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

                . Sequence filename : 				 nucleic_M2944_80x1495_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_M2944_80x1495_2006.phy_FAST_TREE)"
                . 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...

. 494 patterns found. (out of a total of 1495 sites) 

. 1077 sites without polymorphism (72.04%).

. Reading tree...

. This analysis requires at least 21Mo of memory space.

. (    0 sec) [     -9453.0573] [Branch lengths     ]
. (    3 sec) [     -9172.0943] [GTR parameters     ]
. (    4 sec) [     -9068.1813] [Alpha              ][  0.500960]
. (    4 sec) [     -9059.7250] [Branch lengths     ]
. (    6 sec) [     -9059.4877] [GTR parameters     ]
. (    6 sec) [     -9032.5693] [Alpha              ][  0.312406]
. (    7 sec) [     -9029.6706] [Branch lengths     ]
. (    9 sec) [     -9029.4126] [GTR parameters     ]
. (    9 sec) [     -9029.4106] [Alpha              ][  0.311127]
. (   10 sec) [     -9028.4769] [Branch lengths     ]
. (   11 sec) [     -9028.4729] [GTR parameters     ]
. (   11 sec) [     -9028.4726] [Alpha              ][  0.310620]
. (   12 sec) [     -9028.1513] [Branch lengths     ]
. (   13 sec) [     -9028.1502] [GTR parameters     ]
. (   13 sec) [     -9028.1500] [Alpha              ][  0.310176]
. (   14 sec) [     -9028.0496] [Branch lengths     ]
. (   15 sec) [     -9028.0483] [GTR parameters     ]
. (   15 sec) [     -9028.0482] [Alpha              ][  0.309792]
. (   16 sec) [     -9028.0121] [Branch lengths     ]
. (   17 sec) [     -9028.0119] [GTR parameters     ]
. (   17 sec) [     -9028.0119] [Alpha              ][  0.309792]
. (   18 sec) [     -9028.0000] [Branch lengths     ]
. (   18 sec) [     -9028.0000] [GTR parameters     ]
. (   18 sec) [     -9027.9999] [Alpha              ][  0.309465]
. (   19 sec) [     -9027.9955] [Branch lengths     ]
. (   19 sec) [     -9027.9955] [GTR parameters     ]
. (   20 sec) [     -9027.9955] [Alpha              ][  0.309465]
. (   20 sec) [     -9027.9941] [Branch lengths     ]
. (   22 sec) [     -9027.9940] [GTR parameters     ]
. (   22 sec) [     -9027.9940] [Alpha              ][  0.309465]
. (   22 sec) [     -9027.9934] [Branch lengths     ]
. (   23 sec) [     -9027.9934] [GTR parameters     ]
. (   23 sec) [     -9027.9934] [Alpha              ][  0.309465]
. (   23 sec) [     -9027.9934] [GTR parameters     ]
. (   23 sec) [     -9027.9934] [Alpha              ][  0.309465]
. Log likelihood of the current tree: -9027.993405.

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

. Printing the most likely tree in file 'nucleic_M2944_80x1495_2006.phy_phyml_tree.txt'...


. Time used 0h0m40s

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)