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

                . Sequence filename : 				 nucleic_M2946_110x1003_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 (RAxML_result.nucleic_M2946_110x1003_2006.phy_RAXML_CAT)"
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. Compressing sequences...

. 614 patterns found. (out of a total of 1003 sites) 

. 462 sites without polymorphism (46.06%).

. Reading tree...

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

. (    2 sec) [    -18406.5057] [Branch lengths     ]
. (    8 sec) [    -17333.5408] [GTR parameters     ]
. (    9 sec) [    -17060.7424] [Alpha              ][  0.500960]
. (   10 sec) [    -17039.8650] [Branch lengths     ]
. (   12 sec) [    -17037.8224] [GTR parameters     ]
. (   13 sec) [    -17005.8040] [Alpha              ][  0.365940]
. (   14 sec) [    -17003.5099] [Branch lengths     ]
. (   15 sec) [    -17003.0162] [GTR parameters     ]
. (   16 sec) [    -17003.0039] [Alpha              ][  0.363649]
. (   17 sec) [    -17002.2065] [Branch lengths     ]
. (   20 sec) [    -17002.1874] [GTR parameters     ]
. (   20 sec) [    -17002.1871] [Alpha              ][  0.364013]
. (   21 sec) [    -17001.8685] [Branch lengths     ]
. (   23 sec) [    -17001.8631] [GTR parameters     ]
. (   23 sec) [    -17001.8631] [Alpha              ][  0.364013]
. (   25 sec) [    -17001.7467] [Branch lengths     ]
. (   26 sec) [    -17001.7447] [GTR parameters     ]
. (   26 sec) [    -17001.7447] [Alpha              ][  0.364377]
. (   27 sec) [    -17001.7034] [Branch lengths     ]
. (   28 sec) [    -17001.7026] [GTR parameters     ]
. (   28 sec) [    -17001.7026] [Alpha              ][  0.364377]
. (   29 sec) [    -17001.6883] [Branch lengths     ]
. (   30 sec) [    -17001.6881] [GTR parameters     ]
. (   31 sec) [    -17001.6881] [Alpha              ][  0.364012]
. (   32 sec) [    -17001.6831] [Branch lengths     ]
. (   33 sec) [    -17001.6830] [GTR parameters     ]
. (   33 sec) [    -17001.6830] [Alpha              ][  0.364012]
. (   34 sec) [    -17001.6813] [Branch lengths     ]
. (   35 sec) [    -17001.6813] [GTR parameters     ]
. (   35 sec) [    -17001.6813] [Alpha              ][  0.364012]
. (   36 sec) [    -17001.6807] [Branch lengths     ]
. (   37 sec) [    -17001.6807] [GTR parameters     ]
. (   37 sec) [    -17001.6807] [Alpha              ][  0.364012]
. (   37 sec) [    -17001.6807] [GTR parameters     ]
. (   38 sec) [    -17001.6807] [Alpha              ][  0.364012]
. Log likelihood of the current tree: -17001.680679.

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

. Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'...


. Time used 0h1m6s

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)