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

                . Sequence filename : 				 nucleic_M2661_66x1027_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_M2661_66x1027_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 596 patterns found. (out of a total of 1027 sites) 

. 417 sites without polymorphism (40.60%).

. Reading tree...

. This analysis requires at least 21Mo of memory space.

. (    1 sec) [     -9379.4426] [Branch lengths     ]
. (    5 sec) [     -9184.5012] [GTR parameters     ]
. (    5 sec) [     -9148.9025] [Alpha              ][  0.564553]
. (    6 sec) [     -9135.8538] [Branch lengths     ]
. (    8 sec) [     -9134.8937] [GTR parameters     ]
. (    8 sec) [     -9132.9540] [Alpha              ][  0.499630]
. (    9 sec) [     -9131.8902] [Branch lengths     ]
. (   11 sec) [     -9131.8324] [GTR parameters     ]
. (   11 sec) [     -9131.7760] [Alpha              ][  0.489739]
. (   12 sec) [     -9131.6155] [Branch lengths     ]
. (   12 sec) [     -9131.6122] [GTR parameters     ]
. (   12 sec) [     -9131.6085] [Alpha              ][  0.487114]
. (   13 sec) [     -9131.5671] [Branch lengths     ]
. (   13 sec) [     -9131.5667] [GTR parameters     ]
. (   14 sec) [     -9131.5667] [Alpha              ][  0.486627]
. (   14 sec) [     -9131.5570] [Branch lengths     ]
. (   15 sec) [     -9131.5570] [GTR parameters     ]
. (   15 sec) [     -9131.5570] [Alpha              ][  0.486627]
. (   15 sec) [     -9131.5540] [Branch lengths     ]
. (   16 sec) [     -9131.5540] [GTR parameters     ]
. (   16 sec) [     -9131.5540] [Alpha              ][  0.486627]
. (   16 sec) [     -9131.5531] [Branch lengths     ]
. (   17 sec) [     -9131.5531] [GTR parameters     ]
. (   17 sec) [     -9131.5531] [Alpha              ][  0.486627]
. (   17 sec) [     -9131.5531] [GTR parameters     ]
. (   17 sec) [     -9131.5531] [Alpha              ][  0.486627]
. Log likelihood of the current tree: -9131.553098.

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

. Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'...


. Time used 0h0m33s

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)