--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/messages.log	Tue Feb 12 08:53:39 2019 -0500
@@ -0,0 +1,633 @@
+
+Loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Loaded 'IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Loaded 'convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
+Loaded 'libv3/models/codon/MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
+Loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
+Loaded '../tasks/genetic_code.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
+Loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
+Loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
+Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
+Loaded 'GrabBag' from /usr/local/lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
+Overwritten previously defined function:'_sortStringsAux'
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Loaded 'model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
+Already loaded 'DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
+Already loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
+Already loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
+Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
+Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Loaded 'libv3/tasks/estimators.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
+Already loaded '../models/model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
+Loaded '../models/DNA/GTR.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
+Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
+Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
+Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
+Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'libv3/tasks/alignments.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
+Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
+Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'libv3/tasks/trees.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
+Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
+Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
+Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Loaded 'TreeTools' from /usr/local/lib/hyphy/TemplateBatchFiles/TreeTools.ibf
+Loaded 'modules/io_functions.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
+Already loaded 'libv3/convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
+Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Loaded 'modules/selection_lib.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
+Loaded 'libv3/models/codon/BS_REL.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
+Already loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
+Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
+Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
+Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
+Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
+Loaded '../../convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Already loaded 'libv3/convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
+Loaded 'libv3/tasks/mpi.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
+Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
+Already loaded '../models/parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
+Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
+Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
+Loaded 'modules/shared-load-file.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
+Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
+Already loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
+Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
+Variable 'JOYpYPkv.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 '_thZqV_F.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.
+Loaded 'modules/grid_compute.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
+Variable 'QPmholqs.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 'MiVdxtWn.model_pi' was not initialized prior to being used
+Model MiVdxtWn.model assigned to Pig
+Model MiVdxtWn.model assigned to Cow
+Model MiVdxtWn.model assigned to Node3
+Model MiVdxtWn.model assigned to Horse
+Model MiVdxtWn.model assigned to Cat
+Model MiVdxtWn.model assigned to Node2
+Model MiVdxtWn.model assigned to RhMonkey
+Model MiVdxtWn.model assigned to Baboon
+Model MiVdxtWn.model assigned to Node9
+Model MiVdxtWn.model assigned to Human
+Model MiVdxtWn.model assigned to Chimp
+Model MiVdxtWn.model assigned to Node12
+Model MiVdxtWn.model assigned to Node8
+Model MiVdxtWn.model assigned to Node1
+Model MiVdxtWn.model assigned to Rat
+Model MiVdxtWn.model assigned to Mouse
+The tips of the tree:MiVdxtWn.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 is ASSUMED to have a reversible model
+Variable 'USE_LAST_RESULTS' was not initialized prior to being used
+Variable 'MiVdxtWn.tree_0.Pig.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Pig.t=0.3974535884114245
+Variable 'MiVdxtWn.tree_0.Cow.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Cow.t=0.5732857515739808
+Variable 'MiVdxtWn.tree_0.Node3.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Node3.t=0.2285810062933711
+Variable 'MiVdxtWn.tree_0.Horse.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Horse.t=0.445313802634098
+Variable 'MiVdxtWn.tree_0.Cat.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Cat.t=0.7112847618952328
+Variable 'MiVdxtWn.tree_0.Node2.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Node2.t=0.1574326532610344
+Variable 'MiVdxtWn.tree_0.RhMonkey.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.RhMonkey.t=0.00541241057687097
+Variable 'MiVdxtWn.tree_0.Baboon.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Baboon.t=0.008348273981595522
+Variable 'MiVdxtWn.tree_0.Node9.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Node9.t=0.06106219833449517
+Variable 'MiVdxtWn.tree_0.Human.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Human.t=0.01168167424258652
+Variable 'MiVdxtWn.tree_0.Chimp.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Chimp.t=0.00214616181187092
+Variable 'MiVdxtWn.tree_0.Node12.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Node12.t=0.03189158847602433
+Variable 'MiVdxtWn.tree_0.Node8.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Node8.t=0.2735913110261884
+Variable 'MiVdxtWn.tree_0.Node1.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Node1.t=0.9154145654683773
+Variable 'MiVdxtWn.tree_0.Rat.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Rat.t=0.1368762373082833
+Variable 'MiVdxtWn.tree_0.Mouse.t' was not initialized prior to being used
+models.generic.SetBranchLength: MiVdxtWn.tree_0.Mouse.t=0.2630995612925615
+Variable 'MiVdxtWn.MiVdxtWn.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 331-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+MiVdxtWn.model.theta_GT = 0.25
+MiVdxtWn.model.theta_CG = 0.25
+MiVdxtWn.model.theta_CT = 1
+MiVdxtWn.model.theta_AT = 0.25
+MiVdxtWn.model.theta_AC = 0.25
+MiVdxtWn.tree_0.Pig.t = 0.397454
+MiVdxtWn.tree_0.Cow.t = 0.573286
+MiVdxtWn.tree_0.Node3.t = 0.228581
+MiVdxtWn.tree_0.Horse.t = 0.445314
+MiVdxtWn.tree_0.Cat.t = 0.711285
+MiVdxtWn.tree_0.Node2.t = 0.157433
+MiVdxtWn.tree_0.RhMonkey.t = 0.00541241
+MiVdxtWn.tree_0.Baboon.t = 0.00834827
+MiVdxtWn.tree_0.Node9.t = 0.0610622
+MiVdxtWn.tree_0.Human.t = 0.0116817
+MiVdxtWn.tree_0.Chimp.t = 0.00214616
+MiVdxtWn.tree_0.Node12.t = 0.0318916
+MiVdxtWn.tree_0.Node8.t = 0.273591
+MiVdxtWn.tree_0.Node1.t = 0.915415
+MiVdxtWn.tree_0.Rat.t = 0.136876
+MiVdxtWn.tree_0.Mouse.t = 0.2631
+Optimization finished in 24 loop passes.
+1467 likelihood evaluation calls and 10507 matrix exponentiations calls were made
+
+Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
+Variable 'MiVdxtWn.option' was not initialized prior to being used
+Variable 'relax.terms.json.nucleotide_gtr' was not initialized prior to being used
+Variable 'Unknown' was not initialized prior to being used
+Variable 'SRnFPBcA.initial_value' was not initialized prior to being used
+Variable 'FYuAtbni.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 2879-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 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used
+Model FYuAtbni.model_MGREV assigned to Pig
+Model FYuAtbni.model_MGREV assigned to Cow
+Model FYuAtbni.model_MGREV assigned to Node3
+Model FYuAtbni.model_MGREV assigned to Horse
+Model FYuAtbni.model_MGREV assigned to Cat
+Model FYuAtbni.model_MGREV assigned to Node2
+Model FYuAtbni.model_MGREV assigned to RhMonkey
+Model FYuAtbni.model_MGREV assigned to Baboon
+Model FYuAtbni.model_MGREV assigned to Node9
+Model FYuAtbni.model_MGREV assigned to Human
+Model FYuAtbni.model_MGREV assigned to Chimp
+Model FYuAtbni.model_MGREV assigned to Node12
+Model FYuAtbni.model_MGREV assigned to Node8
+Model FYuAtbni.model_MGREV assigned to Node1
+Model FYuAtbni.model_MGREV assigned to Rat
+Model FYuAtbni.model_MGREV assigned to Mouse
+The tips of the tree:FYuAtbni.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 is ASSUMED to have a reversible model
+Variable 'FYuAtbni.FYuAtbni.likelihoodFunction' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.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 187-th LF evaluation.
+Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618
+Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05
+Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063
+Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779
+Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488
+Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799
+Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05
+Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119
+Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06
+Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06
+Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05
+Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07
+Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06
+Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05
+Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+FYuAtbni.model_MGREV.theta_GT = 1
+FYuAtbni.model_MGREV.theta_CT = 1
+FYuAtbni.model_MGREV.theta_AC = 1
+FYuAtbni.model_MGREV.theta_CG = 1
+FYuAtbni.model_MGREV.theta_AT = 1
+FYuAtbni.model_MGREV.omega_0 = 1
+FYuAtbni.model_MGREV.omega_1 = 1
+FYuAtbni.tree_0.Pig.alpha = 0.000173063
+FYuAtbni.tree_0.Cow.alpha = 0.000186779
+FYuAtbni.tree_0.Node3.alpha = 1.15458e-05
+FYuAtbni.tree_0.Horse.alpha = 0.000174488
+FYuAtbni.tree_0.Cat.alpha = 0.000196799
+FYuAtbni.tree_0.Node2.alpha = 0.000173618
+FYuAtbni.model_MGREV.omega_2 = 1
+FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06
+FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06
+FYuAtbni.tree_0.Node9.alpha = 0.000140119
+FYuAtbni.tree_0.Human.alpha = 7.93383e-07
+FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06
+FYuAtbni.tree_0.Node12.alpha = 2.75759e-05
+FYuAtbni.tree_0.Node8.alpha = 4.67029e-05
+FYuAtbni.tree_0.Node1.alpha = 0.1
+FYuAtbni.tree_0.Rat.alpha = 8.26646e-05
+FYuAtbni.tree_0.Mouse.alpha = 0.000107933
+Optimization finished in 37 loop passes.
+3110 likelihood evaluation calls and 18285 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 2926-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 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used
+Model FYuAtbni.model_MGREV assigned to Pig
+Model FYuAtbni.model_MGREV assigned to Cow
+Model FYuAtbni.model_MGREV assigned to Node3
+Model FYuAtbni.model_MGREV assigned to Horse
+Model FYuAtbni.model_MGREV assigned to Cat
+Model FYuAtbni.model_MGREV assigned to Node2
+Model FYuAtbni.model_MGREV assigned to RhMonkey
+Model FYuAtbni.model_MGREV assigned to Baboon
+Model FYuAtbni.model_MGREV assigned to Node9
+Model FYuAtbni.model_MGREV assigned to Human
+Model FYuAtbni.model_MGREV assigned to Chimp
+Model FYuAtbni.model_MGREV assigned to Node12
+Model FYuAtbni.model_MGREV assigned to Node8
+Model FYuAtbni.model_MGREV assigned to Node1
+Model FYuAtbni.model_MGREV assigned to Rat
+Model FYuAtbni.model_MGREV assigned to Mouse
+The tips of the tree:FYuAtbni.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 is ASSUMED to have a reversible model
+Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used
+Variable 'FYuAtbni.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 285-th LF evaluation.
+Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618
+Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05
+Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063
+Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779
+Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488
+Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799
+Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05
+Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119
+Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06
+Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06
+Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05
+Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07
+Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06
+Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05
+Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+FYuAtbni.model_MGREV.theta_CG = 1
+FYuAtbni.model_MGREV.theta_AT = 1
+FYuAtbni.model_MGREV.theta_CT = 1
+FYuAtbni.model_MGREV.theta_GT = 1
+FYuAtbni.model_MGREV.theta_AC = 1
+FYuAtbni.model_MGREV.omega_0 = 1
+FYuAtbni.model_MGREV.omega_1 = 1
+FYuAtbni.tree_0.Pig.alpha = 0.000173063
+FYuAtbni.tree_0.Cow.alpha = 0.000186779
+FYuAtbni.tree_0.Node3.alpha = 1.15458e-05
+FYuAtbni.tree_0.Horse.alpha = 0.000174488
+FYuAtbni.tree_0.Cat.alpha = 0.000196799
+FYuAtbni.tree_0.Node2.alpha = 0.000173618
+FYuAtbni.model_MGREV.omega_2 = 1
+FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06
+FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06
+FYuAtbni.tree_0.Node9.alpha = 0.000140119
+FYuAtbni.tree_0.Human.alpha = 7.93383e-07
+FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06
+FYuAtbni.tree_0.Node12.alpha = 2.75759e-05
+FYuAtbni.tree_0.Node8.alpha = 4.67029e-05
+FYuAtbni.tree_0.Node1.alpha = 0.1
+FYuAtbni.tree_0.Rat.alpha = 8.26646e-05
+FYuAtbni.tree_0.Mouse.alpha = 0.000107933
+Optimization finished in 30 loop passes.
+3225 likelihood evaluation calls and 18018 matrix exponentiations calls were made
+
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Set GUI update interval to every 2992-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 'relax.test_pi' was not initialized prior to being used
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Set GUI update interval to every 2912-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 'relax.reference_pi' was not initialized prior to being used
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Overwritten previously defined function:'GpmgdDcy.rate_generator'
+Set GUI update interval to every 2827-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 'relax.unclassified_pi' 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:RPGDJipv.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
+relax.reference.theta_AC was already constrained in estimators.SetGlobals2
+relax.reference.theta_AG was already constrained in estimators.SetGlobals2
+relax.reference.theta_AT was already constrained in estimators.SetGlobals2
+relax.reference.theta_CG was already constrained in estimators.SetGlobals2
+relax.reference.theta_CT was already constrained in estimators.SetGlobals2
+relax.reference.theta_GT was already constrained in estimators.SetGlobals2
+relax.test.theta_AG was already constrained in estimators.SetGlobals2
+relax.unclassified.theta_AC was already constrained in estimators.SetGlobals2
+relax.unclassified.theta_AG was already constrained in estimators.SetGlobals2
+relax.unclassified.theta_AT was already constrained in estimators.SetGlobals2
+relax.unclassified.theta_CG was already constrained in estimators.SetGlobals2
+relax.unclassified.theta_CT was already constrained in estimators.SetGlobals2
+relax.unclassified.theta_GT was already constrained in estimators.SetGlobals2
+Variable 'RPGDJipv.tree_id_0.Pig.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Pig.t=1.375151388677762
+Variable 'RPGDJipv.tree_id_0.Cow.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cow.t=1.781953803671641
+Variable 'RPGDJipv.tree_id_0.Node3.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node3.t=0.7179600319187995
+Variable 'RPGDJipv.tree_id_0.Horse.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Horse.t=1.501071819834825
+Variable 'RPGDJipv.tree_id_0.Cat.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cat.t=1.973271183104609
+Variable 'RPGDJipv.tree_id_0.Node2.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node2.t=0.4461859649428869
+Variable 'RPGDJipv.tree_id_0.RhMonkey.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.RhMonkey.t=0.02655846610185887
+Variable 'RPGDJipv.tree_id_0.Baboon.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Baboon.t=0.01259838399210765
+Variable 'RPGDJipv.tree_id_0.Node9.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node9.t=0.1891887653227436
+Variable 'RPGDJipv.tree_id_0.Human.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Human.t=0
+Variable 'RPGDJipv.tree_id_0.Chimp.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Chimp.t=0.01302152547854442
+Variable 'RPGDJipv.tree_id_0.Node12.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node12.t=0.1235892304460588
+Variable 'RPGDJipv.tree_id_0.Node8.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node8.t=0.8108545924902142
+Variable 'RPGDJipv.tree_id_0.Node1.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node1.t=2.056868575380766
+Variable 'RPGDJipv.tree_id_0.Rat.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Rat.t=0.485173250741015
+Variable 'RPGDJipv.tree_id_0.Mouse.t' was not initialized prior to being used
+models.generic.SetBranchLength: RPGDJipv.tree_id_0.Mouse.t=0.8522851263393678
+Variable 'RPGDJipv.RPGDJipv.likelihoodFunction' was not initialized prior to being used
+Set GUI update interval to every 26-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+relax.test.theta_GT = 0.315401
+relax.test.theta_CT = 0.98654
+relax.test.theta_AC = 0.578523
+relax.test.theta_CG = 0.469908
+relax.test.theta_AT = 0.267066
+relax.reference.bsrel_mixture_aux_1 = 0.818182
+relax.reference.omega1 = 0.145496
+relax.reference.omega2 = 0.4601
+relax.reference.bsrel_mixture_aux_0 = 0.45
+relax.reference.omega3 = 7.27482
+relax.unclassified.omega3 = 1
+relax.unclassified.bsrel_mixture_aux_1 = 0.5
+relax.unclassified.omega2 = 1
+relax.unclassified.omega1 = 1
+relax.K = 1
+relax.unclassified.bsrel_mixture_aux_0 = 0.5
+RPGDJipv.tree_id_0.Pig.t = 1.37515
+RPGDJipv.tree_id_0.Cow.t = 1.78195
+RPGDJipv.tree_id_0.Node3.t = 0.71796
+RPGDJipv.tree_id_0.Horse.t = 1.50107
+RPGDJipv.tree_id_0.Cat.t = 1.97327
+RPGDJipv.tree_id_0.Node2.t = 0.446186
+RPGDJipv.tree_id_0.RhMonkey.t = 0.0265585
+RPGDJipv.tree_id_0.Baboon.t = 0.0125984
+RPGDJipv.tree_id_0.Node9.t = 0.189189
+RPGDJipv.tree_id_0.Human.t = 0
+RPGDJipv.tree_id_0.Chimp.t = 0.0130215
+RPGDJipv.tree_id_0.Node12.t = 0.123589
+RPGDJipv.tree_id_0.Node8.t = 0.810855
+RPGDJipv.tree_id_0.Node1.t = 2.05687
+RPGDJipv.tree_id_0.Rat.t = 0.485173
+RPGDJipv.tree_id_0.Mouse.t = 0.852285
+Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
+Optimization finished in 156 loop passes.
+19208 likelihood evaluation calls and 408312 matrix exponentiations calls were made
+
+Variable 'MPI_NODE_COUNT' was not initialized prior to being used
+Variable 'esPQwqFL.RPGDJipv.likelihoodFunction' was not initialized prior to being used
+Set GUI update interval to every 24-th LF evaluation.
+Optimization settings:
+	OPTIMIZATION_METHOD = 4
+	OPTIMIZATION_PRECISION = 0.001
+	MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
+
+Initial parameter values
+
+relax.test.theta_GT = 0.272534
+relax.test.theta_CT = 0.989376
+relax.test.theta_AC = 0.472659
+relax.test.theta_CG = 0.409729
+relax.test.theta_AT = 0.213063
+relax.reference.omega2 = 0
+relax.reference.omega3 = 1.81261
+relax.reference.bsrel_mixture_aux_1 = 0.398417
+relax.reference.bsrel_mixture_aux_0 = 0.26934
+relax.reference.omega1 = 0
+relax.unclassified.omega2 = 3.8108
+relax.unclassified.bsrel_mixture_aux_1 = 0.965815
+relax.unclassified.omega3 = 88.0589
+relax.unclassified.omega1 = 0
+relax.unclassified.bsrel_mixture_aux_0 = 0.488814
+RPGDJipv.tree_id_0.Pig.t = 0.288673
+RPGDJipv.tree_id_0.Cow.t = 0.415456
+RPGDJipv.tree_id_0.Node3.t = 0.165342
+RPGDJipv.tree_id_0.Horse.t = 0.373597
+RPGDJipv.tree_id_0.Cat.t = 0.4862
+RPGDJipv.tree_id_0.Node2.t = 0.071002
+RPGDJipv.tree_id_0.RhMonkey.t = 0.0109335
+RPGDJipv.tree_id_0.Baboon.t = 0.00559127
+RPGDJipv.tree_id_0.Node9.t = 0.0891892
+RPGDJipv.tree_id_0.Human.t = 0
+RPGDJipv.tree_id_0.Chimp.t = 0.0054891
+RPGDJipv.tree_id_0.Node12.t = 0.0161348
+RPGDJipv.tree_id_0.Node8.t = 0.405701
+RPGDJipv.tree_id_0.Node1.t = 1.12055
+RPGDJipv.tree_id_0.Rat.t = 0.217643
+RPGDJipv.tree_id_0.Mouse.t = 0.392946
+Optimization finished in 62 loop passes.
+6270 likelihood evaluation calls and 146691 matrix exponentiations calls were made
+
+Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used
\ No newline at end of file