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

                . Sequence filename : 				 nucleic_M2716_79x1252_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_M2716_79x1252_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 280 patterns found. (out of a total of 1252 sites) 

. 984 sites without polymorphism (78.59%).

. Reading tree...

. This analysis requires at least 12Mo of memory space.

. (    1 sec) [     -3427.5090] [Branch lengths     ]
. (    3 sec) [     -3386.2830] [GTR parameters     ]
. (    3 sec) [     -3372.0255] [Alpha              ][  0.500960]
. (    3 sec) [     -3370.7872] [Branch lengths     ]
. (    4 sec) [     -3370.6894] [GTR parameters     ]
. (    4 sec) [     -3362.9228] [Alpha              ][  0.250961]
. (    4 sec) [     -3361.7939] [Branch lengths     ]
. (    5 sec) [     -3361.6422] [GTR parameters     ]
. (    5 sec) [     -3361.4058] [Alpha              ][  0.223818]
. (    6 sec) [     -3361.2798] [Branch lengths     ]
. (    6 sec) [     -3361.2676] [GTR parameters     ]
. (    6 sec) [     -3361.2609] [Alpha              ][  0.219549]
. (    7 sec) [     -3361.2411] [Branch lengths     ]
. (    7 sec) [     -3361.2406] [GTR parameters     ]
. (    7 sec) [     -3361.2404] [Alpha              ][  0.218944]
. (    7 sec) [     -3361.2290] [Branch lengths     ]
. (    8 sec) [     -3361.2290] [GTR parameters     ]
. (    8 sec) [     -3361.2290] [Alpha              ][  0.218725]
. (    8 sec) [     -3361.2184] [Branch lengths     ]
. (    8 sec) [     -3361.2184] [GTR parameters     ]
. (    8 sec) [     -3361.2184] [Alpha              ][  0.218725]
. (    9 sec) [     -3361.2078] [Branch lengths     ]
. (    9 sec) [     -3361.2078] [GTR parameters     ]
. (    9 sec) [     -3361.2078] [Alpha              ][  0.218725]
. (    9 sec) [     -3361.1971] [Branch lengths     ]
. (    9 sec) [     -3361.1971] [GTR parameters     ]
. (    9 sec) [     -3361.1971] [Alpha              ][  0.218725]
. (   10 sec) [     -3361.1863] [Branch lengths     ]
. (   10 sec) [     -3361.1863] [GTR parameters     ]
. (   10 sec) [     -3361.1863] [Alpha              ][  0.218725]
. (   10 sec) [     -3361.1753] [Branch lengths     ]
. (   10 sec) [     -3361.1753] [GTR parameters     ]
. (   11 sec) [     -3361.1753] [Alpha              ][  0.218725]
. (   11 sec) [     -3361.1642] [Branch lengths     ]
. (   11 sec) [     -3361.1642] [GTR parameters     ]
. (   11 sec) [     -3361.1642] [Alpha              ][  0.218725]
. (   11 sec) [     -3361.1540] [Branch lengths     ]
. (   12 sec) [     -3361.1540] [GTR parameters     ]
. (   12 sec) [     -3361.1540] [Alpha              ][  0.218725]
. (   12 sec) [     -3361.1507] [Branch lengths     ]
. (   12 sec) [     -3361.1507] [GTR parameters     ]
. (   12 sec) [     -3361.1507] [Alpha              ][  0.218944]
. (   12 sec) [     -3361.1492] [Branch lengths     ]
. (   13 sec) [     -3361.1492] [GTR parameters     ]
. (   13 sec) [     -3361.1492] [Alpha              ][  0.218944]
. (   13 sec) [     -3361.1486] [Branch lengths     ]
. (   13 sec) [     -3361.1486] [GTR parameters     ]
. (   13 sec) [     -3361.1486] [Alpha              ][  0.219163]
. (   13 sec) [     -3361.1486] [GTR parameters     ]
. (   14 sec) [     -3361.1486] [Alpha              ][  0.219163]
. Log likelihood of the current tree: -3361.148630.

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

. Printing the most likely tree in file 'nucleic_M2716_79x1252_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)