Mercurial > repos > rdvelazquez > hyphy_relax

annotate test-data/messages.log @ 4:7782bb7bc7b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
author rdvelazquez
date Tue, 12 Feb 2019 08:53:39 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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2 Loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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3 Loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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4 Loaded 'IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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5 Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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6 Loaded 'convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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7 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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8 Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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9 Loaded 'libv3/models/codon/MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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10 Loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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11 Loaded '../tasks/genetic_code.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/genetic_code.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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12 Loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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13 Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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14 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
15 Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
16 Loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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17 Loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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18 Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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19 Loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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20 Loaded 'GrabBag' from /usr/local/lib/hyphy/TemplateBatchFiles/Utility/GrabBag.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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21 Overwritten previously defined function:'_sortStringsAux'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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22 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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23 Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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24 Loaded 'model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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25 Already loaded 'DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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26 Already loaded 'parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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27 Already loaded 'frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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28 Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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29 Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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30 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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31 Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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32 Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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33 Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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34 Loaded 'libv3/tasks/estimators.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/estimators.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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35 Already loaded '../models/model_functions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/model_functions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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36 Loaded '../models/DNA/GTR.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA/GTR.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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37 Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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38 Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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39 Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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40 Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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41 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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42 Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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43 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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44 Loaded 'libv3/tasks/alignments.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/alignments.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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45 Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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46 Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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47 Loaded 'libv3/tasks/trees.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/trees.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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48 Already loaded '../IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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49 Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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50 Already loaded '../convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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51 Already loaded '../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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52 Loaded 'TreeTools' from /usr/local/lib/hyphy/TemplateBatchFiles/TreeTools.ibf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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53 Loaded 'modules/io_functions.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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54 Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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55 Already loaded 'libv3/IOFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/IOFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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56 Already loaded 'libv3/convenience/regexp.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/regexp.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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57 Already loaded 'libv3/all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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58 Loaded 'modules/selection_lib.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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59 Loaded 'libv3/models/codon/BS_REL.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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60 Already loaded '../codon.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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61 Already loaded '../DNA.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/DNA.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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62 Already loaded '../parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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63 Already loaded '../frequencies.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/frequencies.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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64 Already loaded '../../UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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65 Already loaded 'MG_REV.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
66 Loaded '../../convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
67 Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
68 Already loaded 'libv3/convenience/math.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/math.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
69 Loaded 'libv3/tasks/mpi.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/tasks/mpi.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
70 Already loaded '../all-terms.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/all-terms.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
71 Already loaded '../models/parameters.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/models/parameters.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
72 Variable 'NORMALIZE_SEQUENCE_NAMES' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
73 Variable 'ASSUME_REVERSIBLE_MODELS' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
74 Loaded 'modules/shared-load-file.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
75 Variable 'MARKDOWN_OUTPUT' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
76 Already loaded 'libv3/convenience/matrix.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/convenience/matrix.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
77 Already loaded 'libv3/UtilityFunctions.bf' from /usr/local/lib/hyphy/TemplateBatchFiles/libv3/UtilityFunctions.bf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
78 Variable 'JOYpYPkv.skipCodeSelectionStep' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
79 Row and/or column partition is empty. All the data will be used by default.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
80 Variable 'NEXUS_FILE_TREE_MATRIX' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
81 Variable 'utility.ToggleEnvVariable.cache' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
82 Variable 'TREE_NODE_NAME_MAPPING' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
83 Variable '_thZqV_F.PROMPT_FOR_FILE' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
84 Variable 'END_OF_FILE' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
85 Variable '_DO_TREE_REBALANCE_' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
86 Variable '_KEEP_I_LABELS_' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
87 Variable 'INCLUDE_MODEL_SPECS' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
88 Variable 'utility.ForEachPair.warn_non_rentrant' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
89 Row and/or column partition is empty. All the data will be used by default.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
90 Row and/or column partition is empty. All the data will be used by default.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
91 Loaded 'modules/grid_compute.ibf' from /usr/local/lib/hyphy/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
92 Variable 'QPmholqs.cache' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
93 Row and/or column partition is empty. All the data will be used by default.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
94 Variable 'COUNT_GAPS_IN_FREQUENCIES' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
95 Variable 'MiVdxtWn.model_pi' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
96 Model MiVdxtWn.model assigned to Pig
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
97 Model MiVdxtWn.model assigned to Cow
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
98 Model MiVdxtWn.model assigned to Node3
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
99 Model MiVdxtWn.model assigned to Horse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
100 Model MiVdxtWn.model assigned to Cat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
101 Model MiVdxtWn.model assigned to Node2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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102 Model MiVdxtWn.model assigned to RhMonkey
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
103 Model MiVdxtWn.model assigned to Baboon
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
104 Model MiVdxtWn.model assigned to Node9
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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105 Model MiVdxtWn.model assigned to Human
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
106 Model MiVdxtWn.model assigned to Chimp
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
107 Model MiVdxtWn.model assigned to Node12
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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108 Model MiVdxtWn.model assigned to Node8
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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109 Model MiVdxtWn.model assigned to Node1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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110 Model MiVdxtWn.model assigned to Rat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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111 Model MiVdxtWn.model assigned to Mouse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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112 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}
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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113
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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114 Pseudo-optimal path's cost 2330 vs 4284 for 1..k=> a 1.83863 x improvement
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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115 Partition 0 is ASSUMED to have a reversible model
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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116 Variable 'USE_LAST_RESULTS' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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117 Variable 'MiVdxtWn.tree_0.Pig.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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118 models.generic.SetBranchLength: MiVdxtWn.tree_0.Pig.t=0.3974535884114245
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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119 Variable 'MiVdxtWn.tree_0.Cow.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
120 models.generic.SetBranchLength: MiVdxtWn.tree_0.Cow.t=0.5732857515739808
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
121 Variable 'MiVdxtWn.tree_0.Node3.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
122 models.generic.SetBranchLength: MiVdxtWn.tree_0.Node3.t=0.2285810062933711
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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123 Variable 'MiVdxtWn.tree_0.Horse.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
124 models.generic.SetBranchLength: MiVdxtWn.tree_0.Horse.t=0.445313802634098
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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125 Variable 'MiVdxtWn.tree_0.Cat.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
126 models.generic.SetBranchLength: MiVdxtWn.tree_0.Cat.t=0.7112847618952328
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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127 Variable 'MiVdxtWn.tree_0.Node2.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
128 models.generic.SetBranchLength: MiVdxtWn.tree_0.Node2.t=0.1574326532610344
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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129 Variable 'MiVdxtWn.tree_0.RhMonkey.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
130 models.generic.SetBranchLength: MiVdxtWn.tree_0.RhMonkey.t=0.00541241057687097
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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131 Variable 'MiVdxtWn.tree_0.Baboon.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
132 models.generic.SetBranchLength: MiVdxtWn.tree_0.Baboon.t=0.008348273981595522
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
133 Variable 'MiVdxtWn.tree_0.Node9.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
134 models.generic.SetBranchLength: MiVdxtWn.tree_0.Node9.t=0.06106219833449517
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
135 Variable 'MiVdxtWn.tree_0.Human.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
136 models.generic.SetBranchLength: MiVdxtWn.tree_0.Human.t=0.01168167424258652
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
137 Variable 'MiVdxtWn.tree_0.Chimp.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
138 models.generic.SetBranchLength: MiVdxtWn.tree_0.Chimp.t=0.00214616181187092
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
139 Variable 'MiVdxtWn.tree_0.Node12.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
140 models.generic.SetBranchLength: MiVdxtWn.tree_0.Node12.t=0.03189158847602433
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
141 Variable 'MiVdxtWn.tree_0.Node8.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
142 models.generic.SetBranchLength: MiVdxtWn.tree_0.Node8.t=0.2735913110261884
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
143 Variable 'MiVdxtWn.tree_0.Node1.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
144 models.generic.SetBranchLength: MiVdxtWn.tree_0.Node1.t=0.9154145654683773
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
145 Variable 'MiVdxtWn.tree_0.Rat.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
146 models.generic.SetBranchLength: MiVdxtWn.tree_0.Rat.t=0.1368762373082833
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
147 Variable 'MiVdxtWn.tree_0.Mouse.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
148 models.generic.SetBranchLength: MiVdxtWn.tree_0.Mouse.t=0.2630995612925615
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
149 Variable 'MiVdxtWn.MiVdxtWn.likelihoodFunction' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
150 Variable 'SAVE_OPT_STATUS_TO' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
151 Set GUI update interval to every 331-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
152 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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153 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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154 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
155 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
156
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
157 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
158
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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159 MiVdxtWn.model.theta_GT = 0.25
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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160 MiVdxtWn.model.theta_CG = 0.25
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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161 MiVdxtWn.model.theta_CT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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162 MiVdxtWn.model.theta_AT = 0.25
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
163 MiVdxtWn.model.theta_AC = 0.25
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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164 MiVdxtWn.tree_0.Pig.t = 0.397454
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
165 MiVdxtWn.tree_0.Cow.t = 0.573286
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
166 MiVdxtWn.tree_0.Node3.t = 0.228581
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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167 MiVdxtWn.tree_0.Horse.t = 0.445314
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
168 MiVdxtWn.tree_0.Cat.t = 0.711285
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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169 MiVdxtWn.tree_0.Node2.t = 0.157433
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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170 MiVdxtWn.tree_0.RhMonkey.t = 0.00541241
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
171 MiVdxtWn.tree_0.Baboon.t = 0.00834827
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
172 MiVdxtWn.tree_0.Node9.t = 0.0610622
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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173 MiVdxtWn.tree_0.Human.t = 0.0116817
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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174 MiVdxtWn.tree_0.Chimp.t = 0.00214616
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
175 MiVdxtWn.tree_0.Node12.t = 0.0318916
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
176 MiVdxtWn.tree_0.Node8.t = 0.273591
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
177 MiVdxtWn.tree_0.Node1.t = 0.915415
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
178 MiVdxtWn.tree_0.Rat.t = 0.136876
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
179 MiVdxtWn.tree_0.Mouse.t = 0.2631
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
180 Optimization finished in 24 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
181 1467 likelihood evaluation calls and 10507 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
182
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
183 Variable 'BRANCH_LENGTH_STENCIL' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
184 Variable 'MiVdxtWn.option' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
185 Variable 'relax.terms.json.nucleotide_gtr' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
186 Variable 'Unknown' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
187 Variable 'SRnFPBcA.initial_value' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
188 Variable 'FYuAtbni.data_filter' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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189 Row and/or column partition is empty. All the data will be used by default.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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190 Set GUI update interval to every 2879-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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191 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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192 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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193 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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194 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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195
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
196 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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197
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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198 frequencies._aux.CF3x4.p0_0 = 0.415775
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
199 frequencies._aux.CF3x4.p0_1 = 0.250343
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
200 frequencies._aux.CF3x4.p0_2 = 0.652625
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
201 frequencies._aux.CF3x4.p1_0 = 0.399465
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
202 frequencies._aux.CF3x4.p1_1 = 0.28317
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
203 frequencies._aux.CF3x4.p1_2 = 0.391304
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
204 frequencies._aux.CF3x4.p2_0 = 0.253743
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
205 frequencies._aux.CF3x4.p2_1 = 0.314941
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
206 frequencies._aux.CF3x4.p2_2 = 0.521444
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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207 Optimization finished in 5 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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208 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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209
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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210 Variable 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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211 Model FYuAtbni.model_MGREV assigned to Pig
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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212 Model FYuAtbni.model_MGREV assigned to Cow
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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213 Model FYuAtbni.model_MGREV assigned to Node3
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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214 Model FYuAtbni.model_MGREV assigned to Horse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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215 Model FYuAtbni.model_MGREV assigned to Cat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
216 Model FYuAtbni.model_MGREV assigned to Node2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
217 Model FYuAtbni.model_MGREV assigned to RhMonkey
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
218 Model FYuAtbni.model_MGREV assigned to Baboon
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
219 Model FYuAtbni.model_MGREV assigned to Node9
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
220 Model FYuAtbni.model_MGREV assigned to Human
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
221 Model FYuAtbni.model_MGREV assigned to Chimp
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
222 Model FYuAtbni.model_MGREV assigned to Node12
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
223 Model FYuAtbni.model_MGREV assigned to Node8
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
224 Model FYuAtbni.model_MGREV assigned to Node1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
225 Model FYuAtbni.model_MGREV assigned to Rat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
226 Model FYuAtbni.model_MGREV assigned to Mouse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
227 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}
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
228
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
229 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
230 Partition 0 is ASSUMED to have a reversible model
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
231 Variable 'FYuAtbni.FYuAtbni.likelihoodFunction' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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232 Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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233 Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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234 Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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235 Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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236 Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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237 Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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238 Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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239 Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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240 Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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241 Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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242 Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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243 Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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244 Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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245 Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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246 Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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247 Variable 'FYuAtbni.tree_0.Mouse.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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248 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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249 Set GUI update interval to every 187-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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250 Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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251 Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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252 Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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253 Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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254 Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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255 Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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256 Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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257 Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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258 Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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259 Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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260 Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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261 Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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262 Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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263 Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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264 Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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265 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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266 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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267 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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268 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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269
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270 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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271
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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272 FYuAtbni.model_MGREV.theta_GT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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273 FYuAtbni.model_MGREV.theta_CT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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274 FYuAtbni.model_MGREV.theta_AC = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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275 FYuAtbni.model_MGREV.theta_CG = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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276 FYuAtbni.model_MGREV.theta_AT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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277 FYuAtbni.model_MGREV.omega_0 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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278 FYuAtbni.model_MGREV.omega_1 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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279 FYuAtbni.tree_0.Pig.alpha = 0.000173063
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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280 FYuAtbni.tree_0.Cow.alpha = 0.000186779
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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281 FYuAtbni.tree_0.Node3.alpha = 1.15458e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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282 FYuAtbni.tree_0.Horse.alpha = 0.000174488
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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283 FYuAtbni.tree_0.Cat.alpha = 0.000196799
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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284 FYuAtbni.tree_0.Node2.alpha = 0.000173618
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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285 FYuAtbni.model_MGREV.omega_2 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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286 FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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287 FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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288 FYuAtbni.tree_0.Node9.alpha = 0.000140119
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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289 FYuAtbni.tree_0.Human.alpha = 7.93383e-07
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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290 FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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291 FYuAtbni.tree_0.Node12.alpha = 2.75759e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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292 FYuAtbni.tree_0.Node8.alpha = 4.67029e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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293 FYuAtbni.tree_0.Node1.alpha = 0.1
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294 FYuAtbni.tree_0.Rat.alpha = 8.26646e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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295 FYuAtbni.tree_0.Mouse.alpha = 0.000107933
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
296 Optimization finished in 37 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
297 3110 likelihood evaluation calls and 18285 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
298
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
299 Row and/or column partition is empty. All the data will be used by default.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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300 Set GUI update interval to every 2926-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
301 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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302 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
303 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
304 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
305
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
306 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
307
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
308 frequencies._aux.CF3x4.p0_0 = 0.415775
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
309 frequencies._aux.CF3x4.p0_1 = 0.250343
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
310 frequencies._aux.CF3x4.p0_2 = 0.652625
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
311 frequencies._aux.CF3x4.p1_0 = 0.399465
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
312 frequencies._aux.CF3x4.p1_1 = 0.28317
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
313 frequencies._aux.CF3x4.p1_2 = 0.391304
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
314 frequencies._aux.CF3x4.p2_0 = 0.253743
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
315 frequencies._aux.CF3x4.p2_1 = 0.314941
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
316 frequencies._aux.CF3x4.p2_2 = 0.521444
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
317 Optimization finished in 5 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
318 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
319
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
320 Variable 'FYuAtbni.model_MGREV_pi' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
321 Model FYuAtbni.model_MGREV assigned to Pig
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
322 Model FYuAtbni.model_MGREV assigned to Cow
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
323 Model FYuAtbni.model_MGREV assigned to Node3
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
324 Model FYuAtbni.model_MGREV assigned to Horse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
325 Model FYuAtbni.model_MGREV assigned to Cat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
326 Model FYuAtbni.model_MGREV assigned to Node2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
327 Model FYuAtbni.model_MGREV assigned to RhMonkey
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
328 Model FYuAtbni.model_MGREV assigned to Baboon
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
329 Model FYuAtbni.model_MGREV assigned to Node9
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
330 Model FYuAtbni.model_MGREV assigned to Human
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
331 Model FYuAtbni.model_MGREV assigned to Chimp
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
332 Model FYuAtbni.model_MGREV assigned to Node12
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
333 Model FYuAtbni.model_MGREV assigned to Node8
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
334 Model FYuAtbni.model_MGREV assigned to Node1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
335 Model FYuAtbni.model_MGREV assigned to Rat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
336 Model FYuAtbni.model_MGREV assigned to Mouse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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337 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}
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
338
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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diff changeset
339 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
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340 Partition 0 is ASSUMED to have a reversible model
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
341 Variable 'FYuAtbni.tree_0.Rat.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
342 Variable 'FYuAtbni.tree_0.Node1.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
343 Variable 'FYuAtbni.tree_0.Node8.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
344 Variable 'FYuAtbni.tree_0.Cat.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
345 Variable 'FYuAtbni.tree_0.Node12.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
346 Variable 'FYuAtbni.tree_0.Chimp.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
347 Variable 'FYuAtbni.tree_0.Human.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
348 Variable 'FYuAtbni.tree_0.Node9.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
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diff changeset
349 Variable 'FYuAtbni.tree_0.Node2.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
350 Variable 'FYuAtbni.tree_0.Baboon.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
351 Variable 'FYuAtbni.tree_0.RhMonkey.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
352 Variable 'FYuAtbni.tree_0.Node3.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
353 Variable 'FYuAtbni.tree_0.Cow.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
354 Variable 'FYuAtbni.tree_0.Pig.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
355 Variable 'FYuAtbni.tree_0.Horse.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
356 Variable 'FYuAtbni.tree_0.Mouse.alpha' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
357 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
358 Set GUI update interval to every 285-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
359 Initial guess for FYuAtbni.tree_0.Node2.alpha is 0.000173618
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
360 Initial guess for FYuAtbni.tree_0.Node3.alpha is 1.15458e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
361 Initial guess for FYuAtbni.tree_0.Pig.alpha is 0.000173063
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
362 Initial guess for FYuAtbni.tree_0.Cow.alpha is 0.000186779
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
363 Initial guess for FYuAtbni.tree_0.Horse.alpha is 0.000174488
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
364 Initial guess for FYuAtbni.tree_0.Cat.alpha is 0.000196799
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
365 Initial guess for FYuAtbni.tree_0.Node8.alpha is 4.67029e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
366 Initial guess for FYuAtbni.tree_0.Node9.alpha is 0.000140119
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
367 Initial guess for FYuAtbni.tree_0.RhMonkey.alpha is 4.64183e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
368 Initial guess for FYuAtbni.tree_0.Baboon.alpha is 1.75863e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
369 Initial guess for FYuAtbni.tree_0.Node12.alpha is 2.75759e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
370 Initial guess for FYuAtbni.tree_0.Human.alpha is 7.93383e-07
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
371 Initial guess for FYuAtbni.tree_0.Chimp.alpha is 1.32491e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
372 Initial guess for FYuAtbni.tree_0.Rat.alpha is 8.26646e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
373 Initial guess for FYuAtbni.tree_0.Mouse.alpha is 0.000107933
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
374 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
375 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
376 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
377 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
378
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
379 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
380
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
381 FYuAtbni.model_MGREV.theta_CG = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
382 FYuAtbni.model_MGREV.theta_AT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
383 FYuAtbni.model_MGREV.theta_CT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
384 FYuAtbni.model_MGREV.theta_GT = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
385 FYuAtbni.model_MGREV.theta_AC = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
386 FYuAtbni.model_MGREV.omega_0 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
387 FYuAtbni.model_MGREV.omega_1 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
388 FYuAtbni.tree_0.Pig.alpha = 0.000173063
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
389 FYuAtbni.tree_0.Cow.alpha = 0.000186779
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
390 FYuAtbni.tree_0.Node3.alpha = 1.15458e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
391 FYuAtbni.tree_0.Horse.alpha = 0.000174488
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
392 FYuAtbni.tree_0.Cat.alpha = 0.000196799
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
393 FYuAtbni.tree_0.Node2.alpha = 0.000173618
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
394 FYuAtbni.model_MGREV.omega_2 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
395 FYuAtbni.tree_0.RhMonkey.alpha = 4.64183e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
396 FYuAtbni.tree_0.Baboon.alpha = 1.75863e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
397 FYuAtbni.tree_0.Node9.alpha = 0.000140119
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
398 FYuAtbni.tree_0.Human.alpha = 7.93383e-07
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
399 FYuAtbni.tree_0.Chimp.alpha = 1.32491e-06
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
400 FYuAtbni.tree_0.Node12.alpha = 2.75759e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
401 FYuAtbni.tree_0.Node8.alpha = 4.67029e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
402 FYuAtbni.tree_0.Node1.alpha = 0.1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
403 FYuAtbni.tree_0.Rat.alpha = 8.26646e-05
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
404 FYuAtbni.tree_0.Mouse.alpha = 0.000107933
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
405 Optimization finished in 30 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
406 3225 likelihood evaluation calls and 18018 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
407
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
408 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
409 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
410 Set GUI update interval to every 2992-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
411 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
412 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
413 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
414 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
415
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
416 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
417
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
418 frequencies._aux.CF3x4.p0_0 = 0.415775
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
419 frequencies._aux.CF3x4.p0_1 = 0.250343
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
420 frequencies._aux.CF3x4.p0_2 = 0.652625
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
421 frequencies._aux.CF3x4.p1_0 = 0.399465
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
422 frequencies._aux.CF3x4.p1_1 = 0.28317
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
423 frequencies._aux.CF3x4.p1_2 = 0.391304
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
424 frequencies._aux.CF3x4.p2_0 = 0.253743
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
425 frequencies._aux.CF3x4.p2_1 = 0.314941
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
426 frequencies._aux.CF3x4.p2_2 = 0.521444
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
427 Optimization finished in 5 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
428 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
429
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
430 Variable 'relax.test_pi' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
431 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
432 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
433 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
434 Set GUI update interval to every 2912-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
435 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
436 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
437 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
438 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
439
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
440 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
441
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
442 frequencies._aux.CF3x4.p0_0 = 0.415775
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
443 frequencies._aux.CF3x4.p0_1 = 0.250343
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
444 frequencies._aux.CF3x4.p0_2 = 0.652625
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
445 frequencies._aux.CF3x4.p1_0 = 0.399465
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
446 frequencies._aux.CF3x4.p1_1 = 0.28317
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
447 frequencies._aux.CF3x4.p1_2 = 0.391304
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
448 frequencies._aux.CF3x4.p2_0 = 0.253743
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
449 frequencies._aux.CF3x4.p2_1 = 0.314941
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
450 frequencies._aux.CF3x4.p2_2 = 0.521444
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
451 Optimization finished in 5 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
452 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
453
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
454 Variable 'relax.reference_pi' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
455 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
456 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
457 Overwritten previously defined function:'GpmgdDcy.rate_generator'
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
458 Set GUI update interval to every 2827-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
459 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
460 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
461 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
462 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
463
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
464 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
465
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
466 frequencies._aux.CF3x4.p0_0 = 0.415775
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
467 frequencies._aux.CF3x4.p0_1 = 0.250343
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
468 frequencies._aux.CF3x4.p0_2 = 0.652625
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
469 frequencies._aux.CF3x4.p1_0 = 0.399465
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
470 frequencies._aux.CF3x4.p1_1 = 0.28317
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
471 frequencies._aux.CF3x4.p1_2 = 0.391304
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
472 frequencies._aux.CF3x4.p2_0 = 0.253743
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
473 frequencies._aux.CF3x4.p2_1 = 0.314941
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
474 frequencies._aux.CF3x4.p2_2 = 0.521444
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
475 Optimization finished in 5 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
476 184 likelihood evaluation calls and 0 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
477
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
478 Variable 'relax.unclassified_pi' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
479 No nodel was assigned to Pig
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
480 No nodel was assigned to Cow
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
481 No nodel was assigned to Node3
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
482 No nodel was assigned to Horse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
483 No nodel was assigned to Cat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
484 No nodel was assigned to Node2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
485 No nodel was assigned to RhMonkey
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
486 No nodel was assigned to Baboon
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
487 No nodel was assigned to Node9
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
488 No nodel was assigned to Human
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
489 No nodel was assigned to Chimp
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
490 No nodel was assigned to Node12
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
491 No nodel was assigned to Node8
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
492 No nodel was assigned to Node1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
493 No nodel was assigned to Rat
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
494 No nodel was assigned to Mouse
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
495 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}
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
496
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
497 Pseudo-optimal path's cost 2286 vs 2927 for 1..k=> a 1.2804 x improvement
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
498 Partition 0 is ASSUMED to have a reversible model
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
499 relax.reference.theta_AC was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
500 relax.reference.theta_AG was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
501 relax.reference.theta_AT was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
502 relax.reference.theta_CG was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
503 relax.reference.theta_CT was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
504 relax.reference.theta_GT was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
505 relax.test.theta_AG was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
506 relax.unclassified.theta_AC was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
507 relax.unclassified.theta_AG was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
508 relax.unclassified.theta_AT was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
509 relax.unclassified.theta_CG was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
510 relax.unclassified.theta_CT was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
511 relax.unclassified.theta_GT was already constrained in estimators.SetGlobals2
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
512 Variable 'RPGDJipv.tree_id_0.Pig.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
513 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Pig.t=1.375151388677762
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
514 Variable 'RPGDJipv.tree_id_0.Cow.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
515 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cow.t=1.781953803671641
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
516 Variable 'RPGDJipv.tree_id_0.Node3.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
517 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node3.t=0.7179600319187995
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
518 Variable 'RPGDJipv.tree_id_0.Horse.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
519 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Horse.t=1.501071819834825
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
520 Variable 'RPGDJipv.tree_id_0.Cat.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
521 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Cat.t=1.973271183104609
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
522 Variable 'RPGDJipv.tree_id_0.Node2.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
523 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node2.t=0.4461859649428869
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
524 Variable 'RPGDJipv.tree_id_0.RhMonkey.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
525 models.generic.SetBranchLength: RPGDJipv.tree_id_0.RhMonkey.t=0.02655846610185887
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
526 Variable 'RPGDJipv.tree_id_0.Baboon.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
527 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Baboon.t=0.01259838399210765
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
528 Variable 'RPGDJipv.tree_id_0.Node9.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
529 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node9.t=0.1891887653227436
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
530 Variable 'RPGDJipv.tree_id_0.Human.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
531 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Human.t=0
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
532 Variable 'RPGDJipv.tree_id_0.Chimp.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
533 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Chimp.t=0.01302152547854442
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
534 Variable 'RPGDJipv.tree_id_0.Node12.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
535 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node12.t=0.1235892304460588
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
536 Variable 'RPGDJipv.tree_id_0.Node8.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
537 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node8.t=0.8108545924902142
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
538 Variable 'RPGDJipv.tree_id_0.Node1.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
539 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Node1.t=2.056868575380766
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
540 Variable 'RPGDJipv.tree_id_0.Rat.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
541 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Rat.t=0.485173250741015
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
542 Variable 'RPGDJipv.tree_id_0.Mouse.t' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
543 models.generic.SetBranchLength: RPGDJipv.tree_id_0.Mouse.t=0.8522851263393678
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
544 Variable 'RPGDJipv.RPGDJipv.likelihoodFunction' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
545 Set GUI update interval to every 26-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
546 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
547 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
548 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
549 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
550
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
551 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
552
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
553 relax.test.theta_GT = 0.315401
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
554 relax.test.theta_CT = 0.98654
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
555 relax.test.theta_AC = 0.578523
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
556 relax.test.theta_CG = 0.469908
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
557 relax.test.theta_AT = 0.267066
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
558 relax.reference.bsrel_mixture_aux_1 = 0.818182
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
559 relax.reference.omega1 = 0.145496
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
560 relax.reference.omega2 = 0.4601
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
561 relax.reference.bsrel_mixture_aux_0 = 0.45
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
562 relax.reference.omega3 = 7.27482
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
563 relax.unclassified.omega3 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
564 relax.unclassified.bsrel_mixture_aux_1 = 0.5
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
565 relax.unclassified.omega2 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
566 relax.unclassified.omega1 = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
567 relax.K = 1
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
568 relax.unclassified.bsrel_mixture_aux_0 = 0.5
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
569 RPGDJipv.tree_id_0.Pig.t = 1.37515
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
570 RPGDJipv.tree_id_0.Cow.t = 1.78195
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
571 RPGDJipv.tree_id_0.Node3.t = 0.71796
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
572 RPGDJipv.tree_id_0.Horse.t = 1.50107
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
573 RPGDJipv.tree_id_0.Cat.t = 1.97327
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
574 RPGDJipv.tree_id_0.Node2.t = 0.446186
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
575 RPGDJipv.tree_id_0.RhMonkey.t = 0.0265585
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
576 RPGDJipv.tree_id_0.Baboon.t = 0.0125984
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
577 RPGDJipv.tree_id_0.Node9.t = 0.189189
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
578 RPGDJipv.tree_id_0.Human.t = 0
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
579 RPGDJipv.tree_id_0.Chimp.t = 0.0130215
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
580 RPGDJipv.tree_id_0.Node12.t = 0.123589
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
581 RPGDJipv.tree_id_0.Node8.t = 0.810855
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
582 RPGDJipv.tree_id_0.Node1.t = 2.05687
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
583 RPGDJipv.tree_id_0.Rat.t = 0.485173
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
584 RPGDJipv.tree_id_0.Mouse.t = 0.852285
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
585 Site 1 evaluated to a 0 probability in ComputeTreeBlockByBranch
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
586 Optimization finished in 156 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
587 19208 likelihood evaluation calls and 408312 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
588
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
589 Variable 'MPI_NODE_COUNT' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
590 Variable 'esPQwqFL.RPGDJipv.likelihoodFunction' was not initialized prior to being used
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
591 Set GUI update interval to every 24-th LF evaluation.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
592 Optimization settings:
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
593 OPTIMIZATION_METHOD = 4
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
594 OPTIMIZATION_PRECISION = 0.001
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
595 MAXIMUM_ITERATIONS_PER_VARIABLE = 5000
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
596
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
597 Initial parameter values
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
598
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
599 relax.test.theta_GT = 0.272534
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
600 relax.test.theta_CT = 0.989376
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
601 relax.test.theta_AC = 0.472659
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
602 relax.test.theta_CG = 0.409729
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
603 relax.test.theta_AT = 0.213063
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
604 relax.reference.omega2 = 0
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
605 relax.reference.omega3 = 1.81261
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
606 relax.reference.bsrel_mixture_aux_1 = 0.398417
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
607 relax.reference.bsrel_mixture_aux_0 = 0.26934
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
608 relax.reference.omega1 = 0
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
609 relax.unclassified.omega2 = 3.8108
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
610 relax.unclassified.bsrel_mixture_aux_1 = 0.965815
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
611 relax.unclassified.omega3 = 88.0589
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
612 relax.unclassified.omega1 = 0
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
613 relax.unclassified.bsrel_mixture_aux_0 = 0.488814
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
614 RPGDJipv.tree_id_0.Pig.t = 0.288673
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
615 RPGDJipv.tree_id_0.Cow.t = 0.415456
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
616 RPGDJipv.tree_id_0.Node3.t = 0.165342
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
617 RPGDJipv.tree_id_0.Horse.t = 0.373597
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
618 RPGDJipv.tree_id_0.Cat.t = 0.4862
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
619 RPGDJipv.tree_id_0.Node2.t = 0.071002
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
620 RPGDJipv.tree_id_0.RhMonkey.t = 0.0109335
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
621 RPGDJipv.tree_id_0.Baboon.t = 0.00559127
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
622 RPGDJipv.tree_id_0.Node9.t = 0.0891892
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
623 RPGDJipv.tree_id_0.Human.t = 0
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
624 RPGDJipv.tree_id_0.Chimp.t = 0.0054891
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
625 RPGDJipv.tree_id_0.Node12.t = 0.0161348
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
626 RPGDJipv.tree_id_0.Node8.t = 0.405701
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
627 RPGDJipv.tree_id_0.Node1.t = 1.12055
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
628 RPGDJipv.tree_id_0.Rat.t = 0.217643
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
629 RPGDJipv.tree_id_0.Mouse.t = 0.392946
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
630 Optimization finished in 62 loop passes.
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
631 6270 likelihood evaluation calls and 146691 matrix exponentiations calls were made
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
632
7782bb7bc7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'40e2bb1e1af10cbc6641632376fd750d6cf5cd46\n'-dirty
rdvelazquez
parents:
diff changeset
633 Variable 'USE_JSON_FOR_MATRIX' was not initialized prior to being used