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

                . Sequence filename : 				 nucleic_M2587_117x1910_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_M2587_117x1910_2006.phy_FAST_TREE)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 1192 patterns found. (out of a total of 1910 sites) 

. 932 sites without polymorphism (48.80%).

. Reading tree...

. This analysis requires at least 74Mo of memory space.

. (    3 sec) [    -16555.4326] [Branch lengths     ]
. (   14 sec) [    -16217.4166] [GTR parameters     ]
. (   14 sec) [    -16152.8868] [Alpha              ][  0.526116]
. (   17 sec) [    -16113.1130] [Branch lengths     ]
. (   22 sec) [    -16113.0068] [GTR parameters     ]
. (   22 sec) [    -16110.1904] [Alpha              ][  0.467804]
. (   24 sec) [    -16085.6950] [Branch lengths     ]
. (   29 sec) [    -16085.6581] [GTR parameters     ]
. (   29 sec) [    -16083.4663] [Alpha              ][  0.423937]
. (   32 sec) [    -16070.5433] [Branch lengths     ]
. (   36 sec) [    -16070.5200] [GTR parameters     ]
. (   37 sec) [    -16069.3255] [Alpha              ][  0.395228]
. (   39 sec) [    -16062.1547] [Branch lengths     ]
. (   42 sec) [    -16062.1432] [GTR parameters     ]
. (   42 sec) [    -16061.5330] [Alpha              ][  0.376349]
. (   45 sec) [    -16057.7308] [Branch lengths     ]
. (   47 sec) [    -16057.7243] [GTR parameters     ]
. (   48 sec) [    -16057.4260] [Alpha              ][  0.363985]
. (   50 sec) [    -16055.3841] [Branch lengths     ]
. (   53 sec) [    -16055.3798] [GTR parameters     ]
. (   53 sec) [    -16055.2334] [Alpha              ][  0.355759]
. (   55 sec) [    -16054.2440] [Branch lengths     ]
. (   58 sec) [    -16054.2415] [GTR parameters     ]
. (   59 sec) [    -16054.1704] [Alpha              ][  0.349934]
. (   61 sec) [    -16053.6424] [Branch lengths     ]
. (   63 sec) [    -16053.6410] [GTR parameters     ]
. (   64 sec) [    -16053.6098] [Alpha              ][  0.346144]
. (   66 sec) [    -16053.3437] [Branch lengths     ]
. (   69 sec) [    -16053.3430] [GTR parameters     ]
. (   69 sec) [    -16053.3275] [Alpha              ][  0.343507]
. (   72 sec) [    -16053.1871] [Branch lengths     ]
. (   73 sec) [    -16053.1868] [GTR parameters     ]
. (   73 sec) [    -16053.1793] [Alpha              ][  0.341683]
. (   76 sec) [    -16053.1076] [Branch lengths     ]
. (   78 sec) [    -16053.1073] [GTR parameters     ]
. (   79 sec) [    -16053.1034] [Alpha              ][  0.340383]
. (   81 sec) [    -16053.0645] [Branch lengths     ]
. (   82 sec) [    -16053.0645] [GTR parameters     ]
. (   83 sec) [    -16053.0625] [Alpha              ][  0.339454]
. (   85 sec) [    -16053.0420] [Branch lengths     ]
. (   86 sec) [    -16053.0420] [GTR parameters     ]
. (   87 sec) [    -16053.0410] [Alpha              ][  0.338780]
. (   89 sec) [    -16053.0296] [Branch lengths     ]
. (   90 sec) [    -16053.0296] [GTR parameters     ]
. (   91 sec) [    -16053.0290] [Alpha              ][  0.338291]
. (   93 sec) [    -16053.0229] [Branch lengths     ]
. (   94 sec) [    -16053.0229] [GTR parameters     ]
. (   95 sec) [    -16053.0227] [Alpha              ][  0.337932]
. (   97 sec) [    -16053.0192] [Branch lengths     ]
. (   98 sec) [    -16053.0192] [GTR parameters     ]
. (   99 sec) [    -16053.0191] [Alpha              ][  0.337594]
. (  101 sec) [    -16053.0172] [Branch lengths     ]
. (  102 sec) [    -16053.0172] [GTR parameters     ]
. (  103 sec) [    -16053.0172] [Alpha              ][  0.337594]
. (  105 sec) [    -16053.0162] [Branch lengths     ]
. (  106 sec) [    -16053.0162] [GTR parameters     ]
. (  107 sec) [    -16053.0161] [Alpha              ][  0.337256]
. (  109 sec) [    -16053.0155] [Branch lengths     ]
. (  110 sec) [    -16053.0155] [GTR parameters     ]
. (  111 sec) [    -16053.0155] [Alpha              ][  0.337256]
. (  112 sec) [    -16053.0155] [GTR parameters     ]
. (  112 sec) [    -16053.0155] [Alpha              ][  0.337256]
. Log likelihood of the current tree: -16053.015455.

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

. Printing the most likely tree in file 'nucleic_M2587_117x1910_2006.phy_phyml_tree.txt'...


. Time used 0h2m52s

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)