Mercurial > repos > stephenshank > hyphy_gard
changeset 1:0ea9da9cd6ad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6da8a2296bb256e47852690cf2221a7c943d8adc-dirty
| author | stephenshank |
|---|---|
| date | Tue, 30 Oct 2018 10:56:18 -0400 |
| parents | 81b2d9fd1284 |
| children | 5501955d58e1 |
| files | errors.log hyphy_gard.xml hyphy_meme.xml macros.xml messages.log test-data/meme-out1.json |
| diffstat | 6 files changed, 10421 insertions(+), 100 deletions(-) [+] |
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--- a/errors.log Wed Sep 12 16:07:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ - -Error:HyPhy killed by signal 2 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_gard.xml Tue Oct 30 10:56:18 2018 -0400 @@ -0,0 +1,78 @@ +<?xml version="1.0"?> +<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0"> + <description>: Recombination Detection</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="1.0.4">translate-gard</requirement> + </expand> + <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} && + ln -s '$input_file' gard_input.fa && + echo `pwd`/gard_input.fa > tool_params && + echo "010010" >> tool_params && + echo $gencodeid >> tool_params && + echo $rate_cond.rate >> tool_params && + #if str($rate_cond.rate) != "1": + echo $rate_cond.rate_classes >> tool_params && + #end if + echo `pwd`/"gard_input.fa.GARD.json" >> tool_params && + @HYPHYMPI_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' && + translate-gard -i gard_input.fa -j gard_input.fa.GARD.json -o gard_input.fa.translated.json + ]]> + </command> + <inputs> + <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> + <param name="gencodeid" type="select" label="Genetic code"> + <option value="1">Universal code</option> + <option value="2">Vertebrate mitochondrial DNA code</option> + <option value="3">Yeast mitochondrial DNA code</option> + <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="5">Invertebrate mitochondrial DNA code</option> + <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> + <option value="7">Echinoderm mitochondrial DNA code</option> + <option value="8">Euplotid Nuclear code</option> + <option value="9">Alternative Yeast Nuclear code</option> + <option value="10">Ascidian mitochondrial DNA code</option> + <option value="11">Flatworm mitochondrial DNA code</option> + <option value="12">Blepharisma Nuclear code</option> + </param> + <conditional name="rate_cond"> + <param name="rate" type="select" label="Rate variation"> + <option value="1">None</option> + <option value="2">General Discrete</option> + <option value="3">Beta-Gamma</option> + </param> + <when value="1" /> + <when value="2"> + <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" /> + </when> + <when value="3"> + <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="gard_log" format="txt" /> + <data name="gard_output" format="json" from_work_dir="gard_input.fa.GARD.json" /> + <data name="translated" format="json" from_work_dir="gard_input.fa.translated.json" /> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fasta" value="gard-in2.fa" /> + <output name="gard_output" file="gard-out1.json" compare="sim_size" /> + <output name="translated" file="gard-out2.json" compare="sim_size" /> + </test> + </tests> + <help> + <![CDATA[ +GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block. + ]]> + </help> + <expand macro="citations"> + <citation type="doi">10.1093/molbev/msl051</citation> + </expand> +</tool>
--- a/hyphy_meme.xml Wed Sep 12 16:07:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -<?xml version="1.0"?> -<tool id="hyphy_gard" name="HyPhy-MEME" version="@VERSION@+galaxy0"> - <description>: Recombination Detection</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> - <command detect_errors="exit_code"> - <![CDATA[ - export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} && - ln -s '$input_file' meme_input.fa && - ln -s '$input_nhx' meme_input.nhx && - echo $gencodeid > tool_params && - echo `pwd`/meme_input.fa >> tool_params && - echo `pwd`/meme_input.nhx >> tool_params && - echo "1" >> tool_params && - echo "0.1" >> tool_params && - @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log' - ]]> - </command> - <inputs> - <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> - <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> - <param name="gencodeid" type="select" label="Genetic code"> - <option value="1">Universal code</option> - <option value="2">Vertebrate mitochondrial DNA code</option> - <option value="3">Yeast mitochondrial DNA code</option> - <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> - <option value="5">Invertebrate mitochondrial DNA code</option> - <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> - <option value="7">Echinoderm mitochondrial DNA code</option> - <option value="8">Euplotid Nuclear code</option> - <option value="9">Alternative Yeast Nuclear code</option> - <option value="10">Ascidian mitochondrial DNA code</option> - <option value="11">Flatworm mitochondrial DNA code</option> - <option value="12">Blepharisma Nuclear code</option> - </param> - <conditional name="rate_cond"> - <param name="rate" type="select" label="Rate variation"> - <option value="1">None</option> - <option value="2">General Discrete</option> - <option value="3">Beta-Gamma</option> - </param> - <when value="1" /> - <when value="2"> - <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" /> - </when> - <when value="3"> - <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" /> - </when> - </conditional> - </inputs> - <outputs> - <data name="meme_log" format="txt" /> - <data name="meme_output" format="json" from_work_dir="meme_input.fa.MEME.json" /> - </outputs> - <tests> - <test> - <param name="input_file" ftype="fasta" value="meme-in1.fa" /> - <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" /> - <output name="meme_output" file="meme-out1.json" compare="sim_size" /> - </test> - </tests> - <help> - <![CDATA[ -MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches. - ]]> - </help> - <expand macro="citations"> - <citation type="doi">10.1371/journal.pgen.1002764</citation> - </expand> -</tool>
--- a/macros.xml Wed Sep 12 16:07:49 2018 -0400 +++ b/macros.xml Tue Oct 30 10:56:18 2018 -0400 @@ -6,7 +6,7 @@ <yield /> </citations> </xml> - <token name="@VERSION@">2.3.12</token> + <token name="@VERSION@">2.3.14</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> @@ -18,4 +18,9 @@ export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]> </token> + <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && +export HYPHY_PATH=`dirname \$HYPHY` && +export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && +cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]> + </token> </macros> \ No newline at end of file
--- a/messages.log Wed Sep 12 16:07:49 2018 -0400 +++ b/messages.log Tue Oct 30 10:56:18 2018 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Tue Oct 30 10:56:18 2018 -0400 @@ -0,0 +1,9816 @@ +{ + "analysis":{ + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "version":"2.0.1", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "contact":"spond@temple.edu", + "requirements":"in-frame codon alignment and a phylogenetic tree" + }, + "fits":{ + "Nucleotide GTR":{ + "Log Likelihood":-4394.17778442101, + "estimated parameters":47, + "AIC-c":8882.482274823486, + "Equilibrium frequencies":[ + [0.3460163217230355], + [0.1876507375623983], + [0.2296889898480005], + [0.2366439508665657] + ], + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337, + "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039, + "Substitution rate from nucleotide C to nucleotide T":1.290725939052547, + "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102 + }, + "display order":0 + }, + "Global MG94xREV":{ + "Log Likelihood":-4272.739394378317, + "estimated parameters":54, + "AIC-c":8653.980859587502, + "Equilibrium frequencies":[ + [0.04794212053691846], + [0.02918423386756777], + [0.03061835466109362], + [0.03395226455636327], + [0.02063374857573568], + [0.01256056547467788], + [0.01317779490778274], + [0.01461267216775245], + [0.02309512129134449], + [0.01405889880167917], + [0.01474975672164567], + [0.01635579860179934], + [0.03032452824999034], + [0.01845972006369387], + [0.01936683547765817], + [0.02147561255447049], + [0.02137643485619778], + [0.01301266750638816], + [0.01365211335015547], + [0.01513863724385318], + [0.009200176740799796], + [0.005600505497450756], + [0.005875715784779066], + [0.006515498921838312], + [0.01029765371767897], + [0.006268582428525358], + [0.0065766221888793], + [0.007292724214466442], + [0.01352110201678854], + [0.00823082081030041], + [0.008635285471781717], + [0.009575547089413102], + [0.03891475766269277], + [0.02368892689369449], + [0.02485300688252417], + [0.02755915117048418], + [0.01674847329457107], + [0.01019544726180969], + [0.01069645417478218], + [0.01186114818960848], + [0.0187463766345312], + [0.01141164874946168], + [0.01197242011780667], + [0.01327604894903844], + [0.02461450713626915], + [0.01498380807429274], + [0.01572011627491417], + [0.01743181671681681], + [0.02096427272215724], + [0.0243893513506083], + [0.01482209656025475], + [0.009022786801619234], + [0.009466168876559794], + [0.0104969020572672], + [0.01009910316608133], + [0.0105953757052942], + [0.01174906369078435], + [0.02178339453036125], + [0.01326039969204127], + [0.01391201915942615], + [0.01542684315477715] + ], + "Rate Distributions":{ + "non-synonymous/synonymous rate ratio for *test*":[ + [0.2936035676191999, 1] + ] + }, + "display order":1 + } + }, + "timers":{ + "Total time":{ + "timer":816, + "order":0 + }, + "Model fitting":{ + "timer":12, + "order":1 + }, + "MEME analysis":{ + "timer":803, + "order":2 + } + }, + "tested":{ + "0":{ + "TREESPARROW_HENAN_1_2004":"test", + "TREESPARROW_HENAN_3_2004":"test", + "Node6":"test", + "TREESPARROW_HENAN_4_2004":"test", + "Node5":"test", + "CHICKEN_HEBEI_326_2005":"test", + "SWINE_ANHUI_1_2004":"test", + "TREESPARROW_HENAN_2_2004":"test", + "Node12":"test", + "Node10":"test", + "Node4":"test", + "CHICKEN_HONGKONG_915_97":"test", + "GOOSE_HONGKONG_W355_97":"test", + "DUCK_HONGKONG_Y283_97":"test", + "Node19":"test", + "Node17":"test", + "HONGKONG_1_97_98":"test", + "Node16":"test", + "HONGKONG_1_538_97":"test", + "Node15":"test", + "Node3":"test", + "DUCK_GUANGZHOU_20_2005":"test", + "GOOSE_SHANTOU_2216_2005":"test", + "Node26":"test", + "PEREGRINEFALCON_HK_D0028_2004":"test", + "Node25":"test", + "CK_HK_WF157_2003":"test", + "Node24":"test", + "Node2":"test", + "HUMAN_VIETNAM_CL105_2005":"test", + "DUCK_VIETNAM_376_2005":"test", + "Node33":"test", + "HUMAN_VIETNAM_3062_2004":"test", + "Node32":"test", + "MALLARD_VIETNAM_16_2003":"test", + "Node31":"test", + "Node1":"test", + "CHICKEN_CK_160_2005":"test", + "DUCK_VIETNAM_272_2005":"test" + } + }, + "input":{ + "file name":"/tmp/tmpv_gXOY/job_working_directory/002/2719/working/meme_input.fa", + "number of sequences":21, + "number of sites":566, + "partition count":1, + "trees":{ + "0":"(((((((TREESPARROW_HENAN_1_2004:0.0111334,TREESPARROW_HENAN_3_2004:0.00619375)Node6:0.000995666,TREESPARROW_HENAN_4_2004:0.00435165)Node5:0.00226776,(CHICKEN_HEBEI_326_2005:0.0210089,(SWINE_ANHUI_1_2004:0.00770239,TREESPARROW_HENAN_2_2004:0.00906278)Node12:0.00209522)Node10:0.00388724)Node4:0.00340492,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1,DUCK_HONGKONG_Y283_97:0.00279842)Node19:0.00289977)Node17:0.00130638,HONGKONG_1_97_98:0.00384493)Node16:0.000182536,HONGKONG_1_538_97:-1)Node15:0.0209617)Node3:0.00313061,(((DUCK_GUANGZHOU_20_2005:0.00629939,GOOSE_SHANTOU_2216_2005:0.00620784)Node26:0.00253061,PEREGRINEFALCON_HK_D0028_2004:0.0036083)Node25:0.0032889,CK_HK_WF157_2003:0.0066313)Node24:0.0046553)Node2:0.0116809,(((HUMAN_VIETNAM_CL105_2005:0.00652152,DUCK_VIETNAM_376_2005:0.00787762)Node33:0.00196789,HUMAN_VIETNAM_3062_2004:0.0016414)Node32:0.000312551,MALLARD_VIETNAM_16_2003:0.00324422)Node31:0.000412598)Node1:0.000340091,CHICKEN_CK_160_2005:0.00616834,DUCK_VIETNAM_272_2005:0.0094653)" + } + }, + "data partitions":{ + "0":{ + "name":"meme.filter.default", + "coverage":[ + [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565] + ] + } + }, + "branch attributes":{ + "0":{ + "TREESPARROW_HENAN_1_2004":{ + "original name":"TREESPARROW_HENAN_1_2004", + "Nucleotide GTR":0.01066479252384179, + "Global 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label", + "display order":566 + } + } + }, + "MLE":{ + "headers":[ + ["alpha;", "Synonymous substitution rate at a site"], + ["β<sup>-</sup>", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"], + ["p<sup>-</sup>", "Mixture distribution weight allocated to β<sup>-</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection"], + ["β<sup>+</sup>", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"], + ["p<sup>+</sup>", "Mixture distribution weight allocated to β<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection"], + ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> > 0 <emph>and<emph> β<sup>+</sup> > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β<sup>+</sup> rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ], + "content":{ + "0":[ + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [3.518153136581004e-17, 3.243045519502881e-17, 1.022166200682819e-08, 1.291751771813077, 0.999999989778338, 0.5894186108086057, 0.4058674930166563, 1, 0.3590955405423049], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1.015244473805534e-08, 2.805293595854978, 0.9999999898475552, 1.564165559839974, 0.2310493931422519, 2, 0.7798467493791119], + [3.097517451103013, 3.633546560692318e-13, 0.006739028294327419, 0, 0.9932609717056726, 0, 0.6666666666666666, 0, 0.3592491319023247], + [0, 0, 1.066894692458495e-08, 2.051552228725943, 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