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

                . Sequence filename : 				 nucleic_M2975_93x982_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_M2975_93x982_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 725 patterns found. (out of a total of 982 sites) 

. 454 sites without polymorphism (46.23%).

. Reading tree...

. This analysis requires at least 36Mo of memory space.

. (    2 sec) [    -13008.0208] [Branch lengths     ]
. (    8 sec) [    -12453.6129] [GTR parameters     ]
. (    9 sec) [    -12326.9210] [Alpha              ][  0.500960]
. (   10 sec) [    -12319.4408] [Branch lengths     ]
. (   15 sec) [    -12318.9321] [GTR parameters     ]
. (   15 sec) [    -12309.7112] [Alpha              ][  0.399919]
. (   17 sec) [    -12308.8126] [Branch lengths     ]
. (   21 sec) [    -12308.7518] [GTR parameters     ]
. (   21 sec) [    -12308.7455] [Alpha              ][  0.397512]
. (   22 sec) [    -12308.6649] [Branch lengths     ]
. (   23 sec) [    -12308.6648] [GTR parameters     ]
. (   23 sec) [    -12308.6645] [Alpha              ][  0.396990]
. (   24 sec) [    -12308.6568] [Branch lengths     ]
. (   25 sec) [    -12308.6568] [GTR parameters     ]
. (   25 sec) [    -12308.6568] [Alpha              ][  0.396593]
. (   27 sec) [    -12308.6558] [Branch lengths     ]
. (   28 sec) [    -12308.6558] [GTR parameters     ]
. (   28 sec) [    -12308.6558] [Alpha              ][  0.396593]
. (   29 sec) [    -12308.6556] [Branch lengths     ]
. (   30 sec) [    -12308.6556] [GTR parameters     ]
. (   30 sec) [    -12308.6556] [Alpha              ][  0.396593]
. (   31 sec) [    -12308.6556] [GTR parameters     ]
. (   32 sec) [    -12308.6556] [Alpha              ][  0.396593]
. Log likelihood of the current tree: -12308.655558.

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

. Printing the most likely tree in file 'nucleic_M2975_93x982_2006.phy_phyml_tree.txt'...


. Time used 0h1m1s

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)