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

                . Sequence filename : 				 nucleic_M2862_54x1011_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_M2862_54x1011_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 587 patterns found. (out of a total of 1011 sites) 

. 443 sites without polymorphism (43.82%).

. Reading tree...

. This analysis requires at least 16Mo of memory space.

. (    1 sec) [    -17638.8109] [Branch lengths     ]
. (    1 sec) [    -17140.2888] [GTR parameters     ]
. (    2 sec) [    -16885.4780] [Alpha              ][  0.500960]
. (    3 sec) [    -16879.9503] [Branch lengths     ]
. (    6 sec) [    -16385.8149] [GTR parameters     ]
. (    6 sec) [    -16318.8661] [Alpha              ][  0.312653]
. (    7 sec) [    -16294.6537] [Branch lengths     ]
. (   10 sec) [    -16280.5742] [GTR parameters     ]
. (   10 sec) [    -16279.2006] [Alpha              ][  0.293592]
. (   10 sec) [    -16268.4738] [Branch lengths     ]
. (   14 sec) [    -16265.9367] [GTR parameters     ]
. (   14 sec) [    -16265.9345] [Alpha              ][  0.292801]
. (   14 sec) [    -16260.4650] [Branch lengths     ]
. (   17 sec) [    -16259.6643] [GTR parameters     ]
. (   17 sec) [    -16259.6622] [Alpha              ][  0.292018]
. (   18 sec) [    -16257.4772] [Branch lengths     ]
. (   20 sec) [    -16257.1795] [GTR parameters     ]
. (   20 sec) [    -16257.1772] [Alpha              ][  0.291194]
. (   21 sec) [    -16256.3149] [Branch lengths     ]
. (   22 sec) [    -16256.1892] [GTR parameters     ]
. (   22 sec) [    -16256.1856] [Alpha              ][  0.290190]
. (   23 sec) [    -16255.8649] [Branch lengths     ]
. (   25 sec) [    -16255.8160] [GTR parameters     ]
. (   25 sec) [    -16255.8150] [Alpha              ][  0.289636]
. (   25 sec) [    -16255.6817] [Branch lengths     ]
. (   26 sec) [    -16255.6618] [GTR parameters     ]
. (   27 sec) [    -16255.6612] [Alpha              ][  0.289174]
. (   27 sec) [    -16255.6108] [Branch lengths     ]
. (   29 sec) [    -16255.6020] [GTR parameters     ]
. (   30 sec) [    -16255.6020] [Alpha              ][  0.289174]
. (   30 sec) [    -16255.5790] [Branch lengths     ]
. (   31 sec) [    -16255.5762] [GTR parameters     ]
. (   32 sec) [    -16255.5758] [Alpha              ][  0.288775]
. (   32 sec) [    -16255.5670] [Branch lengths     ]
. (   33 sec) [    -16255.5655] [GTR parameters     ]
. (   33 sec) [    -16255.5655] [Alpha              ][  0.288775]
. (   34 sec) [    -16255.5616] [Branch lengths     ]
. (   36 sec) [    -16255.5609] [GTR parameters     ]
. (   36 sec) [    -16255.5609] [Alpha              ][  0.288775]
. (   36 sec) [    -16255.5593] [Branch lengths     ]
. (   38 sec) [    -16255.5591] [GTR parameters     ]
. (   38 sec) [    -16255.5591] [Alpha              ][  0.288775]
. (   38 sec) [    -16255.5584] [Branch lengths     ]
. (   39 sec) [    -16255.5582] [GTR parameters     ]
. (   40 sec) [    -16255.5582] [Alpha              ][  0.288775]
. (   41 sec) [    -16255.5582] [GTR parameters     ]
. (   41 sec) [    -16255.5582] [Alpha              ][  0.288775]
. Log likelihood of the current tree: -16255.558163.

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

. Printing the most likely tree in file 'nucleic_M2862_54x1011_2006.phy_phyml_tree.txt'...


. Time used 0h0m55s

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)