Reading tree tree_1
Executing blformat command...
Number of sites in sequences set to 58171
Branch lengths assumed to be in units of numbers of substitutions per site
All branch lengths multipled by the 58171 sites in the sequence
Branch lengths rounded to nearest integer
(This may not be a good idea when using CALIBRATE on ultrametric user supplied input trees. Use ROUND=NO then)
0 zero-length branches collapsed
Defining clade name: CNIDARIA
Defining clade name: HYDROZOA
Defining clade name: SCYPHOZOA
Defining clade name: OCTOCORALLIA
Defining clade name: HEXACORALLIA
Defining clade name: BILATERIA
Defining clade name: DEUTEROSTOMIA
Defining clade name: LOPHOTROCHOZOA
Defining clade name: HYDRACTINIA
Defining clade name: ROOT
Fixing age of CNIDARIA at 570.000000
 (The age of this node will no longer be estimated.)
 (This command overides any previous age constraints for this node.)
 (The total number of fixed ages is now 1)
Setting minimum age constraint for taxon HYDROZOA to 500.000000
********************* WARNING **********************

Times and rates unavailable

****************************************************
[Printing tree 1]

[TREE DESCRIPTION of tree tree_1]

tree tree_1 = ((Mlei:0.000000,(Tadh:0.000000,(((Apla:0.000000,Skow:0.000000)DEUTEROSTOMIA:0.000000,(Lgig:0.000000,Paus:0.000000)LOPHOTROCHOZOA:0.000000)BILATERIA:0.000000,((((Adig:0.000000,(Ofav:0.000000,Pdam:0.000000):0.000000):0.000000,(Epal:0.000000,Nvec:0.000000):0.000000)HEXACORALLIA:0.000000,(Dgig:0.000000,Rmue:0.000000)OCTOCORALLIA:0.000000):570.000000,(((Chem:0.000000,(Hech:0.000000,Hsym:0.000000)HYDRACTINIA:0.000000):0.000000,Hmag:0.000000)HYDROZOA:0.000000,(Mvir:0.000000,(Nnom:0.000000,(Aaurb:0.000000,Aaurp:0.000000):0.000000)SCYPHOZOA:0.000000):0.000000):570.000000)CNIDARIA:-570.000000):0.000000):0.000000):0.000000,Aque:0.000000)ROOT;
********************* WARNING **********************

You are trying to estimate the age of the root
but with the given constraints it is possible that a range of solutions exist

****************************************************


----------------------------------------


LINEAGE RATE/TIME ANALYSIS FOR TREE tree_1

Method = Langley and Fitch
Optimization via Truncated-Newton (TN) method with bound constraints

----------------------------------------
Substitution Model
	Rates are equal across sites
Global/Local Search Parameters
	Number of searches from random starts = 3
	Number of restarts after each search = 1
	Local perturbation on restarts = 0.01
	Local fractional tolerance after restarts = 0.01
Optimization parameters set automatically by TN routine
Length of tree input =  1.07676e+06
Number of taxa  =  22
Number of sites in sequences =  58171

----------------------------------------
Starting optimization (random starting point 1)
...Checking the starting point...(for some barrier constant)...
...Passed...now optimizing...
...Initial solution=69742.362718
......starting perturbation 1
......solution for perturbation 1=69742.362718...best=69742.362718
*** Using analytical formula for gradient in check gradient step ***
...checking gradient of the solution...

	Norm for free parameters in gradient (0.000021) should be less than cutoff (151.182974)
	Checking active constraints for node times only (activeEpsilon=0.001000 and window [actEps*rootage]=1.219294)
	Param	Estimate	Gradient	Active*	Taxon
	[1]	1219.294272	-0.000000	0	ROOT
	[2]	749.401717	0.000001	0	
	[3]	687.945534	-0.000005	0	
	[4]	637.483184	0.000001	0	
	[5]	514.477292	0.000001	0	BILATERIA
	[6]	415.922672	-0.000005	0	DEUTEROSTOMIA
	[7]	396.546216	-0.000005	0	LOPHOTROCHOZOA
	[8]	497.558359	-0.000002	0	
	[9]	342.457166	0.000008	0	HEXACORALLIA
	[10]	161.829881	0.000000	0	
	[11]	108.778685	0.000006	0	
	[12]	243.046190	-0.000000	0	
	[13]	232.483920	0.000003	0	OCTOCORALLIA
	[14]	538.925507	0.000005	0	
	[15]	500.000000	-644.095004	-1	HYDROZOA
	[16]	417.893346	0.000001	0	
	[17]	19.282414	0.000001	0	HYDRACTINIA
	[18]	466.938588	0.000004	0	
	[19]	207.178438	-0.000004	0	SCYPHOZOA
	[20]	45.663198	0.000003	0	

	Gradients for rate parameters (if any)
	Param	Estimate	Gradient
	[21]	105.643118	-0.000012
------------------------------------------------------------------------------
*Key
	+1 = maximum age constraint is reached (gradient may not be 0)
	-1 = minimum age constraint is reached (gradient may not be 0)
	 0 = no constraint present or constraint not reached (gradient should be 0)

	 (note that small gradient values (< |0.015118|) are not examined with respect to active constraints to avoid spurious roundoff issues)

*** Gradient check passed ***
Starting optimization (random starting point 2)
...Checking the starting point...(for some barrier constant)...
...Passed...now optimizing...
...Initial solution=69742.362718
......starting perturbation 1
......solution for perturbation 1=69742.362718...best=69742.362718
*** Using analytical formula for gradient in check gradient step ***
...checking gradient of the solution...

	Norm for free parameters in gradient (0.000005) should be less than cutoff (151.182974)
	Checking active constraints for node times only (activeEpsilon=0.001000 and window [actEps*rootage]=1.219294)
	Param	Estimate	Gradient	Active*	Taxon
	[1]	1219.294270	-0.000000	0	ROOT
	[2]	749.401714	0.000001	0	
	[3]	687.945531	-0.000001	0	
	[4]	637.483182	-0.000001	0	
	[5]	514.477287	0.000002	0	BILATERIA
	[6]	415.922665	-0.000000	0	DEUTEROSTOMIA
	[7]	396.546210	-0.000000	0	LOPHOTROCHOZOA
	[8]	497.558360	-0.000001	0	
	[9]	342.457173	0.000001	0	HEXACORALLIA
	[10]	161.829885	-0.000001	0	
	[11]	108.778689	-0.000001	0	
	[12]	243.046193	0.000000	0	
	[13]	232.483922	0.000000	0	OCTOCORALLIA
	[14]	538.925508	-0.000003	0	
	[15]	500.000000	-644.094998	-1	HYDROZOA
	[16]	417.893347	-0.000000	0	
	[17]	19.282414	0.000000	0	HYDRACTINIA
	[18]	466.938590	0.000000	0	
	[19]	207.178436	0.000001	0	SCYPHOZOA
	[20]	45.663198	-0.000001	0	

	Gradients for rate parameters (if any)
	Param	Estimate	Gradient
	[21]	105.643118	-0.000002
------------------------------------------------------------------------------
*Key
	+1 = maximum age constraint is reached (gradient may not be 0)
	-1 = minimum age constraint is reached (gradient may not be 0)
	 0 = no constraint present or constraint not reached (gradient should be 0)

	 (note that small gradient values (< |0.015118|) are not examined with respect to active constraints to avoid spurious roundoff issues)

*** Gradient check passed ***
Starting optimization (random starting point 3)
...Checking the starting point...(for some barrier constant)...
...Passed...now optimizing...
...Initial solution=69742.362718
......starting perturbation 1
......solution for perturbation 1=69742.362718...best=69742.362718
*** Using analytical formula for gradient in check gradient step ***
...checking gradient of the solution...

	Norm for free parameters in gradient (0.000004) should be less than cutoff (151.182974)
	Checking active constraints for node times only (activeEpsilon=0.001000 and window [actEps*rootage]=1.219294)
	Param	Estimate	Gradient	Active*	Taxon
	[1]	1219.294271	0.000000	0	ROOT
	[2]	749.401716	-0.000001	0	
	[3]	687.945533	-0.000001	0	
	[4]	637.483183	-0.000001	0	
	[5]	514.477288	-0.000000	0	BILATERIA
	[6]	415.922666	0.000000	0	DEUTEROSTOMIA
	[7]	396.546210	0.000000	0	LOPHOTROCHOZOA
	[8]	497.558360	0.000000	0	
	[9]	342.457174	-0.000001	0	HEXACORALLIA
	[10]	161.829885	0.000001	0	
	[11]	108.778689	-0.000002	0	
	[12]	243.046195	-0.000001	0	
	[13]	232.483922	0.000001	0	OCTOCORALLIA
	[14]	538.925508	0.000002	0	
	[15]	500.000000	-644.095000	-1	HYDROZOA
	[16]	417.893347	0.000000	0	
	[17]	19.282414	-0.000000	0	HYDRACTINIA
	[18]	466.938590	0.000000	0	
	[19]	207.178436	0.000001	0	SCYPHOZOA
	[20]	45.663198	0.000000	0	

	Gradients for rate parameters (if any)
	Param	Estimate	Gradient
	[21]	105.643117	-0.000001
------------------------------------------------------------------------------
*Key
	+1 = maximum age constraint is reached (gradient may not be 0)
	-1 = minimum age constraint is reached (gradient may not be 0)
	 0 = no constraint present or constraint not reached (gradient should be 0)

	 (note that small gradient values (< |0.015118|) are not examined with respect to active constraints to avoid spurious roundoff issues)

*** Gradient check passed ***

Using optimization from starting point 2 as best estimate
Test of molecular clock on soln. 2 (best): Chi squared = 261886.774961 (df=21)


Parameter estimates:

	       1         2         3  

Times
p[ 1]	   0.021     0.021     0.021  
p[ 2]	  0.0129    0.0129    0.0129  
p[ 3]	  0.0118    0.0118    0.0118  
p[ 4]	   0.011     0.011     0.011  
p[ 5]	 0.00884   0.00884   0.00884  
p[ 6]	 0.00715   0.00715   0.00715  
p[ 7]	 0.00682   0.00682   0.00682  
p[ 8]	 0.00855   0.00855   0.00855  
p[ 9]	 0.00589   0.00589   0.00589  
p[10]	 0.00278   0.00278   0.00278  
p[11]	 0.00187   0.00187   0.00187  
p[12]	 0.00418   0.00418   0.00418  
p[13]	   0.004     0.004     0.004  
p[14]	 0.00926   0.00926   0.00926  
p[15]	  0.0086    0.0086    0.0086  
p[16]	 0.00718   0.00718   0.00718  
p[17]	 0.000331   0.000331   0.000331  
p[18]	 0.00803   0.00803   0.00803  
p[19]	 0.00356   0.00356   0.00356  
p[20]	 0.000785   0.000785   0.000785  

Rates (substitutions per site per unit time)
p[21]	 0.00182   0.00182   0.00182  

	  PASSED    PASSED    PASSED  
__________________
Result codes:
PASSED = OK
FAILED(1) = Optimization routine returned error
FAILED(2) = Solution's gradient was not 0
__________________


Obj->	-69742.363  -69742.363  -69742.363  
[Printing tree 1]

[CHRONOGRAM of tree tree_1]
                +---------------------------Mlei
                |
                | +-------------------------Tadh
                | |
+---------------+2|         +---------------Apla
|               | |     +---+DEUTEROSTOMIA
|               | |     |   +---------------Skow
|               | | +---+BILATERIA
|               | | |   |    +--------------Lgig
|               +-+4|   +----+LOPHOTROCHOZOA
|                 | |        +--------------Paus
|                 | |
|                 | |                +------Adig
|                 | |         +------+17
|                 | |         |      | +----Ofav
|                 | |         |      +-+19
|                 +-+6   +----+HEXACORALLIA-Pdam
|                   |    |    |
|                   |    |    |   +---------Epal
|                   | +--+15  +---+22
|                   | |  |        +---------Never
|                   | |  |
|                   | |  |        +---------Dgig
+ROOT               | |  +--------+OCTOCORALLIA
|                   | |           +---------Rmue
|                   +-+CNIDARIA
|                     |     +---------------Chem
|                     |  +--+30
|                     |  |  |             +-Hech
|                     |+-+HYDROZOA--------+HYDRACTINIA
|                     || |                +-Hsym
|                     || |
|                     ++28------------------Hmag
|                      |
|                      |  +-----------------Mvir
|                      +--+36
|                         |        +--------Nnom
|                         +--------+SCYPHOZOA
|                                  |     +--Aaurb
|                                  +-----+40
|                                        +--Aaurp
|
+-------------------------------------------Aque

[Printing tree 1]

[TREE DESCRIPTION of tree tree_1]

tree tree_1 = ((Mlei:749.401714,(Tadh:687.945531,(((Apla:415.922665,Skow:415.922665)DEUTEROSTOMIA:98.554621,(Lgig:396.546210,Paus:396.546210)LOPHOTROCHOZOA:117.931077)BILATERIA:123.005895,((((Adig:161.829885,(Ofav:108.778689,Pdam:108.778689):53.051196):180.627287,(Epal:243.046193,Nvec:243.046193):99.410979)HEXACORALLIA:155.101188,(Dgig:232.483922,Rmue:232.483922)OCTOCORALLIA:265.074438):72.441640,(((Chem:417.893347,(Hech:19.282414,Hsym:19.282414)HYDRACTINIA:398.610933):82.106653,Hmag:500.000000)HYDROZOA:38.925508,(Mvir:466.938590,(Nnom:207.178436,(Aaurb:45.663198,Aaurp:45.663198):161.515237)SCYPHOZOA:259.760154):71.986918):31.074492)CNIDARIA:67.483182):50.462349):61.456183):469.892556,Aque:1219.294270)ROOT;
