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

                . Sequence filename : 				 nucleic_M2856_61x970_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_M2856_61x970_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 686 patterns found. (out of a total of 970 sites) 

. 322 sites without polymorphism (33.20%).

. Reading tree...

. This analysis requires at least 22Mo of memory space.

. (    1 sec) [    -26373.9390] [Branch lengths     ]
. (    1 sec) [    -25696.0850] [GTR parameters     ]
. (    1 sec) [    -25466.6599] [Alpha              ][  0.500960]
. (    2 sec) [    -25447.2460] [Branch lengths     ]
. (    6 sec) [    -25150.1225] [GTR parameters     ]
. (    6 sec) [    -25138.9313] [Alpha              ][  0.426507]
. (    6 sec) [    -25130.5139] [Branch lengths     ]
. (   10 sec) [    -25128.4287] [GTR parameters     ]
. (   10 sec) [    -25128.3056] [Alpha              ][  0.419603]
. (   10 sec) [    -25125.5162] [Branch lengths     ]
. (   12 sec) [    -25125.2024] [GTR parameters     ]
. (   12 sec) [    -25125.2000] [Alpha              ][  0.420568]
. (   13 sec) [    -25123.8071] [Branch lengths     ]
. (   15 sec) [    -25123.6747] [GTR parameters     ]
. (   16 sec) [    -25123.6742] [Alpha              ][  0.421014]
. (   16 sec) [    -25123.0490] [Branch lengths     ]
. (   19 sec) [    -25122.9845] [GTR parameters     ]
. (   19 sec) [    -25122.9841] [Alpha              ][  0.421435]
. (   19 sec) [    -25122.6055] [Branch lengths     ]
. (   21 sec) [    -25122.5691] [GTR parameters     ]
. (   21 sec) [    -25122.5691] [Alpha              ][  0.421435]
. (   22 sec) [    -25122.3789] [Branch lengths     ]
. (   24 sec) [    -25122.3585] [GTR parameters     ]
. (   24 sec) [    -25122.3585] [Alpha              ][  0.421435]
. (   24 sec) [    -25122.2367] [Branch lengths     ]
. (   26 sec) [    -25122.2248] [GTR parameters     ]
. (   26 sec) [    -25122.2248] [Alpha              ][  0.421435]
. (   27 sec) [    -25122.1636] [Branch lengths     ]
. (   29 sec) [    -25122.1535] [GTR parameters     ]
. (   29 sec) [    -25122.1535] [Alpha              ][  0.421435]
. (   30 sec) [    -25122.1093] [Branch lengths     ]
. (   32 sec) [    -25122.1050] [GTR parameters     ]
. (   32 sec) [    -25122.1050] [Alpha              ][  0.421435]
. (   33 sec) [    -25122.0805] [Branch lengths     ]
. (   33 sec) [    -25122.0784] [GTR parameters     ]
. (   34 sec) [    -25122.0784] [Alpha              ][  0.421435]
. (   34 sec) [    -25122.0624] [Branch lengths     ]
. (   36 sec) [    -25122.0596] [GTR parameters     ]
. (   36 sec) [    -25122.0596] [Alpha              ][  0.421435]
. (   37 sec) [    -25122.0499] [Branch lengths     ]
. (   39 sec) [    -25122.0489] [GTR parameters     ]
. (   39 sec) [    -25122.0489] [Alpha              ][  0.421435]
. (   39 sec) [    -25122.0424] [Branch lengths     ]
. (   41 sec) [    -25122.0417] [GTR parameters     ]
. (   41 sec) [    -25122.0417] [Alpha              ][  0.421435]
. (   41 sec) [    -25122.0381] [Branch lengths     ]
. (   42 sec) [    -25122.0377] [GTR parameters     ]
. (   43 sec) [    -25122.0377] [Alpha              ][  0.421435]
. (   43 sec) [    -25122.0352] [Branch lengths     ]
. (   45 sec) [    -25122.0344] [GTR parameters     ]
. (   45 sec) [    -25122.0344] [Alpha              ][  0.421435]
. (   45 sec) [    -25122.0329] [Branch lengths     ]
. (   47 sec) [    -25122.0326] [GTR parameters     ]
. (   47 sec) [    -25122.0326] [Alpha              ][  0.421435]
. (   47 sec) [    -25122.0315] [Branch lengths     ]
. (   48 sec) [    -25122.0314] [GTR parameters     ]
. (   48 sec) [    -25122.0314] [Alpha              ][  0.421435]
. (   49 sec) [    -25122.0306] [Branch lengths     ]
. (   50 sec) [    -25122.0305] [GTR parameters     ]
. (   50 sec) [    -25122.0305] [Alpha              ][  0.421435]
. (   50 sec) [    -25122.0305] [GTR parameters     ]
. (   50 sec) [    -25122.0305] [Alpha              ][  0.421435]
. Log likelihood of the current tree: -25122.030454.

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

. Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'...


. Time used 0h1m8s

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)