec) [     -3486.4618] [Alpha              ][  0.267128]
. (   14 sec) [     -3486.4618] [GTR parameters     ]
. (   15 sec) [     -3486.4618] [Alpha              ][  0.267128]
. Log likelihood of the current tree: -3486.461766.

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

. Printing the most likely tree in file 'nucleic_M2916_143x897_2006.phy_phyml_tree.txt'...


. Time used 0h0m28s

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)