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

                . Sequence filename : 				 nucleic_M2708_78x1107_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 (RAxML_result.nucleic_M2708_78x1107_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 616 patterns found. (out of a total of 1107 sites) 

. 505 sites without polymorphism (45.62%).

. Reading tree...

. This analysis requires at least 25Mo of memory space.

. (    1 sec) [     -6728.5867] [Branch lengths     ]
. (    4 sec) [     -6603.8300] [GTR parameters     ]
. (    5 sec) [     -6554.8935] [Alpha              ][  0.500960]
. (    5 sec) [     -6541.7697] [Branch lengths     ]
. (    7 sec) [     -6541.0149] [GTR parameters     ]
. (    7 sec) [     -6536.5503] [Alpha              ][  0.408956]
. (    8 sec) [     -6532.5514] [Branch lengths     ]
. (   10 sec) [     -6532.3821] [GTR parameters     ]
. (   10 sec) [     -6531.7073] [Alpha              ][  0.379225]
. (   11 sec) [     -6530.5153] [Branch lengths     ]
. (   12 sec) [     -6530.4755] [GTR parameters     ]
. (   13 sec) [     -6530.2868] [Alpha              ][  0.364739]
. (   13 sec) [     -6529.8986] [Branch lengths     ]
. (   14 sec) [     -6529.8879] [GTR parameters     ]
. (   14 sec) [     -6529.8250] [Alpha              ][  0.356848]
. (   15 sec) [     -6529.6986] [Branch lengths     ]
. (   16 sec) [     -6529.6955] [GTR parameters     ]
. (   16 sec) [     -6529.6734] [Alpha              ][  0.352063]
. (   17 sec) [     -6529.6266] [Branch lengths     ]
. (   18 sec) [     -6529.6255] [GTR parameters     ]
. (   18 sec) [     -6529.6186] [Alpha              ][  0.349404]
. (   19 sec) [     -6529.6026] [Branch lengths     ]
. (   19 sec) [     -6529.6023] [GTR parameters     ]
. (   19 sec) [     -6529.6000] [Alpha              ][  0.347887]
. (   20 sec) [     -6529.5942] [Branch lengths     ]
. (   21 sec) [     -6529.5940] [GTR parameters     ]
. (   21 sec) [     -6529.5933] [Alpha              ][  0.347030]
. (   22 sec) [     -6529.5912] [Branch lengths     ]
. (   22 sec) [     -6529.5912] [GTR parameters     ]
. (   23 sec) [     -6529.5910] [Alpha              ][  0.346529]
. (   23 sec) [     -6529.5902] [Branch lengths     ]
. (   24 sec) [     -6529.5901] [GTR parameters     ]
. (   24 sec) [     -6529.5901] [Alpha              ][  0.346182]
. (   24 sec) [     -6529.5901] [GTR parameters     ]
. (   25 sec) [     -6529.5901] [Alpha              ][  0.346182]
. Log likelihood of the current tree: -6529.590083.

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

. Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'...


. Time used 0h0m42s

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)