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

                . Sequence filename : 				 nucleic_M2921_54x966_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_M2921_54x966_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...

. 397 patterns found. (out of a total of 966 sites) 

. 643 sites without polymorphism (66.56%).

. Reading tree...

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

. (    0 sec) [     -7021.4767] [Branch lengths     ]
. (    3 sec) [     -6630.5426] [GTR parameters     ]
. (    3 sec) [     -6514.6673] [Alpha              ][  0.500960]
. (    4 sec) [     -6508.0344] [Branch lengths     ]
. (    5 sec) [     -6507.7238] [GTR parameters     ]
. (    5 sec) [     -6447.9166] [Alpha              ][  0.250961]
. (    5 sec) [     -6447.1588] [Branch lengths     ]
. (    7 sec) [     -6446.3687] [GTR parameters     ]
. (    7 sec) [     -6444.6688] [Alpha              ][  0.221450]
. (    7 sec) [     -6444.6073] [Branch lengths     ]
. (    8 sec) [     -6444.5721] [GTR parameters     ]
. (    8 sec) [     -6444.5688] [Alpha              ][  0.220176]
. (    8 sec) [     -6444.5595] [Branch lengths     ]
. (    9 sec) [     -6444.5594] [GTR parameters     ]
. (    9 sec) [     -6444.5593] [Alpha              ][  0.219945]
. (    9 sec) [     -6444.5582] [Branch lengths     ]
. (    9 sec) [     -6444.5582] [GTR parameters     ]
. (    9 sec) [     -6444.5582] [Alpha              ][  0.219945]
. (   10 sec) [     -6444.5580] [Branch lengths     ]
. (   10 sec) [     -6444.5580] [GTR parameters     ]
. (   10 sec) [     -6444.5580] [Alpha              ][  0.219945]
. (   10 sec) [     -6444.5580] [GTR parameters     ]
. (   10 sec) [     -6444.5580] [Alpha              ][  0.219945]
. Log likelihood of the current tree: -6444.558001.

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

. Printing the most likely tree in file 'nucleic_M2921_54x966_2006.phy_phyml_tree.txt'...


. Time used 0h0m20s

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)