diff messages.log @ 1:bb04851a0da1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 74206c79038a0dbd29a5581bf66e08721a4dfda2-dirty

--- a/messages.log	Mon Sep 10 15:39:35 2018 -0400
+++ b/messages.log	Thu Jan 17 14:10:34 2019 -0500
@@ -1,16 +1,11 @@
 
+Loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
 Loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
 Loaded 'IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
 Loaded 'convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
-Loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
 Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
-Loaded 'libv3/stats.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/stats.bf
-Loaded 'libv3/tasks/ancestral.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/ancestral.bf
-Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
-Loaded 'libv3/tasks/alignments.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/alignments.bf
-Already loaded '../IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
-Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
 Loaded 'libv3/tasks/estimators.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/estimators.bf
 Loaded '../models/model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf
 Loaded 'DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
@@ -35,22 +30,30 @@
 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
 Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
 Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'libv3/tasks/alignments.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/alignments.bf
+Already loaded '../IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
+Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'libv3/models/codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
+Loaded '../tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
+Loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
+Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
 Loaded 'libv3/tasks/trees.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/trees.bf
 Already loaded '../IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
 Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
 Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
 Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
 Loaded 'TreeTools' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/TreeTools.ibf
-Loaded 'libv3/tasks/mpi.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/mpi.bf
-Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
-Already loaded '../models/parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
+Already loaded 'libv3/tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
+Loaded 'modules/io_functions.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
+Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
+Already loaded 'libv3/convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
+Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'modules/selection_lib.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
 Loaded 'libv3/models/codon/BS_REL.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
-Loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
-Loaded '../tasks/genetic_code.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/tasks/genetic_code.bf
-Loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
-Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
-Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
-Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded '../codon.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon.bf
 Already loaded '../DNA.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA.bf
 Already loaded '../parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
 Already loaded '../frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
@@ -64,16 +67,510 @@
 Loaded '../../convenience/math.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/math.bf
 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
 Already loaded 'libv3/convenience/math.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/math.bf
-Loaded 'modules/io_functions.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
-Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
-Already loaded 'libv3/IOFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/IOFunctions.bf
-Already loaded 'libv3/convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
-Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
-Loaded 'modules/selection_lib.ibf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
 Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
 Loaded 'modules/shared-load-file.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
 Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
 Already loaded 'libv3/convenience/matrix.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/matrix.bf
 Already loaded 'libv3/UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
-Variable 'bRvPSZrO.skipCodeSelectionStep' was not initialized prior to being used
-HyPhy killed by signal 2
\ No newline at end of file
+Variable 'OWzuGPhH.skipCodeSelectionStep' was not initialized prior to being used
+Row and/or column partition is empty. All the data will be used by default.
+Variable 'NEXUS_FILE_TREE_MATRIX' was not initialized prior to being used
+Variable 'utility.ToggleEnvVariable.cache' was not initialized prior to being used
+Variable 'TREE_NODE_NAME_MAPPING' was not initialized prior to being used
+Variable 'Gibbjnoz.PROMPT_FOR_FILE' was not initialized prior to being used
+Variable 'END_OF_FILE' was not initialized prior to being used
+Variable '_DO_TREE_REBALANCE_' was not initialized prior to being used
+Variable '_KEEP_I_LABELS_' was not initialized prior to being used
+Variable 'INCLUDE_MODEL_SPECS' was not initialized prior to being used
+Variable 'utility.ForEachPair.warn_non_rentrant' was not initialized prior to being used
+Row and/or column partition is empty. All the data will be used by default.
+Row and/or column partition is empty. All the data will be used by default.
+Variable 'zpqXEbDu.cache' was not initialized prior to being used
+Row and/or column partition is empty. All the data will be used by default.
+Variable 'COUNT_GAPS_IN_FREQUENCIES' was not initialized prior to being used
+Variable 'NRSKiVtk.model_pi' was not initialized prior to being used
+Model NRSKiVtk.model assigned to Pig
+Model NRSKiVtk.model assigned to Cow
+Model NRSKiVtk.model assigned to Node3
+Model NRSKiVtk.model assigned to Horse
+Model NRSKiVtk.model assigned to Cat
+Model NRSKiVtk.model assigned to Node2
+Model NRSKiVtk.model assigned to RhMonkey
+Model NRSKiVtk.model assigned to Baboon
+Model NRSKiVtk.model assigned to Node9
+Model NRSKiVtk.model assigned to Human
+Model NRSKiVtk.model assigned to Chimp
+Model NRSKiVtk.model assigned to Node12
+Model NRSKiVtk.model assigned to Node8
+Model NRSKiVtk.model assigned to Node1
+Model NRSKiVtk.model assigned to Rat
+Model NRSKiVtk.model assigned to Mouse
+The tips of the tree:NRSKiVtk.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
+
+Pseudo-optimal path's cost 2330 vs 4284 for 1..k=> a 1.83863 x improvement
+Partition 0 reversible model flag computed as 1
+Variable 'USE_LAST_RESULTS' was not initialized prior to being used
+Variable 'NRSKiVtk.tree_0.Pig.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Pig.t=0.3974535884114245
+Variable 'NRSKiVtk.tree_0.Cow.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Cow.t=0.5732857515739808
+Variable 'NRSKiVtk.tree_0.Node3.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Node3.t=0.2285810062933711
+Variable 'NRSKiVtk.tree_0.Horse.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Horse.t=0.445313802634098
+Variable 'NRSKiVtk.tree_0.Cat.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Cat.t=0.7112847618952328
+Variable 'NRSKiVtk.tree_0.Node2.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Node2.t=0.1574326532610344
+Variable 'NRSKiVtk.tree_0.RhMonkey.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.RhMonkey.t=0.00541241057687097
+Variable 'NRSKiVtk.tree_0.Baboon.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Baboon.t=0.008348273981595522
+Variable 'NRSKiVtk.tree_0.Node9.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Node9.t=0.06106219833449517
+Variable 'NRSKiVtk.tree_0.Human.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Human.t=0.01168167424258652
+Variable 'NRSKiVtk.tree_0.Chimp.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Chimp.t=0.00214616181187092
+Variable 'NRSKiVtk.tree_0.Node12.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Node12.t=0.03189158847602433
+Variable 'NRSKiVtk.tree_0.Node8.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Node8.t=0.2735913110261884
+Variable 'NRSKiVtk.tree_0.Node1.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Node1.t=0.9154145654683773
+Variable 'NRSKiVtk.tree_0.Rat.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Rat.t=0.1368762373082833
+Variable 'NRSKiVtk.tree_0.Mouse.t' was not initialized prior to being used
+models.generic.SetBranchLength: NRSKiVtk.tree_0.Mouse.t=0.2630995612925615
+Variable 'NRSKiVtk.NRSKiVtk.likelihoodFunction' was not initialized prior to being used
+Variable 'SAVE_OPT_STATUS_TO' was not initialized prior to being used
+Set GUI update interval to every 357-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+NRSKiVtk.model.theta_GT = 0.25
+NRSKiVtk.model.theta_CG = 0.25
+NRSKiVtk.model.theta_CT = 1
+NRSKiVtk.model.theta_AT = 0.25
+NRSKiVtk.model.theta_AC = 0.25
+NRSKiVtk.tree_0.Pig.t = 0.397454
+NRSKiVtk.tree_0.Cow.t = 0.573286
+NRSKiVtk.tree_0.Node3.t = 0.228581
+NRSKiVtk.tree_0.Horse.t = 0.445314
+NRSKiVtk.tree_0.Cat.t = 0.711285
+NRSKiVtk.tree_0.Node2.t = 0.157433
+NRSKiVtk.tree_0.RhMonkey.t = 0.00541241
+NRSKiVtk.tree_0.Baboon.t = 0.00834827
+NRSKiVtk.tree_0.Node9.t = 0.0610622
+NRSKiVtk.tree_0.Human.t = 0.0116817
+NRSKiVtk.tree_0.Chimp.t = 0.00214616
+NRSKiVtk.tree_0.Node12.t = 0.0318916
+NRSKiVtk.tree_0.Node8.t = 0.273591
+NRSKiVtk.tree_0.Node1.t = 0.915415
+NRSKiVtk.tree_0.Rat.t = 0.136876
+NRSKiVtk.tree_0.Mouse.t = 0.2631
+Optimization finished in 25 loop passes.
+1667 likelihood evaluation calls and 12169 matrix exponentiations calls were made
+
+Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
+Variable 'NRSKiVtk.option' was not initialized prior to being used
+Variable 'busted.terms.json.nucleotide_gtr' was not initialized prior to being used
+Variable 'Unknown' was not initialized prior to being used
+Variable 'ThTEDPSn.initial_value' was not initialized prior to being used
+Variable 'dIONygHy.data_filter' was not initialized prior to being used
+Row and/or column partition is empty. All the data will be used by default.
+Set GUI update interval to every 2834-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+frequencies._aux.CF3x4.p0_0 = 0.415775
+frequencies._aux.CF3x4.p0_1 = 0.250343
+frequencies._aux.CF3x4.p0_2 = 0.652625
+frequencies._aux.CF3x4.p1_0 = 0.399465
+frequencies._aux.CF3x4.p1_1 = 0.28317
+frequencies._aux.CF3x4.p1_2 = 0.391304
+frequencies._aux.CF3x4.p2_0 = 0.253743
+frequencies._aux.CF3x4.p2_1 = 0.314941
+frequencies._aux.CF3x4.p2_2 = 0.521444
+Optimization finished in 5 loop passes.
+184 likelihood evaluation calls and 0 matrix exponentiations calls were made
+
+Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
+Model dIONygHy.model_MGREV assigned to Pig
+Model dIONygHy.model_MGREV assigned to Cow
+Model dIONygHy.model_MGREV assigned to Node3
+Model dIONygHy.model_MGREV assigned to Horse
+Model dIONygHy.model_MGREV assigned to Cat
+Model dIONygHy.model_MGREV assigned to Node2
+Model dIONygHy.model_MGREV assigned to RhMonkey
+Model dIONygHy.model_MGREV assigned to Baboon
+Model dIONygHy.model_MGREV assigned to Node9
+Model dIONygHy.model_MGREV assigned to Human
+Model dIONygHy.model_MGREV assigned to Chimp
+Model dIONygHy.model_MGREV assigned to Node12
+Model dIONygHy.model_MGREV assigned to Node8
+Model dIONygHy.model_MGREV assigned to Node1
+Model dIONygHy.model_MGREV assigned to Rat
+Model dIONygHy.model_MGREV assigned to Mouse
+The tips of the tree:dIONygHy.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
+
+Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
+Partition 0 reversible model flag computed as 1
+Variable 'dIONygHy.dIONygHy.likelihoodFunction' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
+Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
+Set GUI update interval to every 208-th LF evaluation.
+Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
+Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
+Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
+Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
+Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
+Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
+Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
+Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
+Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
+Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
+Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
+Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
+Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
+Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
+Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+dIONygHy.model_MGREV.theta_CT = 1
+dIONygHy.model_MGREV.theta_GT = 1
+dIONygHy.model_MGREV.theta_CG = 1
+dIONygHy.model_MGREV.theta_AC = 1
+dIONygHy.model_MGREV.theta_AT = 1
+dIONygHy.model_MGREV.omega_0 = 1
+dIONygHy.tree_0.Pig.alpha = 0.000173063
+dIONygHy.tree_0.Cow.alpha = 0.000186779
+dIONygHy.tree_0.Node3.alpha = 1.15458e-05
+dIONygHy.tree_0.Horse.alpha = 0.000174488
+dIONygHy.tree_0.Cat.alpha = 0.000196799
+dIONygHy.tree_0.Node2.alpha = 0.000173618
+dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
+dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
+dIONygHy.tree_0.Node9.alpha = 0.000140119
+dIONygHy.tree_0.Human.alpha = 7.93383e-07
+dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
+dIONygHy.tree_0.Node12.alpha = 2.75759e-05
+dIONygHy.tree_0.Node8.alpha = 4.67029e-05
+dIONygHy.tree_0.Node1.alpha = 0.1
+dIONygHy.tree_0.Rat.alpha = 8.26646e-05
+dIONygHy.tree_0.Mouse.alpha = 0.000107933
+Optimization finished in 35 loop passes.
+3927 likelihood evaluation calls and 23083 matrix exponentiations calls were made
+
+Row and/or column partition is empty. All the data will be used by default.
+Set GUI update interval to every 2909-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+frequencies._aux.CF3x4.p0_0 = 0.415775
+frequencies._aux.CF3x4.p0_1 = 0.250343
+frequencies._aux.CF3x4.p0_2 = 0.652625
+frequencies._aux.CF3x4.p1_0 = 0.399465
+frequencies._aux.CF3x4.p1_1 = 0.28317
+frequencies._aux.CF3x4.p1_2 = 0.391304
+frequencies._aux.CF3x4.p2_0 = 0.253743
+frequencies._aux.CF3x4.p2_1 = 0.314941
+frequencies._aux.CF3x4.p2_2 = 0.521444
+Optimization finished in 5 loop passes.
+184 likelihood evaluation calls and 0 matrix exponentiations calls were made
+
+Variable 'dIONygHy.model_MGREV_pi' was not initialized prior to being used
+Model dIONygHy.model_MGREV assigned to Pig
+Model dIONygHy.model_MGREV assigned to Cow
+Model dIONygHy.model_MGREV assigned to Node3
+Model dIONygHy.model_MGREV assigned to Horse
+Model dIONygHy.model_MGREV assigned to Cat
+Model dIONygHy.model_MGREV assigned to Node2
+Model dIONygHy.model_MGREV assigned to RhMonkey
+Model dIONygHy.model_MGREV assigned to Baboon
+Model dIONygHy.model_MGREV assigned to Node9
+Model dIONygHy.model_MGREV assigned to Human
+Model dIONygHy.model_MGREV assigned to Chimp
+Model dIONygHy.model_MGREV assigned to Node12
+Model dIONygHy.model_MGREV assigned to Node8
+Model dIONygHy.model_MGREV assigned to Node1
+Model dIONygHy.model_MGREV assigned to Rat
+Model dIONygHy.model_MGREV assigned to Mouse
+The tips of the tree:dIONygHy.tree_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
+
+Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
+Partition 0 reversible model flag computed as 1
+Variable 'dIONygHy.tree_0.Node1.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node8.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Rat.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node12.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Cat.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Chimp.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Human.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node9.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Baboon.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node2.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.RhMonkey.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Node3.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Cow.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Pig.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Horse.alpha' was not initialized prior to being used
+Variable 'dIONygHy.tree_0.Mouse.alpha' was not initialized prior to being used
+Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
+Set GUI update interval to every 269-th LF evaluation.
+Initial guess for dIONygHy.tree_0.Node2.alpha is 0.000173618
+Initial guess for dIONygHy.tree_0.Node3.alpha is 1.15458e-05
+Initial guess for dIONygHy.tree_0.Pig.alpha is 0.000173063
+Initial guess for dIONygHy.tree_0.Cow.alpha is 0.000186779
+Initial guess for dIONygHy.tree_0.Horse.alpha is 0.000174488
+Initial guess for dIONygHy.tree_0.Cat.alpha is 0.000196799
+Initial guess for dIONygHy.tree_0.Node8.alpha is 4.67029e-05
+Initial guess for dIONygHy.tree_0.Node9.alpha is 0.000140119
+Initial guess for dIONygHy.tree_0.RhMonkey.alpha is 4.64183e-06
+Initial guess for dIONygHy.tree_0.Baboon.alpha is 1.75863e-06
+Initial guess for dIONygHy.tree_0.Node12.alpha is 2.75759e-05
+Initial guess for dIONygHy.tree_0.Human.alpha is 7.93383e-07
+Initial guess for dIONygHy.tree_0.Chimp.alpha is 1.32491e-06
+Initial guess for dIONygHy.tree_0.Rat.alpha is 8.26646e-05
+Initial guess for dIONygHy.tree_0.Mouse.alpha is 0.000107933
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+dIONygHy.model_MGREV.theta_CG = 1
+dIONygHy.model_MGREV.theta_AT = 1
+dIONygHy.model_MGREV.theta_CT = 1
+dIONygHy.model_MGREV.theta_GT = 1
+dIONygHy.model_MGREV.theta_AC = 1
+dIONygHy.model_MGREV.omega_0 = 1
+dIONygHy.tree_0.Pig.alpha = 0.000173063
+dIONygHy.tree_0.Cow.alpha = 0.000186779
+dIONygHy.tree_0.Node3.alpha = 1.15458e-05
+dIONygHy.tree_0.Horse.alpha = 0.000174488
+dIONygHy.tree_0.Cat.alpha = 0.000196799
+dIONygHy.tree_0.Node2.alpha = 0.000173618
+dIONygHy.tree_0.RhMonkey.alpha = 4.64183e-06
+dIONygHy.tree_0.Baboon.alpha = 1.75863e-06
+dIONygHy.tree_0.Node9.alpha = 0.000140119
+dIONygHy.tree_0.Human.alpha = 7.93383e-07
+dIONygHy.tree_0.Chimp.alpha = 1.32491e-06
+dIONygHy.tree_0.Node12.alpha = 2.75759e-05
+dIONygHy.tree_0.Node8.alpha = 4.67029e-05
+dIONygHy.tree_0.Node1.alpha = 0.1
+dIONygHy.tree_0.Rat.alpha = 8.26646e-05
+dIONygHy.tree_0.Mouse.alpha = 0.000107933
+Optimization finished in 35 loop passes.
+3276 likelihood evaluation calls and 21044 matrix exponentiations calls were made
+
+Overwritten previously defined function:'IIsiGihg.rate_generator'
+Overwritten previously defined function:'IIsiGihg.rate_generator'
+Set GUI update interval to every 3023-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+frequencies._aux.CF3x4.p0_0 = 0.415775
+frequencies._aux.CF3x4.p0_1 = 0.250343
+frequencies._aux.CF3x4.p0_2 = 0.652625
+frequencies._aux.CF3x4.p1_0 = 0.399465
+frequencies._aux.CF3x4.p1_1 = 0.28317
+frequencies._aux.CF3x4.p1_2 = 0.391304
+frequencies._aux.CF3x4.p2_0 = 0.253743
+frequencies._aux.CF3x4.p2_1 = 0.314941
+frequencies._aux.CF3x4.p2_2 = 0.521444
+Optimization finished in 5 loop passes.
+184 likelihood evaluation calls and 0 matrix exponentiations calls were made
+
+Variable 'busted.test_pi' was not initialized prior to being used
+Overwritten previously defined function:'IIsiGihg.rate_generator'
+Overwritten previously defined function:'IIsiGihg.rate_generator'
+Overwritten previously defined function:'IIsiGihg.rate_generator'
+Set GUI update interval to every 3010-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+frequencies._aux.CF3x4.p0_0 = 0.415775
+frequencies._aux.CF3x4.p0_1 = 0.250343
+frequencies._aux.CF3x4.p0_2 = 0.652625
+frequencies._aux.CF3x4.p1_0 = 0.399465
+frequencies._aux.CF3x4.p1_1 = 0.28317
+frequencies._aux.CF3x4.p1_2 = 0.391304
+frequencies._aux.CF3x4.p2_0 = 0.253743
+frequencies._aux.CF3x4.p2_1 = 0.314941
+frequencies._aux.CF3x4.p2_2 = 0.521444
+Optimization finished in 5 loop passes.
+184 likelihood evaluation calls and 0 matrix exponentiations calls were made
+
+Variable 'busted.background_pi' was not initialized prior to being used
+Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
+No nodel was assigned to Pig
+No nodel was assigned to Cow
+No nodel was assigned to Node3
+No nodel was assigned to Horse
+No nodel was assigned to Cat
+No nodel was assigned to Node2
+No nodel was assigned to RhMonkey
+No nodel was assigned to Baboon
+No nodel was assigned to Node9
+No nodel was assigned to Human
+No nodel was assigned to Chimp
+No nodel was assigned to Node12
+No nodel was assigned to Node8
+No nodel was assigned to Node1
+No nodel was assigned to Rat
+No nodel was assigned to Mouse
+The tips of the tree:CPXgZuSs.tree_id_0 were matched with the species names from the data in the following numeric order (0-based) {5,4,6,7,3,2,0,1,9,8}
+
+Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
+Partition 0 is ASSUMED to have a reversible model
+busted.test.theta_AG was already constrained in estimators.SetGlobals2
+Variable 'CPXgZuSs.tree_id_0.Pig.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Pig.t=1.377886710534728
+Variable 'CPXgZuSs.tree_id_0.Cow.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cow.t=1.774251775766245
+Variable 'CPXgZuSs.tree_id_0.Node3.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node3.t=0.727900992785442
+Variable 'CPXgZuSs.tree_id_0.Horse.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Horse.t=1.51058601207266
+Variable 'CPXgZuSs.tree_id_0.Cat.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Cat.t=1.957296993203762
+Variable 'CPXgZuSs.tree_id_0.Node2.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node2.t=0.4612561973173576
+Variable 'CPXgZuSs.tree_id_0.RhMonkey.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.RhMonkey.t=0.02659579655381833
+Variable 'CPXgZuSs.tree_id_0.Baboon.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Baboon.t=0.01267390527294645
+Variable 'CPXgZuSs.tree_id_0.Node9.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node9.t=0.1855677984720407
+Variable 'CPXgZuSs.tree_id_0.Human.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Human.t=0
+Variable 'CPXgZuSs.tree_id_0.Chimp.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Chimp.t=0.01307822802283968
+Variable 'CPXgZuSs.tree_id_0.Node12.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node12.t=0.1279673910082466
+Variable 'CPXgZuSs.tree_id_0.Node8.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node8.t=0.7824909790907859
+Variable 'CPXgZuSs.tree_id_0.Node1.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Node1.t=2.034207610785829
+Variable 'CPXgZuSs.tree_id_0.Rat.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Rat.t=0.4799151894651191
+Variable 'CPXgZuSs.tree_id_0.Mouse.t' was not initialized prior to being used
+models.generic.SetBranchLength: CPXgZuSs.tree_id_0.Mouse.t=0.859781481367942
+Variable 'CPXgZuSs.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
+Set GUI update interval to every 17-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+busted.test.theta_AC = 0.575889
+busted.test.theta_AT = 0.266515
+busted.test.omega1 = 0
+busted.test.bsrel_mixture_aux_0 = 0.7
+busted.test.theta_CG = 0.470944
+busted.test.omega3 = 9.52381
+busted.test.omega2 = 0.238095
+busted.test.theta_CT = 0.973284
+busted.test.bsrel_mixture_aux_1 = 0.666667
+busted.test.theta_GT = 0.315964
+CPXgZuSs.tree_id_0.Pig.t = 1.37789
+CPXgZuSs.tree_id_0.Cow.t = 1.77425
+CPXgZuSs.tree_id_0.Node3.t = 0.727901
+CPXgZuSs.tree_id_0.Horse.t = 1.51059
+CPXgZuSs.tree_id_0.Cat.t = 1.9573
+CPXgZuSs.tree_id_0.Node2.t = 0.461256
+CPXgZuSs.tree_id_0.RhMonkey.t = 0.0265958
+CPXgZuSs.tree_id_0.Baboon.t = 0.0126739
+CPXgZuSs.tree_id_0.Node9.t = 0.185568
+CPXgZuSs.tree_id_0.Human.t = 0
+CPXgZuSs.tree_id_0.Chimp.t = 0.0130782
+CPXgZuSs.tree_id_0.Node12.t = 0.127967
+CPXgZuSs.tree_id_0.Node8.t = 0.782491
+CPXgZuSs.tree_id_0.Node1.t = 2.03421
+CPXgZuSs.tree_id_0.Rat.t = 0.479915
+CPXgZuSs.tree_id_0.Mouse.t = 0.859781
+Optimization finished in 26 loop passes.
+2990 likelihood evaluation calls and 70968 matrix exponentiations calls were made
+
+Variable 'KIGDLXKi.CPXgZuSs.likelihoodFunction' was not initialized prior to being used
+Set GUI update interval to every 28-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+busted.test.theta_AC = 0.468589
+busted.test.omega1 = 0.210733
+busted.test.bsrel_mixture_aux_0 = 0.412135
+busted.test.theta_AT = 0.215633
+busted.test.omega2 = 0.105287
+busted.test.bsrel_mixture_aux_1 = 0.404693
+busted.test.theta_CT = 0.973171
+busted.test.theta_GT = 0.273282
+busted.test.theta_CG = 0.415669
+CPXgZuSs.tree_id_0.Pig.t = 0.410826
+CPXgZuSs.tree_id_0.Cow.t = 0.555921
+CPXgZuSs.tree_id_0.Node3.t = 0.241332
+CPXgZuSs.tree_id_0.Horse.t = 0.483056
+CPXgZuSs.tree_id_0.Cat.t = 0.61829
+CPXgZuSs.tree_id_0.Node2.t = 0.117184
+CPXgZuSs.tree_id_0.RhMonkey.t = 0.00689772
+CPXgZuSs.tree_id_0.Baboon.t = 0.0034792
+CPXgZuSs.tree_id_0.Node9.t = 0.051855
+CPXgZuSs.tree_id_0.Human.t = 0
+CPXgZuSs.tree_id_0.Chimp.t = 0.00344635
+CPXgZuSs.tree_id_0.Node12.t = 0.0343399
+CPXgZuSs.tree_id_0.Node8.t = 0.253166
+CPXgZuSs.tree_id_0.Node1.t = 0.86218
+CPXgZuSs.tree_id_0.Rat.t = 0.138343
+CPXgZuSs.tree_id_0.Mouse.t = 0.279774
+Optimization finished in 14 loop passes.
+1338 likelihood evaluation calls and 35802 matrix exponentiations calls were made
+
+Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used
\ No newline at end of file