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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
author stephenshank
date Mon, 10 Sep 2018 16:01:07 -0400
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children c5f1257ff9f5
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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/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
Loaded 'frequencies.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/frequencies.bf
Already loaded '../all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.bf
Loaded 'parameters.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/parameters.bf
Loaded 'GrabBag' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/Utility/GrabBag.bf
Overwritten previously defined function:'_sortStringsAux'
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 'model_functions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/model_functions.bf
Already loaded 'libv3/all-terms.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/all-terms.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
Already loaded '../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Already loaded '../convenience/regexp.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/convenience/regexp.bf
Loaded '../models/DNA/GTR.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/DNA/GTR.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
Already loaded '../../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 '../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/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
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 '../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
Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
Loaded 'MG_REV.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/models/codon/MG_REV.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
Already loaded '../../UtilityFunctions.bf' from /Users/stephenshank/Documents/hyphy/res/TemplateBatchFiles/libv3/UtilityFunctions.bf
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