..........................                                      
 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 (RAxML_result.nucleic_M2944_80x1495_2006.phy_RAXML_CAT)"
                . 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.

. (    1 sec) [     -9404.8733] [Branch lengths     ]
. (    4 sec) [     -9128.9499] [GTR parameters     ]
. (    5 sec) [     -9020.4329] [Alpha              ][  0.500960]
. (    5 sec) [     -9019.0082] [Branch lengths     ]
. (    7 sec) [     -9018.6960] [GTR parameters     ]
. (    7 sec) [     -8992.9614] [Alpha              ][  0.316877]
. (    8 sec) [     -8992.1357] [Branch lengths     ]
. (    9 sec) [     -8991.8660] [GTR parameters     ]
. (   10 sec) [     -8991.8616] [Alpha              ][  0.314992]
. (   10 sec) [     -8991.5112] [Branch lengths     ]
. (   11 sec) [     -8991.5094] [GTR parameters     ]
. (   11 sec) [     -8991.5094] [Alpha              ][  0.314677]
. (   12 sec) [     -8991.3794] [Branch lengths     ]
. (   14 sec) [     -8991.3784] [GTR parameters     ]
. (   14 sec) [     -8991.3784] [Alpha              ][  0.314363]
. (   15 sec) [     -8991.3373] [Branch lengths     ]
. (   16 sec) [     -8991.3371] [GTR parameters     ]
. (   16 sec) [     -8991.3371] [Alpha              ][  0.314363]
. (   16 sec) [     -8991.3217] [Branch lengths     ]
. (   17 sec) [     -8991.3216] [GTR parameters     ]
. (   18 sec) [     -8991.3216] [Alpha              ][  0.314048]
. (   18 sec) [     -8991.3165] [Branch lengths     ]
. (   18 sec) [     -8991.3165] [GTR parameters     ]
. (   19 sec) [     -8991.3165] [Alpha              ][  0.314048]
. (   19 sec) [     -8991.3146] [Branch lengths     ]
. (   20 sec) [     -8991.3146] [GTR parameters     ]
. (   20 sec) [     -8991.3146] [Alpha              ][  0.314048]
. (   20 sec) [     -8991.3140] [Branch lengths     ]
. (   21 sec) [     -8991.3139] [GTR parameters     ]
. (   21 sec) [     -8991.3139] [Alpha              ][  0.314048]
. (   22 sec) [     -8991.3139] [GTR parameters     ]
. (   22 sec) [     -8991.3139] [Alpha              ][  0.314048]
. Log likelihood of the current tree: -8991.313885.

. 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 0h0m39s

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)